diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/debian/changelog golang-github-brentp-irelate-0.0.1+ds/debian/changelog --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/debian/changelog 2020-07-11 14:43:01.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/debian/changelog 2020-07-12 14:16:55.000000000 +0000 @@ -1,3 +1,11 @@ +golang-github-brentp-irelate (0.0.1+ds-1) unstable; urgency=medium + + * Update Build-Deps - drop vendor + * Modify watch to use tags + * New upstream version 0.0.1+ds + + -- Nilesh Patra Sun, 12 Jul 2020 19:46:55 +0530 + golang-github-brentp-irelate (0.0~git20180801.1bf7c8f+ds-2) unstable; urgency=medium * Source-only upload for migration to testing diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/debian/control golang-github-brentp-irelate-0.0.1+ds/debian/control --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/debian/control 2020-07-11 14:43:01.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/debian/control 2020-07-12 14:16:55.000000000 +0000 @@ -10,6 +10,8 @@ golang-github-biogo-hts-dev, golang-gopkg-check.v1-dev, golang-github-pkg-errors-dev, + golang-github-brentp-vcfgo-dev, + golang-github-brentp-bix-dev, samtools Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/go-team/packages/golang-github-brentp-irelate diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/debian/watch golang-github-brentp-irelate-0.0.1+ds/debian/watch --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/debian/watch 2020-07-11 14:43:01.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/debian/watch 2020-07-12 14:15:03.000000000 +0000 @@ -1,11 +1,4 @@ version=4 -opts="mode=git, pgpmode=none,repacksuffix=+ds,dversionmangle=auto" \ - https://github.com/brentp/irelate.git \ - HEAD debian - -# Use the following when upstream starts to tag releases: -# -#version=4 -#opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%golang-github-brentp-irelate-$1.tar.gz%,\ -# uversionmangle=s/(\d)[_\.\-\+]?(RC|rc|pre|dev|beta|alpha)[.]?(\d*)$/\$1~\$2\$3/" \ -# https://github.com/brentp/irelate/tags .*/v?(\d\S*)\.tar\.gz debian +opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%golang-github-brentp-irelate-$1.tar.gz%,\ + uversionmangle=s/(\d)[_\.\-\+]?(RC|rc|pre|dev|beta|alpha)[.]?(\d*)$/\$1~\$2\$3/,repacksuffix=+ds,dversionmangle=auto" \ + https://github.com/brentp/irelate/tags .*/v?(\d\S*)\.tar\.gz debian diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/bix/bix.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/bix/bix.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/bix/bix.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/bix/bix.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,517 +0,0 @@ -// Tabix queries for go -package bix - -import ( - "bufio" - "bytes" - "compress/gzip" - "io" - "log" - "os" - "strconv" - "strings" - "time" - "unsafe" - - "github.com/biogo/hts/bgzf" - "github.com/biogo/hts/bgzf/index" - "github.com/biogo/hts/tabix" - "github.com/brentp/irelate/interfaces" - "github.com/brentp/irelate/parsers" - "github.com/brentp/vcfgo" - "github.com/pkg/errors" -) - -// Bix provides read access to tabix files. -type Bix struct { - Index - bgzf *bgzf.Reader - path string - workers int - - VReader *vcfgo.Reader - // index for 'ref' and 'alt' columns if they were present. - refalt []int - - file *os.File - buf *bufio.Reader -} - -func (tbx *Bix) init() error { - if tbx.file != nil { - return nil - } - var err error - tbx.file, err = os.Open(tbx.path) - if err != nil { - return errors.Wrapf(err, "bix: error (re)opening %s", tbx.path) - } - tbx.bgzf, err = bgzf.NewReader(tbx.file, tbx.workers) - if err != nil { - return errors.Wrapf(err, "bix: error creating new bgzf reader for %v", tbx.path) - } - return nil -} - -// create a new bix that does as little as possible from the old bix -func newShort(old *Bix) (*Bix, error) { - tbx := &Bix{ - Index: old.Index, - path: old.path, - workers: old.workers, - VReader: old.VReader, - refalt: old.refalt, - } - var err error - tbx.file, err = os.Open(tbx.path) - if err != nil { - return nil, errors.Wrapf(err, "bix: error (re)opening %s", tbx.path) - } - tbx.bgzf, err = bgzf.NewReader(tbx.file, old.workers) - if err != nil { - return nil, errors.Wrapf(err, "bix: error creating new bgzf reader for %v", tbx.path) - } - return tbx, nil -} - -func exists(path string) bool { - _, err := os.Stat(path) - return err == nil -} - -func getModTime(path string) time.Time { - if t, err := os.Stat(path); err != nil { - // ignore the error because we know the file exists from check below. - return time.Time{} - } else { - return t.ModTime() - } -} - -// New returns a &Bix -func New(path string, workers ...int) (*Bix, error) { - var idx Index - var ext string - - if exists(path + ".csi") { - ext = ".csi" - } else { - ext = ".tbi" - } - if getModTime(path).After(getModTime(path + ext)) { - log.Printf("warning: data file %s is modified more recently than its index.", path) - } - - f, err := os.Open(path + ext) - if err != nil { - return nil, errors.Wrapf(err, "bix: error on opening %s%s", path, ext) - } - defer f.Close() - - gz, err := gzip.NewReader(f) - if err != nil { - return nil, errors.Wrapf(err, "bix: error on reading tabix index: %s%s", path, ext) - } - defer gz.Close() - - if ext == ".tbi" { - t, err := tabix.ReadFrom(gz) - if err != nil { - return nil, errors.Wrapf(err, "bix: error parsing tabix index from: %s.tbi", path) - } - idx = tIndex{t} - } else { - idx, err = NewCSI(gz) - if err != nil { - return nil, errors.Wrapf(err, "bix: error parsing tabix index from: %s.csi", path) - } - } - n := 1 - if len(workers) > 0 { - n = workers[0] - } - - b, err := os.Open(path) - if err != nil { - return nil, err - } - bgz, err := bgzf.NewReader(b, n) - if err != nil { - return nil, errors.Wrapf(err, "bix: error opening bgzf reader for %s", path) - } - - var h []string - tbx := &Bix{bgzf: bgz, path: path, file: b, workers: n} - - buf := bufio.NewReader(bgz) - l, err := buf.ReadString('\n') - if err != nil { - return tbx, errors.Wrapf(err, "bix: error reading line from %s", path) - } - - for i := 0; i < int(idx.Skip()) || rune(l[0]) == idx.MetaChar(); i++ { - h = append(h, l) - l, err = buf.ReadString('\n') - if err != nil { - return tbx, errors.Wrapf(err, "bix: error reading line from %s", path) - } - } - header := strings.Join(h, "") - - if len(h) > 0 && (strings.HasSuffix(tbx.path, ".vcf.gz") || strings.HasSuffix(tbx.path, ".vcf.bgz")) { - var err error - h := strings.NewReader(header) - - tbx.VReader, err = vcfgo.NewReader(h, true) - if err != nil { - return nil, err - } - } else if len(h) > 0 { - htab := strings.Split(strings.TrimSpace(h[len(h)-1]), "\t") - // try to find ref and alternate columns to make an IREFALT - for i, hdr := range htab { - if l := strings.ToLower(hdr); l == "ref" || l == "reference" { - tbx.refalt = append(tbx.refalt, i) - break - } - } - for i, hdr := range htab { - if l := strings.ToLower(hdr); l == "alt" || l == "alternate" { - tbx.refalt = append(tbx.refalt, i) - break - } - } - if len(tbx.refalt) != 2 { - tbx.refalt = nil - } - } - tbx.buf = buf - tbx.Index = idx - return tbx, nil -} - -func (b *Bix) Close() error { - b.bgzf.Close() - b.file.Close() - return nil -} - -func (tbx *Bix) toPosition(toks [][]byte) interfaces.Relatable { - isVCF := tbx.VReader != nil - var g *parsers.Interval - - if isVCF { - v := tbx.VReader.Parse(toks) - return interfaces.AsRelatable(v) - - } else { - g, _ = newgeneric(toks, tbx.Index.NameColumn()-1, tbx.Index.BeginColumn()-1, - tbx.Index.EndColumn()-1, tbx.Index.ZeroBased()) - } - if tbx.refalt != nil { - ra := parsers.RefAltInterval{Interval: *g, HasEnd: tbx.Index.EndColumn() != tbx.Index.BeginColumn()} - ra.SetRefAlt(tbx.refalt) - return &ra - } - return g -} - -func unsafeString(b []byte) string { - return *(*string)(unsafe.Pointer(&b)) -} - -// return an interval using the info from the tabix index -func newgeneric(fields [][]byte, chromCol int, startCol int, endCol int, zeroBased bool) (*parsers.Interval, error) { - s, err := strconv.Atoi(unsafeString(fields[startCol])) - if err != nil { - return nil, err - } - if !zeroBased { - s -= 1 - } - e, err := strconv.Atoi(unsafeString(fields[endCol])) - if err != nil { - return nil, err - } - return parsers.NewInterval(string(fields[chromCol]), uint32(s), uint32(e), fields, uint32(0), nil), nil -} - -func (tbx *Bix) ChunkedReader(chrom string, start, end int) (io.ReadCloser, error) { - chunks, err := tbx.Chunks(chrom, start, end) - if err == index.ErrNoReference { - if strings.HasPrefix(chrom, "chr") { - chunks, err = tbx.Chunks(chrom[3:], start, end) - } else { - chunks, err = tbx.Chunks("chr"+chrom, start, end) - } - } - if err == index.ErrInvalid { - return index.NewChunkReader(tbx.bgzf, []bgzf.Chunk{}) - } else if err == index.ErrNoReference { - log.Printf("chromosome %s not found in %s\n", chrom, tbx.path) - return index.NewChunkReader(tbx.bgzf, []bgzf.Chunk{}) - } else if err != nil { - return nil, errors.Wrapf(err, "bix: error reading Chunks from %s", tbx.path) - } - cr, err := index.NewChunkReader(tbx.bgzf, chunks) - if err != nil { - return nil, errors.Wrapf(err, "bix: error creating chunked reader from %s", tbx.path) - } - return cr, nil -} - -// bixerator meets interfaces.RelatableIterator -type bixerator struct { - rdr io.ReadCloser - buf *bufio.Reader - tbx *Bix - - region interfaces.IPosition -} - -func makeFields(line []byte) [][]byte { - fields := make([][]byte, 9) - copy(fields[:8], bytes.SplitN(line, []byte{'\t'}, 8)) - s := 0 - for i, f := range fields { - if i == 7 { - break - } - s += len(f) + 1 - } - /* - if s >= len(line) { - c := make([]string, len(fields)) - for k, f := range fields { - c[k] = string(f) - } - log.Println(s, string(line), c) - } - */ - e := bytes.IndexByte(line[s:], '\t') - if e == -1 { - e = len(line) - } else { - e += s - } - - fields[7] = line[s:e] - if len(line) > e+1 { - fields[8] = line[e+1:] - } else { - fields = fields[:8] - } - - return fields -} - -func (b bixerator) Next() (interfaces.Relatable, error) { - - for { - line, err := b.buf.ReadBytes('\n') - - if err == io.EOF && len(line) == 0 { - return nil, io.EOF - } else if err != nil { - return nil, errors.Wrapf(err, "bix: error iterating on %s", b.tbx.path) - } - if len(line) == 0 { - return nil, io.EOF - } - if line[len(line)-1] == '\n' { - line = line[:len(line)-1] - } - in := true - var toks [][]byte - if b.region != nil { - var err error - - in, err, toks = b.inBounds(line) - if err != nil { - return nil, err - } - } else { - if b.tbx.VReader != nil { - toks = makeFields(line) - } else { - toks = bytes.Split(line, []byte{'\t'}) - } - } - - if in { - return b.tbx.toPosition(toks), nil - } - } - return nil, io.EOF -} - -func (b bixerator) Close() error { - if b.rdr != nil { - b.rdr.Close() - } - return b.tbx.Close() -} - -var _ interfaces.RelatableIterator = bixerator{} - -// FastQuery allows extracting intervals from an indexed file. Use this function if -// concurrency is *not* required, otherwise use Query -func (tbx *Bix) FastQuery(region interfaces.IPosition) (interfaces.RelatableIterator, error) { - if err := tbx.init(); err != nil { - return nil, err - } - cr, err := tbx.ChunkedReader(region.Chrom(), int(region.Start()), int(region.End())) - if err != nil { - if cr != nil { - cr.Close() - tbx.Close() - } - return nil, err - } - return bixerator{cr, bufio.NewReader(cr), tbx, region}, nil -} - -// Query allows extracting intervals from an indexed file. Use this function if -// concurrency is required, otherwise use FastQuery -func (tbx *Bix) Query(region interfaces.IPosition) (interfaces.RelatableIterator, error) { - tbx2, err := newShort(tbx) - if err != nil { - return nil, err - } - if region == nil { - var l string - var err error - buf := bufio.NewReader(tbx2.bgzf) - l, err = buf.ReadString('\n') - for i := 0; i < tbx2.Index.Skip() || rune(l[0]) == tbx2.Index.MetaChar(); i++ { - l, err = buf.ReadString('\n') - if err != nil { - return nil, err - } - } - if tbx2.Index.Skip() == 0 && rune(l[0]) != tbx2.Index.MetaChar() { - buf = bufio.NewReader(io.MultiReader(strings.NewReader(l), buf)) - } - return bixerator{nil, buf, tbx2, region}, nil - } - - cr, err := tbx2.ChunkedReader(region.Chrom(), int(region.Start()), int(region.End())) - if err != nil { - if cr != nil { - cr.Close() - tbx2.Close() - } - return nil, err - } - return bixerator{cr, bufio.NewReader(cr), tbx2, region}, nil -} - -func (tbx *Bix) AddInfoToHeader(id, number, vtype, desc string) { - if tbx.VReader == nil { - return - } - tbx.VReader.AddInfoToHeader(id, number, vtype, desc) -} - -func (tbx *Bix) GetHeaderType(field string) string { - if tbx.VReader == nil { - return "" - } - return tbx.VReader.GetHeaderType(field) -} - -func (tbx *Bix) GetHeaderDescription(field string) string { - if tbx.VReader == nil { - return "" - } - if h, ok := tbx.VReader.Header.Infos[field]; ok { - return h.Description - } - return "" -} - -func (tbx *Bix) GetHeaderNumber(field string) string { - if tbx.VReader == nil { - return "1" - } - if h, ok := tbx.VReader.Header.Infos[field]; ok { - return h.Number - } - return "1" -} - -func (b *bixerator) inBounds(line []byte) (bool, error, [][]byte) { - - var readErr error - line = bytes.TrimRight(line, "\r\n") - var toks [][]byte - if b.tbx.VReader != nil { - toks = makeFields(line) - } else { - toks = bytes.Split(line, []byte{'\t'}) - } - - s, err := strconv.Atoi(unsafeString(toks[b.tbx.BeginColumn()-1])) - if err != nil { - return false, err, toks - } - - pos := s - if !b.tbx.ZeroBased() { - pos -= 1 - } - if pos >= int(b.region.End()) { - return false, io.EOF, toks - } - - if b.tbx.EndColumn() != 0 { - e, err := strconv.Atoi(unsafeString(toks[b.tbx.EndColumn()-1])) - if err != nil { - return false, err, toks - } - if e < int(b.region.Start()) { - return false, readErr, toks - } - return true, readErr, toks - } else if b.tbx.VReader != nil { - start := int(b.region.Start()) - alt := strings.Split(string(toks[4]), ",") - lref := len(toks[3]) - if start >= pos+lref { - for _, a := range alt { - if a[0] != '<' || a == "" { - e := pos + lref - if e > start { - return true, readErr, toks - } - } else if strings.HasPrefix(a, " start { - return true, readErr, toks - } - return false, readErr, toks - } else { - log.Println("no end:", b.tbx.path, string(toks[0]), pos, string(toks[3]), a) - } - } - } - } else { - return true, readErr, toks - } - return false, readErr, toks - } - return false, readErr, toks - -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/bix/csi.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/bix/csi.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/bix/csi.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/bix/csi.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,128 +0,0 @@ -// Tabix queries for go -package bix - -import ( - "bytes" - "encoding/binary" - "io" - "strings" - - "github.com/biogo/hts/bgzf" - "github.com/biogo/hts/csi" - "github.com/biogo/hts/tabix" -) - -// Index unifies CSI and tabix. -type Index interface { - Chunks(string, int, int) ([]bgzf.Chunk, error) - NameColumn() int - BeginColumn() int - EndColumn() int - ZeroBased() bool - MetaChar() rune - Skip() int -} - -type tIndex struct{ *tabix.Index } - -func (t tIndex) NameColumn() int { - return int(t.Index.NameColumn) -} -func (t tIndex) BeginColumn() int { - return int(t.Index.BeginColumn) -} - -func (t tIndex) EndColumn() int { - return int(t.Index.EndColumn) -} - -func (t tIndex) ZeroBased() bool { - return t.Index.ZeroBased -} - -func (t tIndex) MetaChar() rune { - return t.Index.MetaChar -} - -func (t tIndex) Skip() int { - return int(t.Index.Skip) -} - -type cIndex struct { - *csi.Index - chroms []string - nameColumn int - beginColumn int - endColumn int - metaChar rune - zeroBased bool - skip int -} - -func (c cIndex) NameColumn() int { - return c.nameColumn -} -func (c cIndex) BeginColumn() int { - return c.beginColumn -} - -func (c cIndex) EndColumn() int { - return c.endColumn -} - -func (c cIndex) ZeroBased() bool { - return c.zeroBased -} - -func (c cIndex) MetaChar() rune { - return c.metaChar -} - -func (c cIndex) Skip() int { - return c.skip -} - -// StripChr removes the "chr" prefix if it is present -func stripChr(c string) string { - if strings.HasPrefix(c, "chr") { - return c[3:] - } - return c -} - -func (c cIndex) Chunks(chrom string, start int, end int) ([]bgzf.Chunk, error) { - idx := -1 - chrom = stripChr(chrom) - for i, ichrom := range c.chroms { - if stripChr(ichrom) == chrom { - idx = i - break - } - - } - return c.Index.Chunks(idx, start, end), nil -} - -func NewCSI(r io.Reader) (cIndex, error) { - c, err := csi.ReadFrom(r) - ci := cIndex{Index: c} - if err != nil { - return ci, err - } - aux := c.Auxilliary - - ci.nameColumn = int(binary.LittleEndian.Uint32(aux[4:8])) - ci.beginColumn = int(binary.LittleEndian.Uint32(aux[8:12])) - ci.endColumn = int(binary.LittleEndian.Uint32(aux[12:16])) - ci.metaChar = rune(binary.LittleEndian.Uint32(aux[16:20])) - ci.skip = int(binary.LittleEndian.Uint32(aux[20:24])) - - L := int(binary.LittleEndian.Uint32(aux[24:28])) - // ends in trailing '0' so we take all but the last one byte. - chroms := bytes.Split(aux[28:28+L-1], []byte{0}) - ci.chroms = make([]string, len(chroms)) - for i, chrom := range chroms { - ci.chroms[i] = string(chrom) - } - return ci, nil -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/bix/csi_test.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/bix/csi_test.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/bix/csi_test.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/bix/csi_test.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,39 +0,0 @@ -package bix - -import ( - "compress/gzip" - "os" - "testing" - - . "gopkg.in/check.v1" -) - -func Test(t *testing.T) { TestingT(t) } - -type BixSuite struct{} - -var _ = Suite(&BixSuite{}) - -func (s *BixSuite) TestReadCSI(c *C) { - f, err := os.Open("tests/csitest.bed.gz.csi") - if err != nil { - c.Fatal(err) - } - g, err := gzip.NewReader(f) - if err != nil { - c.Fatal(err) - } - - cs, err := NewCSI(g) - if err != nil { - c.Fatal(err) - } - c.Check(cs.NameColumn(), Equals, 1) - c.Check(cs.BeginColumn(), Equals, 2) - c.Check(cs.EndColumn(), Equals, 3) - c.Check(cs.Skip(), Equals, 0) - c.Check(cs.NumRefs(), Equals, len(cs.chroms)) - c.Check(cs.MetaChar(), Equals, '#') - c.Check(cs.chroms, DeepEquals, []string{"1", "2", "3", "4", "5", "6", "9"}) - -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/bix/LICENSE golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/bix/LICENSE --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/bix/LICENSE 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/bix/LICENSE 1970-01-01 00:00:00.000000000 +0000 @@ -1,22 +0,0 @@ -The MIT License (MIT) - -Copyright (c) 2015 Brent Pedersen - Bioinformatics - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. - diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/bix/main/main.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/bix/main/main.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/bix/main/main.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/bix/main/main.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,68 +0,0 @@ -package main - -import ( - "fmt" - "log" - "os" - "strconv" - - "github.com/brentp/bix" - "github.com/brentp/irelate/interfaces" -) - -func check(e error) { - if e != nil { - log.Fatal(e) - } -} - -func min(a, b int) int { - if a < b { - return a - } - return b -} - -type loc struct { - chrom string - start int - end int -} - -func (s loc) Chrom() string { - return s.chrom -} -func (s loc) Start() uint32 { - return uint32(s.start) -} -func (s loc) End() uint32 { - return uint32(s.end) -} - -func main() { - - f := os.Args[1] - tbx, err := bix.New(f) - check(err) - - chrom := os.Args[2] - - s, err := strconv.Atoi(os.Args[3]) - check(err) - - e, err := strconv.Atoi(os.Args[4]) - check(err) - - vals, _ := tbx.Query(loc{chrom, s, e}) - i := 0 - for { - v, err := vals.Next() - if err != nil { - break - } - fmt.Println(v.(interfaces.IVariant).String()[:40]) - i++ - } - tbx.Close() - -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/bix/main/test.py golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/bix/main/test.py --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/bix/main/test.py 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/bix/main/test.py 1970-01-01 00:00:00.000000000 +0000 @@ -1,60 +0,0 @@ -""" -This compares the output of the tabix commandline tool from htslib to -this version built with the biogo bindings. -""" - -import sys -import os -import subprocess -import gzip - -F = sys.argv[1] if len(sys.argv) > 1 else "NA12878.wham.del.vcf.gz" - -positions = [] -for i, x in enumerate(gzip.open(F)): - if x[0] == "#": continue - if i > 2000000: break - positions.append((x.split("\t")[0], int(x.split("\t")[1]))) -print(positions[:100]) -print(len(positions)) - -p = subprocess.Popen("go build -o main main.go", shell=True) -p.wait() - -def tbxrun(query, chrom, start, end): - p = subprocess.Popen("tabix %s %s:%d-%d" % (query, chrom, start+1, end), - shell=True, stdout=subprocess.PIPE) - return p#.stdout.read().rstrip() - - -def btrun(query, chrom, start, end): - with open("t.bed", "w") as fin: - fin.write("%s\t%d\t%d" % (chrom, start, end)) - p = subprocess.Popen("bedtools intersect -b t.bed -a %s" % query, - shell=True, stdout=subprocess.PIPE) - try: - return p.stdout.read().rstrip() - finally: - os.unlink("t.bed") - -def bxrun(query, chrom, start, end): - cmd = "./main %s %s %d %d" % (query, chrom, start, end) - p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE) - return p, cmd#.stdout.read().rstrip(), cmd - -for chrom, position in positions: - print position - for j in range(position-5, position+5): - for l in range(1, 3): - - #btres = btrun(F, '1', j, j + 5) - bxres, cmd = bxrun(F, chrom, j, j + l) - tbres = tbxrun(F, chrom, j, j + l) - bxres = bxres.stdout.read().strip() - tbres = tbres.stdout.read().strip() - - #lbt = len(btres.split("\n")) - lbx = len(bxres.split("\n")) if bxres else 0 - ltb = len(tbres.split("\n")) if tbres else 0 - - assert ltb == lbx, (F, chrom, position, j, j + l, ltb, lbx, cmd) diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/bix/README.md golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/bix/README.md --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/bix/README.md 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/bix/README.md 1970-01-01 00:00:00.000000000 +0000 @@ -1,38 +0,0 @@ -bix -=== - -Tabix files in go. - -[![GoDoc](https://godoc.org/github.com/brentp/bix?status.png)](https://godoc.org/github.com/brentp/bix) - - -`Bix`is a pure go tabix reader. Tabix has a minimum resolution of 16K bases. So, for dense annotations -like ExAC, repeated queries will have to re-parse the same intervals. To mitigate this, `Bix` caches -all annotations for the blocks from each query and re-uses them for later querires to the same block. -In practice, this results in 10X-100X speedup for any type of data. - - - - -```go -tbx, err := bix.New(f) - -// Query returns an io.Reader -ph := true // print header ? -rdr, err := tbx.Query(chrom, start, end, ph) -buf := bufio.NewReader(rdr) -for { - line, err := bufr.ReadString('\n') - if err == io.EOF { - break - } - fmt.Println(line) -} -// or - -intervals := tbx.Get(chrom, start, end) - - -``` - -where intervals will be either a vcfgo.Variant or an Interval object with a Chrom(), Start(), and End() method. diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/bench.sh golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/bench.sh --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/bench.sh 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/bench.sh 1970-01-01 00:00:00.000000000 +0000 @@ -1 +0,0 @@ -go test -cpu=1,2,4 -bench . -run NOTHING -benchtime 3s -cpuprofile cpu.prof diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/bench_test.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/bench_test.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/bench_test.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/bench_test.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -package vcfgo - -import ( - "os" - "testing" -) - -func benchmarkReader(lazy bool, b *testing.B) { - - for n := 0; n < b.N; n++ { - f, err := os.Open("examples/test.query.vcf") - if err != nil { - panic(err) - } - rdr, err := NewReader(f, lazy) - if err != nil { - panic(err) - } - - j := 0 - for { - v := rdr.Read() - if v == nil { - break - } - j++ - } - } -} - -func BenchmarkLazy(b *testing.B) { benchmarkReader(true, b) } -func BenchmarkEager(b *testing.B) { benchmarkReader(false, b) } diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/doc_test.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/doc_test.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/doc_test.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/doc_test.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,28 +0,0 @@ -package vcfgo_test - -import ( - "fmt" - "os" - - "github.com/brentp/vcfgo" -) - -func Example() { - f, _ := os.Open("examples/test.auto_dom.no_parents.vcf") - rdr, err := vcfgo.NewReader(f, false) - if err != nil { - panic(err) - } - for { - variant := rdr.Read() - if variant == nil { - break - } - fmt.Printf("%s\t%d\t%s\t%s\n", variant.Chromosome, variant.Pos, variant.Ref(), variant.Alt()) - dp, _ := variant.Info().Get("DP") - fmt.Printf("%v", dp.(int) > 10) - // Output: asdf - } - // Print all accumulated errors to stderr - fmt.Fprintln(os.Stderr, rdr.Error()) -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/examples/main.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/examples/main.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/examples/main.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/examples/main.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,79 +0,0 @@ -package main - -import ( - "flag" - "fmt" - "io" - "log" - "os" - - "github.com/brentp/vcfgo" -) - -func main() { - - flag.Parse() - files := flag.Args() - f, err := os.Open(files[0]) - - r := io.Reader(f) - vr, err := vcfgo.NewReader(r, false) - if err != nil { - panic(err) - } - fmt.Printf("%v\n", vr) - - variant := vr.Read() - fmt.Println(vr.Error()) - fmt.Println("variant:", variant) - if len(variant.Samples) > 0 { - if _, ok := vr.Header.SampleFormats["PL"]; ok { - if vr.Header.SampleFormats["PL"].Type == "Integer" { - fmt.Println(variant.GetGenotypeField(variant.Samples[0], "PL", int(-1))) - } else { - fmt.Println(variant.GetGenotypeField(variant.Samples[0], "PL", float32(-1))) - } - } - } - fmt.Println(vr.Error()) - vr.Clear() - for { - variant = vr.Read() - if variant == nil { - if e := vr.Error(); e != io.EOF && e != nil { - vr.Clear() - } - break - } - if vr.Error() != nil { - fmt.Println(vr.Error()) - } - vr.Clear() - if len(variant.Samples) > 0 { - var pl interface{} - if _, ok := vr.Header.SampleFormats["PL"]; ok { - if vr.Header.SampleFormats["PL"].Type == "Integer" { - pl, err = variant.GetGenotypeField(variant.Samples[0], "PL", int(-1)) - } else { - pl, err = variant.GetGenotypeField(variant.Samples[0], "PL", float32(-1)) - } - } - fmt.Println("ERR:", err) - fmt.Println(variant.Samples[0]) - if err != nil && variant.Samples[0] != nil { - log.Println("BBBBBBBBBBBBBBBBBBB") - if _, ok := vr.Header.SampleFormats["PL"]; ok { - fmt.Println("") - fmt.Println(variant.Samples[0]) - log.Println("DDDDDDDDDDDDDDDDD") - log.Fatal(err) - } - } - - if variant.Samples[0] != nil { - fmt.Println("PL:", pl, "GQ:", variant.Samples[0].GQ, "DP:", variant.Samples[0].DP) - } - } - } - fmt.Println("OK") -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/examples/test.auto_dom.no_parents.vcf golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/examples/test.auto_dom.no_parents.vcf --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/examples/test.auto_dom.no_parents.vcf 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/examples/test.auto_dom.no_parents.vcf 1970-01-01 00:00:00.000000000 +0000 @@ -1,127 +0,0 @@ -##fileformat=VCFv4.1 -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/M10478.conc.on.pos.realigned.bam, bam/M10475.conc.on.pos.realigned.bam, bam/M10500.conc.on.pos.realigned.bam, bam/M128215.conc.on.pos.realigned.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=10 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false" -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##reference=file:///m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa -##INFO= -##SnpEffVersion="SnpEff 3.0g (build 2012-08-31), by Pablo Cingolani" -##SnpEffCmd="SnpEff -i vcf -o vcf GRCh37.66 test4.vep.vcf " -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1_dad 1_mom 1_kid 2_dad 2_mom 2_kid 3_dad 3_mom 3_kid -chr10 1142208 . T C 3404.3 . AC=8;AF=1.00;AN=8;DP=122;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.6747;MQ=36.00;MQ0=0;QD=27.90;CSQ=intron_variant|||ENSG00000047056|WDR37|ENST00000263150|||,downstream_gene_variant|||ENSG00000047056|WDR37|ENST00000436154|||,intron_variant|||ENSG00000047056|WDR37|ENST00000358220|||,stop_lost|Tga/Cga|*/R|ENSG00000047056|WDR37|ENST00000381329|9/9||;EFF=DOWNSTREAM(MODIFIER||||208|WDR37|protein_coding|CODING|ENST00000436154|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000263150|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000358220|),STOP_LOST(HIGH|MISSENSE|Tga/Cga|*250R|249|WDR37|protein_coding|CODING|ENST00000381329|exon_10_1142110_1142566) GT:AD:DP:GQ:PL 0/0:1,37:39:87.16:940,87,0 0/0:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 0/0:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/0:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 -chr10 1142208 . T C 3404.3 . AC=8;AF=1.00;AN=8;DP=122;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.6747;MQ=36.00;MQ0=0;QD=27.90;CSQ=intron_variant|||ENSG00000047056|WDR37|ENST00000263150|||,downstream_gene_variant|||ENSG00000047056|WDR37|ENST00000436154|||,intron_variant|||ENSG00000047056|WDR37|ENST00000358220|||,stop_lost|Tga/Cga|*/R|ENSG00000047056|WDR37|ENST00000381329|9/9||;EFF=DOWNSTREAM(MODIFIER||||208|WDR37|protein_coding|CODING|ENST00000436154|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000263150|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000358220|),STOP_LOST(HIGH|MISSENSE|Tga/Cga|*250R|249|WDR37|protein_coding|CODING|ENST00000381329|exon_10_1142110_1142566) GT:AD:DP:GQ:PL 0/1:1,37:39:17.16:940,87,1 0/1:0,29:29:78.20:899,78,0 1/1:0,24:24:66.14:729,66,0 0/1:1,37:59:87.16:940,87,0 0/1:0,29:49:78.20:899,78,0 1/1:0,24:64:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 -chr10 48003992 . C T 1047.87 . AC=4;AF=0.50;AN=8;BaseQRankSum=-0.053;DP=165;Dels=0.00;FS=6.377;HRun=0;HaplotypeScore=4.3830;MQ=20.94;MQ0=0;MQRankSum=-0.368;QD=9.53;ReadPosRankSum=1.346;CSQ=missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000420079|16/17|benign(0)|tolerated(1),missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000426610|17/18|benign(0)|tolerated(1);EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C540Y|610|ASAH2C|protein_coding|CODING|ENST00000420079|exon_10_48003968_48004056),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C552Y|622|ASAH2C|protein_coding|CODING|ENST00000426610|exon_10_48003968_48004056) GT:AD:DP:GQ:PL 0/0:1,37:39:17.16:940,87,0 0/0:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 0/0:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/0:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 -chr10 48004992 . C T 1047.87 . AC=4;AF=0.50;AN=8;BaseQRankSum=-0.053;DP=165;Dels=0.00;FS=6.377;HRun=0;HaplotypeScore=4.3830;MQ=20.94;MQ0=0;MQRankSum=-0.368;QD=9.53;ReadPosRankSum=1.346;CSQ=missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000420079|16/17|benign(0)|tolerated(1),missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000426610|17/18|benign(0)|tolerated(1);EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C540Y|610|ASAH2C|protein_coding|CODING|ENST00000420079|exon_10_48003968_48004056),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C552Y|622|ASAH2C|protein_coding|CODING|ENST00000426610|exon_10_48003968_48004056) GT:AD:DP:GQ:PL 0/0:1,37:39:47.16:940,27,0 0/0:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 0/0:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/0:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 -chr10 135336656 . G A 38.34 . AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS=0.000;HRun=4;HaplotypeScore=0.0000;MQ=37.00;MQ0=0;QD=19.17;CSQ=upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000418356|||,intron_variant&nc_transcript_variant|||ENSG00000214279||ENST00000488261|||,intron_variant|||ENSG00000203772|SPRN|ENST00000541506|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000541261|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000421586|||,intron_variant|||ENSG00000130649|CYP2E1|ENST00000463117|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000252945|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000541080|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000477500|||,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000480558|||,intron_variant|||ENSG00000214279||ENST00000356567|||;EFF=INTRON(MODIFIER||||151|SPRN|protein_coding|CODING|ENST00000541506|),INTRON(MODIFIER||||493|CYP2E1|protein_coding|CODING|ENST00000463117|),INTRON(MODIFIER||||693|RP11-108K14.4.1|protein_coding|CODING|ENST00000356567|),INTRON(MODIFIER|||||RP11-108K14.4.1|retained_intron|CODING|ENST00000488261|),UPSTREAM(MODIFIER||||305|CYP2E1|protein_coding|CODING|ENST00000418356|),UPSTREAM(MODIFIER||||355|CYP2E1|protein_coding|CODING|ENST00000421586|),UPSTREAM(MODIFIER||||493|CYP2E1|protein_coding|CODING|ENST00000252945|),UPSTREAM(MODIFIER||||85|CYP2E1|protein_coding|CODING|ENST00000541261|),UPSTREAM(MODIFIER|||||CYP2E1|processed_transcript|CODING|ENST00000477500|),UPSTREAM(MODIFIER|||||CYP2E1|processed_transcript|CODING|ENST00000480558|) GT:AD:DP:GQ:PL 0/1:1,37:39:77.16:148,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/1:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 0/1:1,37:39:87.16:940,87,0 0/0:0,29:29:78.20:899,78,0 0/1:0,24:24:66.14:729,66,0 diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/examples/test.query.vcf golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/examples/test.query.vcf --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/examples/test.query.vcf 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/examples/test.query.vcf 1970-01-01 00:00:00.000000000 +0000 @@ -1,1001 +0,0 @@ -##fileformat=VCFv4.1 -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/all.conc.on.pos.dedup.realigned.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=10 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false" -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##reference=file:///home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa -##SnpEffVersion="SnpEff 3.1b (build 2012-11-14), by Pablo Cingolani" -##SnpEffCmd="SnpEff GRCh37.68 -c /Users/arq5x/src/other/snpEff_3_1/snpEff.config -i vcf -o vcf rs-exome.all.raw.nobaq.2012-Nov-15.vcf " -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1094PC0005 1094PC0009 1094PC0012 1094PC0013 1094PC0016 1094PC0017 1094PC0018 1094PC0019 1094PC0020 1094PC0021 1094PC0022 1094PC0023 1094PC0025 1478PC0001B 1478PC0002 1478PC0003 1478PC0004 1478PC0005 1478PC0006B 1478PC0007B 1478PC0008B 1478PC0009B 1478PC0010 1478PC0011 1478PC0012 1478PC0013B 1478PC0014B 1478PC0015B 1478PC0016 1478PC0017B 1478PC0018 1478PC0019 1478PC0020 1478PC0021 1478PC0022B 1478PC0023B 1478PC0024B 1478PC0025 1719PC0001 1719PC0002 1719PC0003 1719PC0004 1719PC0005 1719PC0006 1719PC0007 1719PC0008 1719PC0009 1719PC0010 1719PC0011 1719PC0012 1719PC0013 1719PC0014 1719PC0015 1719PC0016 1719PC0017 1719PC0018 1719PC0019 1719PC0020 1719PC0021 1719PC0022 -chr1 30548 . T G 50.09 . AC=6;AF=0.429;AN=14;BaseQRankSum=0.000;DP=7;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=29.00;MQ0=0;MQRankSum=-0.550;QD=16.70;ReadPosRankSum=0.937;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),EXON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|1),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000473358|||||lincRNA|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000469289|1/2||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000417324|||||lincRNA|1,downstream_gene_variant|||ENSG00000243485|MIR1302-10|ENST00000607096|||||miRNA|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000461467|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 1/1:0,1:1:3.01:33,3,0 ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. -chr1 30860 . G C 54.3 . AC=3;AF=0.058;AN=52;BaseQRankSum=2.815;DP=61;Dels=0.00;FS=2.403;HRun=0;HaplotypeScore=0.6396;InbreedingCoeff=-0.0048;MQ=36.25;MQ0=0;MQRankSum=0.396;QD=13.57;ReadPosRankSum=2.148;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|2),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000473358|||||lincRNA|1,intron_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000469289|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000417324|||||lincRNA|1,downstream_gene_variant|||ENSG00000243485|MIR1302-10|ENST00000607096|||||miRNA|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000461467|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1 GT:AD:DP:GQ:PL 0/0:7,0:7:15.04:0,15,177 0/0:2,0:2:3.01:0,3,39 0/0:6,0:6:12.02:0,12,143 0/0:4,0:4:9.03:0,9,119 ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. 0/0:3,0:3:6.02:0,6,73 0/0:2,0:2:6.02:0,6,80 0/0:1,0:1:3:0,3,27 ./. ./. 0/0:1,0:1:3.01:0,3,32 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. 0/0:2,0:2:3.01:0,3,38 ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,35 0/0:3,0:3:9.02:0,9,105 0/0:2,0:2:6.02:0,6,67 1/1:0,2:2:6.02:80,6,0 0/0:3,0:3:3.01:0,3,39 ./. 0/0:2,0:2:3:0,3,29 ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1:1,1:2:33.99:34,0,34 ./. 0/0:1,0:1:3.01:0,3,31 ./. 0/0:2,0:2:3.01:0,3,32 ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,34 0/0:2,0:2:6.02:0,6,73 ./. ./. ./. ./. ./. ./. ./. -chr1 30867 . CCT C 49.48 . AC=6;AF=0.107;AN=56;BaseQRankSum=0.900;DP=65;FS=0.000;HRun=0;HaplotypeScore=12.2055;InbreedingCoeff=-0.1167;MQ=36.09;MQ0=0;MQRankSum=1.148;QD=3.81;ReadPosRankSum=0.124;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|2),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|);CSQ=intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000243485|MIR1302-10|ENST00000473358|||||lincRNA|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000243485|MIR1302-10|ENST00000469289|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000417324|||||lincRNA|1,downstream_gene_variant|||ENSG00000243485|MIR1302-10|ENST00000607096|||||miRNA|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000461467|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1 GT:AD:DP:GQ:PL 0/0:8,0:8:18.06:0,18,283 0/0:3,0:3:6.01:0,6,60 0/1:5,1:6:17.12:17,0,215 0/0:5,0:5:9.03:0,9,142 ./. ./. 0/0:1,0:1:3.01:0,3,47 ./. 0/0:3,0:3:5.99:0,6,69 0/1:1,1:2:29.16:29,0,41 0/0:1,0:1:3.01:0,3,47 ./. ./. 0/0:1,0:1:3.01:0,3,47 0/0:2,0:2:3.01:0,3,47 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,47 ./. ./. 0/1:1,1:2:29.16:29,0,41 ./. 0/0:1,0:1:3.01:0,3,47 1/1:0,1:1:3.01:35,3,0 0/0:3,0:3:9.03:0,9,142 0/0:2,0:2:6.02:0,6,94 0/0:2,0:2:6.01:0,6,60 0/0:3,0:3:6.02:0,6,94 ./. 0/0:2,0:2:6.02:0,6,80 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,47 ./. ./. ./. ./. 0/1:1,1:2:29.16:29,0,41 ./. 0/0:1,0:1:3.01:0,3,47 ./. 0/0:1,1:2:3.01:0,3,47 0/0:1,0:1:3:0,3,27 ./. 0/0:1,0:1:3.01:0,3,47 0/0:1,0:1:3.01:0,3,47 0/0:1,0:1:3.01:0,3,47 0/0:2,0:2:6.02:0,6,94 ./. ./. ./. ./. ./. ./. ./. -chr1 30895 . T C 51.79 . AC=4;AF=0.069;AN=58;BaseQRankSum=-0.230;DP=63;Dels=0.00;FS=11.041;HRun=0;HaplotypeScore=0.2091;InbreedingCoeff=-0.0237;MQ=36.09;MQ0=0;MQRankSum=1.212;QD=3.98;ReadPosRankSum=0.230;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|2),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000473358|||||lincRNA|1,intron_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000469289|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000417324|||||lincRNA|1,downstream_gene_variant|||ENSG00000243485|MIR1302-10|ENST00000607096|||||miRNA|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000461467|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1 GT:AD:DP:GQ:PL 0/1:7,1:8:8.58:9,0,188 0/1:1,2:3:29.23:33,0,29 0/0:6,0:6:18.04:0,18,206 0/0:5,0:5:12.03:0,12,139 ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. 0/0:3,0:3:9.03:0,9,119 0/0:2,0:2:6.02:0,6,80 0/0:1,0:1:3.01:0,3,40 ./. 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,38 ./. ./. 0/0:2,0:2:6.02:0,6,79 ./. ./. 0/0:1,0:1:3.01:0,3,32 0/0:3,0:3:9.03:0,9,110 0/0:2,0:2:6.02:0,6,79 1/1:0,2:2:6.02:77,6,0 0/0:2,0:2:6.02:0,6,76 ./. 0/0:2,0:2:6.02:0,6,79 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,34 ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,77 ./. 0/0:1,0:1:3.01:0,3,40 ./. 0/0:2,0:2:6.02:0,6,74 0/0:1,0:1:3:0,3,25 ./. ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,76 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. ./. ./. ./. -chr1 30923 . G T 601.49 . AC=30;AF=1.000;AN=30;DP=17;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=-0.1858;MQ=35.61;MQ0=0;QD=35.38;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|2),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000473358|||||lincRNA|1,intron_variant&nc_transcript_variant|||ENSG00000243485|MIR1302-10|ENST00000469289|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000488147|||||unprocessed_pseudogene|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000417324|||||lincRNA|1,downstream_gene_variant|||ENSG00000243485|MIR1302-10|ENST00000607096|||||miRNA|1,downstream_gene_variant|||ENSG00000237613|FAM138A|ENST00000461467|||||lincRNA|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000538476|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000438504|||||unprocessed_pseudogene|1,upstream_gene_variant|||ENSG00000227232|WASH7P|ENST00000423562|||||unprocessed_pseudogene|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 ./. 1/1:0,1:1:3.01:40,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 1/1:0,1:1:3.01:40,3,0 1/1:0,1:1:3.01:40,3,0 1/1:0,1:1:3.01:40,3,0 ./. 1/1:0,1:1:3.01:40,3,0 ./. 1/1:0,2:2:6.02:78,6,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:34,3,0 1/1:0,1:1:3.01:30,3,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 ./. 1/1:0,2:2:6.02:77,6,0 1/1:0,1:1:3:25,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 1/1:0,1:1:3.01:40,3,0 ./. ./. ./. ./. ./. ./. -chr1 69270 . A G 2971.02 . AC=53;AF=0.946;AN=56;BaseQRankSum=1.675;DP=100;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0340;InbreedingCoeff=0.1553;MQ=31.06;MQ0=0;MQRankSum=-0.742;QD=31.61;ReadPosRankSum=-1.925;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S60|305|OR4F5|protein_coding|CODING|ENST00000335137|);CSQ=synonymous_variant|tcA/tcG|S|ENSG00000186092|OR4F5|ENST00000335137|1/1|||60/305|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 1/1:0,3:3:9.03:106,9,0 1/1:0,6:6:18.05:203,18,0 1/1:0,7:7:21.06:236,21,0 1/1:0,1:1:3.01:33,3,0 1/1:0,9:9:27.08:309,27,0 1/1:0,7:7:21.06:244,21,0 1/1:0,4:4:12.03:140,12,0 ./. 1/1:0,7:7:18.05:206,18,0 ./. ./. 1/1:0,2:2:6.02:67,6,0 1/1:0,3:3:9.03:106,9,0 1/1:0,2:2:6.02:67,6,0 1/1:0,2:2:6.02:73,6,0 ./. ./. 1/1:0,6:6:18.05:206,18,0 1/1:0,2:2:6.02:69,6,0 1/1:0,4:4:6.02:73,6,0 ./. ./. ./. 1/1:0,2:2:6.02:71,6,0 1/1:0,2:2:6.02:67,6,0 ./. 1/1:0,4:4:12.03:140,12,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,6:6:18.05:212,18,0 1/1:0,3:3:9.03:112,9,0 1/1:1,2:3:6.02:73,6,0 1/1:0,1:1:3.01:32,3,0 ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. 0/1:2,1:3:24.41:24,0,58 ./. ./. 1/1:0,2:2:6.02:69,6,0 ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. 0/0:3,0:3:9.03:0,9,112 ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 -chr1 69428 . T G 938.56 . AC=3;AF=0.0283;AN=106;BaseQRankSum=-0.638;DP=5013;DS;Dels=0.00;FS=2.607;HRun=0;HaplotypeScore=2.5603;InbreedingCoeff=0.3557;MQ=29.79;MQ0=0;MQRankSum=-5.524;QD=18.40;ReadPosRankSum=4.047;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F113C|305|OR4F5|protein_coding|CODING|ENST00000335137|);CSQ=missense_variant|tTt/tGt|F/C|ENSG00000186092|OR4F5|ENST00000335137|1/1|possibly_damaging(0.568)|deleterious(0)|113/305|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.01:0,6,62 0/0:79,0:79:99:0,201,1853 0/0:87,0:87:99:0,243,2236 0/0:107,0:107:99:0,294,2744 0/0:128,0:128:99:0,378,3442 0/0:165,0:165:99:0,486,4434 0/0:250,0:250:99:0,735,6705 0/0:173,0:174:99:0,504,4669 0/0:129,0:129:99:0,387,3547 ./. 0/0:133,0:133:99:0,390,3764 ./. ./. 0/0:111,0:111:99:0,315,3067 0/0:112,1:113:99:0,297,2962 0/0:156,0:156:99:0,426,4417 0/0:109,0:109:99:0,300,3096 0/0:2,0:2:5.99:0,6,49 0/0:98,1:99:99:0,251,2648 0/0:249,0:249:99:0,705,6903 0/0:216,0:216:99:0,585,5798 0/0:248,1:249:99:0,684,6939 0/0:94,0:94:99:0,249,2574 ./. 0/0:2,0:2:5.99:0,6,49 0/0:89,0:89:99:0,243,2463 0/0:111,0:111:99:0,309,3050 0/0:1,0:1:3:0,3,25 0/0:235,0:235:99:0,657,6464 0/0:1,0:1:3:0,3,25 0/0:1,0:1:3:0,3,25 0/0:99,0:99:99:0,276,2796 0/0:113,0:113:99:0,315,3121 0/0:145,0:145:99:0,396,3880 0/0:106,0:106:99:0,297,2864 0/0:111,0:111:99:0,312,3136 0/0:120,1:121:99:0,342,3428 0/0:122,0:122:99:0,339,3227 0/0:87,0:87:99:0,231,2383 0/0:30,0:30:86.95:0,87,802 0/0:71,0:71:99:0,201,1905 0/0:36,0:36:99:0,102,1010 0/0:50,0:50:99:0,138,1359 0/0:41,0:41:99:0,117,1176 0/0:3,0:3:8.99:0,9,74 0/1:1,1:2:18.69:19,0,19 1/1:3,46:49:73.52:1002,74,0 0/0:95,0:95:99:0,252,2781 0/0:73,0:73:99:0,201,1974 0/0:2,1:3:6.01:0,6,65 0/0:78,1:79:99:0,228,2259 0/0:56,0:56:99:0,150,1526 0/0:139,0:139:99:0,375,3773 0/0:68,0:68:99:0,189,1813 0/0:1,0:1:3.01:0,3,42 0/0:177,0:177:99:0,471,5073 ./. ./. ./. 0/0:42,0:42:99:0,105,1086 -chr1 69511 . A G 101944.44 . AC=79;AF=0.878;AN=90;BaseQRankSum=-1.592;DP=3853;DS;Dels=0.00;FS=20.586;HRun=0;HaplotypeScore=3.0494;InbreedingCoeff=0.1357;MQ=33.24;MQ0=0;MQRankSum=-12.858;QD=26.51;ReadPosRankSum=-1.756;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T141A|305|OR4F5|protein_coding|CODING|ENST00000335137|);CSQ=missense_variant|Aca/Gca|T/A|ENSG00000186092|OR4F5|ENST00000335137|1/1|benign(0.003)|tolerated(0.63)|141/305|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/1:2,4:6:15.70:16,0,40 0/1:2,2:4:21.59:22,0,40 1/1:0,4:4:6.02:67,6,0 0/1:2,4:6:37.36:55,0,37 0/1:5,4:9:38.25:38,0,102 1/1:0,2:2:3:29,3,0 0/1:1,5:7:12.68:78,0,13 ./. 1/1:1,3:4:3.01:33,3,0 0/0:1,0:1:3.01:0,3,40 ./. 1/1:0,130:131:99:3915,369,0 1/1:0,115:117:99:3317,321,0 1/1:0,153:155:99:4531,438,0 1/1:0,120:121:99:3353,324,0 ./. 1/1:1,89:91:99:2470,246,0 1/1:0,249:250:99:7207,717,0 1/1:1,223:228:99:6363,598,0 1/1:0,249:250:99:6985,690,0 1/1:0,93:96:99:2711,267,0 ./. ./. 1/1:0,114:114:99:3155,321,0 1/1:0,113:113:99:3241,318,0 ./. 1/1:1,249:250:99:6915,705,0 ./. ./. 1/1:1,101:103:99:2770,239,0 1/1:0,131:132:99:3728,366,0 1/1:0,131:131:99:3508,342,0 1/1:0,104:106:99:2935,291,0 1/1:1,110:111:99:3253,306,0 1/1:0,134:137:99:3791,378,0 1/1:0,129:132:99:3403,360,0 1/1:1,89:91:99:2649,222,0 1/1:0,33:33:93.02:937,93,0 1/1:0,45:46:99:1385,135,0 1/1:0,36:36:99:991,99,0 1/1:0,54:54:99:1556,147,0 1/1:1,49:51:99:1435,106,0 ./. ./. ./. 0/1:71,27:98:99:559,0,2203 1/1:0,59:60:99:1553,153,0 1/1:0,2:2:3.01:37,3,0 1/1:0,82:83:99:2374,225,0 1/1:0,65:65:99:1808,186,0 1/1:0,134:135:99:3522,348,0 1/1:0,66:67:99:1769,183,0 0/0:2,0:2:6.02:0,6,82 0/1:82,97:179:99:2493,0,2281 ./. ./. 1/1:0,1:1:3:25,3,0 1/1:0,34:34:90.08:964,90,0 -chr1 69761 . A T 1026.71 . AC=8;AF=0.091;AN=88;BaseQRankSum=1.333;DP=574;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.3806;InbreedingCoeff=0.5887;MQ=32.18;MQ0=0;MQRankSum=-2.342;QD=21.39;ReadPosRankSum=-3.271;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D224V|305|OR4F5|protein_coding|CODING|ENST00000335137|);CSQ=missense_variant|gAt/gTt|D/V|ENSG00000186092|OR4F5|ENST00000335137|1/1|benign(0.072)|tolerated(0.1)|224/305|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,33 0/1:6,1:7:12.39:12,0,177 0/0:12,0:12:36.11:0,36,442 0/0:9,0:9:27.08:0,27,324 0/0:6,0:6:18.05:0,18,212 0/0:25,0:25:75.23:0,75,904 0/0:26,0:26:78.24:0,78,946 1/1:0,21:21:63.19:761,63,0 0/0:14,0:14:39.10:0,39,447 ./. 0/0:11,0:11:33.10:0,33,409 ./. ./. 0/0:15,0:15:42.12:0,42,492 0/0:15,0:15:45.14:0,45,553 0/1:7,6:13:99:167,0,202 0/0:19,0:19:57.17:0,57,685 0/0:1,0:1:3:0,3,25 0/0:12,0:12:30.07:0,30,337 0/0:25,0:25:75.22:0,75,899 0/0:14,0:14:39.12:0,39,464 0/0:40,0:40:99:0,117,1412 0/0:19,0:19:57.14:0,57,660 ./. ./. 0/0:15,0:15:45.13:0,45,523 0/0:21,0:21:60.18:0,60,714 ./. 0/0:20,0:20:60.18:0,60,715 ./. ./. 0/0:7,0:7:21.06:0,21,252 0/0:15,0:15:45.13:0,45,527 0/0:10,0:10:30.09:0,30,346 0/0:16,0:16:48.15:0,48,588 0/0:16,0:16:48.14:0,48,562 0/0:12,0:12:36.11:0,36,441 0/0:16,0:16:48.14:0,48,575 0/0:7,0:7:21.06:0,21,230 1/1:0,3:3:9.03:106,9,0 0/0:5,0:5:15.05:0,15,183 0/0:7,0:7:21.06:0,21,245 0/0:3,0:3:9.03:0,9,116 0/0:5,0:5:15.05:0,15,185 ./. ./. ./. 0/0:12,0:12:36.10:0,36,417 1/1:0,3:4:9.03:106,9,0 ./. 0/0:14,0:14:39.11:0,39,462 0/0:7,0:7:21.06:0,21,258 0/0:22,0:22:66.19:0,66,775 0/0:7,0:7:21.06:0,21,244 ./. 0/0:23,0:23:66.20:0,66,798 ./. ./. ./. 0/0:2,0:2:6.02:0,6,67 -chr1 69871 . G A 82.97 . AC=2;AF=0.025;AN=80;BaseQRankSum=-0.646;DP=154;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.1095;InbreedingCoeff=0.1693;MQ=31.10;MQ0=0;MQRankSum=-0.154;QD=20.74;ReadPosRankSum=-0.292;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D261N|305|OR4F5|protein_coding|CODING|ENST00000335137|);CSQ=missense_variant|Gat/Aat|D/N|ENSG00000186092|OR4F5|ENST00000335137|1/1|probably_damaging(0.968)|tolerated(0.06)|261/305|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:4,0:4:12.02:0,12,129 0/0:2,0:2:6.02:0,6,67 0/0:2,0:2:6.02:0,6,73 0/0:8,0:8:24.06:0,24,265 0/0:16,0:16:48.12:0,48,538 0/0:10,0:10:30.09:0,30,358 0/0:5,0:5:15.03:0,15,164 0/0:5,0:5:15.04:0,15,179 ./. 0/0:2,0:2:6.02:0,6,67 0/0:2,0:2:5.99:0,6,49 ./. 0/0:3,0:3:9.03:0,9,111 0/0:2,0:2:6.02:0,6,73 0/0:6,0:6:18.04:0,18,202 0/0:4,0:4:12.03:0,12,140 ./. 0/0:3,0:3:9.03:0,9,106 0/0:4,0:4:12.04:0,12,145 0/0:4,0:4:12.04:0,12,144 0/0:11,0:11:33.10:0,33,401 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:4,0:4:12.03:0,12,140 ./. 0/0:9,0:9:27.07:0,27,314 ./. ./. 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:3.01:0,3,33 1/1:0,4:4:12.03:140,12,0 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,67 0/0:3,0:3:9.03:0,9,104 0/0:2,0:2:6.02:0,6,77 0/0:5,0:5:15.03:0,15,157 ./. ./. 0/0:2,0:2:6.01:0,6,63 ./. 0/0:4,0:4:12.03:0,12,140 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:3,0:3:9.03:0,9,102 0/0:2,0:2:6.02:0,6,76 ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:6,0:7:18.02:0,18,183 ./. ./. 0/0:4,0:4:12.04:0,12,153 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 -chr1 69897 . T C 2544.15 . AC=52;AF=0.813;AN=64;BaseQRankSum=-0.912;DP=92;Dels=0.00;FS=58.362;HRun=1;HaplotypeScore=0.1549;InbreedingCoeff=0.0561;MQ=30.68;MQ0=0;MQRankSum=3.326;QD=28.59;ReadPosRankSum=1.059;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S269|305|OR4F5|protein_coding|CODING|ENST00000335137|);CSQ=synonymous_variant|tcT/tcC|S|ENSG00000186092|OR4F5|ENST00000335137|1/1|||269/305|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,3:3:9.01:96,9,0 1/1:0,4:4:12.03:139,12,0 1/1:0,2:2:6.02:73,6,0 0/1:1,4:5:9.66:119,0,10 1/1:0,8:8:24.07:285,24,0 1/1:0,5:5:15.05:185,15,0 0/1:1,6:7:3.64:185,0,4 1/1:0,2:2:6:58,6,0 ./. 1/1:0,1:1:3.01:39,3,0 0/0:1,0:1:3:0,3,25 ./. 1/1:0,4:4:12.04:151,12,0 0/1:2,1:3:24.43:24,0,40 0/1:1,2:3:15.67:58,0,16 1/1:0,3:3:9.02:97,9,0 ./. ./. 1/1:0,3:3:9.03:106,9,0 1/1:0,3:3:9.03:106,9,0 1/1:0,5:5:15.04:176,15,0 1/1:0,1:1:3.01:39,3,0 ./. ./. 1/1:0,2:2:6.02:72,6,0 ./. ./. 0/1:1,5:6:9.65:125,0,10 ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. 0/0:1,0:1:3.01:0,3,39 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:32,3,0 1/1:0,2:2:6.02:79,6,0 1/1:0,4:4:12.03:127,12,0 ./. ./. 1/1:0,2:2:6.02:73,6,0 ./. 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/1:2,1:3:24.41:24,0,64 ./. ./. ./. ./. 1/1:0,2:2:6:58,6,0 ./. ./. ./. ./. ./. ./. ./. -chr1 861008 . G C 1110.54 . AC=40;AF=0.870;AN=46;BaseQRankSum=1.889;DP=38;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=0.1855;MQ=56.89;MQ0=0;MQRankSum=1.660;QD=33.65;ReadPosRankSum=-1.946;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|1),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|1),UPSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1,upstream_gene_variant|||ENSG00000223764|RP11-54O7.3|ENST00000609207|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:35,3,0 ./. ./. ./. 1/1:0,1:1:3.01:37,3,0 1/1:0,1:1:3.01:34,3,0 ./. 1/1:0,6:6:18.04:222,18,0 1/1:0,4:4:12.04:164,12,0 ./. ./. ./. ./. ./. ./. 1/1:0,2:2:6.02:82,6,0 ./. ./. ./. 0/0:1,0:1:3:0,3,25 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. 1/1:0,1:1:3.01:37,3,0 0/0:1,0:1:3.01:0,3,39 ./. ./. 1/1:0,2:2:6.01:66,6,0 ./. ./. ./. 0/0:1,0:1:3:0,3,25 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:3.01:45,3,0 ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:40,3,0 1/1:0,1:1:3.01:33,3,0 1/1:0,2:2:3.01:45,3,0 ./. ./. 1/1:0,2:2:6.02:79,6,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 1/1:0,1:1:3.01:37,3,0 ./. ./. ./. ./. -chr1 861605 . C T 52.33 . AC=1;AF=0.0085;AN=118;BaseQRankSum=-0.110;DP=330;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.2194;InbreedingCoeff=-0.0688;MQ=57.00;MQ0=0;MQRankSum=-0.597;QD=10.47;ReadPosRankSum=-1.210;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|2),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|2),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|2);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.01:0,6,63 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,39 0/0:5,0:5:12.04:0,12,153 0/0:2,0:2:6.02:0,6,81 0/0:5,0:5:12.04:0,12,155 0/1:2,3:5:48.88:99,0,49 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:9.03:0,9,111 0/0:4,0:4:9.03:0,9,117 0/0:3,0:3:9.03:0,9,118 0/0:4,0:4:12.04:0,12,154 0/0:2,0:2:3.01:0,3,35 0/0:1,0:1:3.01:0,3,41 0/0:5,0:5:12.04:0,12,155 ./. 0/0:5,0:5:15.05:0,15,190 0/0:3,0:3:9.03:0,9,120 0/0:6,0:6:18.06:0,18,227 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.04:0,12,162 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,72 0/0:2,0:2:3.01:0,3,41 0/0:5,0:5:15.05:0,15,187 0/0:3,0:3:6.02:0,6,70 0/0:5,0:5:12.04:0,12,159 0/0:5,0:5:12.02:0,12,139 0/0:2,0:2:6.02:0,6,83 0/0:6,0:6:18.06:0,18,233 0/0:3,0:3:9.02:0,9,103 0/0:5,0:5:12.04:0,12,147 0/0:8,0:8:24.07:0,24,300 0/0:8,0:9:21.07:0,21,281 0/0:8,0:8:18.06:0,18,241 0/0:13,0:13:39.12:0,39,486 0/0:9,0:9:18.06:0,18,240 0/0:3,0:3:9.03:0,9,121 0/0:12,0:12:36.11:0,36,450 0/0:4,0:4:12.04:0,12,158 0/0:6,0:6:15.04:0,15,176 0/0:7,0:7:15.04:0,15,179 0/0:17,0:17:48.15:0,48,622 0/0:8,0:8:24.07:0,24,279 0/0:6,0:6:18.06:0,18,229 0/0:20,0:20:51.13:0,51,602 0/0:18,0:18:51.15:0,51,633 0/0:10,0:10:30.06:0,30,343 0/0:10,0:10:24.08:0,24,301 0/0:4,0:4:12.04:0,12,154 0/0:9,0:9:27.08:0,27,343 0/0:6,0:6:12.04:0,12,152 0/0:15,0:15:36.11:0,36,463 0/0:3,0:3:6.02:0,6,75 0/0:9,0:9:18.06:0,18,249 0/0:7,0:7:21.06:0,21,256 -chr1 861630 . G A 5677.14 . AC=75;AF=0.7212;AN=104;BaseQRankSum=-3.827;DP=239;Dels=0.00;FS=4.448;HRun=0;HaplotypeScore=0.6050;InbreedingCoeff=0.2720;MQ=57.64;MQ0=0;MQRankSum=-2.334;QD=28.82;ReadPosRankSum=-1.755;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|2),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|2),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|2);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:5.99:61,6,0 ./. 0/1:2,1:3:30.98:31,0,67 0/0:2,0:2:6.02:0,6,81 1/1:0,1:1:3.01:39,3,0 0/1:1,6:7:19.58:202,0,20 1/1:0,3:3:9.03:108,9,0 1/1:0,4:4:9.03:118,9,0 1/1:0,4:4:9.03:115,9,0 1/1:0,2:2:6.02:81,6,0 1/1:0,2:2:3.01:35,3,0 0/1:2,2:4:54.65:65,0,55 1/1:0,2:2:3.01:38,3,0 0/1:1,1:2:25.53:26,0,34 1/1:0,3:3:9.03:119,9,0 ./. ./. 1/1:0,3:3:6.02:83,6,0 ./. 0/1:1,3:4:28.61:110,0,29 1/1:0,2:2:6.02:71,6,0 1/1:0,5:5:15.05:191,15,0 0/0:1,0:1:3.01:0,3,42 1/1:0,3:3:9.03:118,9,0 ./. 0/0:2,0:2:6.02:0,6,81 ./. 1/1:0,3:4:9.03:119,9,0 1/1:0,3:3:9.03:116,9,0 1/1:0,5:5:12.03:140,12,0 1/1:0,3:3:6.02:79,6,0 ./. 0/0:2,0:2:6.02:0,6,82 0/0:3,0:3:9.03:0,9,120 1/1:0,3:3:6.02:82,6,0 0/1:2,3:5:62.58:97,0,63 0/0:7,0:7:18.06:0,18,229 0/1:1,5:6:23.18:168,0,23 1/1:0,8:8:24.08:314,24,0 1/1:0,7:7:18.06:235,18,0 1/1:0,2:2:6.02:83,6,0 1/1:0,6:6:18.06:235,18,0 1/1:0,2:2:6.02:78,6,0 0/1:3,2:5:59.19:59,0,67 1/1:0,5:5:15.04:183,15,0 0/1:5,6:12:99:212,0,177 0/0:6,0:6:18.06:0,18,227 1/1:0,4:4:9.03:124,9,0 0/1:7,9:16:99:246,0,201 0/0:11,0:12:33.11:0,33,444 1/1:0,7:8:21.03:246,21,0 1/1:0,6:6:18.05:224,18,0 1/1:0,3:3:6.02:81,6,0 1/1:0,3:3:9.02:104,9,0 1/1:0,5:5:15.04:184,15,0 1/1:0,10:10:30.10:394,30,0 0/1:1,1:2:24.58:27,0,25 1/1:0,8:8:21.04:236,21,0 0/0:5,0:5:15.05:0,15,195 -chr1 861808 . A G 1231.98 . AC=34;AF=1.000;AN=34;DP=36;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0587;InbreedingCoeff=-0.1349;MQ=57.39;MQ0=0;QD=34.22;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|2),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|2),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|2);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3.01:38,3,0 1/1:0,3:3:9.03:113,9,0 1/1:0,2:2:6.02:76,6,0 1/1:0,6:6:18.05:219,18,0 1/1:0,2:2:6.02:81,6,0 ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:41,3,0 ./. 1/1:0,2:2:6.02:81,6,0 ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,3:3:6.02:87,6,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,6:6:12.03:143,12,0 ./. ./. ./. ./. ./. 1/1:0,2:2:6.02:83,6,0 ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 ./. 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,2:2:6.02:76,6,0 ./. ./. -chr1 864938 . G A 38.62 . AC=4;AF=0.67;AN=6;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=4.771;HRun=0;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;MQRankSum=-0.736;QD=19.31;ReadPosRankSum=0.736;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|2),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|2),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|2);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,35 -chr1 865219 . G A 271.52 . AC=14;AF=0.226;AN=62;BaseQRankSum=-0.335;DP=65;Dels=0.00;FS=1.303;HRun=0;HaplotypeScore=0.1417;InbreedingCoeff=0.1395;MQ=57.84;MQ0=0;MQRankSum=0.625;QD=14.29;ReadPosRankSum=-0.407;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|2),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|2),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|2);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,68 0/0:7,0:7:21.07:0,21,268 0/1:3,1:4:24.09:24,0,103 0/1:1,1:2:31.78:32,0,35 ./. 1/1:0,2:2:6.02:81,6,0 0/1:2,1:3:27.95:28,0,71 0/0:1,0:1:3.01:0,3,41 0/0:5,0:5:15.05:0,15,194 0/0:5,0:5:15.05:0,15,183 0/1:2,2:4:66.54:67,0,69 0/0:3,0:3:9.03:0,9,122 1/1:0,1:1:3.01:38,3,0 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,35 1/1:0,1:1:3.01:37,3,0 ./. 0/0:3,0:3:9.03:0,9,113 ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,73 0/0:3,0:3:6.02:0,6,72 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,75 ./. ./. -chr1 865367 . G T 48.93 . AC=2;AF=0.022;AN=90;BaseQRankSum=-0.637;DP=186;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3749;InbreedingCoeff=0.1476;MQ=55.90;MQ0=0;MQRankSum=2.051;QD=16.31;ReadPosRankSum=0.013;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|2),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|2),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|2);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3.01:0,3,34 0/0:2,0:2:6.02:0,6,77 0/0:4,0:4:12.04:0,12,156 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:6.02:0,6,82 0/0:5,0:5:12.04:0,12,156 ./. 0/0:6,0:6:12.04:0,12,161 0/0:5,0:5:9.03:0,9,116 0/0:3,0:3:9.03:0,9,124 0/0:3,0:3:9.03:0,9,111 0/0:3,0:3:9.03:0,9,112 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,80 ./. ./. ./. ./. 0/0:1,0:1:3:0,3,29 0/0:3,0:3:6.02:0,6,68 0/0:3,0:3:9.03:0,9,117 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,41 ./. 0/0:3,0:3:9.03:0,9,108 ./. ./. ./. ./. 1/1:0,3:3:9.01:103,9,0 0/0:4,0:4:8.99:0,9,83 0/0:4,0:4:12.04:0,12,164 0/0:9,0:9:18.05:0,18,222 0/0:9,0:9:18.05:0,18,230 0/0:3,0:3:6.02:0,6,75 0/0:6,0:6:12.04:0,12,159 0/0:5,0:5:12.03:0,12,145 0/0:7,0:7:15.03:0,15,172 0/0:5,0:5:15.05:0,15,195 0/0:8,0:8:21.07:0,21,270 0/0:3,0:3:9.01:0,9,97 ./. 0/0:11,0:11:27.09:0,27,351 0/0:7,0:7:21.05:0,21,255 0/0:8,0:8:21.06:0,21,254 0/0:4,0:4:12.04:0,12,165 0/0:7,0:7:21.06:0,21,247 0/0:5,0:5:15.05:0,15,197 0/0:4,0:4:6.02:0,6,82 0/0:4,0:4:9.03:0,9,122 0/0:5,0:5:12.04:0,12,153 0/0:5,0:5:12.04:0,12,164 0/0:2,0:2:6.02:0,6,79 -chr1 865435 . C G 566.25 . AC=2;AF=0.0185;AN=108;BaseQRankSum=1.312;DP=479;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6697;InbreedingCoeff=-0.0645;MQ=56.23;MQ0=0;MQRankSum=-0.467;QD=18.88;ReadPosRankSum=-0.530;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|2),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|2),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|2);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:6.02:0,6,68 ./. 0/0:1,0:1:3:0,3,27 ./. 0/0:6,0:6:18.06:0,18,244 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,73 0/0:9,0:9:27.07:0,27,350 0/1:1,5:6:16.30:180,0,16 0/0:5,0:5:15.05:0,15,188 0/0:6,0:6:18.06:0,18,229 ./. 0/0:1,0:1:3.01:0,3,39 0/0:6,0:6:18.06:0,18,232 0/0:2,0:2:6.02:0,6,78 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 0/0:4,0:4:12.04:0,12,155 0/0:3,0:3:9.03:0,9,111 0/0:3,0:3:9.03:0,9,104 0/0:4,0:4:12.04:0,12,157 ./. 0/0:3,0:3:9.03:0,9,120 0/0:1,0:1:3.01:0,3,36 0/0:3,0:3:6.02:0,6,83 0/0:3,0:3:6.02:0,6,87 0/0:1,0:1:3.01:0,3,39 0/0:6,0:6:15.05:0,15,192 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.02:0,6,84 ./. 0/0:3,0:3:9.03:0,9,118 0/0:3,0:3:9.03:0,9,116 0/0:4,0:4:12.04:0,12,153 0/0:4,0:4:9.03:0,9,119 0/0:6,0:6:12.04:0,12,164 0/0:3,0:3:9.03:0,9,117 0/0:11,0:11:24.05:0,24,300 0/0:17,0:18:45.10:0,45,538 0/0:31,0:31:75.24:0,75,970 0/0:11,0:11:30.09:0,30,377 0/0:14,0:14:39.12:0,39,487 0/0:13,0:13:30.07:0,30,380 0/0:11,1:12:30.09:0,30,381 0/0:30,0:30:84.25:0,84,1043 0/0:33,0:33:87.27:0,87,1082 0/0:1,0:8:3.01:0,3,37 0/0:8,0:8:21.07:0,21,279 0/0:24,0:24:66.20:0,66,834 0/1:10,14:24:99:450,0,271 0/0:23,0:23:63.16:0,63,729 0/0:16,0:16:36.11:0,36,448 0/0:13,0:14:27.08:0,27,342 0/0:17,0:17:45.14:0,45,574 0/0:9,0:9:21.06:0,21,253 0/0:10,0:10:30.09:0,30,375 0/0:16,1:17:42.13:0,42,539 0/0:13,0:13:36.10:0,36,440 0/0:13,0:13:39.12:0,39,478 -chr1 865694 . C T 2783.07 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-1.642;DP=2811;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.6308;InbreedingCoeff=-0.0276;MQ=58.79;MQ0=0;MQRankSum=1.333;QD=13.71;ReadPosRankSum=0.518;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H78Y|108|SAMD11|protein_coding|CODING|ENST00000437963|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H78Y|178|SAMD11|protein_coding|CODING|ENST00000420190|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H78Y|681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=missense_variant|Cac/Tac|H/Y|ENSG00000187634|SAMD11|ENST00000420190|3/7|possibly_damaging(0.493)|tolerated(0.09)|78/179|protein_coding|1,missense_variant|tGc/tAc|C/Y|ENSG00000268179|AL645608.1|ENST00000598827|3/6|possibly_damaging(0.598)||18/112|protein_coding|1,missense_variant|Cac/Tac|H/Y|ENSG00000187634|SAMD11|ENST00000437963|3/5|possibly_damaging(0.493)|tolerated(0.12)|78/109|protein_coding|1,missense_variant|Cac/Tac|H/Y|ENSG00000187634|SAMD11|ENST00000342066|3/14|possibly_damaging(0.493)|tolerated(0.07)|78/681|protein_coding|1,missense_variant|Cac/Tac|H/Y|ENSG00000187634|SAMD11|ENST00000341065|1/12|probably_damaging(0.986)|deleterious(0)|2/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12.04:0,12,145 0/0:3,0:3:9.03:0,9,107 0/0:8,0:8:24.07:0,24,295 0/0:5,0:5:15.04:0,15,169 0/0:6,0:6:18.06:0,18,241 0/0:10,0:10:30.10:0,30,391 0/0:19,0:19:54.17:0,54,710 0/0:11,0:11:33.10:0,33,422 0/0:22,0:22:66.21:0,66,868 0/0:23,0:23:69.17:0,69,861 0/0:11,0:11:33.10:0,33,423 0/0:10,0:10:30.09:0,30,384 0/0:15,0:15:42.10:0,42,526 0/0:43,0:43:99:0,99,1290 0/0:65,0:65:99:0,147,1926 0/0:49,0:49:99:0,117,1585 0/0:63,0:63:99:0,162,2060 0/0:65,0:65:99:0,138,1802 0/0:65,0:65:99:0,166,2183 0/0:61,0:62:99:0,135,1801 0/0:41,0:41:99:0,102,1336 0/0:79,0:79:99:0,178,2301 0/0:58,0:59:99:0,123,1679 0/0:56,0:56:99:0,132,1748 0/0:56,1:57:99:0,141,1846 0/0:61,0:62:99:0,144,1881 0/1:40,31:71:99:737,0,1137 0/0:43,0:43:99:0,99,1275 0/0:63,0:63:99:0,147,1939 0/0:69,0:69:99:0,169,2234 0/0:64,0:64:99:0,153,1988 0/0:37,1:38:67.58:0,68,1114 0/0:53,0:53:99:0,126,1691 0/0:76,0:76:99:0,163,2127 0/1:27,38:66:99:1058,0,681 0/0:56,0:56:99:0,132,1732 0/1:26,40:66:99:1068,0,626 0/0:114,0:114:99:0,265,3537 0/0:49,0:49:99:0,138,1725 0/0:106,0:107:99:0,274,3515 0/0:64,0:64:99:0,159,2072 0/0:50,0:50:99:0,117,1530 0/0:50,0:50:99:0,126,1620 0/0:43,0:43:99:0,108,1381 0/0:44,0:44:99:0,114,1458 0/0:43,0:43:99:0,108,1398 0/0:65,0:65:99:0,162,2066 0/0:42,0:42:99:0,108,1328 0/0:62,0:62:99:0,147,1964 0/0:55,0:55:99:0,153,1924 0/0:55,0:55:99:0,141,1791 0/0:57,0:57:99:0,132,1705 0/0:45,0:45:99:0,114,1410 0/0:48,0:48:99:0,120,1548 0/0:50,0:50:99:0,138,1771 0/0:36,0:36:93.25:0,93,1171 0/0:37,0:37:96.31:0,96,1276 0/0:44,0:44:99:0,114,1476 0/0:42,0:42:96.30:0,96,1282 0/0:30,0:30:87.22:0,87,1099 -chr1 865738 . A G 389.63 . AC=1;AF=0.0083;AN=120;BaseQRankSum=1.098;DP=2190;Dels=0.00;FS=12.943;HRun=2;HaplotypeScore=1.1793;InbreedingCoeff=-0.0108;MQ=58.92;MQ0=0;MQRankSum=1.104;QD=9.28;ReadPosRankSum=0.259;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|3),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|3),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|3);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.04:0,12,153 0/0:4,0:4:12.03:0,12,131 0/0:7,0:7:21.07:0,21,268 0/0:4,0:4:9.03:0,9,104 0/0:10,0:10:30.09:0,30,396 0/0:5,0:5:15.05:0,15,194 0/0:9,0:9:24.07:0,24,304 0/0:10,0:10:30.10:0,30,409 0/0:20,0:21:57.18:0,57,761 0/0:14,0:14:39.13:0,39,521 0/0:16,0:16:48.16:0,48,635 0/0:7,0:7:21.07:0,21,286 0/0:19,0:19:57.19:0,57,759 0/0:42,0:42:99:0,99,1347 0/0:48,0:48:99:0,117,1570 0/0:37,0:37:87.26:0,87,1167 0/0:50,0:50:99:0,132,1730 0/0:48,1:49:99:0,117,1562 0/0:58,0:58:99:0,138,1874 0/0:43,0:43:99:0,102,1357 0/0:27,0:27:66.22:0,66,907 0/0:54,0:54:99:0,132,1759 0/0:40,0:40:99:0,105,1408 0/0:41,0:41:99:0,99,1322 0/0:45,0:45:99:0,120,1575 0/0:48,0:48:99:0,120,1614 0/0:62,0:62:99:0,160,2119 0/0:31,0:31:81.26:0,81,1083 0/0:39,1:40:60.57:0,61,1295 0/0:52,0:52:99:0,120,1613 0/0:55,0:55:99:0,132,1776 0/0:25,0:25:66.22:0,66,881 0/0:30,0:30:72.24:0,72,980 0/0:60,0:60:99:0,147,1903 0/0:53,0:53:99:0,132,1807 0/0:42,0:42:99:0,105,1413 0/0:42,0:42:99:0,102,1352 0/0:86,0:86:99:0,190,2586 0/0:40,0:40:99:0,108,1409 0/0:79,0:79:99:0,193,2516 0/1:27,15:42:99:437,0,851 0/0:46,0:47:99:0,117,1552 0/0:52,0:52:99:0,135,1748 0/0:29,0:29:78.24:0,78,1014 0/0:27,0:27:72.23:0,72,957 0/0:36,0:36:96.31:0,96,1257 0/0:61,0:61:99:0,138,1809 0/0:34,0:35:84.27:0,84,1117 0/0:54,0:54:99:0,129,1745 0/0:47,0:47:99:0,114,1517 0/0:37,0:37:99:0,102,1307 0/0:44,0:44:99:0,105,1423 0/0:47,0:47:99:0,102,1360 0/0:36,0:36:84.27:0,84,1102 0/0:35,0:35:90.29:0,90,1204 0/0:31,0:31:90.28:0,90,1162 0/0:28,0:28:75.23:0,75,1003 0/0:30,0:30:75.25:0,75,1015 0/0:31,0:31:81.26:0,81,1079 0/0:32,0:32:75.24:0,75,1013 -chr1 866319 . G A 53469.99 . AC=118;AF=0.9833;AN=120;BaseQRankSum=1.591;DP=1731;Dels=0.00;FS=7.888;HRun=0;HaplotypeScore=1.0922;InbreedingCoeff=-0.0237;MQ=56.60;MQ0=0;MQRankSum=0.921;QD=30.89;ReadPosRankSum=-0.721;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|3),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|3),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|3);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,4:4:12.04:145,12,0 1/1:0,3:3:3.01:34,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,4:4:12.03:143,12,0 1/1:0,8:8:24.05:308,24,0 1/1:0,11:11:30.10:389,30,0 1/1:0,14:14:42.13:529,42,0 1/1:0,10:10:30.09:398,30,0 1/1:0,14:14:39.13:516,39,0 1/1:0,14:14:42.14:561,42,0 1/1:0,13:13:36.12:466,36,0 1/1:0,8:8:21.07:281,21,0 1/1:0,12:13:27.08:339,27,0 1/1:0,27:27:72.22:939,72,0 1/1:0,36:36:93.27:1180,93,0 1/1:0,18:18:48.13:566,48,0 1/1:0,21:21:54.17:700,54,0 1/1:0,31:31:81.25:1045,81,0 1/1:0,24:24:66.20:839,66,0 1/1:0,34:34:78.24:1010,78,0 1/1:1,23:24:60.18:756,60,0 1/1:0,36:36:84.26:1058,84,0 1/1:0,21:21:54.15:681,54,0 1/1:0,17:17:45.14:577,45,0 1/1:1,26:27:66.20:851,66,0 1/1:0,21:21:60.19:785,60,0 1/1:0,28:28:72.17:900,72,0 1/1:0,26:26:69.17:848,69,0 1/1:0,38:39:93.29:1193,93,0 1/1:0,30:30:81.25:1031,81,0 1/1:0,35:35:90.25:1185,90,0 1/1:0,27:27:66.21:858,66,0 1/1:0,29:29:84.25:1035,84,0 1/1:0,23:23:60.19:791,60,0 1/1:1,28:29:66.18:853,66,0 1/1:0,19:19:48.16:639,48,0 1/1:0,23:23:63.17:777,63,0 1/1:0,48:49:99:1713,129,0 1/1:0,31:32:84.24:1059,84,0 1/1:0,42:43:99:1300,105,0 1/1:0,40:41:99:1278,99,0 1/1:1,30:31:69.22:894,69,0 1/1:1,39:40:99:1259,99,0 1/1:0,43:45:99:1341,102,0 0/1:17,14:32:99:378,0,482 1/1:0,30:30:72.21:935,72,0 1/1:2,49:51:99:1582,126,0 1/1:0,24:24:63.18:825,63,0 1/1:0,47:47:99:1423,108,0 0/1:37,44:81:99:1244,0,958 1/1:0,69:71:99:2237,175,0 1/1:0,42:42:99:1296,105,0 1/1:0,61:65:99:1896,150,0 1/1:0,46:47:99:1347,105,0 1/1:0,32:33:90.25:1145,90,0 1/1:0,40:40:99:1308,102,0 1/1:0,19:19:54.17:687,54,0 1/1:0,38:39:90.26:1139,90,0 1/1:1,36:37:90.28:1154,90,0 1/1:0,26:27:60.19:783,60,0 -chr1 866511 . C CCCCT 58244.04 . AC=74;AF=0.6167;AN=120;BaseQRankSum=-16.318;DP=2662;FS=36.325;HRun=0;HaplotypeScore=234.1454;InbreedingCoeff=-0.0915;MQ=48.89;MQ0=0;MQRankSum=-26.717;QD=25.31;ReadPosRankSum=-3.550;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 1/1:3,3:6:14.41:228,14,0 1/1:5,0:5:12.03:138,12,0 0/0:4,0:4:6.02:0,6,102 1/1:1,1:2:3.01:75,3,0 0/1:7,0:7:26.96:27,0,141 0/0:10,0:10:15.05:0,15,255 0/1:24,4:28:99:404,0,302 1/1:4,1:5:9.03:144,9,0 1/1:30,10:41:60.20:1284,60,0 1/1:18,5:24:39.12:732,39,0 0/1:18,2:20:99:388,0,133 1/1:6,0:6:6.02:68,6,0 0/1:12,0:12:99:132,0,135 0/1:34,10:44:99:1001,0,436 0/1:60,6:66:99:709,0,1203 1/1:12,5:17:24.07:410,24,0 0/1:26,2:28:99:185,0,445 0/1:26,7:33:99:706,0,373 0/1:36,13:50:99:1245,0,400 0/1:40,12:52:99:795,0,1196 0/1:28,4:32:99:488,0,626 0/1:26,22:50:18.06:1675,0,18 0/1:24,9:33:30.41:835,0,30 0/1:30,10:41:99:953,0,431 1/1:15,13:28:3.24:1075,3,0 0/1:28,8:36:99:700,0,472 0/0:62,0:62:99:0,111,1810 0/1:20,10:31:99:947,0,237 1/1:23,18:41:81.27:1729,81,0 0/1:25,18:43:29.28:1415,0,29 1/1:25,19:45:41.39:1767,41,0 1/1:17,16:33:12.28:1279,12,0 0/1:36,10:46:99:906,0,607 0/0:48,0:48:99:0,108,1795 0/0:42,0:42:90.24:0,90,1440 0/1:19,7:26:17.81:643,0,18 0/1:51,3:55:99:261,0,1017 0/0:106,0:107:99:0,209,3529 0/1:40,8:49:99:601,0,892 0/1:54,32:86:5.41:3027,0,5 1/1:40,25:65:99:2323,105,0 1/1:32,23:55:6.52:2096,7,0 0/1:25,22:48:7.63:1899,0,8 1/1:22,13:34:54.18:1188,54,0 0/1:38,5:43:99:434,0,927 1/1:31,28:59:55.22:2238,55,0 0/1:91,17:108:99:1212,0,1929 0/0:45,0:46:99:0,111,1775 0/1:40,19:59:99:1765,0,101 0/1:91,22:116:99:1872,0,1778 0/1:116,19:136:99:1613,0,2200 0/1:43,17:61:44.76:1559,0,45 1/1:49,29:79:99:2925,103,0 1/1:35,17:52:87.16:1620,87,0 1/1:45,28:73:36.62:2451,37,0 1/1:25,18:43:29.24:1623,29,0 1/1:14,18:32:69.22:1624,69,0 0/1:58,13:70:99:1067,0,1182 1/1:27,18:45:87.15:1761,87,0 0/0:42,0:42:78.26:0,78,1240 -chr1 866515 . T TCCCC 28452.17 . AC=52;AF=0.4333;AN=120;BaseQRankSum=20.767;DP=2538;FS=131.119;HRun=4;HaplotypeScore=272.7313;InbreedingCoeff=-0.6682;MQ=48.42;MQ0=0;MQRankSum=-29.484;QD=13.08;ReadPosRankSum=13.879;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/1:6,0:6:37.81:108,0,38 1/1:5,0:5:4.64:24,5,0 0/0:5,0:5:9.03:0,9,145 1/1:2,0:2:3.01:51,3,0 0/0:6,0:6:12.04:0,12,195 0/0:10,0:10:21.05:0,21,332 0/1:24,0:24:99:200,0,566 0/1:6,0:6:41.64:42,0,58 0/1:38,0:38:99:573,0,246 0/1:24,0:25:99:345,0,189 0/1:15,0:15:99:189,0,283 0/0:6,0:6:1.94:0,2,110 0/1:8,0:8:34.11:34,0,181 0/1:42,0:42:99:542,0,684 0/1:65,0:65:99:269,0,1635 0/1:16,0:16:54.14:134,0,54 0/1:25,0:25:21.43:21,0,630 0/1:32,0:33:99:348,0,511 0/1:46,1:47:99:594,0,740 0/1:50,0:50:99:375,0,1471 0/1:32,0:32:99:275,0,798 0/1:47,0:47:99:987,0,251 0/1:30,0:30:99:377,0,358 0/1:38,0:38:99:519,0,656 0/1:26,0:26:99:612,0,171 0/1:34,0:34:99:296,0,760 0/0:57,0:57:99:0,149,2358 0/1:30,0:30:99:486,0,369 0/1:39,0:39:70.67:901,0,71 0/1:38,1:39:99:868,0,299 0/1:43,0:43:99:773,0,306 0/1:31,0:31:99:673,0,213 0/1:41,0:41:99:505,0,733 0/0:46,0:46:99:0,120,2057 0/0:40,0:40:99:0,108,1749 0/1:28,0:28:99:306,0,240 0/1:48,1:49:99:161,0,1378 0/0:103,0:103:99:0,259,4318 0/1:46,0:46:99:220,0,1124 0/1:88,0:88:99:1414,0,506 0/1:62,0:62:99:1197,0,331 0/1:52,0:52:99:1027,0,287 0/1:47,0:47:99:927,0,230 0/1:33,0:33:99:530,0,321 0/1:41,0:41:99:170,0,1164 0/1:57,0:57:99:1139,0,315 0/1:103,0:103:99:472,0,2716 0/0:48,0:48:99:0,123,2021 0/1:57,0:57:99:928,0,431 0/1:113,0:113:99:897,0,2392 0/1:125,0:125:99:801,0,3049 0/1:58,1:59:99:675,0,580 0/1:76,0:76:99:1398,0,344 0/1:50,0:50:99:797,0,210 0/1:71,0:71:99:1374,0,579 0/1:40,1:41:99:866,0,248 0/1:31,0:31:99:769,0,119 0/1:68,0:67:99:479,0,1600 0/1:42,0:42:99:783,0,115 0/0:41,0:41:99:0,111,1680 -chr1 866517 . C G 804.92 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.085;DP=2503;Dels=0.00;FS=17.839;HRun=0;HaplotypeScore=16.1376;InbreedingCoeff=-0.0112;MQ=48.27;MQ0=0;MQRankSum=7.710;QD=18.29;ReadPosRankSum=2.729;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:18.05:0,18,210 0/0:6,0:6:15.04:0,15,182 0/0:5,0:5:15.05:0,15,197 0/0:2,0:2:6.02:0,6,71 0/0:6,0:6:18.06:0,18,239 0/0:10,0:10:27.09:0,27,358 0/0:23,0:23:69.21:0,69,864 0/0:6,0:6:18.05:0,18,217 0/0:37,0:37:99:0,108,1299 0/0:25,0:25:72.17:0,72,879 0/0:14,0:14:42.12:0,42,519 0/0:6,0:6:18.06:0,18,224 0/0:8,0:8:24.08:0,24,308 0/0:42,0:42:99:0,111,1321 0/0:64,0:64:99:0,150,1868 0/0:16,0:16:36.11:0,36,431 0/0:25,0:25:57.13:0,57,706 0/0:31,0:31:87.25:0,87,1048 0/0:48,0:48:99:0,126,1450 0/0:49,0:49:99:0,120,1496 0/0:32,0:32:78.22:0,78,946 0/0:47,0:47:99:0,120,1371 0/0:30,0:30:84.25:0,84,999 0/0:36,1:38:69.66:0,70,1127 0/0:25,0:26:60.18:0,60,716 0/0:35,0:35:96.25:0,96,1133 0/0:55,0:56:99:0,129,1646 0/0:30,0:30:75.22:0,75,904 0/0:38,0:38:99:0,102,1189 0/0:38,0:38:96.28:0,96,1143 0/0:42,0:42:99:0,123,1460 0/0:30,0:30:81.21:0,81,927 0/0:39,0:39:99:0,102,1196 0/1:12,31:44:99:853,0,333 0/0:40,0:40:90.29:0,90,1196 0/0:26,0:26:63.18:0,63,733 0/0:49,0:49:99:0,114,1434 0/0:103,0:103:99:0,247,3239 0/0:46,0:46:99:0,108,1348 0/0:86,0:86:99:0,232,2683 0/0:59,0:59:99:0,159,1790 0/0:50,0:50:99:0,141,1611 0/0:47,0:47:99:0,126,1466 0/0:33,0:33:87.25:0,87,1009 0/0:41,0:41:99:0,108,1373 0/0:56,0:56:99:0,135,1530 0/0:102,0:102:99:0,256,3128 0/0:47,1:48:99:0,114,1451 0/0:54,0:54:99:0,144,1674 0/0:109,0:110:99:0,280,3364 0/0:123,0:123:99:0,325,3929 0/0:59,0:59:99:0,156,1773 0/0:76,0:76:99:0,211,2386 0/0:48,0:48:99:0,132,1485 0/0:71,0:71:99:0,184,2140 0/0:42,0:42:99:0,114,1281 0/0:30,0:30:90.24:0,90,1007 0/0:65,0:65:99:0,159,1954 0/0:42,0:42:99:0,114,1320 0/0:41,0:41:99:0,99,1251 -chr1 866527 . A T 4017.89 . AC=45;AF=0.3750;AN=120;BaseQRankSum=11.973;DP=2186;Dels=0.00;FS=0.676;HRun=0;HaplotypeScore=3.9960;InbreedingCoeff=-0.5937;MQ=46.89;MQ0=0;MQRankSum=0.035;QD=2.40;ReadPosRankSum=-21.689;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/1:4,1:6:30.29:30,0,57 0/1:2,4:6:24.27:121,0,24 0/0:4,0:4:12.04:0,12,141 0/0:1,0:1:3.01:0,3,33 0/1:5,1:6:23.17:23,0,178 0/0:5,1:6:15.04:0,15,178 0/0:16,0:16:48.12:0,48,527 0/1:3,2:5:51.86:52,0,66 0/1:23,5:28:99:106,0,542 0/1:12,6:18:99:180,0,299 0/1:8,4:12:99:107,0,183 0/1:2,1:3:27.96:28,0,51 0/1:6,2:8:53.60:54,0,155 0/1:28,3:35:1.20:1,0,491 0/1:50,5:56:81.94:82,0,606 0/1:7,4:14:79.90:80,0,130 0/1:18,4:23:41.98:42,0,220 0/1:20,3:29:40.88:41,0,453 0/1:34,8:47:60.66:61,0,623 0/0:44,0:45:93.15:0,93,990 0/0:25,3:29:25.53:0,26,538 0/1:34,5:41:39.38:39,0,489 0/1:17,5:24:93.02:93,0,282 0/1:24,5:32:78.68:79,0,395 0/1:15,5:22:33.86:34,0,208 0/1:26,5:33:81.77:82,0,428 0/0:43,1:48:84.15:0,84,932 0/1:20,4:28:49.11:49,0,376 0/1:28,6:35:99:133,0,468 0/1:25,5:32:14.62:15,0,415 0/1:23,11:37:99:202,0,481 0/1:23,4:27:64.71:65,0,455 0/0:31,2:36:3.98:0,4,537 0/0:39,1:40:99:0,102,1174 0/0:29,1:33:66.09:0,66,676 0/1:17,4:22:17.92:18,0,434 0/0:34,2:41:40.48:0,40,708 0/0:84,1:87:99:0,156,1929 0/0:35,2:41:11.27:0,11,712 0/1:51,17:75:99:361,0,1033 0/1:36,8:51:99:109,0,759 0/1:33,7:41:99:120,0,625 0/1:32,7:40:27.91:28,0,652 0/1:21,4:28:69.51:70,0,443 0/1:31,4:38:51.43:51,0,674 0/1:39,7:53:90.61:91,0,751 0/1:77,9:94:0.82:1,0,1357 0/0:44,0:46:81.12:0,81,861 0/1:33,10:48:99:205,0,672 0/1:81,6:93:8.87:9,0,1302 0/1:91,9:107:19.73:20,0,1639 0/1:37,7:51:99:157,0,573 0/1:38,19:62:99:401,0,612 0/1:26,14:42:99:239,0,265 0/1:43,7:56:86.33:86,0,691 0/1:31,5:38:50.52:51,0,469 0/1:24,3:27:41.25:41,0,447 0/1:48,7:60:27.66:28,0,997 0/1:31,8:41:99:134,0,581 0/0:35,0:38:60.05:0,60,631 -chr1 866557 . C T 127.71 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.174;DP=1561;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7669;InbreedingCoeff=-0.0117;MQ=49.50;MQ0=0;MQRankSum=3.050;QD=5.55;ReadPosRankSum=-0.277;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.05:0,15,189 0/0:5,0:5:15.04:0,15,184 0/0:3,0:3:9.03:0,9,120 0/0:3,0:3:9.03:0,9,112 0/0:6,0:6:18.06:0,18,242 0/0:5,0:5:15.05:0,15,193 0/0:15,0:15:45.14:0,45,594 0/0:11,0:11:30.10:0,30,406 0/0:15,0:15:45.15:0,45,610 0/0:20,0:20:60.20:0,60,808 0/0:7,0:7:21.07:0,21,284 0/0:6,0:6:18.05:0,18,224 0/0:5,0:5:15.05:0,15,193 0/0:29,0:29:84.25:0,84,1030 0/0:42,0:42:99:0,120,1526 0/0:11,0:11:33.10:0,33,387 0/0:18,0:18:48.15:0,48,616 0/0:21,0:21:54.16:0,54,675 0/0:29,0:29:81.24:0,81,959 0/0:30,0:30:78.24:0,78,969 0/0:22,0:22:60.18:0,60,735 0/0:33,0:33:87.25:0,87,1010 0/0:14,0:15:42.13:0,42,507 0/0:24,0:24:69.21:0,69,843 0/0:15,0:15:42.12:0,42,501 0/0:29,0:29:87.27:0,87,1088 0/0:36,0:36:90.30:0,90,1223 0/0:19,0:19:57.17:0,57,690 0/0:23,0:23:69.18:0,69,788 0/0:28,0:28:66.18:0,66,767 0/0:20,0:20:54.16:0,54,635 0/0:13,0:13:30.09:0,30,349 0/0:21,0:21:60.18:0,60,727 0/1:16,7:23:99:175,0,544 0/0:22,0:22:57.18:0,57,754 0/0:16,0:16:48.14:0,48,567 0/0:24,1:26:33.65:0,34,845 0/0:57,0:57:99:0,160,2136 0/0:28,0:28:69.21:0,69,874 0/0:52,0:52:99:0,141,1683 0/0:33,0:33:90.23:0,90,1035 0/0:33,0:33:96.28:0,96,1131 0/0:31,0:31:93.27:0,93,1096 0/0:18,0:18:48.14:0,48,564 0/0:29,0:29:84.25:0,84,1041 0/0:45,0:45:99:0,126,1458 0/0:58,0:58:99:0,162,2049 0/0:30,0:30:81.26:0,81,1091 0/0:38,0:38:99:0,108,1285 0/0:71,0:71:99:0,205,2483 0/0:81,0:81:99:0,223,2749 0/0:35,0:35:99:0,99,1161 0/0:36,0:36:99:0,99,1141 0/0:28,0:28:75.22:0,75,869 0/0:40,0:40:99:0,105,1232 0/0:27,0:27:78.23:0,78,922 0/0:20,0:20:57.15:0,57,674 0/0:44,0:44:99:0,114,1395 0/0:27,0:27:72.21:0,72,867 0/0:29,0:29:78.25:0,78,1022 -chr1 866731 . G C 56.38 . AC=1;AF=0.011;AN=90;BaseQRankSum=-0.423;DP=139;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1598;InbreedingCoeff=-0.1061;MQ=53.72;MQ0=0;MQRankSum=0.762;QD=14.09;ReadPosRankSum=-0.131;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3.01:0,3,36 0/0:1,0:1:3.01:0,3,36 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,30 0/0:1,0:1:3.01:0,3,40 ./. ./. 0/0:1,0:1:3.01:0,3,35 ./. 0/0:4,0:4:12.04:0,12,165 0/0:2,0:2:6.02:0,6,80 ./. 0/0:2,0:2:3.01:0,3,33 0/0:1,0:1:3.01:0,3,39 0/0:5,0:5:15.04:0,15,191 ./. ./. 0/0:3,0:3:9.03:0,9,117 ./. 0/0:6,0:6:15.05:0,15,187 0/0:1,0:1:3.01:0,3,40 0/0:4,0:4:12.04:0,12,144 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,79 ./. ./. 0/0:2,0:2:6.02:0,6,75 0/0:1,0:1:3.01:0,3,40 0/0:3,0:3:9.03:0,9,112 ./. 0/0:3,0:3:6.02:0,6,82 ./. 0/0:1,0:1:3.01:0,3,41 0/1:1,3:4:25.76:102,0,26 0/0:2,0:2:6.02:0,6,83 0/0:1,0:1:3.01:0,3,42 0/0:4,0:4:12.04:0,12,151 0/0:6,0:6:15.05:0,15,200 0/0:6,0:6:15.05:0,15,185 0/0:3,0:3:9.02:0,9,100 ./. 0/0:3,0:3:9.03:0,9,127 0/0:5,0:5:15.05:0,15,185 ./. 0/0:4,0:4:12.04:0,12,156 0/0:2,0:2:6.02:0,6,73 0/0:5,0:5:12.04:0,12,166 0/0:3,0:3:9.03:0,9,126 0/0:2,0:2:6.01:0,6,66 0/0:3,0:3:9.03:0,9,112 0/0:10,0:10:30.10:0,30,389 ./. 0/0:7,0:7:15.04:0,15,183 0/0:1,0:1:3.01:0,3,33 0/0:7,0:7:18.06:0,18,229 ./. 0/0:3,0:3:9.03:0,9,115 0/0:3,0:4:9.03:0,9,109 0/0:2,0:2:6.02:0,6,75 0/0:2,0:2:6.02:0,6,78 -chr1 866893 . T C 622.24 . AC=22;AF=0.500;AN=44;BaseQRankSum=-3.378;DP=42;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0452;InbreedingCoeff=0.1880;MQ=58.67;MQ0=0;MQRankSum=1.917;QD=23.93;ReadPosRankSum=-1.917;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,2:2:6.02:69,6,0 1/1:0,3:3:9.03:112,9,0 1/1:0,3:3:9.03:121,9,0 0/1:2,3:5:62.06:98,0,62 0/1:1,1:2:35.21:35,0,35 ./. 0/1:1,1:2:34.63:35,0,35 1/1:0,1:1:3.01:41,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,41 1/1:0,1:1:3.01:39,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:1,0:1:3.01:0,3,42 0/1:1,2:3:33.29:39,0,33 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 ./. ./. ./. 1/1:0,1:1:3.01:32,3,0 ./. 1/1:0,1:1:3.01:38,3,0 ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. 0/0:4,0:4:9.03:0,9,125 ./. 1/1:0,1:1:3.01:34,3,0 0/0:3,0:3:6.02:0,6,87 ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,74 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,34 ./. ./. ./. -chr1 866920 . A G 1246.22 . AC=38;AF=1.000;AN=38;DP=41;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0415;InbreedingCoeff=-0.1594;MQ=58.06;MQ0=0;QD=32.80;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,4:4:12.04:150,12,0 1/1:0,1:1:3.01:33,3,0 1/1:0,8:8:24.08:311,24,0 ./. 1/1:0,1:1:3.01:40,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:83,6,0 1/1:0,1:1:3.01:39,3,0 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:45,3,0 1/1:0,3:3:3.01:45,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,1:1:3.01:39,3,0 1/1:0,5:5:9.03:130,9,0 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. 1/1:0,2:2:6.01:63,6,0 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. -chr1 866938 . G A 218.0 . AC=10;AF=0.278;AN=36;BaseQRankSum=1.425;DP=38;Dels=0.00;FS=4.047;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=0.1861;MQ=59.15;MQ0=0;MQRankSum=0.256;QD=18.17;ReadPosRankSum=-1.863;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:6.01:0,6,63 0/0:5,0:6:15.02:0,15,170 0/1:1,1:2:16.68:35,0,17 0/1:2,3:5:65.60:107,0,66 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:40,3,0 ./. ./. 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,38 ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:39,3,0 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 ./. 0/0:1,0:1:3.01:0,3,41 0/0:6,0:6:12.04:0,12,168 0/0:1,0:1:3.01:0,3,36 ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. ./. -chr1 870645 . T C 290.54 . AC=16;AF=0.320;AN=50;BaseQRankSum=-0.425;DP=42;Dels=0.00;FS=3.173;HRun=0;HaplotypeScore=0.0800;InbreedingCoeff=0.0985;MQ=58.33;MQ0=0;MQRankSum=0.337;QD=13.21;ReadPosRankSum=1.918;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/1:4,1:5:21.40:21,0,109 0/0:2,0:2:6.02:0,6,77 ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. 0/0:1,0:1:3.01:0,3,41 0/1:1,1:2:30.96:31,0,35 ./. 0/0:1,0:1:3.01:0,3,32 ./. 1/1:0,2:2:3.01:45,3,0 1/1:0,1:1:3.01:39,3,0 ./. ./. 1/1:0,2:2:3.01:45,3,0 0/1:1,2:3:29.23:39,0,29 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:4,0:4:6.02:0,6,86 1/1:0,2:2:6.02:71,6,0 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,33 ./. 0/1:1,2:3:33.29:36,0,33 ./. 0/0:1,0:1:3.01:0,3,34 ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,39 1/1:0,1:1:3.01:33,3,0 ./. 1/1:0,1:1:3.01:34,3,0 -chr1 870659 . G T 39.74 . AC=2;AF=0.040;AN=50;BaseQRankSum=1.431;DP=38;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0399;InbreedingCoeff=-0.0066;MQ=57.53;MQ0=0;MQRankSum=0.000;QD=13.25;ReadPosRankSum=1.202;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:4:9.03:0,9,113 0/0:2,0:2:6.02:0,6,77 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,116 ./. 0/0:1,0:1:3.01:0,3,32 ./. 0/0:2,0:2:3.01:0,3,45 0/0:1,0:1:3.01:0,3,37 ./. ./. 0/0:2,0:2:3.01:0,3,45 0/0:3,0:3:6.02:0,6,83 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,34 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,3:3:6.02:87,6,0 0/0:1,0:2:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,42 ./. 0/0:1,0:1:3.01:0,3,37 ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,42 -chr1 870903 . T C 4527.15 . AC=105;AF=0.9722;AN=108;BaseQRankSum=-1.547;DP=151;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=0.3492;InbreedingCoeff=-0.0281;MQ=55.90;MQ0=0;MQRankSum=-1.281;QD=30.59;ReadPosRankSum=-1.215;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:36,3,0 ./. 1/1:0,2:2:5.99:63,6,0 1/1:0,2:2:6.01:56,6,0 1/1:0,5:5:12.04:158,12,0 1/1:0,3:3:3.01:35,3,0 1/1:0,6:6:18.06:236,18,0 1/1:0,3:3:6.02:82,6,0 1/1:0,2:2:3.01:41,3,0 1/1:0,1:1:3.01:36,3,0 1/1:0,2:2:6.02:75,6,0 1/1:0,2:2:3.01:35,3,0 1/1:0,6:6:12.04:156,12,0 ./. 1/1:0,4:4:9.03:118,9,0 1/1:0,2:2:6.02:80,6,0 1/1:0,5:5:12.04:147,12,0 1/1:0,5:5:12.04:155,12,0 ./. 1/1:0,1:2:3.01:40,3,0 1/1:0,1:1:3.01:42,3,0 1/1:0,2:2:6.02:71,6,0 1/1:0,3:3:9.03:118,9,0 1/1:0,3:3:9.03:121,9,0 1/1:0,3:3:9.03:113,9,0 1/1:0,3:3:6.02:80,6,0 1/1:0,4:4:12.04:157,12,0 1/1:0,2:2:6.02:76,6,0 1/1:0,7:7:15.05:200,15,0 1/1:0,1:1:3.01:38,3,0 1/1:0,2:2:6.02:78,6,0 ./. 1/1:0,3:3:9.03:113,9,0 1/1:0,2:2:6.02:76,6,0 1/1:0,1:1:3.01:32,3,0 1/1:0,3:3:9.03:103,9,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:42,3,0 1/1:0,6:6:15.05:186,15,0 1/1:0,3:3:6.02:79,6,0 1/1:0,4:4:9.02:95,9,0 1/1:0,1:1:3.01:40,3,0 0/0:1,0:1:3.01:0,3,41 1/1:0,2:2:6.02:78,6,0 1/1:0,1:1:3.01:31,3,0 1/1:0,2:2:6.02:67,6,0 1/1:0,1:1:3.01:42,3,0 0/1:3,2:6:68.41:68,0,105 1/1:0,8:8:18.06:232,18,0 1/1:0,2:2:6.02:78,6,0 1/1:0,1:2:3.01:38,3,0 1/1:0,4:4:12.03:144,12,0 ./. 1/1:0,2:2:6.02:75,6,0 1/1:0,2:2:3.01:41,3,0 1/1:0,3:3:6.02:78,6,0 1/1:0,1:1:3.01:32,3,0 1/1:0,1:1:3.01:41,3,0 -chr1 871020 . G A 123.6 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.361;DP=922;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6728;InbreedingCoeff=-0.0124;MQ=58.46;MQ0=0;MQRankSum=0.878;QD=12.36;ReadPosRankSum=0.658;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.01:0,6,60 0/0:6,0:6:15.05:0,15,199 0/0:3,0:3:9.03:0,9,116 0/0:5,0:5:15.04:0,15,176 0/0:11,0:11:30.08:0,30,375 0/0:14,0:14:42.13:0,42,540 0/0:17,0:17:51.17:0,51,685 0/0:13,0:13:39.12:0,39,506 0/0:23,0:23:69.22:0,69,884 0/0:35,0:35:99:0,102,1336 0/0:15,0:15:45.14:0,45,596 0/0:11,0:11:33.07:0,33,394 0/0:22,0:22:63.20:0,63,825 0/0:27,0:27:66.21:0,66,865 0/0:18,0:18:51.16:0,51,630 0/0:11,0:11:30.10:0,30,402 0/0:16,0:16:48.16:0,48,628 0/0:19,0:19:51.16:0,51,646 0/0:17,0:17:42.12:0,42,519 0/0:23,0:23:60.20:0,60,800 0/0:19,0:19:57.17:0,57,699 0/0:20,0:20:54.15:0,54,671 0/0:14,0:14:39.13:0,39,509 0/0:12,0:12:30.10:0,30,409 0/0:15,0:15:42.12:0,42,535 0/0:18,0:18:51.15:0,51,655 0/0:12,0:12:30.10:0,30,402 0/0:17,0:17:48.14:0,48,620 0/0:20,0:20:54.17:0,54,684 0/0:13,0:13:39.13:0,39,505 0/0:22,1:23:26.88:0,27,758 0/0:18,0:18:51.16:0,51,657 0/1:4,6:10:94.84:171,0,95 0/0:16,0:16:45.14:0,45,585 0/0:8,0:8:18.06:0,18,231 0/0:12,0:12:36.12:0,36,479 0/0:15,0:15:45.15:0,45,588 0/0:29,0:29:84.25:0,84,1073 0/0:10,0:10:27.08:0,27,346 0/0:19,0:19:51.16:0,51,662 0/0:20,0:21:51.16:0,51,665 0/0:16,0:16:42.12:0,42,520 0/0:10,0:10:30.09:0,30,371 0/0:12,0:12:36.12:0,36,482 0/0:13,0:13:36.12:0,36,469 0/0:16,0:16:45.14:0,45,563 0/0:34,0:35:90.28:0,90,1144 0/0:6,0:6:15.05:0,15,186 0/0:12,0:12:30.10:0,30,392 0/0:22,1:23:35.53:0,36,750 0/0:20,0:20:54.17:0,54,682 0/0:19,0:19:54.17:0,54,679 0/0:13,0:13:39.12:0,39,496 0/0:18,0:18:54.17:0,54,704 0/0:7,0:7:21.06:0,21,263 0/0:12,0:12:33.09:0,33,405 0/0:13,0:13:33.11:0,33,426 0/0:11,0:11:33.10:0,33,417 0/0:10,0:10:30.10:0,30,391 0/0:7,0:7:15.05:0,15,196 -chr1 871042 . C CA 1121.53 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-3.932;DP=1196;FS=4.192;HRun=1;HaplotypeScore=68.0502;InbreedingCoeff=-0.0178;MQ=58.64;MQ0=0;MQRankSum=0.039;QD=20.77;ReadPosRankSum=1.478;EFF=INTRON(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|4),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|4),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|4),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:8,0:8:18.06:0,18,233 0/0:7,0:7:21.07:0,21,272 0/0:6,0:6:15.05:0,15,195 0/0:6,0:6:15.05:0,15,195 0/0:17,0:17:45.15:0,45,585 0/0:14,0:14:39.12:0,39,500 0/0:20,0:20:57.18:0,57,736 0/0:16,0:16:48.16:0,48,621 0/0:27,0:27:81.26:0,81,1048 0/0:34,0:34:96.31:0,96,1242 0/0:15,0:15:42.13:0,42,534 0/0:16,0:16:45.15:0,45,583 0/0:29,0:29:81.26:0,81,1043 0/0:30,0:29:84.27:0,84,1091 0/0:20,0:20:60.19:0,60,773 0/0:12,0:12:33.11:0,33,429 0/0:23,0:23:66.21:0,66,848 0/0:24,0:24:69.22:0,69,896 0/0:28,0:28:78.25:0,78,1013 0/1:18,12:30:99:500,0,500 0/0:21,0:21:63.20:0,63,816 0/0:22,0:22:63.20:0,63,812 0/0:22,0:22:63.20:0,63,818 0/0:24,0:24:72.23:0,72,920 0/0:20,0:20:57.18:0,57,728 0/1:7,17:23:99:696,0,158 0/0:18,0:18:51.16:0,51,655 0/0:20,0:19:60.19:0,60,771 0/0:24,0:24:69.21:0,69,882 0/0:21,0:21:60.19:0,60,777 0/0:38,0:38:99:0,114,1472 0/0:20,0:20:60.17:0,60,752 0/0:14,0:14:42.14:0,42,546 0/0:24,0:24:72.23:0,72,927 0/0:11,0:11:30.10:0,30,390 0/0:20,0:20:60.20:0,60,779 0/0:22,0:22:63.20:0,63,812 0/0:34,0:34:96.31:0,96,1247 0/0:10,0:10:24.08:0,24,310 0/0:24,0:23:69.22:0,69,896 0/0:21,0:21:51.16:0,51,653 0/0:19,0:19:45.15:0,45,585 0/0:18,0:18:48.63:0,49,623 0/0:17,0:17:45.15:0,45,585 0/0:14,0:14:39.13:0,39,505 0/0:26,0:26:66.21:0,66,858 0/0:45,0:45:99:0,123,1583 0/0:10,0:10:24.08:0,24,312 0/0:14,0:14:39.12:0,39,500 0/0:27,0:27:78.25:0,78,1004 0/0:30,0:30:75.24:0,75,974 0/0:21,0:21:55.42:0,55,704 0/0:20,0:20:60.20:0,60,779 0/0:26,0:26:75.24:0,75,965 0/0:10,0:10:27.09:0,27,351 0/0:17,0:17:48.15:0,48,610 0/0:15,0:15:39.13:0,39,507 0/0:12,0:12:36.12:0,36,468 0/0:11,0:11:33.10:0,33,420 0/0:8,0:8:24.07:0,24,300 -chr1 871215 . C G 3347.1 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.247;DP=4311;Dels=0.00;FS=7.397;HRun=1;HaplotypeScore=1.9160;InbreedingCoeff=-0.0257;MQ=58.16;MQ0=0;MQRankSum=2.137;QD=13.44;ReadPosRankSum=0.832;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P123|178|SAMD11|protein_coding|CODING|ENST00000420190|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccG|P123|681|SAMD11|protein_coding|CODING|ENST00000342066|),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,synonymous_variant|ccC/ccG|P|ENSG00000187634|SAMD11|ENST00000420190|5/7|||123/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,synonymous_variant|ccC/ccG|P|ENSG00000187634|SAMD11|ENST00000342066|5/14|||123/681|protein_coding|1,synonymous_variant|ccC/ccG|P|ENSG00000187634|SAMD11|ENST00000341065|3/12|||47/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:14,0:14:33.10:0,33,389 0/0:17,0:17:42.11:0,42,489 0/0:9,0:9:24.08:0,24,318 0/0:8,0:8:21.07:0,21,281 0/0:25,1:26:75.24:0,75,993 0/0:35,0:35:93.30:0,93,1224 0/0:44,0:44:99:0,129,1670 0/0:25,0:25:75.22:0,75,955 0/0:54,0:54:99:0,160,2065 0/0:58,0:59:99:0,166,2147 0/0:33,0:33:96.29:0,96,1249 0/0:23,0:23:63.19:0,63,809 0/0:44,0:44:99:0,123,1563 0/0:69,0:69:99:0,156,2056 0/0:107,0:107:99:0,244,3240 0/0:60,0:60:99:0,153,2024 0/0:74,0:74:99:0,196,2517 0/0:83,0:84:99:0,190,2463 0/0:96,1:97:99:0,229,3013 0/0:87,0:87:99:0,211,2839 0/0:89,0:89:99:0,199,2623 0/0:92,0:92:99:0,193,2533 0/0:82,0:83:99:0,184,2428 0/0:65,0:66:99:0,163,2148 0/0:76,0:76:99:0,181,2282 0/0:75,0:75:99:0,169,2231 0/1:42,41:84:99:1038,0,964 0/0:60,0:60:99:0,132,1781 0/0:75,1:76:99:0,187,2380 0/0:62,1:63:99:0,139,2056 0/0:107,0:107:99:0,244,3220 0/0:88,0:88:99:0,178,2385 0/0:65,0:65:99:0,160,2111 0/0:85,0:85:99:0,193,2555 0/1:37,28:66:99:672,0,934 0/0:93,1:95:99:0,202,2654 0/1:43,56:99:99:1637,0,1077 0/0:112,0:112:99:0,274,3584 0/0:65,0:65:99:0,153,1953 0/0:133,2:135:99:0,328,4193 0/0:129,0:129:99:0,283,3653 0/0:90,0:90:99:0,199,2609 0/0:85,0:86:99:0,199,2594 0/0:69,1:70:99:0,159,2103 0/0:45,2:47:99:0,117,1497 0/0:77,2:79:99:0,202,2573 0/0:136,0:136:99:0,325,4128 0/0:52,0:53:99:0,114,1489 0/0:103,0:103:99:0,214,2779 0/0:119,1:121:99:0,289,3731 0/0:110,0:111:99:0,277,3541 0/0:73,1:74:99:0,196,2474 0/0:60,0:60:99:0,144,1842 0/0:74,0:75:99:0,175,2232 0/0:79,0:79:99:0,181,2358 0/0:68,0:68:99:0,163,2108 0/0:40,0:40:84.27:0,84,1104 0/0:86,2:88:99:0,184,2395 0/0:66,2:70:99:0,138,1832 0/0:80,1:82:99:0,175,2292 -chr1 871306 . G A 333.26 . AC=1;AF=0.0085;AN=118;BaseQRankSum=0.027;DP=2068;Dels=0.00;FS=3.159;HRun=0;HaplotypeScore=2.0683;InbreedingCoeff=-0.0097;MQ=57.05;MQ0=0;MQRankSum=0.683;QD=9.52;ReadPosRankSum=0.829;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|5),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|5),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:9.02:0,9,100 0/0:8,0:8:24.06:0,24,268 0/0:7,0:7:21.06:0,21,257 ./. 0/0:12,0:12:33.11:0,33,447 0/0:9,0:9:27.08:0,27,354 0/0:19,0:19:57.18:0,57,746 0/0:13,0:13:39.12:0,39,506 0/0:23,0:23:69.23:0,69,939 0/0:24,0:24:72.23:0,72,949 0/0:8,0:8:24.08:0,24,325 0/0:12,0:12:33.10:0,33,405 0/0:14,0:14:42.11:0,42,541 0/0:33,0:34:84.26:0,84,1086 0/0:29,0:29:78.25:0,78,1030 0/0:30,0:30:78.24:0,78,1006 0/0:30,0:30:84.26:0,84,1069 0/0:42,0:42:99:0,108,1397 0/0:39,0:39:99:0,102,1270 0/0:32,0:32:84.27:0,84,1091 0/0:32,0:33:84.22:0,84,1062 0/1:20,15:35:99:381,0,638 0/0:29,0:29:78.23:0,78,1011 0/0:19,0:19:54.17:0,54,674 0/0:37,0:38:99:0,99,1259 0/0:30,0:30:81.26:0,81,1075 0/0:36,0:36:99:0,99,1285 0/0:29,0:29:69.22:0,69,899 0/0:48,0:48:99:0,117,1488 0/0:30,0:30:78.25:0,78,1014 0/0:47,0:47:99:0,129,1594 0/0:26,0:26:66.21:0,66,847 0/0:28,0:28:72.22:0,72,932 0/0:30,0:30:81.24:0,81,1036 0/0:24,0:24:63.19:0,63,802 0/0:28,0:28:69.22:0,69,907 0/0:45,0:45:99:0,102,1321 0/0:52,0:55:99:0,129,1669 0/0:63,0:63:99:0,150,1856 0/0:70,0:70:99:0,183,2258 0/0:66,0:66:99:0,156,1963 0/0:34,0:34:87.27:0,87,1097 0/0:53,0:53:99:0,114,1522 0/0:39,0:39:99:0,99,1275 0/0:29,0:29:72.21:0,72,874 0/0:46,0:46:99:0,114,1389 0/0:84,0:86:99:0,190,2397 0/0:30,0:30:60.16:0,60,762 0/0:50,0:50:99:0,123,1555 0/0:68,0:68:99:0,162,2002 0/0:71,0:71:99:0,178,2231 0/0:46,0:47:99:0,111,1385 0/0:27,0:27:69.21:0,69,860 0/0:52,0:52:99:0,129,1632 0/0:57,0:57:99:0,132,1651 0/0:37,0:37:99:0,99,1261 0/0:19,0:19:51.16:0,51,629 0/0:44,0:44:99:0,105,1316 0/0:35,0:35:90.23:0,90,1114 0/0:44,0:44:96.29:0,96,1231 -chr1 871334 . G T 28303.7 . AC=78;AF=0.6500;AN=120;BaseQRankSum=-4.675;DP=1477;Dels=0.00;FS=1.219;HRun=0;HaplotypeScore=0.8602;InbreedingCoeff=-0.1122;MQ=57.60;MQ0=0;MQRankSum=3.104;QD=21.15;ReadPosRankSum=-0.389;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|5),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|5),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,3:3:9.02:103,9,0 1/1:0,5:5:12.04:149,12,0 0/1:3,2:5:59.66:60,0,103 1/1:0,1:1:3.01:39,3,0 0/1:5,5:10:99:125,0,169 0/1:1,3:4:27.28:103,0,27 0/1:8,5:13:99:114,0,262 1/1:0,5:5:15.03:178,15,0 0/1:11,6:17:99:158,0,322 0/1:8,14:22:99:437,0,193 0/1:3,3:6:91.71:92,0,95 1/1:1,8:9:21.06:257,21,0 0/1:2,6:8:54.73:139,0,55 0/1:10,11:21:99:354,0,265 0/1:11,16:27:99:397,0,299 0/1:14,13:27:99:357,0,429 0/1:11,7:18:99:186,0,318 0/1:17,13:30:99:382,0,421 0/1:12,14:26:99:416,0,302 0/1:12,13:25:99:411,0,370 0/1:8,11:19:99:349,0,241 1/1:0,19:19:48.14:615,48,0 1/1:0,20:20:57.17:705,57,0 0/1:6,9:15:99:230,0,197 1/1:0,27:28:69.20:872,69,0 0/1:18,7:25:99:156,0,580 0/0:15,0:15:33.10:0,33,428 0/1:6,10:16:99:310,0,139 1/1:0,23:24:63.20:792,63,0 1/1:0,24:24:69.22:900,69,0 1/1:0,30:30:78.17:930,78,0 1/1:0,18:19:42.13:524,42,0 0/1:11,7:19:99:179,0,384 0/0:16,0:16:48.14:0,48,608 0/0:20,0:20:51.16:0,51,667 1/1:0,16:16:42.12:537,42,0 0/1:13,23:36:99:583,0,384 0/0:43,1:44:99:0,114,1472 0/1:17,24:41:99:759,0,366 1/1:1,51:52:98.95:1596,99,0 0/1:22,20:42:99:508,0,679 0/1:13,6:19:99:120,0,390 1/1:1,43:44:99:1385,111,0 1/1:0,25:25:63.17:765,63,0 0/1:9,17:26:99:451,0,206 1/1:0,34:34:99:1187,99,0 0/1:30,38:69:99:789,0,865 0/0:17,0:17:48.15:0,48,631 1/1:0,33:33:84.26:1064,84,0 0/1:27,32:59:99:823,0,762 0/1:32,22:54:99:497,0,873 1/1:2,43:45:99:1350,111,0 1/1:1,24:25:51.14:601,51,0 1/1:0,35:35:90.25:1129,90,0 1/1:2,42:44:96.28:1201,96,0 0/1:17,11:28:99:336,0,455 1/1:0,17:17:42.11:496,42,0 0/1:13,15:28:99:323,0,420 1/1:0,26:26:66.18:786,66,0 0/0:27,0:27:66.19:0,66,851 -chr1 871406 . C T 373.38 . AC=1;AF=0.0083;AN=120;BaseQRankSum=1.644;DP=663;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.3801;InbreedingCoeff=-0.0188;MQ=58.43;MQ0=0;MQRankSum=0.382;QD=14.94;ReadPosRankSum=0.041;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|5),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|5),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,upstream_gene_variant|||ENSG00000268179|AL645608.1|ENST00000598827||||-/112|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,39 0/0:5,0:5:15.04:0,15,171 0/0:4,0:4:12.04:0,12,160 0/0:3,0:3:9.02:0,9,105 0/0:9,0:9:27.09:0,27,351 0/0:5,0:5:15.05:0,15,202 0/0:7,0:7:21.07:0,21,282 0/0:6,0:6:18.06:0,18,244 0/0:8,0:8:21.07:0,21,280 0/0:19,0:19:57.19:0,57,762 0/0:11,0:11:30.10:0,30,409 0/0:4,0:4:9.03:0,9,115 0/0:9,0:9:27.09:0,27,357 0/0:5,0:5:15.05:0,15,203 0/0:15,0:15:39.13:0,39,516 0/0:9,0:9:24.08:0,24,320 0/0:9,0:9:24.08:0,24,315 0/0:13,0:13:36.12:0,36,471 0/0:7,0:8:21.05:0,21,249 0/0:8,0:8:21.07:0,21,284 0/0:10,0:10:27.09:0,27,368 0/0:10,0:10:27.09:0,27,350 0/0:8,0:8:18.06:0,18,253 0/0:9,0:9:27.09:0,27,367 0/0:13,0:13:33.10:0,33,431 0/0:9,0:9:24.05:0,24,285 0/0:7,0:7:21.07:0,21,270 0/0:3,0:3:9.03:0,9,121 0/0:9,0:9:27.09:0,27,353 0/0:14,0:14:39.13:0,39,518 0/0:13,0:13:36.09:0,36,460 0/0:7,0:7:21.07:0,21,275 0/0:5,0:5:15.05:0,15,185 0/0:5,0:5:15.05:0,15,202 0/0:7,0:7:21.06:0,21,271 0/0:3,0:3:9.03:0,9,124 0/0:11,0:11:33.11:0,33,442 0/0:17,0:17:51.17:0,51,687 0/0:21,0:21:48.15:0,48,613 0/0:21,0:21:63.20:0,63,831 0/0:17,0:17:51.17:0,51,678 0/0:13,0:13:39.11:0,39,511 0/0:17,0:17:48.15:0,48,628 0/0:11,0:11:27.08:0,27,337 0/0:13,0:13:36.12:0,36,478 0/0:16,0:16:45.15:0,45,609 0/0:32,0:32:90.25:0,90,1148 0/0:4,0:4:9.03:0,9,116 0/0:19,0:19:45.13:0,45,579 0/1:13,12:25:99:421,0,378 0/0:20,0:21:45.15:0,45,597 0/0:17,0:17:48.15:0,48,634 0/0:16,0:16:48.15:0,48,631 0/0:15,0:15:42.09:0,42,541 0/0:15,0:15:39.10:0,39,509 0/0:10,0:10:30.10:0,30,388 0/0:11,0:11:30.09:0,30,377 0/0:11,0:11:30.09:0,30,387 0/0:12,0:12:33.08:0,33,421 0/0:8,0:8:21.07:0,21,268 -chr1 871513 . C T 90.88 . AC=2;AF=0.0196;AN=102;BaseQRankSum=0.045;DP=143;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1691;InbreedingCoeff=0.0569;MQ=57.57;MQ0=0;MQRankSum=-0.474;QD=22.72;ReadPosRankSum=-0.123;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|5),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|5),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,69 ./. 0/0:3,0:3:9.03:0,9,114 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,81 ./. 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.04:0,12,162 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3.01:0,3,38 0/0:2,0:2:6.02:0,6,75 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:12.03:0,12,144 0/0:2,0:2:3.01:0,3,39 0/0:4,0:4:12.04:0,12,161 ./. 0/0:2,0:2:6.02:0,6,77 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,116 0/0:3,0:3:6.02:0,6,87 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,84 0/0:2,0:2:6.01:0,6,69 ./. 0/0:2,0:2:6.01:0,6,67 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:6.02:0,6,72 0/0:3,0:3:9.03:0,9,123 ./. 0/0:4,0:4:6.02:0,6,85 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,32 0/0:2,0:2:6.02:0,6,75 0/0:5,0:5:12.04:0,12,158 0/0:5,0:5:15.05:0,15,192 0/0:5,0:5:12.04:0,12,155 0/0:2,0:2:3.01:0,3,42 0/0:4,0:4:12.04:0,12,157 ./. 0/0:4,0:4:9.03:0,9,121 0/0:2,0:2:6.02:0,6,84 0/0:8,0:8:24.07:0,24,302 1/1:0,4:4:12.03:148,12,0 0/0:3,0:3:9.03:0,9,125 0/0:4,0:4:12.02:0,12,130 0/0:6,0:6:12.04:0,12,166 0/0:5,0:5:12.03:0,12,142 0/0:4,0:4:12.04:0,12,154 0/0:4,0:4:9.03:0,9,112 0/0:5,0:5:12.04:0,12,163 0/0:2,0:2:3.01:0,3,40 ./. ./. 0/0:4,0:4:12.04:0,12,153 0/0:3,0:3:9.03:0,9,120 -chr1 871683 . G A 69.81 . AC=6;AF=0.375;AN=16;BaseQRankSum=0.684;DP=8;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.2498;MQ=58.46;MQ0=0;MQRankSum=1.221;QD=23.27;ReadPosRankSum=0.684;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|5),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|5),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. ./. ./. ./. ./. -chr1 874314 . G A 306.48 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.210;DP=904;Dels=0.00;FS=2.007;HRun=2;HaplotypeScore=0.6052;InbreedingCoeff=-0.0150;MQ=58.05;MQ0=0;MQRankSum=-1.582;QD=10.95;ReadPosRankSum=0.649;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|5),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|5),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.04:0,12,148 0/0:4,0:4:9:0,9,96 0/0:2,0:2:6:0,6,59 0/0:3,0:3:9.01:0,9,99 0/0:5,0:5:15.05:0,15,202 0/0:5,0:5:15.05:0,15,193 0/0:4,0:4:12.04:0,12,159 0/0:4,0:4:9.03:0,9,117 0/0:10,0:10:30.09:0,30,391 0/0:13,0:13:36.11:0,36,464 0/0:8,0:8:24.08:0,24,316 0/0:6,0:6:18.06:0,18,235 0/0:6,0:6:18.04:0,18,224 0/0:13,0:13:39.13:0,39,520 0/0:14,0:14:36.11:0,36,467 0/0:7,0:7:21.07:0,21,283 0/0:16,0:16:42.13:0,42,557 0/0:10,0:10:27.08:0,27,350 0/0:15,1:16:45.15:0,45,590 0/0:14,0:14:39.13:0,39,513 0/0:15,0:16:42.14:0,42,549 0/0:17,0:17:48.15:0,48,621 0/0:12,0:12:33.11:0,33,447 0/0:14,0:14:39.12:0,39,499 0/0:10,0:10:30.10:0,30,399 0/0:14,0:14:36.11:0,36,469 0/0:10,0:10:24.08:0,24,319 0/0:12,0:12:30.10:0,30,391 0/0:16,0:16:48.16:0,48,633 0/0:17,0:17:51.16:0,51,670 0/0:15,0:15:42.13:0,42,542 0/0:15,0:15:42.14:0,42,568 0/0:17,0:17:48.15:0,48,628 0/0:11,0:11:33.11:0,33,449 0/0:9,0:9:27.09:0,27,359 0/0:15,0:15:45.15:0,45,594 0/0:11,0:11:33.10:0,33,421 0/0:20,0:20:54.17:0,54,721 0/0:21,0:21:57.18:0,57,755 0/0:39,0:40:99:0,102,1267 0/0:30,0:30:75.23:0,75,976 0/0:18,0:18:39.12:0,39,512 0/0:18,0:18:54.17:0,54,710 0/0:16,0:16:36.11:0,36,465 0/0:21,0:21:57.17:0,57,700 0/0:23,0:23:60.19:0,60,776 0/0:39,0:40:99:0,102,1318 0/0:13,0:13:36.11:0,36,470 0/0:13,0:13:36.11:0,36,451 0/0:40,0:40:99:0,99,1272 0/1:16,12:28:99:354,0,518 0/0:23,1:24:29.74:0,30,718 0/0:30,0:30:69.21:0,69,884 0/0:26,0:26:66.20:0,66,841 0/0:17,0:17:42.14:0,42,565 0/0:11,0:11:27.09:0,27,355 0/0:15,0:15:36.12:0,36,483 0/0:16,0:16:45.12:0,45,552 0/0:19,0:19:48.12:0,48,592 0/0:10,0:10:24.08:0,24,321 -chr1 874415 . C T 459.1 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.071;DP=2210;Dels=0.00;FS=0.832;HRun=0;HaplotypeScore=1.8123;InbreedingCoeff=-0.0101;MQ=58.23;MQ0=0;MQRankSum=1.495;QD=12.08;ReadPosRankSum=0.643;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),INTRON(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|5),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|5),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.04:0,15,177 0/0:7,0:7:18.05:0,18,221 0/0:4,0:4:12.04:0,12,158 0/0:4,0:4:12.03:0,12,143 0/0:7,0:7:21.07:0,21,283 0/0:7,0:7:15.05:0,15,198 0/0:18,0:18:48.16:0,48,659 0/0:10,0:10:30.10:0,30,401 0/0:24,0:24:69.23:0,69,933 0/0:20,0:20:60.19:0,60,788 0/0:9,0:9:27.09:0,27,365 0/0:11,0:11:33.10:0,33,414 0/0:15,0:15:45.12:0,45,560 0/0:40,0:40:87.28:0,87,1191 0/0:50,2:52:69.59:0,70,1455 0/0:24,0:24:60.19:0,60,788 0/0:36,0:36:87.27:0,87,1170 0/0:33,0:33:84.25:0,84,1094 0/0:54,0:54:99:0,126,1712 0/0:45,0:45:99:0,111,1502 0/0:48,0:48:99:0,120,1593 0/0:34,0:34:84.27:0,84,1124 0/0:45,0:45:99:0,111,1503 0/0:44,0:44:93.29:0,93,1257 0/0:37,0:37:90.28:0,90,1193 0/0:32,0:32:81.26:0,81,1075 0/0:40,0:40:96.30:0,96,1267 0/0:25,0:25:66.21:0,66,866 0/0:50,0:50:99:0,120,1597 0/0:42,0:42:99:0,99,1356 0/0:52,0:52:99:0,129,1724 0/0:46,0:46:99:0,108,1447 0/0:54,0:54:99:0,141,1886 0/0:50,0:50:99:0,129,1707 0/1:18,20:38:99:507,0,482 0/0:46,0:46:99:0,108,1446 0/0:51,0:51:99:0,123,1643 0/0:47,0:47:99:0,114,1543 0/0:34,0:34:72.21:0,72,916 0/0:54,0:54:99:0,120,1570 0/0:72,0:72:99:0,163,2119 0/0:30,0:30:69.22:0,69,902 0/0:32,0:32:72.23:0,72,943 0/0:31,0:31:72.23:0,72,955 0/0:26,0:26:75.21:0,75,943 0/0:50,0:50:99:0,129,1638 0/0:76,0:76:99:0,172,2211 0/0:35,0:35:87.28:0,87,1138 0/0:50,0:50:99:0,111,1482 0/0:71,0:71:99:0,166,2164 0/0:57,0:57:99:0,132,1720 0/0:37,0:37:84.26:0,84,1096 0/0:55,0:55:99:0,132,1716 0/0:52,0:52:99:0,117,1527 0/0:45,0:45:99:0,114,1512 0/0:32,0:32:84.27:0,84,1121 0/0:38,0:38:87.28:0,87,1182 0/0:35,0:35:84.26:0,84,1066 0/0:50,0:50:99:0,102,1327 0/0:42,0:42:93.27:0,93,1251 -chr1 874665 . G A 1190.84 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.904;DP=2083;Dels=0.00;FS=5.872;HRun=0;HaplotypeScore=1.2968;InbreedingCoeff=-0.0278;MQ=57.54;MQ0=0;MQRankSum=1.122;QD=14.35;ReadPosRankSum=0.856;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L177|178|SAMD11|protein_coding|CODING|ENST00000420190|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L177|681|SAMD11|protein_coding|CODING|ENST00000342066|),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=synonymous_variant|ctG/ctA|L|ENSG00000187634|SAMD11|ENST00000420190|7/7|||177/179|protein_coding|1,synonymous_variant|ctG/ctA|L|ENSG00000187634|SAMD11|ENST00000342066|7/14|||177/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,synonymous_variant|ctG/ctA|L|ENSG00000187634|SAMD11|ENST00000455979|1/7|||4/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,synonymous_variant|ctG/ctA|L|ENSG00000187634|SAMD11|ENST00000341065|5/12|||101/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:9.02:0,9,99 0/0:9,0:10:18.04:0,18,206 0/0:12,0:12:33.09:0,33,396 0/0:3,0:3:9.01:0,9,91 0/0:14,0:14:42.13:0,42,530 0/0:14,0:14:36.11:0,36,448 0/0:24,0:25:60.18:0,60,743 0/0:11,0:11:30.09:0,30,384 0/0:31,0:32:93.27:0,93,1188 0/0:43,0:43:99:0,108,1300 0/0:15,0:15:36.11:0,36,459 0/0:13,0:13:36.07:0,36,422 0/0:21,0:21:60.18:0,60,764 0/0:24,0:25:63.20:0,63,819 0/0:20,0:20:54.17:0,54,716 0/0:14,0:15:42.12:0,42,519 0/0:22,0:22:48.15:0,48,636 0/0:20,0:20:51.17:0,51,675 0/0:22,0:24:57.18:0,57,739 0/0:32,0:32:78.24:0,78,1007 0/1:13,11:24:99:348,0,333 0/0:31,0:31:81.25:0,81,1025 0/0:33,0:34:87.26:0,87,1113 0/0:23,0:23:51.17:0,51,689 0/0:27,1:28:60.17:0,60,762 0/0:24,1:25:30.64:0,31,805 0/1:12,16:28:99:494,0,313 0/0:19,0:19:42.13:0,42,556 0/0:29,0:29:75.24:0,75,995 0/0:21,0:21:57.18:0,57,737 0/0:33,0:33:84.27:0,84,1104 0/0:34,0:34:93.30:0,93,1203 0/0:23,0:23:60.19:0,60,773 0/1:14,16:31:99:430,0,404 0/0:16,0:16:39.12:0,39,502 0/0:22,0:22:63.20:0,63,802 0/0:22,0:22:57.19:0,57,763 0/0:29,0:29:75.24:0,75,989 0/0:37,0:37:84.24:0,84,1078 0/0:82,0:82:99:0,205,2612 0/0:71,0:71:99:0,190,2359 0/0:51,0:52:99:0,132,1711 0/0:42,0:43:99:0,105,1391 0/0:45,0:45:99:0,108,1394 0/0:37,1:38:84.25:0,84,1110 0/0:39,0:39:99:0,111,1427 0/0:88,0:88:99:0,244,3064 0/0:35,0:35:84.26:0,84,1050 0/0:71,0:72:99:0,147,1951 0/0:88,0:89:99:0,229,2856 0/0:69,0:69:99:0,181,2245 0/0:62,0:63:99:0,166,2079 0/0:79,0:79:99:0,190,2450 0/0:54,0:54:99:0,135,1741 0/0:55,0:55:99:0,138,1765 0/0:54,0:54:99:0,126,1648 0/0:40,0:41:87.27:0,87,1133 0/0:40,0:40:99:0,111,1410 0/0:47,0:47:99:0,108,1445 0/0:42,0:42:99:0,102,1280 -chr1 874816 . C CT 2431.73 . AC=13;AF=0.1083;AN=120;BaseQRankSum=-3.645;DP=2129;FS=0.000;HRun=1;HaplotypeScore=136.3097;InbreedingCoeff=0.2233;MQ=55.95;MQ0=0;MQRankSum=-0.937;QD=9.11;ReadPosRankSum=-4.095;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),FRAME_SHIFT(HIGH||-/T|-228?|681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,frameshift_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000342066|7/14|||228/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,frameshift_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000455979|1/7|||55/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:18.06:0,18,252 0/0:16,0:16:45.15:0,45,630 0/0:15,0:15:39.10:0,39,503 0/0:13,0:13:33.11:0,33,462 0/0:22,0:22:63.21:0,63,876 0/0:23,0:23:66.21:0,66,904 0/0:48,0:48:99:0,129,1768 0/0:23,0:23:45.12:0,45,610 0/0:62,0:62:99:0,172,2340 0/0:56,0:56:99:0,144,1965 0/0:25,0:25:63.21:0,63,871 0/0:25,0:25:69.23:0,69,953 0/0:43,0:43:99:0,111,1526 0/0:23,0:23:66.22:0,66,916 0/0:25,0:25:72.24:0,72,982 0/0:9,0:9:27.07:0,27,360 0/0:20,0:20:57.19:0,57,777 0/0:6,0:6:18.06:0,18,252 0/1:10,1:11:13.90:14,0,378 0/1:13,4:17:99:235,0,369 0/0:15,0:15:42.12:0,42,553 0/0:20,0:20:57.19:0,57,798 0/1:17,0:17:28.82:29,0,370 0/0:20,0:20:57.19:0,57,785 0/0:12,0:12:36.12:0,36,492 0/1:10,3:13:99:177,0,278 0/0:21,0:21:63.21:0,63,861 0/0:10,0:10:27.09:0,27,369 0/0:29,0:29:84.28:0,84,1151 0/0:22,0:22:57.18:0,57,763 0/0:15,0:15:42.14:0,42,581 0/0:17,0:17:51.17:0,51,708 0/0:18,0:18:48.09:0,48,639 0/0:21,0:21:54.18:0,54,756 0/1:3,4:7:56.74:170,0,57 0/1:10,4:14:99:181,0,300 0/0:12,0:12:33.11:0,33,459 1/1:3,10:13:36.11:535,36,0 0/0:56,0:56:99:0,144,1976 0/0:86,0:86:99:0,247,3361 0/0:68,0:68:99:0,193,2648 0/0:81,0:81:99:0,220,3012 0/0:61,0:61:99:0,166,2269 0/0:37,0:37:99:0,108,1476 0/1:52,7:59:99:197,0,1755 0/0:49,0:49:99:0,132,1804 0/1:56,10:66:99:414,0,1739 0/1:32,9:41:99:306,0,1123 0/0:61,0:61:99:0,172,2311 0/0:106,0:106:99:0,295,4049 0/0:96,0:96:99:0,271,3720 0/0:72,0:72:99:0,196,2663 0/0:75,0:75:99:0,205,2755 0/0:74,0:74:99:0,208,2847 0/0:64,1:65:99:0,144,2322 0/0:64,0:64:99:0,184,2523 0/0:39,0:39:99:0,107,1457 0/0:48,0:48:99:0,135,1877 0/0:31,0:31:90.30:0,90,1233 1/1:1,8:9:25.33:366,25,0 -chr1 874817 . C T 196.11 . AC=5;AF=0.0417;AN=120;BaseQRankSum=-3.463;DP=2129;Dels=0.00;FS=3.213;HRun=0;HaplotypeScore=3.1349;InbreedingCoeff=-0.0440;MQ=55.95;MQ0=0;MQRankSum=1.345;QD=2.84;ReadPosRankSum=-3.888;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P228L|681|SAMD11|protein_coding|CODING|ENST00000342066|),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,missense_variant|cCc/cTc|P/L|ENSG00000187634|SAMD11|ENST00000342066|7/14|benign(0.003)|tolerated(0.26)|228/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,missense_variant|cCc/cTc|P/L|ENSG00000187634|SAMD11|ENST00000455979|1/7|benign(0.086)|tolerated(0.06)|55/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:18.05:0,18,219 0/0:16,0:16:45.13:0,45,549 0/0:15,0:15:42.11:0,42,494 0/0:13,0:13:30.09:0,30,381 0/0:22,0:22:66.21:0,66,858 0/0:23,0:23:69.19:0,69,833 0/0:47,0:48:99:0,126,1602 0/0:23,0:23:45.14:0,45,557 0/0:62,0:62:99:0,178,2318 0/0:56,0:56:99:0,150,1865 0/0:25,0:25:66.18:0,66,803 0/0:25,0:25:69.20:0,69,869 0/0:43,0:43:99:0,108,1315 0/0:23,0:23:66.21:0,66,869 0/0:25,0:25:69.22:0,69,913 0/0:9,0:9:27.08:0,27,348 0/0:20,0:20:54.16:0,54,688 0/0:6,0:6:18.06:0,18,240 0/0:11,0:11:27.09:0,27,357 0/1:14,3:17:57.86:58,0,499 0/0:15,0:15:39.13:0,39,517 0/0:20,0:20:54.18:0,54,725 0/1:9,8:17:99:175,0,297 0/0:20,0:20:48.15:0,48,629 0/0:12,0:12:36.11:0,36,461 0/1:11,2:13:6.21:6,0,365 0/0:21,0:21:48.15:0,48,636 0/0:10,0:10:24.06:0,24,294 0/0:29,0:29:72.23:0,72,953 0/0:22,0:22:51.16:0,51,663 0/0:15,0:15:42.13:0,42,528 0/0:17,0:17:51.16:0,51,664 0/0:18,0:18:45.12:0,45,579 0/0:21,0:21:48.16:0,48,646 0/0:7,0:7:18.06:0,18,228 0/0:13,1:14:4.33:0,4,446 0/0:12,0:12:30.10:0,30,393 0/1:11,2:13:39.94:40,0,321 0/0:55,0:56:99:0,126,1632 0/0:86,0:86:99:0,223,2869 0/0:68,0:68:99:0,168,2130 0/0:80,0:81:99:0,178,2333 0/0:61,0:61:99:0,150,1894 0/0:37,0:37:96.29:0,96,1235 0/0:59,0:59:99:0,144,1833 0/0:49,0:49:99:0,120,1533 0/0:62,4:66:64.10:0,64,1952 0/0:41,0:41:99:0,108,1362 0/0:61,0:61:99:0,153,1963 0/0:106,0:106:99:0,256,3198 0/0:95,0:96:99:0,253,3184 0/0:72,0:72:99:0,169,2132 0/0:74,0:75:99:0,181,2309 0/0:74,0:74:99:0,169,2152 0/0:65,0:65:99:0,147,1894 0/0:64,0:64:99:0,162,2057 0/0:38,1:39:54.16:0,54,1126 0/0:48,0:48:99:0,126,1612 0/0:30,0:31:78.22:0,78,972 0/1:8,1:9:10.71:11,0,284 -chr1 874825 . C G 56.5 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.967;DP=2039;Dels=0.00;FS=3.631;HRun=0;HaplotypeScore=3.2093;InbreedingCoeff=-0.0100;MQ=55.77;MQ0=0;MQRankSum=0.586;QD=4.71;ReadPosRankSum=-3.947;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Gac|H231D|681|SAMD11|protein_coding|CODING|ENST00000342066|),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,missense_variant|Cac/Gac|H/D|ENSG00000187634|SAMD11|ENST00000342066|7/14|benign(0)|tolerated(0.23)|231/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,missense_variant|Cac/Gac|H/D|ENSG00000187634|SAMD11|ENST00000455979|1/7|benign(0.001)|tolerated(0.22)|58/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:18.03:0,18,201 0/0:17,0:17:45.11:0,45,540 0/0:14,0:14:33.09:0,33,392 0/0:11,0:11:27.07:0,27,312 0/0:26,0:26:72.21:0,72,907 0/0:25,0:25:69.20:0,69,852 0/0:47,0:47:99:0,117,1384 0/0:22,0:22:48.12:0,48,553 0/0:62,0:62:99:0,169,2182 0/0:67,0:67:99:0,169,2139 0/0:26,0:26:69.20:0,69,820 0/0:23,0:23:63.20:0,63,813 0/0:47,0:47:99:0,123,1513 0/0:20,0:20:57.15:0,57,685 0/0:22,0:22:60.16:0,60,698 0/0:8,0:8:21.03:0,21,235 0/0:17,0:17:45.13:0,45,550 0/0:5,0:5:15.05:0,15,185 0/0:10,0:10:24.06:0,24,281 0/0:13,0:13:33.10:0,33,397 0/0:11,0:11:24.07:0,24,284 0/0:20,0:20:51.15:0,51,616 0/0:13,0:13:33.08:0,33,399 0/0:18,0:18:39.11:0,39,473 0/0:11,0:11:30.08:0,30,355 0/0:10,0:10:27.08:0,27,337 0/0:19,0:19:42.11:0,42,515 0/0:11,0:11:21.05:0,21,247 0/0:23,0:23:51.15:0,51,632 0/0:17,0:17:42.13:0,42,523 0/0:12,0:12:33.08:0,33,363 0/0:15,0:15:42.10:0,42,467 0/0:17,0:17:39.10:0,39,472 0/0:21,0:21:48.08:0,48,557 0/0:6,0:6:12.04:0,12,143 0/0:13,1:14:36.11:0,36,428 0/0:11,0:11:30.08:0,30,350 0/1:7,5:12:99:104,0,196 0/0:56,0:56:99:0,129,1524 0/0:77,0:77:99:0,205,2404 0/0:65,0:65:99:0,153,1855 0/0:81,0:81:99:0,183,2227 0/0:61,0:62:99:0,144,1653 0/0:37,0:37:84.19:0,84,996 0/0:56,0:56:99:0,132,1570 0/0:48,0:48:99:0,111,1304 0/0:52,1:53:99:0,126,1473 0/0:42,3:45:15.79:0,16,1068 0/0:58,0:58:99:0,141,1703 0/0:103,0:103:99:0,238,2781 0/0:98,0:98:99:0,238,2725 0/0:68,0:68:99:0,156,1850 0/0:69,0:69:99:0,156,1780 0/0:70,0:70:99:0,159,1907 0/0:62,0:62:99:0,138,1658 0/0:58,0:58:99:0,132,1540 0/0:42,0:43:96.25:0,96,1179 0/0:45,1:46:99:0,114,1320 0/0:29,0:29:75.20:0,75,896 0/0:6,0:6:15.05:0,15,185 -chr1 874826 . A G 43.49 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-4.114;DP=2017;Dels=0.00;FS=12.409;HRun=0;HaplotypeScore=2.9313;InbreedingCoeff=-0.0145;MQ=55.77;MQ0=0;MQRankSum=1.636;QD=3.62;ReadPosRankSum=-1.153;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H231R|681|SAMD11|protein_coding|CODING|ENST00000342066|),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,missense_variant|cAc/cGc|H/R|ENSG00000187634|SAMD11|ENST00000342066|7/14|benign(0)|tolerated(0.37)|231/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,missense_variant|cAc/cGc|H/R|ENSG00000187634|SAMD11|ENST00000455979|1/7|benign(0)|tolerated(0.36)|58/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:6:15.03:0,15,165 0/0:15,0:17:33.09:0,33,403 0/0:13,0:14:27.07:0,27,315 0/0:10,1:11:18.05:0,18,215 0/0:24,0:26:48.13:0,48,611 0/0:22,0:24:42.09:0,42,499 0/0:38,0:47:66.16:0,66,794 0/0:14,2:24:24.06:0,24,286 0/0:58,0:62:99:0,135,1627 0/0:55,1:67:99:0,108,1326 0/0:21,0:26:36.11:0,36,437 0/0:21,0:22:48.11:0,48,583 0/0:36,1:46:72.18:0,72,869 0/0:20,0:20:51.07:0,51,525 0/0:16,0:21:36.06:0,36,390 0/0:5,0:7:9.02:0,9,96 0/0:16,0:17:39.10:0,39,456 0/0:5,0:5:9.03:0,9,114 0/0:7,0:10:11.99:0,12,121 0/0:10,0:13:27.06:0,27,305 0/0:8,0:11:15.04:0,15,177 0/0:17,0:19:36:0,36,347 0/0:11,0:14:27.07:0,27,314 0/0:14,0:17:21.07:0,21,267 0/0:10,0:11:24.01:0,24,250 0/0:8,0:10:24.07:0,24,290 0/0:16,0:19:33.05:0,33,367 0/0:9,1:11:15.03:0,15,172 0/0:19,0:22:30.09:0,30,361 0/0:17,0:17:33.06:0,33,372 0/0:10,0:10:18.02:0,18,183 0/0:13,0:15:24.06:0,24,260 0/0:14,0:17:30.03:0,30,320 0/0:16,0:21:33.06:0,33,371 0/0:4,0:6:11.99:0,12,117 0/0:11,1:13:33.07:0,33,358 0/0:10,0:11:27.02:0,27,262 0/1:6,5:12:91.19:91,0,160 0/0:46,3:55:63.61:0,64,1067 0/0:71,0:76:99:0,162,1805 0/0:55,0:64:99:0,117,1361 0/0:72,0:80:99:0,147,1708 0/0:49,0:60:99:0,105,1179 0/0:35,1:37:60.12:0,60,694 0/0:50,1:56:99:0,105,1241 0/0:43,0:48:87.17:0,87,961 0/0:44,4:53:90.25:0,90,1078 0/0:36,4:45:7.20:0,7,686 0/0:51,0:58:99:0,108,1252 0/0:91,0:103:99:0,201,2201 0/0:81,2:95:99:0,177,1967 0/0:57,0:66:99:0,105,1249 0/0:58,2:67:96.12:0,96,1040 0/0:61,2:70:99:0,123,1460 0/0:54,1:62:99:0,102,1234 0/0:48,1:58:96.19:0,96,1117 0/0:39,0:43:84.17:0,84,984 0/0:36,1:45:84.15:0,84,947 0/0:26,0:29:66.15:0,66,746 0/0:4,0:5:12.01:0,12,123 -chr1 874864 . CT C 864.62 . AC=4;AF=0.0333;AN=120;BaseQRankSum=2.646;DP=1615;FS=13.206;HRun=1;HaplotypeScore=111.2623;InbreedingCoeff=-0.0402;MQ=54.48;MQ0=0;MQRankSum=-2.660;QD=5.84;ReadPosRankSum=-2.656;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:9.03:0,9,141 0/0:15,0:15:33.11:0,33,517 0/0:14,0:14:30.10:0,30,470 0/0:10,0:10:15.05:0,15,235 0/0:22,0:22:51.17:0,51,787 0/0:23,0:23:54.16:0,54,780 0/0:44,0:43:97.87:0,98,1439 0/0:21,0:21:45.15:0,45,695 0/0:48,0:48:99:0,129,1929 0/0:65,0:65:99:0,144,2190 0/0:18,0:18:45.15:0,45,669 0/0:25,0:25:51.16:0,51,744 0/0:35,0:35:80.91:0,81,1134 0/0:6,0:6:18.06:0,18,282 0/0:10,0:10:30.10:0,30,466 0/0:4,0:4:12.04:0,12,188 0/0:10,0:10:24.08:0,24,376 0/0:4,0:4:12.04:0,12,188 0/0:8,0:8:24.07:0,24,338 0/0:14,0:14:39.13:0,39,583 0/0:4,0:4:12.04:0,12,188 0/0:9,0:9:27.09:0,27,421 0/1:7,1:8:17.90:18,0,304 0/0:8,0:8:24.08:0,24,375 0/0:4,0:4:12.04:0,12,186 0/0:9,0:9:21.07:0,21,324 0/0:12,0:12:36.12:0,36,542 0/0:8,0:8:21.06:0,21,298 0/0:13,0:13:39.13:0,39,597 0/0:9,0:9:27.08:0,27,395 0/0:10,0:10:30.10:0,30,465 0/1:5,1:6:26.94:27,0,173 0/0:11,0:11:27.09:0,27,405 0/0:11,0:11:33.11:0,33,514 0/0:6,0:6:18.06:0,18,280 0/0:9,0:9:27.09:0,27,405 0/0:6,0:6:15.05:0,15,214 0/0:14,0:14:42.14:0,42,656 0/0:45,0:45:99:0,126,1932 0/0:64,1:65:99:0,181,2759 0/0:45,1:46:78.60:0,79,1762 0/0:53,0:53:99:0,144,2166 0/0:57,2:59:90.60:0,91,2525 0/0:34,1:35:60.36:0,60,1505 0/0:49,0:49:99:0,135,2084 0/0:37,2:39:69.39:0,69,1616 0/0:56,1:57:99:0,115,2297 0/0:36,0:36:99:0,108,1680 0/0:51,1:52:96.47:0,96,2025 0/1:68,12:80:99:431,0,2448 0/0:74,0:74:99:0,207,3138 0/0:53,1:54:99:0,112,2241 0/0:44,3:47:6.80:0,7,1739 0/1:42,12:54:99:490,0,1457 0/0:55,0:55:99:0,151,2331 0/0:50,1:51:99:0,109,2223 0/0:34,0:34:87.28:0,87,1315 0/0:28,2:30:43:0,43,1186 0/0:22,0:22:57.19:0,57,880 0/0:19,0:19:57.19:0,57,891 -chr1 874878 . T C 30.73 . AC=4;AF=0.0333;AN=120;BaseQRankSum=-11.417;DP=1417;Dels=0.00;FS=9.439;HRun=4;HaplotypeScore=1.6844;InbreedingCoeff=-0.0402;MQ=53.55;MQ0=0;MQRankSum=0.037;QD=0.29;ReadPosRankSum=-3.513;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,1:7:9.03:0,9,109 0/0:12,3:15:9.40:0,9,339 0/0:11,3:14:18.04:0,18,211 0/0:8,4:12:12.04:0,12,147 0/0:12,5:17:27.08:0,27,335 0/1:15,6:22:48.27:48,0,289 0/1:28,7:35:38.57:39,0,522 0/1:15,5:21:22.96:23,0,306 0/0:34,16:50:45.48:0,45,788 0/0:40,10:51:60.13:0,60,716 0/0:11,3:14:21.06:0,21,247 0/0:16,3:19:32.98:0,33,352 0/1:16,9:27:0.55:1,0,271 0/0:6,0:6:15.05:0,15,183 0/0:8,0:8:24.07:0,24,287 0/0:3,0:3:9.03:0,9,107 0/0:9,0:9:18.05:0,18,220 0/0:4,0:4:12.03:0,12,144 0/0:7,1:8:15.05:0,15,193 0/0:12,0:12:27.08:0,27,320 0/0:3,0:3:9.03:0,9,105 0/0:7,0:7:15.03:0,15,172 0/0:8,0:8:21.04:0,21,224 0/0:9,0:9:18.05:0,18,220 0/0:7,0:7:18.05:0,18,210 0/0:9,0:9:18.03:0,18,189 0/0:8,0:8:15.05:0,15,204 0/0:6,0:6:18.05:0,18,212 0/0:9,0:9:21.06:0,21,255 0/0:7,0:7:12.02:0,12,138 0/0:8,0:8:21.06:0,21,256 0/0:5,0:5:12.04:0,12,145 0/0:7,1:8:15.02:0,15,158 0/0:10,0:10:27.06:0,27,306 0/0:6,0:6:15.02:0,15,152 0/0:8,0:8:18.05:0,18,217 0/0:3,0:3:9.03:0,9,113 0/0:14,0:14:42.11:0,42,471 0/0:35,0:36:81.21:0,81,952 0/0:53,2:56:99:0,135,1618 0/0:39,2:42:81.22:0,81,975 0/0:42,0:43:99:0,114,1389 0/0:51,1:52:99:0,114,1386 0/0:34,0:34:84.23:0,84,1000 0/0:41,0:42:93.25:0,93,1142 0/0:33,1:34:90.25:0,90,1043 0/0:50,1:51:99:0,126,1465 0/0:33,0:33:81.21:0,81,941 0/0:46,0:46:99:0,105,1265 0/0:58,7:66:99:0,144,1627 0/0:62,0:64:99:0,141,1677 0/0:48,1:49:94.60:0,95,1384 0/0:39,0:39:99:0,99,1192 0/0:44,0:44:99:0,102,1231 0/0:51,1:52:99:0,129,1536 0/0:42,1:43:99:0,108,1347 0/0:31,1:32:32.51:0,33,691 0/0:25,1:26:43.46:0,43,724 0/0:21,0:21:51.13:0,51,596 0/0:21,0:22:57.13:0,57,627 -chr1 874927 . A G 459.72 . AC=5;AF=0.0439;AN=114;BaseQRankSum=2.529;DP=728;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5050;InbreedingCoeff=0.1366;MQ=49.13;MQ0=0;MQRankSum=-1.720;QD=7.93;ReadPosRankSum=0.425;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:9,0:9:27.08:0,27,316 0/0:8,0:8:24.05:0,24,287 0/0:8,0:8:21.06:0,21,245 0/0:10,0:10:27.04:0,27,306 0/0:15,0:15:45.14:0,45,568 0/0:15,0:15:45.12:0,45,527 0/0:25,0:25:69.21:0,69,880 0/0:13,0:13:33.09:0,33,386 0/0:25,0:25:72.21:0,72,903 0/0:22,0:22:66.21:0,66,857 0/0:15,0:15:42.12:0,42,493 0/0:12,0:14:33.10:0,33,405 0/0:19,0:20:57.12:0,57,631 0/0:2,0:2:6.01:0,6,60 0/0:6,0:6:18.05:0,18,215 ./. 0/0:4,0:4:12.03:0,12,134 0/0:4,0:4:12.04:0,12,149 0/0:6,0:6:18.05:0,18,217 0/0:3,0:3:9.03:0,9,108 0/0:2,0:3:6.02:0,6,76 0/0:3,0:3:6.02:0,6,75 ./. 0/0:5,0:5:15.04:0,15,172 0/0:4,0:4:9.02:0,9,100 0/0:6,0:6:18.05:0,18,214 0/0:1,0:1:3.01:0,3,36 0/0:2,0:2:6.02:0,6,71 ./. 0/0:4,0:4:12.01:0,12,131 0/0:4,0:4:9.03:0,9,110 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:12.01:0,12,134 0/0:3,0:3:6.02:0,6,85 0/1:5,2:7:52.38:52,0,151 0/0:7,0:7:21.05:0,21,247 1/1:0,1:1:3.01:33,3,0 0/0:7,0:7:21.05:0,21,247 0/0:21,0:21:45.13:0,45,543 0/0:34,0:34:93.20:0,93,1070 0/0:22,0:23:63.18:0,63,727 0/0:13,0:14:36.08:0,36,407 0/0:23,1:24:60.17:0,60,714 0/0:14,0:14:36.10:0,36,422 0/1:11,5:16:99:107,0,345 0/0:12,0:13:30.07:0,30,346 0/0:34,0:35:84.24:0,84,1026 0/0:11,0:11:27.07:0,27,304 0/0:19,0:19:51.15:0,51,601 0/1:19,14:34:99:361,0,500 0/0:31,0:31:81.25:0,81,1005 0/0:28,0:28:69.19:0,69,832 0/0:8,0:9:21.06:0,21,237 0/0:13,0:14:39.10:0,39,457 0/0:23,1:24:66.16:0,66,778 0/0:16,0:16:42.11:0,42,498 0/0:17,0:17:42.13:0,42,537 0/0:16,0:16:39.09:0,39,448 0/0:13,0:13:36.09:0,36,405 0/0:15,0:16:45.11:0,45,511 -chr1 874933 . G A 71.83 . AC=2;AF=0.0175;AN=114;BaseQRankSum=-2.598;DP=677;Dels=0.00;FS=12.021;HRun=0;HaplotypeScore=0.5171;InbreedingCoeff=0.3582;MQ=48.55;MQ0=0;MQRankSum=-2.054;QD=17.96;ReadPosRankSum=-0.568;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:9,0:9:27.07:0,27,323 0/0:8,0:8:24.06:0,24,291 0/0:9,0:9:24.07:0,24,286 0/0:9,0:9:24.05:0,24,291 0/0:13,0:13:39.13:0,39,512 0/0:14,0:14:42.11:0,42,504 0/0:23,0:23:63.20:0,63,828 0/0:13,0:13:36.11:0,36,451 0/0:28,0:28:84.26:0,84,1091 0/0:17,0:17:51.16:0,51,662 0/0:15,0:15:42.13:0,42,517 0/0:16,0:16:45.13:0,45,562 0/0:18,0:18:51.15:0,51,620 0/0:2,0:2:6.02:0,6,67 0/0:6,0:6:18.05:0,18,214 ./. 1/1:0,4:4:12.03:131,12,0 0/0:4,0:4:9.03:0,9,109 0/0:5,0:5:15.04:0,15,179 0/0:3,0:3:9.02:0,9,106 0/0:3,0:3:9.02:0,9,102 0/0:2,0:2:3.01:0,3,42 ./. 0/0:5,0:5:15.04:0,15,172 0/0:4,0:4:9.02:0,9,100 0/0:6,0:6:15.04:0,15,175 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,39 ./. 0/0:4,0:4:12.04:0,12,148 0/0:3,0:3:9.02:0,9,100 0/0:1,0:1:3.01:0,3,40 0/0:4,0:4:12.04:0,12,149 0/0:3,0:3:6.02:0,6,85 0/0:5,0:5:15.04:0,15,169 0/0:7,0:7:21.06:0,21,262 0/0:1,0:1:3.01:0,3,33 0/0:8,0:8:24.07:0,24,299 0/0:20,0:20:48.15:0,48,597 0/0:30,0:31:87.25:0,87,1044 0/0:20,0:21:57.16:0,57,664 0/0:12,0:12:33.10:0,33,394 0/0:21,0:21:60.15:0,60,699 0/0:13,0:13:33.10:0,33,395 0/0:15,0:16:42.13:0,42,531 0/0:10,0:10:30.09:0,30,363 0/0:28,0:28:66.21:0,66,848 0/0:10,0:10:27.08:0,27,307 0/0:18,0:18:45.13:0,45,537 0/0:31,0:32:87.25:0,87,995 0/0:28,0:28:75.21:0,75,929 0/0:27,0:27:69.21:0,69,857 0/0:7,0:7:15.03:0,15,159 0/0:12,0:12:33.10:0,33,408 0/0:22,1:23:38.53:0,39,740 0/0:15,0:15:45.13:0,45,545 0/0:17,0:17:39.12:0,39,496 0/0:16,0:17:45.11:0,45,528 0/0:11,0:12:27.08:0,27,325 0/0:13,0:13:39.10:0,39,444 -chr1 874949 . G GAC 180.07 . AC=12;AF=0.1091;AN=110;BaseQRankSum=4.227;DP=513;FS=1.980;HRun=0;HaplotypeScore=80.8744;InbreedingCoeff=-0.1326;MQ=45.53;MQ0=0;MQRankSum=0.812;QD=1.55;ReadPosRankSum=-6.278;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:17.55:0,18,253 0/0:3,0:4:9.03:0,9,134 0/0:8,0:8:21:0,21,329 0/0:7,0:7:20.43:0,20,281 0/1:11,0:11:0.15:0,0,411 0/0:14,0:14:16.23:0,16,487 0/1:9,1:10:15.76:16,0,319 0/0:12,2:14:1.24:0,1,475 0/0:19,0:19:53.92:0,54,819 0/1:10,4:14:99:155,0,349 0/1:13,1:14:1.98:2,0,402 0/0:14,0:14:41.79:0,42,604 0/0:13,0:13:39.13:0,39,616 0/0:2,0:2:5.61:0,6,59 0/0:4,0:4:10.88:0,11,80 ./. 0/1:4,0:4:17.29:17,0,52 0/0:4,0:4:8.62:0,9,107 0/1:4,1:5:5.90:6,0,148 0/0:4,0:4:11.52:0,12,124 0/0:2,0:2:6.02:0,6,98 0/0:1,0:1:2.80:0,3,13 ./. 0/1:4,1:5:19.81:20,0,176 0/0:4,0:4:11.40:0,11,155 0/0:4,0:4:12.04:0,12,196 ./. 0/0:1,0:1:3.01:0,3,49 ./. 0/0:2,0:2:5.61:0,6,59 0/1:3,1:4:31.82:32,0,92 ./. 0/0:2,0:2:6.02:0,6,98 0/0:1,0:1:3.01:0,3,49 0/0:4,0:4:11.36:0,11,57 0/0:6,0:6:17.93:0,18,257 0/0:1,0:1:2.50:0,2,9 0/0:5,0:5:13.56:0,14,130 0/1:14,0:14:10.91:11,0,166 0/0:21,0:21:62.41:0,62,867 0/1:15,0:15:23.40:23,0,458 0/0:14,0:15:17.61:0,18,342 0/0:17,0:17:34.17:0,34,464 0/1:11,0:11:11.17:11,0,252 0/0:6,0:6:16.79:0,17,148 0/1:9,0:9:30:30,0,272 0/0:23,0:23:45.11:0,45,750 0/0:8,0:8:16.21:0,16,188 0/0:15,0:16:36.63:0,37,444 0/0:21,0:21:58.13:0,58,576 0/0:19,0:19:37.61:0,38,687 0/0:23,0:23:64.96:0,65,928 0/0:8,0:8:19.38:0,19,129 0/0:9,0:9:25.50:0,26,252 0/0:10,0:10:27.49:0,27,328 0/0:9,0:9:25.74:0,26,259 0/0:16,0:16:44.63:0,45,610 0/0:13,0:13:35.15:0,35,542 0/0:10,0:10:29.45:0,29,384 0/0:7,0:7:17.15:0,17,180 -chr1 874950 . T C 171.91 . AC=11;AF=0.1000;AN=110;BaseQRankSum=-0.909;DP=513;Dels=0.00;FS=2.116;HRun=3;HaplotypeScore=3.7881;InbreedingCoeff=-0.1427;MQ=45.53;MQ0=0;MQRankSum=5.553;QD=1.55;ReadPosRankSum=-4.349;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:18.05:0,18,211 0/0:3,1:4:6.02:0,6,77 0/0:8,0:8:21.06:0,21,247 0/0:7,0:7:18.05:0,18,209 0/0:9,2:11:0.47:0,0,318 0/1:12,2:14:3.21:3,0,355 0/1:8,1:10:15.24:15,0,251 0/1:12,2:14:4.57:5,0,327 0/0:19,0:19:54.14:0,54,649 0/1:9,5:14:99:136,0,285 0/1:12,1:14:0.21:0,0,361 0/0:14,0:14:39.12:0,39,491 0/0:13,0:13:39.11:0,39,461 0/0:2,0:2:6.02:0,6,67 0/0:4,0:4:12.01:0,12,129 ./. 0/1:2,2:4:54.83:60,0,55 0/0:4,0:4:6:0,6,56 0/1:4,1:5:23.53:24,0,126 0/0:4,0:4:12.03:0,12,140 0/0:2,0:2:6.02:0,6,69 0/0:1,0:1:3.01:0,3,33 ./. 0/1:4,1:5:23.53:24,0,119 0/0:4,0:4:12.03:0,12,131 0/0:4,0:4:12.02:0,12,129 ./. 0/0:1,0:1:3.01:0,3,39 ./. 0/0:2,0:2:6.02:0,6,71 0/0:3,1:4:4.90:0,5,65 ./. 0/0:2,0:2:6.02:0,6,73 0/0:1,0:1:3.01:0,3,37 0/0:4,0:4:12.03:0,12,133 0/0:6,0:6:15.05:0,15,186 0/0:1,0:1:3.01:0,3,32 0/0:5,0:5:15.04:0,15,178 0/1:12,2:14:5.49:5,0,303 0/0:21,0:21:60.15:0,60,698 0/0:14,1:15:6.55:0,7,435 0/0:13,1:15:3.53:0,4,399 0/0:16,1:17:9.88:0,10,446 0/0:11,0:11:30.08:0,30,342 0/0:6,0:6:18.02:0,18,195 0/1:8,1:9:7.48:7,0,215 0/0:23,0:23:48.14:0,48,583 0/0:8,0:8:24.04:0,24,250 0/0:16,0:16:45.13:0,45,513 0/0:21,0:21:63.14:0,63,680 0/0:19,0:19:48.14:0,48,598 0/0:23,0:23:60.16:0,60,718 0/1:7,1:8:12.96:13,0,183 0/0:9,0:9:21.06:0,21,240 0/0:10,0:10:27.07:0,27,301 0/0:9,0:9:27.07:0,27,302 0/0:16,0:16:42.10:0,42,490 0/0:13,0:13:24.07:0,24,299 0/0:10,0:10:30.07:0,30,330 0/0:7,0:7:21.06:0,21,234 -chr1 874950 . T TCCCTGGAGGACC 52769.69 . AC=82;AF=0.7455;AN=110;BaseQRankSum=-5.074;DP=556;FS=0.992;HRun=0;HaplotypeScore=89.5226;InbreedingCoeff=-0.2281;MQ=43.74;MQ0=0;MQRankSum=-13.823;QD=95.42;ReadPosRankSum=1.894;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/1:7,1:8:99:354,0,158 0/1:5,0:5:99:352,0,211 0/1:9,0:9:99:821,0,203 0/1:7,1:8:99:528,0,180 0/1:11,0:11:99:396,0,544 1/1:14,0:15:27.09:1200,27,0 0/1:11,0:11:99:570,0,306 0/1:12,1:13:99:816,0,439 0/1:19,0:20:99:1071,0,759 0/1:16,1:17:99:1376,0,403 1/1:12,4:16:45.15:2185,45,0 0/1:12,1:14:99:604,0,592 0/1:13,0:13:99:1133,0,470 1/1:2,1:3:9.03:551,9,0 1/1:1,3:4:12.04:584,12,0 ./. 1/1:3,1:4:12.04:425,12,0 0/1:3,1:4:99:175,0,186 0/1:4,1:5:96.88:522,0,97 1/1:2,2:4:9.02:393,9,0 0/1:2,0:2:99:178,0,106 1/1:0,1:1:3.01:184,3,0 ./. 1/1:5,0:5:15.05:770,15,0 0/1:3,1:4:99:520,0,100 0/1:4,0:4:99:356,0,212 ./. 1/1:1,0:1:3.01:31,3,0 ./. 1/1:1,1:2:3.01:184,3,0 1/1:3,1:4:12.04:645,12,0 ./. 0/0:2,0:2:6.02:0,6,224 0/0:1,0:1:3.01:0,3,112 1/1:0,3:4:12.04:731,12,0 0/1:5,1:6:99:172,0,323 1/1:0,1:1:3.01:183,3,0 1/1:3,3:6:15.05:619,15,0 1/1:5,5:14:33.11:1721,33,0 0/1:20,4:24:99:1412,0,1026 1/1:11,4:15:42.14:2308,42,0 0/1:9,6:15:99:1142,0,544 1/1:10,7:18:45.15:2318,45,0 1/1:4,5:10:24.08:1353,24,0 1/1:3,4:7:15.05:916,15,0 1/1:7,2:9:24.08:1168,24,0 0/1:21,3:26:99:1412,0,1177 1/1:5,5:10:30.10:1839,30,0 1/1:9,6:17:36.12:2111,36,0 1/1:13,11:24:63.22:3633,63,0 0/1:18,3:22:99:1380,0,1280 0/1:19,4:23:99:894,0,1444 1/1:3,3:8:21.07:1125,21,0 1/1:9,3:13:24.08:1323,24,0 1/1:9,3:13:33.11:1761,33,0 1/1:5,5:10:30.10:1523,30,0 0/1:13,2:16:99:609,0,921 0/1:13,1:14:99:852,0,747 1/1:8,4:12:33.11:1756,33,0 1/1:5,4:9:27.09:1584,27,0 -chr1 874955 . C G 162.26 . AC=15;AF=0.1364;AN=110;BaseQRankSum=-1.052;DP=411;Dels=0.00;FS=15.434;HRun=0;HaplotypeScore=3.6422;InbreedingCoeff=-0.1058;MQ=46.15;MQ0=0;MQRankSum=4.641;QD=1.62;ReadPosRankSum=-7.007;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:12.04:0,12,143 0/0:6,0:6:15.04:0,15,178 0/0:5,0:5:12.04:0,12,143 0/0:6,0:6:15.04:0,15,178 0/0:8,0:8:21.07:0,21,279 0/0:7,0:7:18.05:0,18,213 0/1:6,1:7:20.16:20,0,215 0/1:8,2:10:50.25:50,0,269 0/1:12,1:13:2.11:2,0,411 0/0:18,0:18:54.17:0,54,678 0/1:8,1:9:16.58:17,0,217 0/1:10,1:11:8.14:8,0,335 0/0:7,0:7:21.07:0,21,273 0/0:2,0:2:6.02:0,6,67 0/1:3,1:4:25.76:26,0,88 ./. 0/0:3,0:3:9.03:0,9,102 0/0:4,0:4:9.03:0,9,105 0/0:3,0:3:9.03:0,9,114 0/1:2,1:3:20.60:21,0,58 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:2:3.01:0,3,39 0/0:2,0:2:6.02:0,6,67 0/0:2,0:2:6.02:0,6,76 ./. 1/1:0,1:1:3.01:35,3,0 ./. 0/0:1,0:1:3.01:0,3,33 0/0:2,1:3:3.01:0,3,33 ./. 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,40 0/0:4,0:4:12.03:0,12,134 0/0:4,0:4:12.04:0,12,141 0/0:1,0:1:3.01:0,3,33 0/1:4,2:6:57.54:58,0,118 0/0:12,0:12:33.09:0,33,368 0/0:18,1:19:13.33:0,13,533 0/0:7,0:7:21.06:0,21,239 0/0:16,0:16:42.13:0,42,500 0/0:11,0:11:30.08:0,30,329 0/1:6,1:7:19.75:20,0,149 0/0:5,0:5:15.04:0,15,167 0/1:5,1:6:19.74:20,0,151 0/0:23,0:23:57.17:0,57,689 0/0:8,0:8:24.07:0,24,266 0/0:10,0:10:27.05:0,27,287 0/0:15,0:15:42.12:0,42,468 0/0:20,0:20:51.16:0,51,638 0/0:19,1:20:19.37:0,19,621 0/0:6,0:6:18.05:0,18,202 0/0:9,0:9:21.06:0,21,232 0/1:7,1:8:13.73:14,0,210 0/1:7,1:8:13.76:14,0,199 0/0:13,0:14:36.10:0,36,432 0/0:10,0:10:21.06:0,21,256 0/1:6,1:7:17.20:17,0,149 0/0:6,0:6:18.04:0,18,195 -chr1 875159 . AGCCAGTGGACGCCGACCT A 727.04 . AC=15;AF=0.500;AN=30;BaseQRankSum=3.932;DP=27;FS=0.000;HRun=0;HaplotypeScore=24.4581;InbreedingCoeff=0.3261;MQ=51.25;MQ0=0;MQRankSum=-2.825;QD=80.78;ReadPosRankSum=2.534;EFF=DOWNSTREAM(MODIFIER||||108|SAMD11|protein_coding|CODING|ENST00000437963|),DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),UPSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000437963||||-/109|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/1:1,1:2:99:147,0,171 ./. ./. 0/0:1,0:1:3.01:0,3,261 ./. ./. 0/0:5,0:5:15.05:0,15,817 0/0:6,0:6:18.06:0,18,978 1/1:0,1:1:3.01:53,3,0 1/1:0,1:1:3.01:53,3,0 1/1:0,1:1:3.01:53,3,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:153,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,261 ./. ./. ./. ./. 1/1:0,1:1:3.01:153,3,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,153 0/0:1,0:1:3.01:0,3,228 ./. ./. ./. 1/1:0,1:1:3.01:53,3,0 1/1:0,1:1:3.01:153,3,0 ./. 0/0:2,0:2:3.01:0,3,261 ./. ./. -chr1 876498 . GA G 1427.8 . AC=48;AF=0.4000;AN=120;BaseQRankSum=-5.371;DP=794;FS=21.973;HRun=1;HaplotypeScore=83.2253;InbreedingCoeff=-0.3157;MQ=58.06;MQ0=0;MQRankSum=0.970;QD=2.48;ReadPosRankSum=-12.769;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|1),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),INTRON(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|1),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000474461|1/4||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:2.97:0,3,20 0/0:2,0:2:0.22:0,0,1 0/1:1,0:1:0:0,0,0 0/0:1,0:1:1.82:0,2,5 1/1:7,0:7:0.23:2,0,0 0/1:7,0:7:0.90:31,0,1 0/1:11,0:11:16.82:22,0,17 1/1:9,0:9:5.69:38,6,0 0/1:15,0:15:26.64:64,0,27 0/1:13,0:13:4.87:5,0,280 1/1:2,0:2:3.01:36,3,0 0/1:6,0:6:2.83:29,0,3 0/1:3,0:3:0.14:0,0,0 0/1:15,0:15:34.25:34,0,57 0/0:12,0:12:17.35:0,17,71 0/0:5,0:5:3.66:0,4,8 0/0:13,0:13:12.63:0,13,30 0/0:15,0:15:21.99:0,22,58 0/0:11,0:11:12.15:0,12,39 0/1:16,0:16:7.90:49,0,8 0/1:7,0:7:21.17:21,0,37 0/1:12,0:12:10.36:48,0,10 0/0:6,0:6:16.61:0,17,232 0/1:6,0:6:16.75:33,0,17 0/1:7,0:7:19.24:21,0,19 0/1:9,1:10:10.49:58,0,10 0/1:14,0:14:16.62:17,0,28 0/1:12,0:12:10.27:35,0,10 0/1:18,0:18:36.14:36,0,67 0/1:7,1:8:23.30:28,0,23 0/1:14,0:14:36.76:43,0,37 0/1:4,0:4:2.94:24,0,3 0/1:10,0:10:3.31:43,0,3 0/0:10,0:10:7.75:0,8,19 0/1:12,0:12:23.66:54,0,24 0/1:9,1:10:6.37:61,0,6 1/1:7,0:7:1.86:61,2,0 0/1:19,0:19:32.70:41,0,33 0/1:9,0:9:14.67:15,0,25 0/1:24,1:25:43.41:46,0,43 0/0:22,0:22:23.24:0,23,97 0/0:20,0:20:17.55:0,18,572 0/1:16,0:16:11.65:12,0,26 0/1:15,0:15:17.94:50,0,18 0/1:14,0:14:20.37:53,0,20 0/1:19,0:19:35.69:81,0,36 0/0:41,0:41:41.48:0,41,165 0/1:7,0:7:6.23:26,0,6 0/1:17,0:17:27.80:30,0,28 0/0:35,0:35:55.13:0,55,1022 0/1:45,0:45:32.15:32,0,948 0/1:25,0:24:54.30:128,0,54 0/1:32,0:32:61.52:122,0,62 0/1:12,1:13:27.64:28,0,41 0/1:16,0:16:36.19:37,0,36 0/1:13,0:13:20.26:44,0,20 0/1:13,0:13:0.57:1,0,333 0/1:22,0:22:18.66:19,0,29 0/0:17,0:17:17.71:0,18,45 0/0:7,0:7:9.70:0,10,23 -chr1 876499 . A G 22430.37 . AC=114;AF=0.9500;AN=120;BaseQRankSum=2.512;DP=794;Dels=0.01;FS=0.566;HRun=6;HaplotypeScore=0.6449;InbreedingCoeff=-0.0691;MQ=58.06;MQ0=0;MQRankSum=0.580;QD=28.25;ReadPosRankSum=0.704;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|1),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|7),INTRON(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|1),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|1/4||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,1:1:2.99:23,3,0 1/1:0,2:2:6.02:81,6,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:37,3,0 1/1:0,7:7:21.07:281,21,0 1/1:0,7:7:21.07:279,21,0 1/1:0,11:11:30.09:372,30,0 1/1:0,9:9:24.08:314,24,0 1/1:0,15:15:42.13:549,42,0 0/1:7,6:13:99:184,0,240 1/1:0,2:2:6.02:81,6,0 1/1:0,6:6:15.05:194,15,0 1/1:0,3:3:9.03:115,9,0 1/1:0,15:15:39.09:464,39,0 1/1:0,12:12:27.09:350,27,0 1/1:0,5:5:12.04:160,12,0 1/1:0,13:13:27.09:356,27,0 1/1:0,15:15:30.08:384,30,0 1/1:0,11:11:27.08:340,27,0 1/1:0,16:16:36.12:485,36,0 1/1:0,7:7:9.03:134,9,0 1/1:0,12:12:27.09:356,27,0 0/1:5,1:6:22.75:23,0,139 1/1:0,6:6:9.02:111,9,0 1/1:0,7:7:21.06:249,21,0 1/1:0,9:9:27.09:342,27,0 1/1:0,14:14:36.12:470,36,0 1/1:0,12:12:30.10:386,30,0 1/1:0,18:18:33.11:442,33,0 1/1:0,7:7:21.05:248,21,0 1/1:0,14:14:33.09:414,33,0 1/1:0,4:4:12.04:150,12,0 1/1:0,10:10:27.09:353,27,0 1/1:0,10:10:21.07:292,21,0 1/1:0,12:12:30.08:375,30,0 1/1:0,9:9:27.09:343,27,0 1/1:0,6:7:18.06:224,18,0 1/1:0,19:19:45.13:573,45,0 1/1:0,9:9:27.06:325,27,0 1/1:0,24:24:54.16:682,54,0 1/1:0,22:22:57.18:712,57,0 0/1:12,8:20:99:210,0,305 1/1:0,16:16:42.13:531,42,0 1/1:0,15:15:42.13:520,42,0 1/1:0,14:14:36.11:462,36,0 1/1:0,19:19:48.15:620,48,0 1/1:1,40:41:99:1289,105,0 1/1:0,7:7:18.06:226,18,0 1/1:0,17:17:45.13:554,45,0 0/1:23,12:35:99:284,0,638 0/1:25,20:45:99:580,0,466 1/1:2,23:25:36.97:821,37,0 1/1:0,32:32:87.24:1042,87,0 1/1:0,12:12:33.09:399,33,0 1/1:0,16:16:45.13:552,45,0 1/1:0,13:13:36.11:455,36,0 0/1:8,5:13:99:118,0,264 1/1:0,22:22:54.17:697,54,0 1/1:0,17:17:42.13:541,42,0 1/1:0,7:7:18.06:234,18,0 -chr1 876595 . C T 278.95 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.357;DP=1272;Dels=0.00;FS=1.349;HRun=0;HaplotypeScore=0.7550;InbreedingCoeff=-0.0197;MQ=57.15;MQ0=0;MQRankSum=0.060;QD=13.28;ReadPosRankSum=-2.131;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),EXON(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|2),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P260S|681|SAMD11|protein_coding|CODING|ENST00000342066|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,missense_variant|Ccc/Tcc|P/S|ENSG00000187634|SAMD11|ENST00000342066|8/14|probably_damaging(0.987)|deleterious(0)|260/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|1/4||||retained_intron|1,missense_variant|Ccc/Tcc|P/S|ENSG00000187634|SAMD11|ENST00000455979|2/7|probably_damaging(0.999)|deleterious(0)|87/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000478729|2/3||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,missense_variant|Ccc/Tcc|P/S|ENSG00000187634|SAMD11|ENST00000341065|6/12|probably_damaging(0.999)|tolerated(0.05)|168/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,32 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:9.03:0,9,114 0/0:6,0:6:18.05:0,18,231 0/0:6,0:6:18.05:0,18,229 0/0:13,0:13:39.12:0,39,509 0/0:13,0:13:36.10:0,36,457 0/0:15,0:15:45.15:0,45,598 0/0:13,0:13:39.12:0,39,493 0/0:7,0:7:18.06:0,18,237 0/0:8,0:9:21.06:0,21,262 0/0:5,0:6:15.05:0,15,190 0/0:13,0:13:30.10:0,30,413 0/0:12,0:12:24.08:0,24,335 0/0:8,0:8:21.06:0,21,277 0/0:11,0:11:27.08:0,27,333 0/0:13,0:13:27.07:0,27,326 0/0:15,0:15:36.09:0,36,435 0/0:8,0:8:21.07:0,21,268 0/0:6,0:7:15.04:0,15,187 0/0:16,0:16:36.12:0,36,490 0/0:7,0:7:15.05:0,15,196 0/0:16,0:16:33.07:0,33,410 0/0:11,0:12:27.08:0,27,347 0/0:16,0:16:39.13:0,39,515 0/0:11,0:11:30.09:0,30,396 0/0:13,0:13:27.09:0,27,363 0/0:16,0:16:42.13:0,42,543 0/0:8,0:8:24.08:0,24,302 0/0:18,0:18:42.13:0,42,545 0/0:5,0:5:12.04:0,12,146 0/0:13,0:13:30.09:0,30,384 0/0:10,0:10:21.04:0,21,269 0/0:12,0:12:30.07:0,30,382 0/0:11,0:11:30.10:0,30,408 0/0:10,0:10:24.07:0,24,301 0/0:19,0:19:33.11:0,33,471 0/0:32,0:32:81.21:0,81,995 0/0:72,0:72:99:0,187,2255 0/0:52,0:53:99:0,126,1635 0/0:32,0:32:81.24:0,81,1010 0/0:38,0:38:96.30:0,96,1218 0/0:32,0:32:93.30:0,93,1213 0/0:29,0:30:78.23:0,78,955 0/0:33,0:33:96.26:0,96,1210 0/0:64,0:64:99:0,162,1999 0/0:27,0:27:69.19:0,69,864 0/1:11,10:21:99:327,0,321 0/0:73,0:74:99:0,190,2394 0/0:68,0:69:99:0,175,2211 0/0:48,0:48:99:0,126,1562 0/0:44,0:44:99:0,117,1462 0/0:36,0:37:90.28:0,90,1158 0/0:31,0:31:72.20:0,72,913 0/0:37,0:37:99:0,99,1246 0/0:16,0:16:42.13:0,42,526 0/0:36,0:36:93.27:0,93,1179 0/0:29,0:29:75.21:0,75,905 0/0:23,0:23:69.22:0,69,882 -chr1 876908 . G A 134.68 . AC=1;AF=0.013;AN=80;BaseQRankSum=1.386;DP=184;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.2023;InbreedingCoeff=-0.0861;MQ=56.39;MQ0=0;MQRankSum=0.341;QD=14.96;ReadPosRankSum=1.908;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|8),INTRON(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|2),INTRON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|1),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,25 0/0:2,0:2:6.02:0,6,79 ./. 0/0:1,0:1:3.01:0,3,32 0/0:3,0:3:9.03:0,9,122 0/0:2,0:2:6.02:0,6,71 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:12.04:0,12,163 0/0:5,0:5:15.03:0,15,178 0/0:3,0:3:9.03:0,9,117 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.02:0,6,72 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,35 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:2,0:2:6.02:0,6,77 0/0:11,0:11:30.09:0,30,381 0/0:9,0:9:24.08:0,24,315 0/0:7,0:7:21.07:0,21,273 0/0:7,0:7:18.06:0,18,225 0/0:3,0:3:9.03:0,9,123 0/1:3,6:9:84.58:180,0,85 0/0:14,0:14:42.13:0,42,538 0/0:12,0:12:33.11:0,33,444 0/0:6,0:6:18.06:0,18,248 0/0:2,0:2:6.02:0,6,80 0/0:6,0:6:18.06:0,18,238 0/0:5,0:5:15.05:0,15,206 0/0:5,0:5:15.05:0,15,186 0/0:3,0:3:6.02:0,6,73 0/0:8,0:8:18.06:0,18,231 0/0:5,0:5:15.05:0,15,199 0/0:8,0:8:24.08:0,24,308 0/0:10,0:10:27.08:0,27,334 0/0:4,0:4:12.04:0,12,164 0/0:6,0:6:18.06:0,18,249 0/0:6,0:6:18.06:0,18,228 -chr1 877147 . G A 43.79 . AC=6;AF=0.273;AN=22;BaseQRankSum=-0.925;DP=17;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;InbreedingCoeff=0.2867;MQ=52.81;MQ0=0;MQRankSum=0.185;QD=14.60;ReadPosRankSum=0.740;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|8),INTRON(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|2),INTRON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|1),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),UPSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,upstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. 1/1:0,1:1:3.01:34,3,0 ./. ./. ./. ./. 0/0:1,1:2:3.01:0,3,41 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,39 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,35 ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,36 ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. 0/0:2,0:2:6.02:0,6,76 ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. -chr1 877715 . C G 5039.18 . AC=98;AF=0.9423;AN=104;BaseQRankSum=1.292;DP=191;Dels=0.00;FS=2.185;HRun=3;HaplotypeScore=0.2807;InbreedingCoeff=-0.0534;MQ=53.91;MQ0=0;MQRankSum=-0.346;QD=26.66;ReadPosRankSum=0.008;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|1),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|9),INTRON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|1),INTRON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|2);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000464948|1/2||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3.01:34,3,0 ./. ./. ./. 1/1:0,2:2:6.02:76,6,0 0/1:5,5:10:99:169,0,163 1/1:0,3:3:6.02:73,6,0 1/1:0,11:11:33.09:408,33,0 0/1:6,4:10:99:128,0,199 1/1:0,3:3:9.03:124,9,0 1/1:0,1:1:3.01:35,3,0 1/1:0,3:3:9.03:116,9,0 ./. 1/1:0,2:2:6.02:82,6,0 1/1:0,1:1:3.01:39,3,0 1/1:0,3:3:6.02:80,6,0 1/1:0,1:1:3.01:42,3,0 1/1:1,1:2:3.01:39,3,0 1/1:0,4:4:9.03:117,9,0 1/1:0,6:6:18.06:233,18,0 1/1:0,6:6:12.04:147,12,0 0/1:4,2:6:24.96:25,0,133 1/1:0,1:1:3.01:39,3,0 1/1:0,3:3:9.02:108,9,0 1/1:0,6:6:15.04:185,15,0 1/1:0,1:1:2.98:22,3,0 ./. 1/1:0,3:3:3:25,3,0 ./. 1/1:0,8:8:12.03:149,12,0 1/1:0,3:3:6.02:79,6,0 1/1:0,6:6:12.04:160,12,0 1/1:0,8:10:21.06:260,21,0 1/1:0,3:3:6.02:75,6,0 1/1:0,6:6:18.05:215,18,0 1/1:0,4:4:12.04:153,12,0 1/1:1,6:7:18.06:228,18,0 1/1:0,3:3:9.02:94,9,0 1/1:0,2:2:6.02:70,6,0 1/1:0,4:4:6.02:73,6,0 1/1:2,1:3:3.01:39,3,0 1/1:0,2:2:6.02:67,6,0 1/1:0,1:1:3.01:42,3,0 1/1:0,2:2:6.02:73,6,0 1/1:0,3:3:6.02:73,6,0 1/1:0,5:5:12.04:148,12,0 ./. 1/1:0,5:5:9.03:120,9,0 1/1:0,4:4:6.02:67,6,0 0/1:3,1:4:27.97:28,0,49 1/1:0,2:2:6.01:61,6,0 1/1:0,2:2:6.02:69,6,0 1/1:0,2:2:6.02:83,6,0 1/1:0,2:2:3.01:39,3,0 1/1:0,1:1:3.01:37,3,0 0/0:1,0:1:3.01:0,3,32 1/1:0,1:1:3.01:42,3,0 1/1:0,4:4:9.03:117,9,0 1/1:0,1:1:3.01:33,3,0 -chr1 877782 . C G 59.43 . AC=4;AF=0.0357;AN=112;BaseQRankSum=-0.568;DP=212;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0665;InbreedingCoeff=0.0350;MQ=54.31;MQ0=0;MQRankSum=1.437;QD=5.40;ReadPosRankSum=0.130;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|1),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|9),INTRON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|1),INTRON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|2);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000464948|1/2||||retained_intron|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3.01:0,3,38 ./. 0/0:6,0:6:15.03:0,15,175 0/0:2,0:2:6.02:0,6,82 0/0:4,0:4:9.03:0,9,121 0/0:1,0:1:3:0,3,28 0/0:3,0:3:9.03:0,9,114 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 ./. 0/0:2,0:2:6.02:0,6,69 0/0:3,0:3:6.02:0,6,83 0/0:2,0:2:3.01:0,3,45 0/0:3,0:3:6.02:0,6,83 0/0:2,0:2:6.02:0,6,76 0/0:4,0:4:12.04:0,12,147 0/0:3,0:3:9.03:0,9,121 0/0:5,0:5:9.03:0,9,112 0/0:4,0:4:9.03:0,9,110 0/0:10,0:10:21.05:0,21,265 0/0:2,0:2:6.02:0,6,72 0/0:4,0:4:9.03:0,9,119 0/0:8,0:8:15.04:0,15,192 1/1:0,3:3:6.02:76,6,0 0/0:3,0:3:3.01:0,3,45 0/0:4,0:4:12.01:0,12,132 0/0:3,0:3:3.01:0,3,45 0/0:7,0:7:15.05:0,15,187 0/0:6,0:6:15.05:0,15,190 0/0:11,0:11:21.07:0,21,285 0/0:6,0:6:18.06:0,18,232 0/1:3,2:5:32.73:33,0,101 0/0:6,0:6:12.04:0,12,162 0/1:2,1:3:32.56:33,0,35 0/0:4,0:4:12.04:0,12,162 0/0:5,0:5:9.03:0,9,117 0/0:5,0:5:6.02:0,6,84 0/0:3,0:3:9.03:0,9,112 0/0:4,0:4:12.04:0,12,145 0/0:3,0:3:9.03:0,9,102 0/0:1,0:1:3.01:0,3,32 0/0:2,0:2:6.02:0,6,67 0/0:4,0:4:6.02:0,6,83 0/0:8,0:8:18.05:0,18,221 0/0:2,0:2:6.02:0,6,69 0/0:2,0:2:6.02:0,6,75 0/0:5,0:5:12.01:0,12,135 0/0:4,0:4:9.03:0,9,114 0/0:5,0:5:15.04:0,15,167 0/0:3,0:3:9.03:0,9,106 0/0:5,0:5:9.03:0,9,117 0/0:4,0:4:12.03:0,12,151 0/0:4,0:4:12.04:0,12,154 0/0:1,0:1:3.01:0,3,37 0/0:3,0:3:6.02:0,6,78 0/0:3,0:3:9.03:0,9,115 0/0:3,0:3:9.03:0,9,105 -chr1 877831 . T C 5022.11 . AC=102;AF=1.0000;AN=102;BaseQRankSum=1.709;DP=173;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.1329;InbreedingCoeff=-0.0991;MQ=53.24;MQ0=0;MQRankSum=1.638;QD=29.20;ReadPosRankSum=-0.772;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|1),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|2),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W343R|681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,missense_variant|Tgg/Cgg|W/R|ENSG00000187634|SAMD11|ENST00000342066|10/14|benign(0)|tolerated(1)|343/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000464948|1/2||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000466827|2/2||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|3/4||||retained_intron|1,missense_variant|Tgg/Cgg|W/R|ENSG00000187634|SAMD11|ENST00000455979|4/7|benign(0)|tolerated(1)|170/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,missense_variant|Tgg/Cgg|W/R|ENSG00000187634|SAMD11|ENST00000341065|8/12|benign(0)|tolerated(1)|251/589|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3.01:38,3,0 ./. ./. 1/1:0,3:3:6.02:69,6,0 1/1:0,1:1:3.01:41,3,0 ./. 1/1:0,3:3:9.03:120,9,0 ./. 1/1:0,4:4:12.04:164,12,0 1/1:0,1:1:3.01:39,3,0 1/1:0,1:1:3.01:41,3,0 ./. 1/1:0,3:3:6.02:70,6,0 1/1:0,3:3:6.02:80,6,0 1/1:0,2:2:3.01:42,3,0 1/1:0,1:1:3.01:39,3,0 1/1:0,2:2:3.01:45,3,0 1/1:0,3:3:6.02:66,6,0 1/1:0,1:1:3.01:39,3,0 1/1:0,1:1:3.01:36,3,0 1/1:0,5:5:15.05:186,15,0 1/1:0,7:7:18.06:245,18,0 1/1:0,2:2:3.01:39,3,0 1/1:0,1:1:3.01:42,3,0 1/1:0,5:5:12.02:151,12,0 1/1:0,1:1:3.01:42,3,0 1/1:0,3:3:6.02:75,6,0 1/1:0,3:3:9.03:105,9,0 1/1:0,3:3:6.01:66,6,0 1/1:0,4:4:9.03:114,9,0 1/1:0,7:7:15.05:198,15,0 1/1:0,6:6:18.06:227,18,0 1/1:0,8:8:18.06:243,18,0 1/1:0,4:4:6.02:78,6,0 1/1:0,5:5:15.02:178,15,0 1/1:0,2:2:6.02:75,6,0 1/1:0,3:3:6.02:86,6,0 1/1:0,4:4:12.04:149,12,0 1/1:0,4:5:9.01:98,9,0 1/1:0,6:6:9.03:120,9,0 1/1:0,4:4:9.03:114,9,0 1/1:0,2:2:6.02:70,6,0 1/1:0,2:2:6.01:60,6,0 ./. 1/1:0,3:3:9.03:109,9,0 1/1:0,7:7:18.04:207,18,0 ./. 1/1:0,1:1:3.01:33,3,0 1/1:0,5:5:9.02:114,9,0 1/1:0,4:4:12.03:139,12,0 1/1:0,6:7:12.03:139,12,0 1/1:0,2:2:3.01:39,3,0 1/1:0,4:4:9.03:118,9,0 1/1:1,5:6:9.03:110,9,0 1/1:0,3:3:6.02:70,6,0 ./. 1/1:0,3:3:6.02:74,6,0 1/1:0,1:1:3.01:39,3,0 1/1:0,4:4:12.03:140,12,0 -chr1 878314 . G C 762.28 . AC=11;AF=0.0917;AN=120;BaseQRankSum=0.711;DP=450;Dels=0.00;FS=2.520;HRun=0;HaplotypeScore=0.3685;InbreedingCoeff=-0.1321;MQ=57.76;MQ0=0;MQRankSum=1.717;QD=9.30;ReadPosRankSum=1.114;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|4),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G480|681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,synonymous_variant|ggG/ggC|G|ENSG00000187634|SAMD11|ENST00000342066|11/14|||480/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|4/4||||retained_intron|1,synonymous_variant|ggG/ggC|G|ENSG00000187634|SAMD11|ENST00000455979|5/7|||307/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,synonymous_variant|ggG/ggC|G|ENSG00000187634|SAMD11|ENST00000341065|9/12|||388/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,37 0/0:2,0:2:6.02:0,6,69 0/0:1,0:1:3.01:0,3,40 0/0:4,0:4:6.02:0,6,78 0/0:7,0:7:18.06:0,18,240 0/0:9,0:9:21.07:0,21,273 0/0:12,0:12:33.11:0,33,426 0/1:3,3:6:42.20:93,0,42 0/0:22,0:22:66.19:0,66,820 0/0:16,0:16:45.14:0,45,581 0/0:7,0:7:15.05:0,15,201 0/0:8,0:8:21.06:0,21,255 0/0:8,0:8:15.03:0,15,170 0/0:9,0:9:21.05:0,21,257 0/0:5,0:5:15.05:0,15,190 0/1:2,2:4:35.74:72,0,36 0/0:2,0:2:6.01:0,6,69 0/0:5,0:5:12.04:0,12,160 0/0:3,0:3:6.02:0,6,85 0/0:8,0:8:18.06:0,18,245 0/0:9,0:9:24.07:0,24,297 0/0:8,0:8:21.06:0,21,272 0/0:2,0:2:3.01:0,3,45 0/0:5,0:5:15.05:0,15,193 0/1:1,1:2:31.78:33,0,32 0/0:2,0:2:6.02:0,6,76 0/0:8,0:8:18.06:0,18,246 0/1:3,6:9:65.29:154,0,65 0/0:7,0:7:18.04:0,18,222 0/0:6,0:6:15.05:0,15,198 0/0:5,0:5:15.05:0,15,188 0/0:4,0:4:12.03:0,12,147 0/1:4,2:6:32.73:33,0,109 0/0:8,0:8:18.06:0,18,231 0/0:4,0:4:12.02:0,12,144 0/0:3,0:3:6.02:0,6,77 0/0:5,0:5:15.05:0,15,189 0/0:13,0:13:36.12:0,36,483 0/0:4,0:4:12.04:0,12,152 0/0:10,0:10:27.08:0,27,332 0/0:9,0:9:24.07:0,24,296 0/0:5,0:5:15.04:0,15,174 0/1:7,5:12:99:153,0,227 0/1:6,4:10:99:112,0,187 0/0:9,0:9:27.09:0,27,351 0/1:5,3:8:93.08:93,0,162 0/0:21,1:22:54.17:0,54,704 0/0:1,0:1:3.01:0,3,39 0/1:4,3:7:95.76:96,0,130 0/1:13,1:14:6.13:6,0,363 0/0:14,0:14:36.11:0,36,459 0/0:6,0:6:15.05:0,15,202 0/0:13,0:13:33.10:0,33,417 0/0:16,0:16:39.12:0,39,492 0/0:9,0:9:24.08:0,24,324 0/0:8,0:8:24.08:0,24,326 0/1:2,2:4:62.04:69,0,62 0/0:8,0:8:24.08:0,24,313 0/0:7,0:7:15.04:0,15,188 0/0:8,0:9:21.07:0,21,273 -chr1 878331 . C T 170.27 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.516;DP=507;Dels=0.00;FS=13.852;HRun=0;HaplotypeScore=0.4065;InbreedingCoeff=-0.0252;MQ=57.83;MQ0=0;MQRankSum=0.921;QD=21.28;ReadPosRankSum=-1.361;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),EXON(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|4),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P486L|681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,missense_variant|cCg/cTg|P/L|ENSG00000187634|SAMD11|ENST00000342066|11/14|benign(0.007)|tolerated(0.12)|486/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187634|SAMD11|ENST00000474461|4/4||||retained_intron|1,missense_variant|cCg/cTg|P/L|ENSG00000187634|SAMD11|ENST00000455979|5/7|benign(0.029)|tolerated(0.09)|313/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,missense_variant|cCg/cTg|P/L|ENSG00000187634|SAMD11|ENST00000341065|9/12|benign(0.006)|tolerated(0.18)|394/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:15.05:0,15,184 0/0:3,0:3:9.03:0,9,120 0/0:2,0:2:6.02:0,6,75 0/0:3,0:3:9.01:0,9,101 0/1:2,6:8:17.51:218,0,18 0/0:6,0:7:15.05:0,15,201 0/0:12,0:12:36.12:0,36,474 0/0:6,0:6:15.03:0,15,176 0/0:29,0:29:87.24:0,87,1106 0/0:16,1:17:9.58:0,10,570 0/0:10,0:10:27.08:0,27,352 0/0:6,0:6:15.05:0,15,196 0/0:10,0:10:21.05:0,21,257 0/0:7,0:7:18.06:0,18,243 0/0:6,0:6:18.06:0,18,231 0/0:4,0:4:9.03:0,9,127 0/0:1,0:1:3.01:0,3,35 0/0:5,0:5:15.05:0,15,199 0/0:4,0:4:9.03:0,9,125 0/0:8,0:8:21.07:0,21,274 0/0:7,0:7:18.05:0,18,223 0/0:6,1:7:18.06:0,18,235 0/0:2,0:2:6.02:0,6,79 0/0:4,0:4:12.04:0,12,158 0/0:2,0:2:6.02:0,6,77 0/0:1,0:1:3.01:0,3,42 0/0:8,0:8:18.06:0,18,245 0/0:9,0:9:18.06:0,18,257 0/0:8,0:8:21.07:0,21,272 0/0:5,0:5:12.04:0,12,157 0/0:5,0:5:15.03:0,15,181 0/0:3,0:3:9.02:0,9,101 0/0:4,0:4:9.03:0,9,119 0/0:8,0:8:18.05:0,18,223 0/0:5,0:5:15.05:0,15,195 0/0:4,0:4:9.03:0,9,118 0/0:4,0:4:12.04:0,12,156 0/0:12,0:12:36.12:0,36,465 0/0:7,0:7:18.06:0,18,248 0/0:13,0:13:36.11:0,36,462 0/0:10,0:10:30.10:0,30,387 0/0:6,0:6:15.04:0,15,180 0/0:17,0:17:51.16:0,51,659 0/0:11,0:11:30.09:0,30,362 0/0:12,0:12:27.09:0,27,351 0/0:10,0:10:30.07:0,30,381 0/0:25,0:25:60.19:0,60,789 0/0:3,0:3:9.03:0,9,117 0/0:9,0:9:15.05:0,15,196 0/0:22,0:22:54.16:0,54,670 0/0:16,0:17:39.12:0,39,494 0/0:7,0:7:18.06:0,18,234 0/0:17,0:17:42.10:0,42,531 0/0:16,0:16:36.09:0,36,452 0/0:13,0:13:36.12:0,36,476 0/0:10,0:10:24.07:0,24,308 0/0:4,0:4:12.02:0,12,143 0/0:10,0:10:27.09:0,27,363 0/0:6,1:7:18.05:0,18,218 0/0:9,0:9:18.06:0,18,227 -chr1 878516 . GA G 725.28 . AC=4;AF=0.0333;AN=120;BaseQRankSum=4.091;DP=1587;FS=6.039;HRun=5;HaplotypeScore=109.1933;InbreedingCoeff=-0.0395;MQ=57.40;MQ0=0;MQRankSum=0.773;QD=10.67;ReadPosRankSum=1.454;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|11);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:12.04:0,12,162 0/0:10,0:10:30.09:0,30,393 0/0:8,0:8:24.08:0,24,324 0/0:8,0:8:24.08:0,24,328 0/0:16,0:16:45.15:0,45,609 0/0:14,0:14:39.13:0,39,521 0/0:25,0:25:69.23:0,69,925 0/0:19,0:19:45.15:0,45,602 0/0:23,0:23:57.19:0,57,767 0/0:42,0:42:99:0,120,1606 0/0:18,0:18:48.16:0,48,657 0/0:11,0:11:27.09:0,27,364 0/0:15,0:15:45.15:0,45,616 0/0:8,0:8:21.07:0,21,286 0/0:9,0:9:24.08:0,24,319 0/0:3,0:3:9.03:0,9,123 0/0:11,0:11:33.11:0,33,450 0/0:11,0:11:33.11:0,33,443 0/0:12,0:12:30.10:0,30,410 0/0:9,0:9:24.08:0,24,328 0/1:4,1:5:22.01:22,0,110 0/0:12,0:12:36.12:0,36,491 0/0:11,0:11:30.10:0,30,410 0/0:14,0:14:33.11:0,33,434 0/0:8,0:8:24.08:0,24,327 0/0:6,0:6:15.05:0,15,205 0/1:9,2:11:99:106,0,216 0/0:9,0:9:27.09:0,27,368 0/0:7,0:7:18.06:0,18,244 0/0:15,0:14:42.14:0,42,574 0/0:4,0:4:9.03:0,9,123 0/0:8,0:8:15.05:0,15,205 0/0:7,0:7:18.06:0,18,245 0/1:8,4:12:99:100,0,266 0/0:7,0:7:18.06:0,18,238 0/0:11,0:11:27.09:0,27,361 0/0:11,0:11:27.09:0,27,369 0/0:15,1:16:8.09:0,8,491 0/0:42,0:42:99:0,108,1470 0/0:80,0:80:99:0,211,2821 0/0:60,0:60:99:0,166,2187 0/0:42,0:42:90.28:0,90,1188 0/0:47,0:47:99:0,129,1722 0/0:47,0:47:99:0,126,1680 0/1:23,17:40:99:599,0,460 0/0:49,0:49:99:0,135,1814 0/0:97,0:97:99:0,259,3457 0/0:38,0:38:99:0,102,1385 0/0:46,0:46:99:0,105,1420 0/0:66,0:66:99:0,175,2345 0/0:66,0:66:99:0,172,2303 0/0:42,0:42:99:0,114,1505 0/0:61,0:61:99:0,163,2185 0/0:56,0:55:99:0,144,1894 0/0:42,0:41:99:0,123,1670 0/0:39,0:39:99:0,108,1433 0/0:34,0:34:84.28:0,84,1139 0/0:59,0:59:99:0,169,2281 0/0:37,0:37:99:0,102,1386 0/0:45,0:45:99:0,126,1680 -chr1 878761 . A AG 102.98 . AC=2;AF=0.0167;AN=120;BaseQRankSum=0.641;DP=955;FS=3.593;HRun=7;HaplotypeScore=63.6389;InbreedingCoeff=-0.0174;MQ=56.57;MQ0=0;MQRankSum=0.356;QD=4.90;ReadPosRankSum=-0.194;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|12);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,splice_region_variant&intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,splice_region_variant&intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,splice_region_variant&intron_variant&feature_elongation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12.02:0,12,116 0/0:9,0:9:18:0,18,165 0/0:8,0:8:21.03:0,21,201 0/0:3,0:3:7.83:0,8,63 0/0:20,0:20:54.08:0,54,520 0/0:19,0:19:42.06:0,42,405 0/0:27,0:27:60.08:0,60,579 0/0:21,0:21:44.40:0,44,389 0/0:41,0:41:91.02:0,91,870 0/0:38,0:38:89.85:0,90,828 0/0:17,0:17:45.02:0,45,425 0/0:23,0:23:42.05:0,42,405 0/0:24,0:24:54.08:0,54,518 0/0:12,0:12:27.04:0,27,261 0/0:27,0:27:60.07:0,60,571 0/0:9,0:9:21.03:0,21,201 0/0:6,0:6:9.01:0,9,87 0/0:23,0:23:54.07:0,54,512 0/0:19,0:19:42.06:0,42,403 0/0:18,0:18:48.07:0,48,463 0/0:14,0:14:38.97:0,39,370 0/0:19,0:19:57.08:0,57,542 0/0:17,0:17:51.08:0,51,491 0/0:13,0:13:30.04:0,30,288 0/0:13,0:13:30.04:0,30,286 0/0:12,0:12:27.04:0,27,261 0/0:12,0:12:30.04:0,30,286 0/0:7,0:7:18.03:0,18,174 0/0:16,0:16:41.92:0,42,383 0/0:15,0:15:39.06:0,39,375 0/0:15,0:14:30.04:0,30,289 0/0:10,0:10:27.04:0,27,261 0/0:21,0:21:51.08:0,51,490 0/0:16,0:16:36.01:0,36,338 0/0:7,0:7:12.01:0,12,116 0/1:12,1:13:0.24:0,0,272 0/0:20,0:20:48.07:0,48,461 0/0:33,0:33:72.07:0,72,679 0/0:6,0:6:15.02:0,15,145 0/0:18,0:18:42.06:0,42,404 0/0:13,0:13:33.05:0,33,317 0/0:10,0:10:18.02:0,18,171 0/0:14,0:14:21.03:0,21,203 0/0:9,0:9:21.03:0,21,202 0/0:19,0:20:48.33:0,48,437 0/0:9,0:9:15.02:0,15,145 0/0:27,0:27:53.52:0,54,518 0/1:4,4:8:35.63:160,0,36 0/0:15,0:15:33.05:0,33,317 0/0:24,0:24:22.79:0,23,458 0/0:32,1:33:57.54:0,58,549 0/0:12,0:12:27.03:0,27,261 0/0:13,0:13:21.03:0,21,201 0/0:18,0:18:36.05:0,36,347 0/0:9,0:9:21.03:0,21,203 0/0:8,0:8:18.02:0,18,174 0/0:10,0:10:24.03:0,24,232 0/0:13,1:14:31.56:0,32,285 0/0:12,0:12:24.03:0,24,231 0/0:11,0:11:27.04:0,27,261 -chr1 878764 . G C 139.53 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.470;DP=938;Dels=0.00;FS=7.307;HRun=0;HaplotypeScore=0.9091;InbreedingCoeff=-0.0119;MQ=56.61;MQ0=0;MQRankSum=1.683;QD=9.97;ReadPosRankSum=2.283;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|12);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.04:0,12,149 0/0:10,0:10:24.06:0,24,299 0/0:7,0:7:18.06:0,18,235 0/0:3,0:3:9.03:0,9,114 0/0:23,0:23:63.18:0,63,787 0/0:19,0:19:51.16:0,51,660 0/0:27,0:27:72.23:0,72,952 0/0:20,0:20:57.18:0,57,733 0/0:41,0:41:99:0,117,1508 0/0:39,0:39:99:0,117,1485 0/0:17,0:17:48.15:0,48,619 0/0:24,0:24:66.21:0,66,839 0/0:26,0:26:69.22:0,69,890 0/0:12,0:12:27.09:0,27,346 0/0:25,0:25:60.20:0,60,813 0/0:8,0:8:21.06:0,21,260 0/0:4,0:4:12.04:0,12,156 0/0:22,0:22:48.15:0,48,643 0/0:19,0:19:51.16:0,51,658 0/0:18,0:18:42.13:0,42,566 0/1:7,7:14:99:187,0,198 0/0:20,0:20:48.16:0,48,641 0/0:17,0:17:42.13:0,42,546 0/0:13,0:13:30.10:0,30,394 0/0:13,0:13:33.10:0,33,433 0/0:12,0:12:27.08:0,27,354 0/0:12,0:12:30.10:0,30,398 0/0:7,0:7:18.06:0,18,245 0/0:16,0:16:36.12:0,36,489 0/0:15,0:15:39.12:0,39,499 0/0:15,0:15:30.09:0,30,393 0/0:10,0:10:30.10:0,30,393 0/0:22,0:22:51.16:0,51,655 0/0:16,0:16:36.08:0,36,449 0/0:6,0:6:15.04:0,15,180 0/0:13,0:13:36.11:0,36,464 0/0:20,0:20:54.16:0,54,689 0/0:30,0:30:69.22:0,69,889 0/0:5,0:5:15.05:0,15,193 0/0:18,0:18:51.16:0,51,637 0/0:13,0:13:36.10:0,36,434 0/0:8,0:8:18.04:0,18,224 0/0:13,0:13:27.08:0,27,333 0/0:8,0:8:24.08:0,24,313 0/0:19,0:19:48.15:0,48,614 0/0:9,0:9:21.07:0,21,266 0/0:26,0:26:63.17:0,63,789 0/0:8,0:8:21.07:0,21,270 0/0:14,0:14:36.11:0,36,459 0/0:24,0:24:54.18:0,54,720 0/0:30,0:30:78.21:0,78,964 0/0:12,0:12:30.09:0,30,393 0/0:11,0:11:30.09:0,30,376 0/0:17,0:17:33.10:0,33,432 0/0:9,0:9:21.07:0,21,271 0/0:8,0:8:18.06:0,18,247 0/0:10,0:10:24.08:0,24,330 0/0:14,0:14:33.10:0,33,432 0/0:12,0:12:27.09:0,27,354 0/0:11,0:11:27.09:0,27,368 -chr1 878904 . A C 629.76 . AC=27;AF=0.270;AN=100;BaseQRankSum=-10.394;DP=328;Dels=0.01;FS=66.455;HRun=4;HaplotypeScore=5.0793;InbreedingCoeff=-0.3279;MQ=45.67;MQ0=0;MQRankSum=-7.168;QD=2.59;ReadPosRankSum=7.847;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|12);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/1:2,2:4:24.41:24,0,64 0/1:3,3:6:17.59:18,0,97 0/0:4,2:6:12.04:0,12,156 0/0:4,0:4:12.02:0,12,131 0/1:5,9:15:42.98:43,0,146 0/1:11,5:16:41.84:42,0,250 0/1:8,6:15:72.03:72,0,226 0/1:6,6:12:38.99:39,0,193 0/1:22,15:38:66.84:67,0,638 0/1:14,14:28:75.83:76,0,448 0/1:4,10:14:40.10:40,0,87 0/1:8,7:15:19.28:19,0,254 0/1:5,9:14:44.89:45,0,150 0/0:1,0:1:3.01:0,3,36 0/0:4,0:4:12.04:0,12,147 0/1:1,2:4:24.44:40,0,24 ./. 0/0:2,0:2:6.02:0,6,67 0/1:4,2:6:12.63:13,0,115 0/1:3,2:5:46.14:46,0,94 0/0:1,0:1:3.01:0,3,33 0/0:4,2:6:12.03:0,12,134 0/0:4,0:4:12.03:0,12,140 0/1:3,2:5:19.52:20,0,92 0/0:4,0:4:9.03:0,9,105 0/1:3,1:4:14.65:15,0,104 0/1:1,2:3:24.44:46,0,24 0/0:1,0:1:3.01:0,3,33 0/0:4,0:4:6.02:0,6,71 0/1:3,1:4:13.66:14,0,97 0/0:1,1:2:3.01:0,3,34 0/0:3,0:3:9.03:0,9,106 0/1:5,2:7:12.66:13,0,92 ./. 0/0:2,0:2:6.02:0,6,67 0/1:3,1:4:18.56:19,0,93 0/1:3,3:6:21.40:21,0,93 0/1:7,3:10:2.61:3,0,230 ./. 0/0:1,0:1:3.01:0,3,35 0/0:1,1:2:3.01:0,3,37 ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,32 0/0:2,2:4:3.01:0,3,33 1/1:0,1:1:3:25,3,0 0/0:4,3:7:6.02:0,6,67 ./. ./. 0/0:1,0:1:3.01:0,3,35 0/0:4,3:7:12.03:0,12,140 0/0:4,1:5:12.02:0,12,129 ./. ./. 0/1:2,2:4:21.57:22,0,58 1/1:0,1:1:3.01:31,3,0 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,34 ./. ./. -chr1 878906 . CTTT C 498.81 . AC=35;AF=0.407;AN=86;BaseQRankSum=-0.896;DP=307;FS=10.838;HRun=22;HaplotypeScore=48.3314;InbreedingCoeff=0.1154;MQ=44.42;MQ0=0;MQRankSum=-1.401;QD=2.60;ReadPosRankSum=2.748;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|12);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 1/1:3,0:4:1.96:11,2,0 0/0:4,0:5:0:0,0,0 0/0:6,0:6:0.89:0,1,2 ./. 0/1:12,1:15:34.09:38,0,34 1/1:15,0:17:5.71:45,6,0 1/1:13,0:15:7.15:71,7,0 0/0:7,3:10:4.51:0,5,24 1/1:27,4:35:6.66:89,7,0 0/0:23,1:26:3.90:0,4,222 1/1:10,1:13:2.69:27,3,0 0/1:12,1:16:7.88:64,0,8 0/1:8,2:13:13.75:14,0,16 ./. 0/0:3,0:3:0:0,0,0 0/1:1,2:4:20.71:21,0,30 ./. 1/1:0,1:2:2.76:20,3,0 1/1:3,0:6:2.54:20,3,0 0/0:4,0:4:0:0,0,0 ./. 1/1:3,0:6:2.33:20,2,0 0/0:3,0:3:2.97:0,3,20 0/1:4,1:6:34.74:35,0,44 0/0:3,0:4:0:0,0,0 1/1:3,1:4:3:27,3,0 0/0:1,0:3:5.93:0,6,56 0/0:1,0:1:3.01:0,3,46 0/0:3,0:4:0:0,0,0 0/0:5,0:5:3:0,3,25 ./. 0/0:3,0:3:2.97:0,3,20 0/0:6,0:6:11.95:0,12,119 0/0:2,1:4:2.97:0,3,20 0/0:2,0:2:6.02:0,6,72 0/1:2,0:3:13.75:14,0,14 0/1:5,1:6:21.20:21,0,40 0/1:5,0:7:11.77:12,0,26 ./. ./. 0/0:0,1:1:0:0,0,0 1/1:0,0:1:2.97:20,3,0 0/0:1,0:1:0:0,0,0 ./. 1/1:3,0:4:2.94:23,3,0 1/1:0,1:1:3:27,3,0 0/1:5,0:8:12.30:12,0,18 ./. 0/0:1,0:1:1.55:0,2,4 ./. 1/1:5,0:6:2.05:18,2,0 0/0:4,0:5:0:0,0,0 ./. ./. 0/0:4,0:4:0:0,0,0 ./. ./. ./. ./. ./. -chr1 879195 . C T 744.73 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.733;DP=2228;Dels=0.00;FS=2.345;HRun=0;HaplotypeScore=2.3431;InbreedingCoeff=-0.0106;MQ=57.41;MQ0=0;MQRankSum=1.176;QD=11.82;ReadPosRankSum=0.278;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|13);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,missense_variant|Cgc/Tgc|R/C|ENSG00000187634|SAMD11|ENST00000455979|7/7|benign(0.047)|tolerated(0.15)|430/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,110 0/0:10,0:11:27.09:0,27,349 0/0:4,0:4:9.03:0,9,121 0/0:6,0:6:15.05:0,15,182 0/0:16,0:16:48.14:0,48,612 0/0:15,0:15:45.14:0,45,590 0/0:28,0:28:78.25:0,78,1024 0/0:17,0:17:48.16:0,48,635 0/0:41,0:41:99:0,117,1501 0/0:47,1:48:99:0,135,1771 0/0:15,0:15:45.12:0,45,580 0/0:14,1:15:36.11:0,36,458 0/0:20,0:20:57.15:0,57,706 0/0:22,0:22:54.18:0,54,733 0/0:33,0:33:75.24:0,75,1014 0/0:25,0:25:63.20:0,63,849 0/0:23,0:23:54.18:0,54,732 0/0:22,0:22:54.18:0,54,732 0/0:22,0:22:57.18:0,57,746 0/0:22,1:23:57.18:0,57,746 0/0:18,0:18:42.12:0,42,526 0/0:25,0:25:60.18:0,60,773 0/0:20,0:20:48.16:0,48,653 0/0:17,0:17:42.13:0,42,528 0/0:23,0:23:45.15:0,45,609 0/0:25,0:25:57.19:0,57,773 0/0:26,0:26:60.18:0,60,774 0/0:21,0:21:54.16:0,54,702 0/0:21,0:21:57.17:0,57,755 0/0:25,0:25:57.18:0,57,767 0/0:37,0:37:87.26:0,87,1127 0/0:28,0:29:69.21:0,69,900 0/0:27,0:27:57.18:0,57,746 0/0:21,0:21:57.19:0,57,766 0/0:27,0:27:69.20:0,69,862 0/0:17,0:17:51.16:0,51,665 0/0:38,0:38:81.26:0,81,1075 0/0:35,0:35:96.30:0,96,1263 0/1:26,35:62:99:792,0,594 0/0:85,0:85:99:0,193,2464 0/0:68,0:68:99:0,171,2133 0/0:53,0:53:99:0,129,1657 0/0:50,0:51:99:0,114,1444 0/0:58,0:58:99:0,144,1893 0/0:54,0:56:99:0,129,1661 0/0:64,0:65:99:0,153,2007 0/0:100,0:100:99:0,232,2899 0/0:27,0:27:69.20:0,69,867 0/0:68,0:68:99:0,156,1993 0/0:91,0:91:99:0,220,2817 0/0:77,0:79:99:0,172,2239 0/0:65,0:66:99:0,156,2016 0/0:74,1:76:99:0,159,2033 0/0:56,1:57:99:0,105,1680 0/0:52,0:52:99:0,123,1564 0/0:52,0:53:99:0,120,1566 0/0:49,0:49:99:0,117,1513 0/0:50,0:51:99:0,102,1301 0/0:47,0:47:99:0,123,1617 0/0:50,0:52:99:0,111,1452 -chr1 879317 . C T 1801.69 . AC=5;AF=0.0417;AN=120;BaseQRankSum=0.490;DP=1511;Dels=0.00;FS=0.480;HRun=0;HaplotypeScore=0.8559;InbreedingCoeff=-0.0439;MQ=57.96;MQ0=0;MQRankSum=-0.001;QD=13.15;ReadPosRankSum=0.731;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y610|681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,synonymous_variant|taC/taT|Y|ENSG00000187634|SAMD11|ENST00000342066|14/14|||610/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,synonymous_variant|taC/taT|Y|ENSG00000187634|SAMD11|ENST00000455979|7/7|||470/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,synonymous_variant|taC/taT|Y|ENSG00000187634|SAMD11|ENST00000341065|12/12|||518/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:15.04:0,15,182 0/0:9,0:9:24.08:0,24,307 0/0:13,0:13:39.11:0,39,492 0/0:13,0:13:33.10:0,33,408 0/0:27,0:27:69.21:0,69,893 0/0:21,0:21:60.17:0,60,761 0/0:55,0:55:99:0,147,1910 0/1:7,14:21:99:391,0,209 0/0:72,0:72:99:0,193,2503 0/0:65,0:66:99:0,187,2418 0/0:28,0:28:81.22:0,81,1016 0/0:33,0:33:90.28:0,90,1145 0/0:27,0:28:72.22:0,72,915 0/0:21,0:21:51.16:0,51,689 0/0:23,0:24:63.19:0,63,834 0/0:13,0:13:39.12:0,39,483 0/0:12,0:12:33.10:0,33,413 0/0:18,0:18:48.15:0,48,623 0/0:16,0:16:45.14:0,45,582 0/0:22,0:23:60.20:0,60,813 0/0:15,0:15:36.12:0,36,473 0/0:14,0:14:33.10:0,33,427 0/0:10,0:10:27.09:0,27,368 0/0:14,0:14:33.11:0,33,440 0/0:22,0:22:60.19:0,60,788 0/0:17,0:17:39.12:0,39,502 0/0:15,0:15:36.12:0,36,480 0/0:17,0:17:45.14:0,45,600 0/0:24,0:24:57.18:0,57,750 0/0:22,0:22:57.18:0,57,760 0/0:24,1:25:66.20:0,66,853 0/0:14,0:14:36.11:0,36,466 0/1:14,8:22:99:260,0,436 0/1:9,4:13:99:119,0,308 0/0:30,0:30:66.22:0,66,898 0/0:15,0:15:39.13:0,39,527 0/0:24,0:24:66.19:0,66,841 0/0:27,0:27:69.23:0,69,935 0/0:34,0:34:81.25:0,81,1006 0/0:39,0:39:96.25:0,96,1187 0/0:32,0:32:81.26:0,81,1056 0/0:26,0:26:66.18:0,66,829 0/0:30,0:30:69.19:0,69,861 0/0:22,0:22:63.20:0,63,817 0/1:16,8:25:99:245,0,363 0/0:27,0:27:66.18:0,66,803 0/0:52,0:52:99:0,135,1699 0/0:11,0:11:27.08:0,27,350 0/0:22,0:22:60.16:0,60,739 0/1:22,34:56:99:891,0,554 0/0:38,0:38:99:0,105,1347 0/0:36,0:36:93.28:0,93,1215 0/0:43,0:43:99:0,108,1385 0/0:20,0:20:48.13:0,48,586 0/0:20,0:21:57.17:0,57,708 0/0:19,0:19:48.13:0,48,581 0/0:25,0:25:60.18:0,60,773 0/0:20,0:20:48.15:0,48,622 0/0:29,0:29:78.23:0,78,1003 0/0:25,0:25:63.17:0,63,805 -chr1 879376 . G A 35.51 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.159;DP=1323;Dels=0.00;FS=4.217;HRun=1;HaplotypeScore=0.6368;InbreedingCoeff=-0.0128;MQ=58.52;MQ0=0;MQRankSum=2.465;QD=2.96;ReadPosRankSum=0.209;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R630Q|681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,missense_variant|cGa/cAa|R/Q|ENSG00000187634|SAMD11|ENST00000342066|14/14|benign(0.048)|tolerated(0.13)|630/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,missense_variant|cGa/cAa|R/Q|ENSG00000187634|SAMD11|ENST00000455979|7/7|benign(0.024)|tolerated(0.19)|490/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,missense_variant|cGa/cAa|R/Q|ENSG00000187634|SAMD11|ENST00000341065|12/12|benign(0.012)|tolerated(0.16)|538/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:9.03:0,9,121 0/0:15,0:15:36.10:0,36,432 0/0:13,0:13:39.11:0,39,487 0/0:9,0:9:27.08:0,27,336 0/0:35,0:35:99:0,99,1327 0/0:34,0:34:96.31:0,96,1269 0/0:66,0:66:99:0,187,2474 0/0:35,0:35:96.31:0,96,1275 0/0:86,0:86:99:0,250,3261 0/0:93,0:93:99:0,262,3431 0/0:37,0:37:99:0,108,1443 0/0:33,0:33:96.30:0,96,1252 0/0:61,0:61:99:0,175,2208 0/0:22,0:22:60.19:0,60,795 0/0:29,0:29:75.23:0,75,973 0/0:15,0:15:39.13:0,39,519 0/1:8,4:12:83.22:83,0,229 0/0:16,0:16:42.13:0,42,547 0/0:27,0:28:66.18:0,66,842 0/0:23,0:23:54.16:0,54,701 0/0:14,1:15:42.14:0,42,550 0/0:20,0:20:51.14:0,51,663 0/0:15,1:16:42.12:0,42,532 0/0:14,0:14:36.12:0,36,481 0/0:22,0:22:54.18:0,54,730 0/0:20,0:20:51.14:0,51,651 0/0:16,2:18:3.39:0,3,552 0/0:21,0:21:51.16:0,51,657 0/0:19,0:19:36.12:0,36,506 0/0:13,0:13:36.12:0,36,467 0/0:26,0:26:66.20:0,66,852 0/0:15,0:15:45.14:0,45,577 0/0:23,0:23:63.17:0,63,787 0/0:23,0:23:51.16:0,51,681 0/0:29,0:29:69.22:0,69,915 0/0:13,0:13:33.11:0,33,443 0/0:26,0:26:69.19:0,69,867 0/0:21,0:21:54.14:0,54,685 0/0:10,0:10:27.09:0,27,353 0/0:16,0:16:45.15:0,45,604 0/0:14,1:15:42.13:0,42,542 0/0:15,0:15:39.09:0,39,482 0/0:16,0:16:45.14:0,45,573 0/0:5,0:5:15.05:0,15,198 0/0:13,0:13:39.12:0,39,504 0/0:22,0:22:63.19:0,63,790 0/0:24,0:24:57.18:0,57,738 0/0:7,0:7:15.03:0,15,182 0/0:7,0:7:21.07:0,21,274 0/0:21,0:22:54.17:0,54,700 0/0:22,0:22:48.15:0,48,615 0/0:17,0:17:45.15:0,45,601 0/0:22,0:22:51.17:0,51,685 0/0:10,0:10:30.10:0,30,393 0/0:11,0:12:30.09:0,30,383 0/0:12,0:12:33.11:0,33,436 0/0:10,0:10:30.10:0,30,394 0/0:10,0:10:30.10:0,30,384 0/0:7,0:7:21.07:0,21,280 0/0:8,0:8:21.07:0,21,270 -chr1 879482 . G C 516.68 . AC=1;AF=0.0088;AN=114;BaseQRankSum=2.415;DP=1065;Dels=0.00;FS=3.604;HRun=0;HaplotypeScore=0.8043;InbreedingCoeff=-0.0358;MQ=59.14;MQ0=0;MQRankSum=0.854;QD=17.82;ReadPosRankSum=-1.823;EFF=DOWNSTREAM(MODIFIER||||178|SAMD11|protein_coding|CODING|ENST00000420190|),DOWNSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G665|681|SAMD11|protein_coding|CODING|ENST00000342066|);CSQ=downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000420190||||-/179|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,synonymous_variant|ggG/ggC|G|ENSG00000187634|SAMD11|ENST00000342066|14/14|||665/681|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,synonymous_variant|ggG/ggC|G|ENSG00000187634|SAMD11|ENST00000455979|7/7|||525/541|protein_coding|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,synonymous_variant|ggG/ggC|G|ENSG00000187634|SAMD11|ENST00000341065|12/12|||573/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:12,0:12:27.07:0,27,331 0/0:15,0:16:42.12:0,42,508 0/0:19,0:19:57.17:0,57,721 0/0:14,0:14:39.11:0,39,483 0/0:34,0:34:99:0,102,1322 0/0:21,0:21:60.16:0,60,756 0/0:62,0:62:99:0,184,2409 0/1:12,17:29:99:564,0,360 0/0:67,0:67:99:0,196,2575 0/0:90,0:90:99:0,253,3336 0/0:34,0:34:99:0,99,1319 0/0:39,0:39:99:0,114,1443 0/0:49,0:49:99:0,135,1789 0/0:27,0:27:57.18:0,57,757 0/0:27,0:27:69.16:0,69,864 0/0:12,0:12:27.08:0,27,344 0/0:16,0:16:42.10:0,42,499 0/0:20,0:20:48.15:0,48,621 0/0:18,0:18:42.14:0,42,572 0/0:20,0:20:51.17:0,51,689 0/0:22,0:22:57.18:0,57,747 0/0:31,0:31:69.16:0,69,860 0/0:16,0:16:45.14:0,45,565 0/0:23,0:23:63.17:0,63,786 0/0:23,0:23:57.17:0,57,727 0/0:10,0:10:24.05:0,24,292 0/0:18,0:18:45.14:0,45,580 0/0:20,0:20:48.15:0,48,621 0/0:15,0:15:39.13:0,39,513 0/0:17,0:17:36.12:0,36,486 0/0:19,0:19:51.13:0,51,606 0/0:17,1:18:39.12:0,39,508 0/0:32,0:32:75.24:0,75,996 0/0:21,0:21:48.15:0,48,641 0/0:22,0:22:54.16:0,54,696 0/0:25,0:25:57.18:0,57,759 0/0:12,0:12:30.09:0,30,381 0/0:31,0:31:78.24:0,78,1032 0/0:8,0:8:21.04:0,21,262 0/0:2,0:2:6.02:0,6,82 0/0:3,0:3:9.03:0,9,115 0/0:2,0:2:3.01:0,3,42 0/0:2,0:2:6.02:0,6,71 0/0:3,0:3:9.03:0,9,113 0/0:1,0:1:3.01:0,3,33 0/0:5,0:5:12.01:0,12,132 0/0:5,0:5:12.01:0,12,127 0/0:2,0:2:3.01:0,3,45 ./. 0/0:2,0:3:6.02:0,6,67 0/0:7,0:7:21.07:0,21,266 ./. 0/0:4,0:4:12.04:0,12,149 0/0:2,0:2:6.02:0,6,79 0/0:3,0:3:9.03:0,9,111 0/0:3,0:3:9.03:0,9,112 0/0:2,0:2:6.02:0,6,80 0/0:4,0:4:6.02:0,6,83 0/0:3,0:3:9.03:0,9,107 ./. -chr1 879676 . G A 6945.69 . AC=71;AF=0.934;AN=76;BaseQRankSum=-1.592;DP=208;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=0.0908;InbreedingCoeff=0.0037;MQ=56.70;MQ0=0;MQRankSum=-0.599;QD=33.55;ReadPosRankSum=-1.965;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|17),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|5),UTR_3_PRIME(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|14),UTR_3_PRIME(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|19);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000187634|SAMD11|ENST00000342066|14/14|||-/681|protein_coding|1,3_prime_UTR_variant|||ENSG00000188976|NOC2L|ENST00000327044|19/19|||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|5/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|17/17||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187634|SAMD11|ENST00000341065|12/12|||-/589|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,6:7:18.05:218,18,0 1/1:0,7:7:21.05:262,21,0 1/1:0,8:8:24.07:308,24,0 1/1:0,5:5:15.05:187,15,0 1/1:0,11:11:33.11:432,33,0 1/1:0,11:11:33.10:423,33,0 1/1:0,18:18:54.17:711,54,0 1/1:0,10:10:30.10:405,30,0 1/1:0,21:21:63.20:838,63,0 0/1:18,16:34:99:537,0,574 1/1:0,10:10:27.08:334,27,0 1/1:0,6:6:18.06:238,18,0 1/1:0,10:10:30.10:386,30,0 1/1:0,1:1:3.01:40,3,0 1/1:0,4:4:12.04:166,12,0 ./. 1/1:0,3:3:9.03:114,9,0 1/1:0,2:2:6.02:76,6,0 1/1:0,3:3:9.03:116,9,0 1/1:0,1:1:3.01:42,3,0 0/1:1,2:3:30.98:72,0,31 ./. 1/1:0,2:2:6.02:82,6,0 1/1:0,2:2:6.02:75,6,0 1/1:0,3:3:9.03:124,9,0 1/1:0,1:1:3.01:36,3,0 0/1:3,1:4:28.62:29,0,95 1/1:0,1:1:3.01:34,3,0 ./. 1/1:0,2:2:6.02:78,6,0 1/1:0,3:3:9.03:122,9,0 1/1:0,1:1:2.99:23,3,0 1/1:0,2:2:6.02:81,6,0 1/1:0,1:1:3.01:41,3,0 1/1:1,2:3:3.01:45,3,0 ./. 1/1:0,1:1:3.01:40,3,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. 1/1:0,2:2:6.02:79,6,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 1/1:0,1:1:3.01:39,3,0 ./. 1/1:0,2:2:6.02:78,6,0 ./. ./. ./. ./. ./. -chr1 879687 . T C 5518.2 . AC=65;AF=0.956;AN=68;BaseQRankSum=0.725;DP=166;Dels=0.00;FS=1.578;HRun=1;HaplotypeScore=0.1048;InbreedingCoeff=0.0533;MQ=56.43;MQ0=0;MQRankSum=0.068;QD=33.44;ReadPosRankSum=-0.128;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|17),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|5),UTR_3_PRIME(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|14),UTR_3_PRIME(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|19);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000187634|SAMD11|ENST00000342066|14/14|||-/681|protein_coding|1,3_prime_UTR_variant|||ENSG00000188976|NOC2L|ENST00000327044|19/19|||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|5/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|17/17||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187634|SAMD11|ENST00000341065|12/12|||-/589|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,5:5:15.04:181,15,0 1/1:0,6:6:15.05:189,15,0 1/1:0,7:7:21.06:272,21,0 1/1:0,3:3:6.02:80,6,0 1/1:0,12:12:36.12:484,36,0 1/1:0,7:7:21.07:272,21,0 1/1:0,9:9:27.09:353,27,0 1/1:0,8:8:24.08:328,24,0 1/1:0,14:14:42.13:545,42,0 0/1:17,17:34:99:564,0,489 1/1:0,9:9:27.08:334,27,0 1/1:0,4:4:12.04:151,12,0 1/1:0,11:11:33.10:424,33,0 ./. 1/1:0,4:4:12.04:162,12,0 ./. 1/1:0,2:2:6:66,6,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:37,3,0 1/1:0,1:1:3.01:42,3,0 ./. ./. 1/1:0,1:1:3.01:42,3,0 1/1:0,2:2:6.02:81,6,0 1/1:0,2:2:6.02:84,6,0 1/1:0,1:1:3.01:39,3,0 1/1:0,4:4:12.04:157,12,0 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,2:2:6.02:73,6,0 1/1:0,2:2:6.02:78,6,0 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:84,6,0 ./. 1/1:1,2:3:3.01:45,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. 1/1:0,2:2:6.02:77,6,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 1/1:0,1:1:3.01:39,3,0 ./. 1/1:0,2:2:6.02:78,6,0 ./. ./. ./. ./. ./. -chr1 879911 . G A 413.77 . AC=3;AF=0.0254;AN=118;BaseQRankSum=-0.760;DP=308;Dels=0.00;FS=1.528;HRun=1;HaplotypeScore=0.1788;InbreedingCoeff=-0.0710;MQ=57.83;MQ0=0;MQRankSum=0.760;QD=15.32;ReadPosRankSum=0.384;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|17),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|5),UTR_3_PRIME(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|14),UTR_3_PRIME(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|19);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000187634|SAMD11|ENST00000342066|14/14|||-/681|protein_coding|1,3_prime_UTR_variant|||ENSG00000188976|NOC2L|ENST00000327044|19/19|||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|5/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|17/17||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187634|SAMD11|ENST00000341065|12/12|||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.03:0,12,136 0/0:4,0:4:9.03:0,9,114 0/0:9,0:9:27.08:0,27,345 ./. 0/0:2,0:2:6.02:0,6,67 0/0:2,0:2:6.02:0,6,76 0/0:7,0:7:21.07:0,21,281 0/0:7,0:7:21.07:0,21,286 0/0:10,0:10:30.09:0,30,375 0/0:9,0:9:27.09:0,27,362 0/0:3,0:3:9.03:0,9,121 0/0:3,0:3:6.02:0,6,82 0/0:4,0:4:12.04:0,12,161 0/0:6,0:6:15.05:0,15,207 0/0:3,0:3:9.03:0,9,112 0/0:3,0:3:9.02:0,9,103 0/0:7,0:7:18.06:0,18,243 0/0:4,0:4:12.04:0,12,160 0/0:4,0:4:12.03:0,12,139 0/1:2,5:7:59.27:168,0,59 0/0:2,0:2:6.02:0,6,74 0/0:4,0:4:12.04:0,12,161 0/0:4,0:4:12.04:0,12,153 0/0:4,0:4:12.04:0,12,163 0/0:6,0:6:12.04:0,12,169 0/0:9,0:9:24.08:0,24,317 0/0:5,0:5:15.05:0,15,192 0/0:5,0:5:15.05:0,15,187 0/0:10,0:10:27.07:0,27,349 0/0:5,0:5:15.05:0,15,207 0/0:6,0:6:18.05:0,18,212 0/0:1,0:1:3:0,3,25 0/0:2,0:2:6.02:0,6,76 0/0:2,0:2:6.02:0,6,79 0/0:6,0:6:18.06:0,18,247 0/0:5,0:5:12.04:0,12,161 0/0:4,0:4:12.04:0,12,155 0/0:4,0:4:12.03:0,12,140 0/0:7,0:7:21.07:0,21,278 0/1:5,4:9:99:132,0,138 0/0:6,0:6:18.05:0,18,228 0/0:2,0:2:6:0,6,58 0/0:5,0:5:15.05:0,15,196 0/0:5,0:5:15.05:0,15,186 0/0:8,0:8:18.06:0,18,235 0/0:3,0:3:9.03:0,9,113 0/0:17,0:17:39.12:0,39,502 0/0:1,0:1:3.01:0,3,33 0/1:5,6:11:99:192,0,162 0/0:2,0:2:6.02:0,6,79 0/0:9,0:9:24.08:0,24,307 0/0:7,0:7:18.06:0,18,242 0/0:3,0:3:9.03:0,9,122 0/0:2,0:2:3.01:0,3,39 0/0:6,0:6:18.06:0,18,245 0/0:6,0:6:12.04:0,12,155 0/0:4,0:4:9.03:0,9,127 0/0:6,0:6:15.05:0,15,197 0/0:1,0:1:3.01:0,3,42 0/0:5,0:5:9.03:0,9,116 -chr1 880110 . G A 149.9 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.394;DP=1847;Dels=0.00;FS=1.624;HRun=0;HaplotypeScore=0.9203;InbreedingCoeff=-0.0094;MQ=57.47;MQ0=0;MQRankSum=1.220;QD=6.25;ReadPosRankSum=0.988;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|17),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|5),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D738|749|NOC2L|protein_coding|CODING|ENST00000327044|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,synonymous_variant|gaC/gaT|D|ENSG00000188976|NOC2L|ENST00000327044|19/19|||738/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|5/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|17/17||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:9.03:0,9,112 0/0:9,0:9:24.07:0,24,289 0/0:9,0:9:24.08:0,24,305 0/0:9,0:9:24.07:0,24,294 0/0:14,0:14:39.11:0,39,498 0/0:18,0:18:54.16:0,54,675 0/0:39,0:39:99:0,102,1315 0/0:17,0:17:39.12:0,39,515 0/0:47,0:47:99:0,138,1814 0/0:38,0:38:99:0,114,1485 0/0:20,0:20:60.19:0,60,788 0/0:19,0:19:57.18:0,57,737 0/0:21,0:22:63.20:0,63,821 0/0:28,0:28:48.13:0,48,601 0/0:31,0:31:66.21:0,66,872 0/0:18,0:18:45.11:0,45,555 0/0:38,0:38:78.23:0,78,1006 0/0:29,0:29:66.17:0,66,829 0/0:39,0:39:90.26:0,90,1153 0/0:29,0:29:60.15:0,60,754 0/0:25,0:25:54.18:0,54,715 0/0:37,0:37:87.27:0,87,1138 0/0:30,0:32:69.21:0,69,912 0/0:31,0:31:69.22:0,69,920 0/0:25,0:27:51.15:0,51,660 0/0:48,0:49:90.25:0,90,1126 0/0:37,0:37:81.25:0,81,1041 0/0:26,0:28:60.19:0,60,791 0/0:54,0:54:99:0,117,1536 0/0:30,0:30:69.19:0,69,886 0/0:37,0:37:81.20:0,81,991 0/1:15,8:24:99:198,0,410 0/0:31,0:31:60.18:0,60,769 0/0:44,0:44:90.27:0,90,1173 0/0:28,0:29:66.17:0,66,835 0/0:32,0:32:75.23:0,75,966 0/0:30,0:30:60.19:0,60,799 0/0:50,0:51:99:0,105,1366 0/0:29,0:29:60.18:0,60,731 0/0:31,0:32:66.18:0,66,827 0/0:48,0:49:99:0,105,1312 0/0:26,0:26:51.15:0,51,643 0/0:32,0:33:69.19:0,69,891 0/0:29,0:29:66.17:0,66,808 0/0:30,0:31:66.20:0,66,827 0/0:38,0:38:84.25:0,84,1038 0/0:54,0:55:99:0,114,1446 0/0:24,0:24:60.19:0,60,770 0/0:33,0:34:75.22:0,75,949 0/0:42,0:42:81.25:0,81,1046 0/0:53,0:54:99:0,120,1488 0/0:30,0:31:63.17:0,63,780 0/0:32,0:32:63.15:0,63,768 0/0:28,0:28:60.19:0,60,777 0/0:37,0:37:75.24:0,75,985 0/0:30,0:31:69.19:0,69,879 0/0:24,0:24:48.14:0,48,608 0/0:28,0:28:54.18:0,54,719 0/0:27,0:27:42.13:0,42,561 0/0:27,0:27:63.18:0,63,778 -chr1 880238 . A G 43084.12 . AC=114;AF=0.9500;AN=120;BaseQRankSum=-0.613;DP=1203;Dels=0.00;FS=12.344;HRun=1;HaplotypeScore=1.0677;InbreedingCoeff=-0.0525;MQ=58.52;MQ0=0;MQRankSum=-1.859;QD=35.81;ReadPosRankSum=-0.535;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|18),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|4);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,6:6:18.06:228,18,0 1/1:0,13:13:36.11:456,36,0 1/1:0,15:15:45.15:591,45,0 1/1:0,12:12:33.09:402,33,0 1/1:0,25:25:75.25:1006,75,0 1/1:0,23:23:66.19:869,66,0 1/1:0,54:54:99:2124,160,0 1/1:0,26:26:78.26:1040,78,0 1/1:0,55:55:99:2171,163,0 0/1:29,35:64:99:1174,0,887 1/1:0,30:30:90.29:1206,90,0 1/1:0,28:28:84.26:1099,84,0 1/1:0,36:36:99:1387,105,0 1/1:0,13:13:39.13:525,39,0 1/1:0,29:29:87.28:1165,87,0 1/1:0,16:16:42.14:575,42,0 1/1:0,15:15:42.14:573,42,0 1/1:0,20:21:60.19:797,60,0 1/1:0,15:15:45.14:591,45,0 1/1:0,18:18:51.15:659,51,0 1/1:0,23:23:66.22:893,66,0 1/1:0,32:32:90.27:1205,90,0 0/1:7,5:12:99:167,0,238 1/1:0,14:14:39.13:517,39,0 1/1:0,17:18:45.14:592,45,0 1/1:0,17:17:48.16:652,48,0 1/1:0,17:17:48.15:619,48,0 1/1:0,18:18:54.17:705,54,0 1/1:0,24:24:69.22:932,69,0 1/1:0,20:20:57.18:757,57,0 1/1:0,17:18:51.17:685,51,0 1/1:0,23:23:66.21:880,66,0 1/1:0,17:17:45.15:603,45,0 1/1:0,20:20:60.20:811,60,0 1/1:0,17:18:48.15:641,48,0 1/1:0,7:7:21.07:285,21,0 1/1:0,17:17:51.16:680,51,0 1/1:0,27:27:78.23:1045,78,0 1/1:0,11:11:33.11:433,33,0 1/1:0,23:23:69.20:913,69,0 1/1:0,18:18:48.15:620,48,0 0/1:4,6:10:97.28:162,0,97 1/1:0,19:19:54.17:689,54,0 1/1:0,13:13:39.12:504,39,0 1/1:0,25:25:66.21:873,66,0 1/1:0,16:16:42.14:565,42,0 1/1:0,27:27:78.25:1006,78,0 1/1:0,8:8:24.08:312,24,0 1/1:0,11:11:33.11:444,33,0 1/1:0,19:20:57.18:738,57,0 0/1:14,16:30:99:559,0,430 1/1:0,10:10:30.09:388,30,0 1/1:0,17:17:51.15:650,51,0 0/1:1,10:11:11.66:332,0,12 1/1:0,18:18:51.17:680,51,0 1/1:0,13:13:36.11:466,36,0 0/1:7,5:12:99:149,0,260 1/1:0,18:18:48.16:657,48,0 1/1:0,6:6:18.06:235,18,0 1/1:0,10:10:30.10:402,30,0 -chr1 880258 . TAA T 1233.06 . AC=1;AF=0.0083;AN=120;BaseQRankSum=1.890;DP=1382;FS=2.604;HRun=2;HaplotypeScore=131.0286;InbreedingCoeff=-0.0085;MQ=58.89;MQ0=0;MQRankSum=1.259;QD=20.55;ReadPosRankSum=-3.041;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|18),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|4);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:8,0:8:24.08:0,24,457 0/0:13,0:13:39.13:0,39,778 0/0:15,0:15:45.15:0,45,900 0/0:14,0:14:39.13:0,39,793 0/0:24,0:24:72.25:0,72,1424 0/0:28,0:28:81.28:0,81,1641 0/0:46,0:46:99:0,138,2739 0/0:31,0:31:93.32:0,93,1854 0/1:31,29:60:99:1290,0,1547 0/0:70,0:70:99:0,211,4176 0/0:32,0:32:96.33:0,96,1884 0/0:26,0:26:75.26:0,75,1499 0/0:40,0:40:99:0,120,2354 0/0:18,0:18:54.19:0,54,1083 0/0:29,0:29:87.30:0,87,1724 0/0:19,0:19:57.20:0,57,1144 0/0:21,0:21:63.22:0,63,1250 0/0:24,0:24:69.24:0,69,1357 0/0:18,0:18:54.19:0,54,1098 0/0:26,0:26:78.27:0,78,1529 0/0:22,0:22:66.23:0,66,1301 0/0:32,0:32:96.33:0,96,1910 0/0:15,0:15:45.15:0,45,915 0/0:13,0:13:39.13:0,39,772 0/0:18,0:18:54.19:0,54,1083 0/0:22,0:22:66.23:0,66,1342 0/0:25,0:25:75.26:0,75,1525 0/0:15,0:15:42.14:0,42,854 0/0:28,0:28:84.29:0,84,1697 0/0:23,0:23:69.23:0,69,1378 0/0:23,0:23:69.24:0,69,1372 0/0:27,0:27:81.28:0,81,1616 0/0:18,0:18:54.19:0,54,1098 0/0:24,0:24:72.25:0,72,1449 0/0:20,0:20:60.21:0,60,1205 0/0:10,0:10:30.10:0,30,595 0/0:30,0:30:90.31:0,90,1773 0/0:29,0:29:87.30:0,87,1773 0/0:11,0:11:33.11:0,33,671 0/0:31,0:31:93.32:0,93,1867 0/0:18,0:18:54.18:0,54,1052 0/0:14,0:14:42.14:0,42,839 0/0:23,0:23:69.24:0,69,1362 0/0:17,0:17:51.18:0,51,1037 0/0:26,0:26:66.23:0,66,1342 0/0:20,0:20:51.17:0,51,1004 0/0:28,0:28:81.27:0,81,1617 0/0:12,0:12:36.12:0,36,716 0/0:15,0:15:45.15:0,45,899 0/0:23,0:23:69.24:0,69,1403 0/0:33,0:33:99:0,99,1983 0/0:16,0:16:45.15:0,45,900 0/0:20,0:20:60.20:0,60,1144 0/0:15,0:15:45.15:0,45,896 0/0:21,0:21:63.22:0,63,1258 0/0:15,0:15:36.12:0,36,717 0/0:13,0:13:36.12:0,36,704 0/0:33,0:33:96.33:0,96,1906 0/0:9,0:9:24.08:0,24,458 0/0:13,0:13:39.13:0,39,778 -chr1 880367 . G A 795.59 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.447;DP=3095;Dels=0.00;FS=7.414;HRun=0;HaplotypeScore=2.5302;InbreedingCoeff=-0.0084;MQ=58.79;MQ0=0;MQRankSum=0.556;QD=10.61;ReadPosRankSum=0.729;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|18),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|4);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:13,0:13:30.08:0,30,360 0/0:17,0:17:45.11:0,45,538 0/0:14,0:14:39.10:0,39,477 0/0:17,0:17:42.12:0,42,507 0/0:32,0:32:93.30:0,93,1226 0/0:31,0:31:93.29:0,93,1211 0/0:49,0:49:99:0,138,1823 0/0:35,0:35:99:0,99,1303 0/0:77,0:77:99:0,229,2961 0/0:64,0:64:99:0,181,2309 0/0:34,0:34:96.29:0,96,1248 0/0:24,0:24:72.20:0,72,907 0/0:45,0:45:99:0,132,1708 0/0:61,0:61:99:0,169,2162 0/0:77,0:78:99:0,211,2675 0/0:45,0:45:99:0,111,1474 0/0:40,1:41:72.09:0,72,1306 0/0:89,0:91:99:0,235,3003 0/0:67,0:67:99:0,168,2043 0/0:69,0:69:99:0,156,1964 0/0:59,1:60:99:0,105,1764 0/0:91,1:93:99:0,187,2855 0/1:38,32:75:99:843,0,1019 0/0:66,0:67:99:0,165,2080 0/0:71,0:71:99:0,184,2328 0/0:69,0:69:99:0,178,2270 0/0:70,0:70:99:0,174,2232 0/0:50,0:51:99:0,126,1596 0/0:82,0:82:99:0,208,2611 0/0:83,0:83:99:0,217,2712 0/0:91,0:92:99:0,247,3124 0/0:64,0:64:99:0,163,2112 0/0:75,0:75:99:0,202,2558 0/0:63,0:63:99:0,168,2071 0/0:61,0:62:99:0,150,1867 0/0:67,2:70:99:0,169,2163 0/0:91,0:92:99:0,232,2898 0/0:131,0:131:99:0,349,4391 0/0:28,0:29:66.21:0,66,856 0/0:54,1:56:99:0,144,1837 0/0:41,0:41:99:0,99,1239 0/0:34,0:35:87.27:0,87,1089 0/0:28,0:30:69.21:0,69,859 0/0:35,0:35:96.29:0,96,1189 0/0:38,0:41:84.26:0,84,1082 0/0:32,0:34:84.23:0,84,1011 0/0:59,0:62:99:0,141,1778 0/0:22,0:23:48.14:0,48,595 0/0:27,0:29:66.21:0,66,859 0/0:38,0:38:87.27:0,87,1113 0/0:47,0:49:99:0,102,1272 0/0:47,0:47:99:0,117,1474 0/0:43,0:44:99:0,99,1238 0/0:35,0:37:84.26:0,84,1064 0/0:27,0:28:66.21:0,66,867 0/0:28,0:28:63.20:0,63,824 0/0:20,0:22:45.14:0,45,579 0/0:44,0:47:99:0,108,1372 0/0:33,0:33:78.24:0,78,1019 0/0:31,0:33:78.24:0,78,980 -chr1 880390 . C A 4207.41 . AC=4;AF=0.0333;AN=120;BaseQRankSum=-1.360;DP=3838;Dels=0.00;FS=18.983;HRun=0;HaplotypeScore=2.5364;InbreedingCoeff=-0.0345;MQ=58.94;MQ0=0;MQRankSum=0.010;QD=14.76;ReadPosRankSum=1.464;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|18),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|4);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:11,0:11:30.09:0,30,379 0/0:19,0:19:48.15:0,48,611 0/0:12,0:12:36.10:0,36,433 0/0:17,0:17:48.14:0,48,596 0/0:33,0:33:96.31:0,96,1292 0/0:29,0:29:84.27:0,84,1113 0/0:41,0:41:99:0,123,1646 0/1:17,21:38:99:649,0,586 0/0:67,0:67:99:0,199,2673 0/0:62,0:62:99:0,181,2378 0/0:48,0:48:99:0,138,1817 0/0:28,0:28:81.26:0,81,1067 0/0:59,0:59:99:0,163,2129 0/0:88,1:89:99:0,184,2850 0/0:107,0:107:99:0,280,3638 0/0:68,1:69:99:0,156,2092 0/0:69,0:69:99:0,184,2358 0/0:127,0:127:99:0,298,3997 0/0:89,0:89:99:0,211,2714 0/0:90,0:90:99:0,208,2660 0/0:83,0:83:99:0,196,2522 0/0:121,0:121:99:0,301,3912 0/0:91,0:91:99:0,217,2836 0/0:77,0:77:99:0,190,2403 0/0:100,0:100:99:0,244,3194 0/0:94,0:94:99:0,232,2975 0/0:101,0:101:99:0,238,3177 0/0:67,0:67:99:0,159,2071 0/0:117,0:117:99:0,274,3517 0/0:102,0:103:99:0,250,3258 0/0:130,0:130:99:0,304,4022 0/0:85,0:85:99:0,205,2730 0/1:50,57:108:99:1502,0,1420 0/1:39,54:93:99:1439,0,895 0/0:78,0:78:99:0,178,2316 0/0:107,0:107:99:0,256,3315 0/0:125,0:125:99:0,310,4021 0/0:160,0:160:99:0,400,5162 0/0:28,0:28:66.21:0,66,870 0/0:60,0:60:99:0,153,1953 0/0:42,0:42:99:0,99,1274 0/0:43,0:43:96.28:0,96,1207 0/0:31,0:31:75.23:0,75,964 0/0:35,0:35:87.26:0,87,1118 0/0:38,0:38:99:0,99,1229 0/0:37,0:37:96.26:0,96,1170 0/0:75,0:75:99:0,184,2330 0/0:27,0:27:66.20:0,66,838 0/0:36,0:36:84.25:0,84,1064 0/1:24,22:46:99:616,0,606 0/0:54,0:54:99:0,123,1606 0/0:53,0:53:99:0,123,1561 0/0:45,0:45:99:0,114,1432 0/0:42,0:42:99:0,102,1309 0/0:31,0:31:84.23:0,84,1057 0/0:35,0:35:84.26:0,84,1103 0/0:16,0:16:45.14:0,45,573 0/0:52,1:53:99:0,126,1669 0/0:31,0:31:81.26:0,81,1061 0/0:36,0:36:81.25:0,81,1040 -chr1 880483 . A G 739.51 . AC=2;AF=0.0167;AN=120;BaseQRankSum=1.408;DP=5022;DS;Dels=0.00;FS=13.337;HRun=0;HaplotypeScore=2.6561;InbreedingCoeff=-0.0170;MQ=59.08;MQ0=0;MQRankSum=0.004;QD=12.75;ReadPosRankSum=-2.856;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|16),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|4),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D699|749|NOC2L|protein_coding|CODING|ENST00000327044|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,synonymous_variant|gaT/gaC|D|ENSG00000188976|NOC2L|ENST00000327044|18/19|||699/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|4/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|16/17||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:13,0:13:33.10:0,33,419 0/0:18,0:18:48.14:0,48,580 0/0:14,0:14:42.13:0,42,534 0/0:25,0:25:57.15:0,57,685 0/0:34,0:34:99:0,99,1278 0/0:34,0:34:99:0,99,1286 0/0:42,0:42:99:0,117,1529 0/1:12,12:24:99:417,0,412 0/0:69,1:70:99:0,208,2718 0/0:70,0:70:99:0,205,2688 0/0:36,0:37:99:0,105,1384 0/0:33,0:33:96.31:0,96,1267 0/0:37,0:37:99:0,108,1395 0/0:130,0:131:99:0,301,4017 0/0:167,0:167:99:0,409,5451 0/0:100,0:101:99:0,229,3078 0/0:128,0:128:99:0,304,4019 0/0:153,0:154:99:0,367,4881 0/0:166,0:166:99:0,391,5201 0/0:127,0:127:99:0,298,3945 0/0:139,0:139:99:0,328,4366 0/0:173,1:174:99:0,412,5443 0/0:120,0:120:99:0,292,3851 0/0:116,0:116:99:0,280,3693 0/0:121,0:121:99:0,298,3975 0/0:132,0:132:99:0,316,4202 0/0:112,0:112:99:0,268,3590 0/0:110,1:112:99:0,234,3563 0/0:174,0:174:99:0,409,5522 0/0:153,0:153:99:0,352,4693 0/0:169,0:169:99:0,412,5452 0/0:125,0:127:99:0,304,3989 0/0:128,0:128:99:0,319,4242 0/0:162,0:162:99:0,373,5047 0/0:107,0:107:99:0,256,3354 0/0:142,1:143:99:0,337,4439 0/0:170,0:171:99:0,424,5654 0/0:242,0:242:99:0,554,7427 0/0:30,0:31:78.25:0,78,1018 0/0:67,0:67:99:0,163,2119 0/0:63,0:63:99:0,160,2066 0/0:37,0:38:96.30:0,96,1243 0/1:18,16:34:99:388,0,480 0/0:34,0:35:93.30:0,93,1224 0/0:33,0:37:81.26:0,81,1069 0/0:51,0:52:99:0,135,1710 0/0:87,0:89:99:0,211,2674 0/0:28,0:28:63.20:0,63,822 0/0:48,0:49:99:0,105,1434 0/0:59,0:59:99:0,129,1704 0/0:56,0:58:99:0,150,1944 0/0:36,0:37:90.29:0,90,1176 0/0:51,0:52:99:0,105,1404 0/0:42,0:43:99:0,99,1313 0/0:27,0:27:69.20:0,69,854 0/0:41,1:43:99:0,99,1269 0/0:25,0:25:57.18:0,57,751 0/0:39,0:39:99:0,102,1327 0/0:35,0:36:93.30:0,93,1230 0/0:48,0:49:99:0,111,1450 -chr1 880639 . TC T 8144.14 . AC=31;AF=0.2583;AN=120;BaseQRankSum=8.550;DP=921;FS=0.348;HRun=2;HaplotypeScore=54.1306;InbreedingCoeff=-0.1017;MQ=58.66;MQ0=0;MQRankSum=1.840;QD=17.70;ReadPosRankSum=1.996;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|17),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|15),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|3);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,135 0/0:5,0:5:15.05:0,15,214 0/1:5,2:7:59.88:60,0,142 0/1:4,3:7:74.88:102,0,75 0/1:2,3:5:29.95:141,0,30 0/1:4,2:6:59.89:60,0,160 0/0:16,0:16:48.16:0,48,704 0/0:7,0:7:21.07:0,21,314 0/1:2,6:8:57.26:210,0,57 0/1:11,16:27:99:476,0,324 0/1:6,1:7:56.81:57,0,204 0/0:2,0:2:6.02:0,6,90 0/1:4,6:10:62.89:246,0,63 1/1:1,25:26:78.25:1006,78,0 0/1:18,12:30:99:415,0,591 0/0:18,0:18:54.18:0,54,808 0/1:12,7:19:99:222,0,399 0/1:16,13:29:99:464,0,489 0/1:18,5:23:99:126,0,739 0/1:12,6:18:99:218,0,430 0/0:22,0:22:63.21:0,63,943 0/0:22,0:22:62.98:0,63,877 0/0:15,0:15:42.14:0,42,628 0/1:14,14:28:99:531,0,456 0/0:24,0:24:69.23:0,69,1035 0/1:11,13:24:99:434,0,422 0/0:21,1:22:27.24:0,27,865 0/0:24,0:24:71.45:0,71,1011 0/0:23,0:23:59.56:0,60,860 0/0:26,0:26:64.77:0,65,944 0/0:31,0:31:90.30:0,90,1342 0/0:16,0:16:48.16:0,48,719 0/1:12,12:24:99:408,0,286 0/0:25,0:25:75.25:0,75,1125 0/1:6,10:16:99:342,0,222 0/1:15,6:21:99:173,0,570 0/0:16,0:16:45.15:0,45,675 1/1:3,38:41:99:1442,111,0 0/1:5,0:5:23.84:24,0,165 0/0:12,0:12:36.12:0,36,537 0/1:10,9:19:99:294,0,393 0/1:9,3:12:44.84:45,0,372 0/0:8,0:8:24.08:0,24,358 0/0:10,0:10:27.09:0,27,405 0/0:15,0:15:45.15:0,45,675 0/0:13,0:13:36.12:0,36,538 0/1:10,5:15:99:153,0,360 0/0:6,0:6:18.06:0,18,259 0/0:14,0:14:42.14:0,42,628 0/1:8,5:13:99:192,0,220 0/1:6,4:10:99:126,0,239 0/0:14,0:14:36.12:0,36,529 0/0:11,0:11:30.10:0,30,448 0/0:8,0:8:24.08:0,24,348 0/0:11,0:11:30.10:0,30,450 0/0:9,0:9:27.09:0,27,379 0/0:6,0:6:15.05:0,15,225 0/1:5,1:6:23.91:24,0,165 0/0:7,0:7:9.03:0,9,135 1/1:0,4:4:12.04:156,12,0 -chr1 880751 . A G 807.9 . AC=4;AF=0.0333;AN=120;BaseQRankSum=1.558;DP=1112;Dels=0.00;FS=1.129;HRun=1;HaplotypeScore=0.7010;InbreedingCoeff=0.4309;MQ=58.97;MQ0=0;MQRankSum=3.000;QD=18.79;ReadPosRankSum=0.469;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|2),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|17),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|15),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|3);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000496938|2/2||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:18.04:0,18,219 0/0:2,0:2:6.02:0,6,81 0/0:6,0:6:18.05:0,18,227 0/0:4,0:4:12.04:0,12,148 0/0:6,0:6:18.06:0,18,239 0/0:10,0:10:30.10:0,30,400 0/1:8,6:14:99:204,0,275 0/0:11,0:11:33.11:0,33,446 0/0:17,0:17:51.17:0,51,677 0/0:30,0:30:87.29:0,87,1167 0/0:9,0:9:24.08:0,24,325 0/0:5,0:5:15.05:0,15,204 0/0:7,0:7:21.07:0,21,275 0/0:14,0:14:36.12:0,36,473 0/0:31,0:31:90.29:0,90,1179 0/0:17,0:17:45.15:0,45,592 0/0:22,0:22:60.20:0,60,817 0/0:30,0:30:90.26:0,90,1173 0/0:33,0:33:96.29:0,96,1248 0/0:23,0:23:69.22:0,69,907 0/0:26,0:26:78.26:0,78,1043 0/0:27,0:28:78.25:0,78,1044 0/0:25,0:25:72.23:0,72,949 0/0:18,0:18:51.16:0,51,683 0/0:26,0:26:78.25:0,78,1013 0/0:28,0:28:78.25:0,78,1013 0/0:28,1:29:84.27:0,84,1112 0/1:10,7:17:99:226,0,317 0/0:29,0:29:84.26:0,84,1092 0/0:25,0:25:69.22:0,69,899 0/0:29,0:29:87.28:0,87,1167 0/0:25,0:25:75.23:0,75,960 0/0:20,0:20:57.18:0,57,754 0/0:31,0:31:93.26:0,93,1157 0/0:16,0:16:42.14:0,42,576 0/0:17,0:17:48.14:0,48,618 0/0:38,0:38:99:0,111,1423 0/0:43,0:43:99:0,129,1733 0/0:11,0:11:33.11:0,33,430 0/0:12,0:12:30.10:0,30,393 0/0:15,0:15:42.14:0,42,557 0/0:13,0:13:36.12:0,36,480 0/0:17,0:17:48.16:0,48,650 0/0:16,0:16:45.12:0,45,549 0/0:19,0:19:57.16:0,57,740 0/0:19,0:19:57.16:0,57,711 0/0:22,1:23:20.95:0,21,735 1/1:0,12:12:36.11:476,36,0 0/0:15,0:15:36.12:0,36,488 0/0:25,0:27:66.21:0,66,865 0/0:23,0:23:60.18:0,60,771 0/0:29,0:29:84.27:0,84,1127 0/0:8,0:8:24.08:0,24,332 0/0:20,0:20:60.20:0,60,802 0/0:13,0:13:39.12:0,39,499 0/0:10,0:10:27.09:0,27,361 0/0:11,0:11:30.10:0,30,401 0/0:15,0:15:42.10:0,42,527 0/0:13,0:13:33.11:0,33,436 0/0:4,0:4:12.04:0,12,155 -chr1 881027 . C G 2780.96 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.239;DP=6197;DS;Dels=0.00;FS=8.993;HRun=0;HaplotypeScore=3.1641;InbreedingCoeff=-0.0084;MQ=59.26;MQ0=0;MQRankSum=2.376;QD=14.56;ReadPosRankSum=-0.209;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|15),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Cac|D642H|749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,missense_variant|Gac/Cac|D/H|ENSG00000188976|NOC2L|ENST00000327044|17/19|probably_damaging(0.928)|deleterious(0)|642/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|3/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|15/17||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:35,0:35:99:0,99,1242 0/0:39,0:40:99:0,117,1434 0/0:49,0:49:99:0,144,1876 0/0:24,0:24:69.21:0,69,877 0/0:37,0:37:99:0,111,1493 0/0:32,0:32:96.30:0,96,1245 0/0:53,0:53:99:0,160,2113 0/0:52,0:52:99:0,153,2007 0/0:101,0:101:99:0,304,4051 0/0:70,0:70:99:0,208,2725 0/0:42,0:42:99:0,123,1643 0/0:43,0:43:99:0,126,1596 0/0:63,0:63:99:0,187,2431 0/0:155,0:155:99:0,391,5306 0/1:92,99:191:99:2829,0,2558 0/0:120,0:120:99:0,304,4067 0/0:158,0:159:99:0,412,5465 0/0:174,0:174:99:0,415,5580 0/0:163,0:163:99:0,391,5247 0/0:169,0:169:99:0,412,5513 0/0:145,0:145:99:0,346,4631 0/0:160,0:160:99:0,400,5355 0/0:169,0:169:99:0,421,5618 0/0:143,0:143:99:0,346,4640 0/0:146,0:146:99:0,367,4912 0/0:152,0:152:99:0,364,4799 0/0:161,0:161:99:0,385,5195 0/0:122,0:122:99:0,295,3959 0/0:157,0:157:99:0,382,5177 0/0:158,0:158:99:0,406,5328 0/0:195,0:195:99:0,481,6412 0/0:123,0:123:99:0,304,4049 0/0:175,0:175:99:0,418,5577 0/0:167,0:167:99:0,409,5475 0/0:138,0:138:99:0,334,4543 0/0:143,0:143:99:0,355,4799 0/0:170,0:170:99:0,424,5627 0/0:180,0:180:99:0,485,6471 0/0:64,0:65:99:0,157,2081 0/0:90,0:90:99:0,211,2802 0/0:93,0:93:99:0,241,3162 0/0:90,0:91:99:0,220,2934 0/0:85,0:85:99:0,202,2651 0/0:61,0:61:99:0,144,1919 0/0:66,0:66:99:0,172,2275 0/0:91,0:91:99:0,235,3044 0/0:114,0:114:99:0,274,3610 0/0:45,0:45:99:0,114,1501 0/0:72,0:72:99:0,175,2310 0/0:88,0:89:99:0,235,3019 0/0:68,0:68:99:0,172,2233 0/0:63,0:63:99:0,156,2054 0/0:55,1:57:99:0,141,1851 0/0:75,0:75:99:0,193,2549 0/0:87,0:87:99:0,229,3047 0/0:55,0:55:99:0,138,1848 0/0:57,0:57:99:0,135,1833 0/0:79,0:80:99:0,181,2398 0/0:64,0:65:99:0,153,2059 0/0:51,0:52:99:0,123,1624 -chr1 881068 . G A 311.66 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.528;DP=3714;DS;Dels=0.00;FS=2.094;HRun=1;HaplotypeScore=2.7083;InbreedingCoeff=-0.0084;MQ=58.85;MQ0=0;MQRankSum=2.312;QD=14.17;ReadPosRankSum=-1.657;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|14),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|2),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:25,0:25:66.20:0,66,826 0/1:9,12:22:99:359,0,266 0/0:30,0:30:87.28:0,87,1132 0/0:26,0:26:78.22:0,78,998 0/0:39,0:39:99:0,117,1536 0/0:35,0:35:99:0,99,1300 0/0:54,0:54:99:0,162,2126 0/0:33,0:33:99:0,99,1314 0/0:87,0:87:99:0,262,3479 0/0:61,0:61:99:0,181,2350 0/0:34,0:34:99:0,99,1321 0/0:29,0:29:84.26:0,84,1092 0/0:35,0:35:99:0,105,1399 0/0:88,0:89:99:0,244,3187 0/0:117,0:117:99:0,310,4035 0/0:55,0:55:99:0,147,1917 0/0:73,0:74:99:0,205,2666 0/0:91,0:91:99:0,244,3160 0/0:91,1:92:99:0,238,3108 0/0:108,0:109:99:0,295,3895 0/0:80,0:80:99:0,217,2823 0/0:111,0:112:99:0,304,3935 0/0:96,1:97:99:0,236,3336 0/0:91,0:91:99:0,241,3142 0/0:97,0:97:99:0,265,3449 0/0:84,0:84:99:0,235,2999 0/0:95,0:95:99:0,256,3309 0/0:74,0:75:99:0,199,2619 0/0:102,0:102:99:0,274,3616 0/0:80,0:80:99:0,220,2888 0/0:114,0:114:99:0,316,4109 0/0:76,0:76:99:0,214,2748 0/0:100,0:100:99:0,286,3719 0/0:100,0:100:99:0,274,3578 0/0:68,0:68:99:0,196,2554 0/0:70,0:70:99:0,190,2439 0/0:80,1:82:99:0,232,2993 0/0:136,0:136:99:0,382,4950 0/0:33,0:33:87.28:0,87,1135 0/0:53,0:53:99:0,138,1723 0/0:47,0:47:99:0,138,1780 0/0:41,0:41:99:0,111,1480 0/0:42,0:42:99:0,108,1411 0/0:35,0:35:87.27:0,87,1117 0/0:38,0:38:99:0,108,1375 0/0:50,0:51:99:0,144,1851 0/0:66,0:66:99:0,180,2305 0/0:22,0:22:63.20:0,63,820 0/0:37,0:37:99:0,102,1349 0/0:58,0:58:99:0,153,1983 0/0:46,0:46:99:0,126,1614 0/0:34,0:34:87.25:0,87,1120 0/0:40,0:40:99:0,114,1452 0/0:44,0:44:99:0,117,1525 0/0:44,0:44:99:0,120,1610 0/0:27,0:28:81.26:0,81,1090 0/0:34,0:34:93.30:0,93,1236 0/0:48,0:49:99:0,123,1623 0/0:45,0:45:99:0,114,1478 0/0:29,0:29:75.24:0,75,974 -chr1 881214 . A G 121.77 . AC=1;AF=0.0085;AN=118;BaseQRankSum=-0.359;DP=622;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.2865;InbreedingCoeff=-0.0200;MQ=58.09;MQ0=0;MQRankSum=-1.890;QD=15.22;ReadPosRankSum=-1.501;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|14),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|2),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:13,0:13:33.10:0,33,422 0/1:3,5:8:71.89:169,0,72 0/0:9,0:9:27.08:0,27,331 0/0:10,0:10:27.08:0,27,339 0/0:7,0:7:21.07:0,21,281 0/0:11,0:11:30.09:0,30,382 0/0:17,0:17:51.15:0,51,648 0/0:13,0:13:39.13:0,39,516 0/0:29,0:29:84.27:0,84,1126 0/0:26,0:26:75.23:0,75,967 0/0:19,0:19:57.18:0,57,760 0/0:10,0:10:27.08:0,27,347 0/0:28,0:28:84.26:0,84,1086 0/0:8,0:8:15.05:0,15,204 0/0:17,0:17:48.13:0,48,604 0/0:12,0:12:30.09:0,30,380 0/0:11,0:11:30.09:0,30,377 0/0:7,0:7:21.06:0,21,275 0/0:16,0:16:45.14:0,45,574 0/0:11,0:11:33.11:0,33,429 0/0:8,0:8:21.05:0,21,262 0/0:12,0:12:33.07:0,33,411 0/0:10,0:10:27.07:0,27,347 0/0:14,0:14:36.11:0,36,478 0/0:22,0:22:60.19:0,60,777 0/0:10,0:10:30.10:0,30,409 0/0:12,0:12:33.04:0,33,381 0/0:9,1:10:27.09:0,27,358 0/0:18,1:19:54.17:0,54,711 0/0:15,0:15:42.11:0,42,532 0/0:15,0:15:39.11:0,39,501 0/0:11,0:11:30.09:0,30,387 0/0:18,0:18:45.11:0,45,574 0/0:15,0:15:42.10:0,42,511 0/0:5,0:5:15.05:0,15,188 0/0:6,0:7:15.04:0,15,187 0/0:11,0:11:30.10:0,30,405 0/0:16,0:16:48.15:0,48,635 0/0:8,0:8:24.07:0,24,303 0/0:9,0:9:27.09:0,27,356 0/0:4,1:5:12.04:0,12,166 0/0:5,0:5:15.04:0,15,181 0/0:6,0:6:18.05:0,18,238 0/0:4,0:4:12.04:0,12,153 0/0:2,0:2:6.02:0,6,76 0/0:6,0:6:15.05:0,15,186 0/0:8,0:8:21.06:0,21,268 0/0:3,0:3:9.03:0,9,117 ./. 0/0:9,0:9:24.07:0,24,322 0/0:5,0:5:15.05:0,15,200 0/0:5,0:5:15.05:0,15,199 0/0:6,0:6:18.06:0,18,237 0/0:5,0:5:15.04:0,15,182 0/0:6,0:6:18.06:0,18,234 0/0:4,0:4:12.04:0,12,159 0/0:5,0:5:12.04:0,12,157 0/0:3,0:3:6.02:0,6,79 0/0:3,0:3:9.03:0,9,119 0/0:3,0:3:9.03:0,9,116 -chr1 881278 . T C 73.18 . AC=5;AF=0.0472;AN=106;BaseQRankSum=-5.288;DP=225;Dels=0.00;FS=14.303;HRun=2;HaplotypeScore=0.2150;InbreedingCoeff=-0.1298;MQ=55.77;MQ0=0;MQRankSum=-0.007;QD=2.36;ReadPosRankSum=-0.143;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|14),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|2),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:3.01:0,3,41 0/0:1,1:2:3.01:0,3,36 0/1:2,3:5:27.42:27,0,32 0/0:2,1:3:6.02:0,6,81 0/1:1,3:4:17.68:18,0,35 ./. 0/0:1,0:1:3.01:0,3,39 0/1:4,6:10:51.77:52,0,92 0/1:5,4:9:54.52:55,0,109 0/0:2,2:4:6.02:0,6,81 ./. 0/0:3,0:3:9.03:0,9,120 0/0:3,1:4:9.03:0,9,113 0/0:5,1:6:15:0,15,146 0/0:6,0:6:15.05:0,15,186 0/0:2,3:5:2.99:0,3,23 0/1:2,1:3:17.65:18,0,73 0/0:5,3:8:15.04:0,15,171 0/0:5,0:5:15.05:0,15,191 0/0:3,0:3:9.03:0,9,109 0/0:5,3:8:12.04:0,12,150 0/0:4,1:5:12.03:0,12,143 0/0:4,2:6:12.03:0,12,144 0/0:3,3:6:9.02:0,9,96 0/0:6,0:6:9.02:0,9,98 0/0:4,0:4:12.02:0,12,136 0/0:3,0:3:9.03:0,9,113 0/0:5,0:5:12.03:0,12,130 0/0:4,0:4:12.03:0,12,142 0/0:4,1:5:9:0,9,92 0/0:1,0:1:3:0,3,26 0/0:5,1:6:15.05:0,15,183 0/0:4,0:4:12.01:0,12,129 0/0:3,0:3:6.02:0,6,68 0/0:5,2:7:12.01:0,12,131 0/0:3,0:3:9.03:0,9,109 0/0:4,0:4:9.03:0,9,109 0/0:4,0:4:12.03:0,12,146 0/0:5,0:5:15.02:0,15,176 0/0:2,0:2:6.02:0,6,67 ./. 0/0:1,2:3:3.01:0,3,42 0/0:4,0:4:12.04:0,12,156 0/0:1,1:2:3.01:0,3,37 0/0:5,0:5:12.04:0,12,147 0/0:11,0:11:27.05:0,27,322 0/0:1,0:1:3:0,3,29 ./. 0/0:3,0:3:9.02:0,9,103 0/0:2,0:2:6.02:0,6,75 0/0:3,0:3:9.03:0,9,110 0/0:2,1:3:6.02:0,6,76 0/0:1,0:1:3.01:0,3,33 ./. 0/0:2,1:3:6.02:0,6,84 ./. 0/0:1,0:1:3.01:0,3,34 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:3.01:0,3,37 -chr1 881377 . G A 198.25 . AC=3;AF=0.0259;AN=116;BaseQRankSum=0.943;DP=299;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1931;InbreedingCoeff=-0.0772;MQ=57.25;MQ0=0;MQRankSum=1.239;QD=11.01;ReadPosRankSum=1.934;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|14),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|2),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3.01:0,3,39 0/0:3,0:3:9.03:0,9,108 0/0:8,0:8:18.06:0,18,240 0/0:2,0:2:6.02:0,6,76 0/0:2,0:2:6.02:0,6,81 0/0:2,0:2:6.02:0,6,76 ./. 0/0:3,0:3:9.02:0,9,109 0/0:1,0:1:3.01:0,3,41 0/0:8,0:8:24.08:0,24,316 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 0/0:5,0:5:15.05:0,15,194 0/0:5,0:5:12.04:0,12,155 0/0:2,0:2:3.01:0,3,42 ./. 0/0:6,0:6:18.06:0,18,230 0/0:1,0:1:3.01:0,3,39 0/0:5,0:5:12.04:0,12,155 0/0:3,0:3:6.02:0,6,79 0/0:4,0:4:12.04:0,12,157 0/0:3,0:3:9:0,9,103 0/0:8,0:8:24.08:0,24,323 0/0:2,0:2:6.02:0,6,79 0/0:5,0:5:15.05:0,15,205 0/1:6,2:8:20.69:21,0,214 0/0:3,0:3:9.03:0,9,119 0/0:6,0:6:12.04:0,12,167 0/0:6,0:6:15.05:0,15,191 0/0:8,0:8:21.07:0,21,279 0/0:5,0:5:15.05:0,15,205 0/0:7,0:7:21.07:0,21,282 0/0:8,0:8:21.07:0,21,277 0/1:1,2:3:26.22:74,0,26 0/0:7,0:7:18.06:0,18,239 0/1:2,5:7:60.70:180,0,61 0/0:7,0:7:21.06:0,21,256 0/0:4,0:4:12.04:0,12,151 0/0:10,0:10:30.10:0,30,390 0/0:7,0:7:15.05:0,15,193 0/0:3,0:3:9.03:0,9,122 0/0:9,0:9:27.08:0,27,350 0/0:3,0:3:9.03:0,9,123 0/0:6,0:6:15.05:0,15,193 0/0:5,0:5:12.04:0,12,160 0/0:10,0:10:21.07:0,21,278 0/0:1,0:1:3.01:0,3,37 0/0:8,0:8:24.07:0,24,301 0/0:11,0:11:33.10:0,33,417 0/0:11,0:11:33.11:0,33,430 0/0:8,0:8:21.06:0,21,261 0/0:9,0:9:27.08:0,27,330 0/0:4,0:4:12.04:0,12,143 0/0:3,0:3:9.03:0,9,124 0/0:8,0:8:24.08:0,24,313 0/0:4,0:4:12.04:0,12,156 0/0:4,0:4:9.03:0,9,117 0/0:10,0:10:27.09:0,27,354 0/0:2,0:2:6.02:0,6,72 -chr1 881512 . G T 329.45 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.087;DP=1882;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.4710;InbreedingCoeff=-0.0118;MQ=58.18;MQ0=0;MQRankSum=0.210;QD=11.36;ReadPosRankSum=-0.792;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|16),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|14),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|2),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:18.05:0,18,209 0/0:3,0:3:9.03:0,9,117 0/0:7,0:7:21.06:0,21,267 0/0:3,0:3:6.02:0,6,77 0/0:9,0:9:27.09:0,27,360 0/0:13,0:13:36.12:0,36,482 0/0:11,0:11:33.11:0,33,452 0/0:8,0:8:24.07:0,24,311 0/0:21,0:21:63.21:0,63,840 0/0:26,0:26:75.24:0,75,998 0/0:12,0:12:36.12:0,36,494 0/0:4,0:4:12.04:0,12,164 0/0:10,0:10:30.09:0,30,386 0/0:40,1:41:73.13:0,73,1427 0/0:42,0:42:99:0,111,1474 0/0:32,0:32:84.27:0,84,1117 0/0:39,0:39:99:0,108,1438 0/0:38,0:39:99:0,99,1331 0/0:39,0:39:99:0,108,1453 0/0:36,0:36:99:0,102,1324 0/0:25,0:25:75.23:0,75,987 0/0:40,0:40:99:0,99,1271 0/1:16,13:29:99:377,0,528 0/0:34,0:34:99:0,102,1370 0/0:23,0:23:60.17:0,60,782 0/0:31,0:31:87.28:0,87,1151 0/0:55,0:55:99:0,144,1914 0/0:27,0:27:75.22:0,75,964 0/0:34,0:34:93.30:0,93,1250 0/0:46,0:46:99:0,126,1611 0/0:30,0:30:81.26:0,81,1060 0/0:39,0:39:99:0,114,1501 0/0:35,0:35:90.28:0,90,1210 0/0:40,0:40:99:0,99,1282 0/0:48,0:49:99:0,126,1626 0/0:30,1:31:34.43:0,34,876 0/0:41,0:42:99:0,108,1424 0/0:43,0:43:99:0,120,1611 0/0:24,0:25:57.17:0,57,745 0/0:60,0:60:99:0,138,1764 0/0:44,0:44:99:0,102,1345 0/0:27,0:27:63.19:0,63,800 0/0:34,0:35:90.24:0,90,1135 0/0:40,0:40:99:0,102,1325 0/0:35,0:36:87.26:0,87,1115 0/0:32,0:33:78.23:0,78,999 0/0:44,0:45:99:0,105,1322 0/0:26,0:26:60.17:0,60,763 0/0:51,0:51:99:0,111,1398 0/0:58,0:59:99:0,129,1686 0/0:57,0:57:99:0,141,1775 0/0:29,0:29:66.21:0,66,850 0/0:39,0:41:93.22:0,93,1164 0/0:31,0:32:75.22:0,75,945 0/0:31,0:32:75.23:0,75,948 0/0:39,0:39:93.28:0,93,1183 0/0:14,0:14:39.12:0,39,512 0/0:38,0:38:87.27:0,87,1110 0/0:46,0:46:90.27:0,90,1178 0/0:18,0:18:45.14:0,45,588 -chr1 881627 . G A 65058.1 . AC=69;AF=0.5750;AN=120;BaseQRankSum=-0.436;DP=4175;Dels=0.00;FS=7.028;HRun=1;HaplotypeScore=3.6325;InbreedingCoeff=0.0788;MQ=58.73;MQ0=0;MQRankSum=0.133;QD=20.93;ReadPosRankSum=1.488;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|14),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|2),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L615|749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,synonymous_variant|Ctg/Ttg|L|ENSG00000188976|NOC2L|ENST00000327044|16/19|||615/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|2/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|14/17||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,11:11:27.08:321,27,0 1/1:4,7:11:18.04:210,18,0 0/1:9,3:12:95.81:96,0,146 0/1:6,3:9:28.61:29,0,101 0/1:10,7:17:99:189,0,278 0/1:11,11:22:99:257,0,298 0/1:19,17:36:99:498,0,476 0/1:17,9:26:99:200,0,455 0/1:27,22:49:99:542,0,710 0/0:57,0:57:99:0,135,1725 0/1:7,16:23:99:493,0,185 1/1:0,17:17:45.12:554,45,0 0/1:19,8:27:99:186,0,586 0/0:104,0:105:99:0,250,3325 0/1:62,58:120:99:1468,0,1696 1/1:0,57:58:99:1920,147,0 0/1:63,51:115:99:1300,0,1640 0/1:51,39:90:99:1005,0,1394 0/1:48,74:122:99:2184,0,1293 0/1:49,45:94:99:1204,0,1384 0/1:48,47:95:99:1153,0,1280 1/1:0,111:111:99:3404,253,0 0/1:39,54:94:99:1428,0,1013 0/1:61,59:121:99:1542,0,1707 1/1:0,82:82:99:2621,193,0 0/1:54,34:88:99:907,0,1409 0/0:129,0:129:99:0,298,3974 0/1:47,34:81:99:869,0,1257 1/1:1,100:101:99:3178,238,0 1/1:0,115:115:99:3637,274,0 1/1:0,125:125:99:4170,313,0 1/1:0,112:112:99:3617,271,0 0/0:98,0:98:99:0,232,3071 0/0:138,0:138:99:0,298,3971 0/0:87,0:89:99:0,220,2935 0/1:58,41:100:99:946,0,1395 0/1:61,55:116:99:1463,0,1587 0/0:170,0:170:99:0,415,5522 0/1:14,18:32:99:553,0,395 1/1:1,84:85:99:2763,214,0 0/1:23,36:59:99:1007,0,625 0/0:50,0:50:99:0,126,1591 1/1:1,51:52:99:1594,123,0 1/1:1,35:36:93.28:1184,93,0 0/1:27,20:47:99:545,0,680 1/1:1,49:50:88.61:1586,89,0 0/1:45,34:79:99:882,0,1142 0/0:27,1:28:36.09:0,36,848 1/1:4,67:71:99:2216,111,0 0/0:82,0:82:99:0,205,2638 0/0:87,0:87:99:0,235,3059 1/1:3,57:61:73.13:1853,73,0 1/1:1,71:72:99:2178,169,0 1/1:2,41:43:76.12:1404,76,0 1/1:0,41:41:99:1296,99,0 1/1:0,51:51:99:1675,129,0 0/1:6,23:30:99:644,0,164 0/1:29,22:51:99:611,0,724 1/1:1,44:45:81.78:1478,82,0 0/0:32,1:34:46.63:0,47,1082 -chr1 881734 . T C 2395.2 . AC=3;AF=0.0250;AN=120;BaseQRankSum=1.087;DP=3324;Dels=0.00;FS=13.773;HRun=0;HaplotypeScore=2.3394;InbreedingCoeff=-0.0275;MQ=58.22;MQ0=0;MQRankSum=4.896;QD=14.34;ReadPosRankSum=1.344;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|15),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|13),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|1),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,72 0/0:14,0:14:33.08:0,33,379 0/0:14,0:14:42.14:0,42,548 0/0:8,0:8:21.06:0,21,258 0/0:41,0:41:99:0,123,1589 0/0:30,0:30:84.27:0,84,1117 0/0:47,0:47:99:0,138,1809 0/0:20,0:20:60.20:0,60,800 0/0:58,0:58:99:0,172,2213 0/0:58,0:58:99:0,172,2247 0/0:42,0:42:99:0,120,1567 0/0:34,0:34:99:0,99,1261 0/0:28,0:28:78.24:0,78,1024 0/0:53,0:53:99:0,144,1797 0/0:64,0:64:99:0,177,2203 0/0:42,0:42:99:0,111,1421 0/0:48,1:49:99:0,129,1599 0/0:41,0:41:99:0,120,1533 0/0:66,0:66:99:0,172,2184 0/0:50,0:50:99:0,132,1714 0/1:19,32:52:99:972,0,528 0/0:62,0:62:99:0,153,1958 0/0:49,0:49:99:0,135,1679 0/0:68,0:68:99:0,184,2300 0/0:53,0:53:99:0,129,1678 0/0:44,0:44:99:0,114,1488 0/1:26,26:52:99:777,0,702 0/0:47,0:47:99:0,123,1546 0/0:70,0:70:99:0,190,2444 0/0:73,0:74:99:0,199,2538 0/0:64,0:64:99:0,181,2262 0/0:51,0:51:99:0,141,1791 0/0:50,0:50:99:0,138,1760 0/1:38,25:63:99:726,0,1128 0/0:43,0:43:99:0,120,1521 0/0:49,0:49:99:0,138,1705 0/0:82,0:82:99:0,223,2838 0/0:95,0:95:99:0,262,3350 0/0:36,0:36:99:0,99,1295 0/0:111,0:111:99:0,277,3526 0/0:75,1:76:99:0,169,2585 0/0:73,0:73:99:0,174,2225 0/0:60,0:60:99:0,147,1896 0/0:58,0:58:99:0,147,1910 0/0:50,0:50:99:0,129,1634 0/0:57,0:57:99:0,138,1754 0/0:97,0:97:99:0,253,3266 0/0:33,0:34:81.24:0,81,1009 0/0:79,1:80:99:0,187,2425 0/0:103,0:103:99:0,268,3437 0/0:101,0:101:99:0,268,3377 0/0:78,0:78:99:0,208,2602 0/0:97,0:97:99:0,235,2997 0/0:70,0:70:99:0,178,2294 0/0:57,0:57:99:0,144,1893 0/0:54,0:54:99:0,132,1639 0/0:48,0:48:99:0,120,1573 0/0:51,0:51:99:0,126,1620 0/0:50,0:50:99:0,126,1614 0/0:54,0:54:99:0,144,1878 -chr1 881894 . G A 502.77 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.087;DP=3111;Dels=0.00;FS=0.806;HRun=0;HaplotypeScore=1.9434;InbreedingCoeff=-0.0084;MQ=55.95;MQ0=0;MQRankSum=4.130;QD=7.62;ReadPosRankSum=-0.465;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|13),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A564V|749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,missense_variant|gCc/gTc|A/V|ENSG00000188976|NOC2L|ENST00000327044|15/19|probably_damaging(0.911)|deleterious(0)|564/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|1/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|13/17||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:10,0:10:27.08:0,27,314 0/0:19,0:19:51.13:0,51,594 0/0:11,0:11:33.10:0,33,404 0/0:13,0:13:33.08:0,33,379 0/0:67,0:67:99:0,196,2318 0/0:45,0:45:99:0,135,1683 0/0:73,1:74:99:0,169,2468 0/0:40,0:40:99:0,120,1490 0/0:87,0:87:99:0,253,3103 0/0:85,0:85:99:0,247,3004 0/0:40,0:40:99:0,120,1429 0/0:50,0:50:99:0,135,1634 0/0:56,0:57:99:0,156,1899 0/0:38,0:38:87.28:0,87,1162 0/0:42,0:43:99:0,117,1531 0/0:28,0:29:72.23:0,72,949 0/0:25,0:25:66.21:0,66,889 0/0:46,0:47:99:0,105,1415 0/0:32,0:32:93.24:0,93,1202 0/0:35,0:35:93.30:0,93,1238 0/0:41,0:41:99:0,99,1313 0/0:57,0:57:99:0,144,1885 0/0:27,0:27:69.19:0,69,884 0/0:41,0:41:96.30:0,96,1288 0/0:31,0:31:78.23:0,78,998 0/0:28,0:28:72.23:0,72,962 0/0:42,1:43:99:0,105,1398 0/0:35,0:35:93.30:0,93,1243 0/0:25,0:25:66.18:0,66,842 0/0:37,1:38:44.92:0,45,1021 0/0:60,0:60:99:0,150,1952 0/0:36,0:36:87.25:0,87,1103 0/0:32,0:32:84.23:0,84,1099 0/0:39,0:39:99:0,102,1350 0/0:22,0:22:48.16:0,48,645 0/0:32,0:32:84.21:0,84,1074 0/0:35,0:36:93.26:0,93,1188 0/0:57,0:57:99:0,144,1892 0/0:51,0:53:99:0,123,1658 0/0:80,0:80:99:0,202,2639 0/1:41,23:66:99:551,0,1127 0/0:73,0:73:99:0,166,2156 0/0:64,0:64:99:0,168,2137 0/0:59,0:61:99:0,135,1768 0/0:63,0:63:99:0,150,1966 0/0:69,0:69:99:0,172,2213 0/0:113,0:116:99:0,286,3614 0/0:37,0:38:93.28:0,93,1240 0/0:105,0:105:99:0,247,3197 0/0:86,0:87:99:0,211,2707 0/0:98,0:99:99:0,241,3176 0/0:61,0:61:99:0,153,1974 0/0:88,0:88:99:0,199,2568 0/0:79,0:79:99:0,196,2539 0/0:66,0:66:99:0,156,2041 0/0:65,0:66:99:0,153,1958 0/0:45,0:47:99:0,105,1403 0/0:58,0:59:99:0,126,1695 0/0:78,0:79:99:0,172,2217 0/0:65,0:65:99:0,150,1960 -chr1 881918 . G A 4148.23 . AC=6;AF=0.0500;AN=120;BaseQRankSum=0.336;DP=2717;Dels=0.00;FS=3.311;HRun=1;HaplotypeScore=1.8603;InbreedingCoeff=-0.0526;MQ=57.50;MQ0=0;MQRankSum=10.868;QD=13.38;ReadPosRankSum=2.821;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|13),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S556L|749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,missense_variant|tCg/tTg|S/L|ENSG00000188976|NOC2L|ENST00000327044|15/19|benign(0.311)|deleterious(0.03)|556/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|1/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|13/17||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:14,0:14:33.10:0,33,408 0/0:19,0:19:54.16:0,54,656 0/0:19,0:19:45.14:0,45,573 0/0:15,0:17:42.13:0,42,536 0/0:49,0:50:99:0,135,1658 0/0:50,0:50:99:0,144,1831 0/0:72,0:72:99:0,193,2428 0/0:36,1:37:65.34:0,65,1212 0/0:80,0:80:99:0,220,2781 0/0:83,0:83:99:0,226,2850 0/0:47,0:47:99:0,129,1592 0/0:52,0:52:99:0,138,1768 0/0:53,0:54:99:0,147,1821 0/0:29,0:29:75.23:0,75,961 0/0:36,1:37:66.57:0,67,1093 0/0:21,0:21:54.18:0,54,729 0/0:25,0:25:69.22:0,69,884 0/0:39,0:41:87.27:0,87,1155 0/0:23,0:23:63.20:0,63,821 0/1:15,17:32:99:454,0,454 0/0:34,0:34:78.25:0,78,1041 0/0:50,0:50:99:0,120,1598 0/0:23,0:23:45.15:0,45,610 0/0:27,0:28:69.22:0,69,901 0/0:25,0:25:60.15:0,60,763 0/0:25,0:25:63.19:0,63,816 0/0:37,0:37:81.24:0,81,1051 0/0:28,0:28:84.25:0,84,1068 0/0:20,0:20:45.14:0,45,577 0/0:28,0:28:72.23:0,72,933 0/0:44,1:45:99:0,105,1336 0/0:31,0:31:84.25:0,84,1064 0/0:21,0:21:57.16:0,57,717 0/0:26,0:27:75.24:0,75,988 0/0:20,0:20:48.15:0,48,632 0/0:23,0:23:57.18:0,57,746 0/1:12,14:26:99:431,0,369 0/0:45,0:45:99:0,120,1569 0/0:47,0:47:99:0,114,1503 0/1:35,36:71:99:999,0,963 0/0:57,0:58:99:0,132,1741 0/0:67,0:67:99:0,156,2043 0/1:21,23:44:99:706,0,481 0/0:54,0:54:99:0,108,1449 0/0:53,0:53:99:0,135,1739 0/0:65,0:65:99:0,141,1822 0/0:111,0:111:99:0,271,3407 0/0:35,0:35:75.21:0,75,973 0/1:49,39:88:99:937,0,1283 0/0:67,1:68:99:0,159,2053 0/0:87,0:87:99:0,211,2754 0/1:27,22:49:99:621,0,787 0/0:79,2:81:99:0,147,2297 0/0:67,0:68:99:0,169,2155 0/0:61,0:61:99:0,144,1857 0/0:56,0:56:99:0,123,1581 0/0:38,0:39:81.26:0,81,1071 0/0:50,0:50:99:0,111,1474 0/0:72,0:72:99:0,159,2021 0/0:55,0:55:99:0,120,1543 -chr1 882033 . G A 7803.05 . AC=29;AF=0.2417;AN=120;BaseQRankSum=-1.083;DP=803;Dels=0.00;FS=0.805;HRun=1;HaplotypeScore=0.5525;InbreedingCoeff=-0.0708;MQ=56.82;MQ0=0;MQRankSum=1.538;QD=18.99;ReadPosRankSum=-1.493;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),DOWNSTREAM(MODIFIER|||||SAMD11|processed_transcript|CODING|ENST00000478729|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000464948|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000466827|),DOWNSTREAM(MODIFIER|||||SAMD11|retained_intron|CODING|ENST00000474461|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|1),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|14),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|12),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000464948|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000466827|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000474461|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000483767|1/5||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000478729|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:9.03:0,9,114 0/0:8,0:8:24.07:0,24,305 0/1:6,6:12:99:148,0,201 0/1:5,6:11:99:198,0,166 0/1:18,15:33:99:502,0,635 0/1:13,7:20:99:224,0,456 0/0:29,0:29:78.25:0,78,1034 0/0:18,0:18:54.18:0,54,727 0/1:19,21:40:99:682,0,651 0/1:21,20:41:99:678,0,722 0/1:10,18:28:99:604,0,315 0/0:27,0:27:81.26:0,81,1066 0/1:5,17:22:99:595,0,107 1/1:0,4:4:12.04:163,12,0 0/1:2,3:5:67.36:90,0,67 0/0:6,0:6:18.06:0,18,234 0/0:8,0:8:24.08:0,24,328 0/1:1,1:2:32.56:34,0,33 0/1:4,2:6:62.49:62,0,150 0/1:3,9:12:89.11:320,0,89 0/0:7,0:7:21.07:0,21,275 0/0:7,0:7:21.07:0,21,286 0/0:4,0:4:12.04:0,12,149 0/1:3,4:7:94.20:138,0,94 0/0:9,0:9:24.08:0,24,309 0/1:3,3:6:99:105,0,101 0/0:3,0:3:9.03:0,9,116 0/0:7,0:7:21.07:0,21,282 0/0:3,0:3:9.03:0,9,122 0/0:8,0:8:24.07:0,24,304 0/0:8,0:8:24.08:0,24,313 0/0:3,0:3:9.03:0,9,123 0/1:4,2:6:64.96:65,0,96 0/0:9,0:9:24.08:0,24,334 0/1:2,2:4:60.74:61,0,69 0/1:3,3:6:99:102,0,99 0/0:8,0:8:18.04:0,18,229 1/1:0,17:17:48.15:624,48,0 0/1:4,4:8:99:135,0,129 0/0:17,0:17:45.15:0,45,602 0/1:12,2:14:38.77:39,0,383 0/1:5,19:24:99:600,0,140 0/0:21,0:21:60.19:0,60,794 0/0:9,0:9:27.09:0,27,354 0/0:9,0:9:27.09:0,27,359 0/0:14,0:14:36.12:0,36,477 0/1:11,15:26:99:534,0,338 0/0:6,0:6:18.06:0,18,235 0/0:16,0:16:48.15:0,48,629 0/0:27,0:27:72.23:0,72,935 0/1:16,12:28:99:379,0,499 0/0:17,0:17:51.16:0,51,669 0/0:19,0:20:45.14:0,45,598 0/0:15,0:15:45.14:0,45,584 0/0:7,0:7:21.07:0,21,284 0/0:10,0:10:27.09:0,27,357 0/0:9,0:9:24.07:0,24,302 0/1:7,5:12:99:162,0,192 0/0:18,1:19:18.92:0,19,634 1/1:1,16:17:8.90:560,9,0 -chr1 883625 . A G 54754.53 . AC=120;AF=1.0000;AN=120;DP=1639;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=1.0098;InbreedingCoeff=-0.0052;MQ=58.06;MQ0=0;QD=33.41;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|13),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|11),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,2:2:3.01:41,3,0 1/1:0,5:5:15.03:169,15,0 1/1:0,4:4:9.03:118,9,0 1/1:0,3:3:9.03:119,9,0 1/1:0,11:11:33.11:453,33,0 1/1:0,6:6:18.06:246,18,0 1/1:0,11:11:33.10:427,33,0 1/1:0,8:9:24.08:321,24,0 1/1:0,20:20:60.20:801,60,0 1/1:0,18:18:51.17:683,51,0 1/1:0,12:12:30.10:410,30,0 1/1:0,7:7:21.07:281,21,0 1/1:0,10:10:30.10:396,30,0 1/1:0,18:18:48.15:639,48,0 1/1:0,28:28:69.22:920,69,0 1/1:0,8:8:18.06:253,18,0 1/1:0,24:24:54.18:741,54,0 1/1:0,34:34:75.24:1012,75,0 1/1:0,23:23:48.15:639,48,0 1/1:0,15:15:33.10:433,33,0 1/1:0,27:27:66.22:898,66,0 1/1:0,23:23:51.17:701,51,0 1/1:0,26:26:60.18:822,60,0 1/1:0,16:16:42.14:574,42,0 1/1:0,25:27:66.20:854,66,0 1/1:0,23:23:57.19:778,57,0 1/1:0,9:9:27.09:356,27,0 1/1:0,16:16:36.12:493,36,0 1/1:0,29:29:75.24:990,75,0 1/1:0,25:25:66.21:888,66,0 1/1:0,33:33:75.24:1018,75,0 1/1:0,24:24:66.22:885,66,0 1/1:0,23:23:57.19:773,57,0 1/1:0,27:27:63.20:848,63,0 1/1:0,9:9:27.09:371,27,0 1/1:0,22:22:42.14:583,42,0 1/1:0,41:41:99:1326,99,0 1/1:0,31:31:78.26:1058,78,0 1/1:0,23:23:60.19:771,60,0 1/1:0,55:55:99:1904,144,0 1/1:0,49:49:99:1642,126,0 1/1:0,26:28:63.20:822,63,0 1/1:0,49:50:99:1598,123,0 1/1:0,35:35:99:1302,102,0 1/1:0,26:26:72.23:940,72,0 1/1:0,42:42:99:1432,111,0 1/1:0,76:76:99:2639,208,0 1/1:0,23:23:48.09:582,48,0 1/1:0,36:36:90.28:1178,90,0 1/1:0,61:61:99:2132,163,0 1/1:0,62:62:99:2023,153,0 1/1:0,57:57:99:1954,150,0 1/1:1,47:49:99:1670,126,0 1/1:0,46:46:99:1528,114,0 1/1:0,42:42:99:1398,105,0 1/1:0,30:30:72.23:974,72,0 1/1:0,35:35:87.28:1140,87,0 1/1:0,45:45:99:1400,105,0 1/1:0,29:29:78.25:1012,78,0 1/1:0,40:40:99:1395,105,0 -chr1 883699 . C T 453.1 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.101;DP=923;Dels=0.00;FS=14.883;HRun=0;HaplotypeScore=0.5131;InbreedingCoeff=-0.0294;MQ=56.96;MQ0=0;MQRankSum=3.137;QD=12.25;ReadPosRankSum=2.276;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|13),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|11),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12:0,12,125 0/0:5,0:5:15.04:0,15,180 0/0:6,0:6:18.06:0,18,240 0/0:2,0:2:6.02:0,6,69 0/0:9,0:9:27.07:0,27,327 0/0:15,0:15:45.14:0,45,573 0/0:23,0:23:69.22:0,69,917 0/0:18,0:18:54.17:0,54,697 0/0:17,0:17:51.16:0,51,647 0/0:25,0:25:72.22:0,72,922 0/0:14,0:14:42.13:0,42,522 0/0:10,0:10:21.05:0,21,257 0/0:13,0:13:39.12:0,39,498 0/0:11,0:11:33.11:0,33,437 0/0:14,0:14:42.14:0,42,559 0/0:7,0:7:15.05:0,15,189 0/0:8,0:8:21.07:0,21,284 0/0:10,0:10:27.08:0,27,337 0/0:17,0:17:51.15:0,51,655 0/0:7,0:7:21.06:0,21,251 0/1:6,4:10:88.68:89,0,164 0/0:17,0:17:51.17:0,51,680 0/0:12,0:12:33.11:0,33,433 0/0:11,0:11:24.08:0,24,321 0/0:15,0:16:39.13:0,39,524 0/0:9,0:9:27.09:0,27,349 0/1:4,9:13:38.11:274,0,38 0/0:10,0:10:24.08:0,24,322 0/0:15,0:16:42.14:0,42,571 0/0:10,0:10:30.09:0,30,387 0/0:13,0:13:36.12:0,36,481 0/0:10,0:10:21.07:0,21,282 0/0:6,0:6:15.05:0,15,193 0/1:6,6:13:99:170,0,200 0/0:6,0:6:18.05:0,18,227 0/0:13,0:13:39.12:0,39,502 0/0:27,0:27:66.21:0,66,853 0/0:14,0:14:42.13:0,42,553 0/0:12,0:13:30.09:0,30,384 0/0:27,0:27:69.21:0,69,879 0/0:29,0:29:81.23:0,81,1041 0/0:16,0:16:45.14:0,45,578 0/0:24,0:24:69.22:0,69,885 0/0:16,0:16:39.12:0,39,494 0/0:13,0:13:36.10:0,36,456 0/0:23,0:23:57.18:0,57,752 0/0:50,0:50:99:0,135,1707 0/0:17,0:17:45.13:0,45,551 0/0:15,0:15:42.13:0,42,538 0/0:33,0:33:96.28:0,96,1202 0/0:30,0:30:84.25:0,84,1056 0/0:30,0:30:84.26:0,84,1080 0/0:24,0:24:51.12:0,51,620 0/0:16,0:16:39.12:0,39,498 0/0:9,0:10:24.08:0,24,325 0/0:12,0:12:33.11:0,33,436 0/0:18,0:18:48.15:0,48,614 0/0:15,0:15:42.13:0,42,541 0/0:14,0:14:42.13:0,42,529 0/0:15,0:15:42.13:0,42,538 -chr1 883750 . T C 877.5 . AC=3;AF=0.0250;AN=120;BaseQRankSum=1.693;DP=1077;Dels=0.00;FS=5.318;HRun=3;HaplotypeScore=0.3559;InbreedingCoeff=-0.0265;MQ=57.03;MQ0=0;MQRankSum=4.377;QD=17.21;ReadPosRankSum=1.955;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|13),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|11),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:15,0:15:33.10:0,33,407 0/0:11,0:11:33.09:0,33,405 0/0:10,0:10:24.07:0,24,303 0/0:9,0:9:27.06:0,27,321 0/0:14,0:14:39.12:0,39,490 0/0:19,0:19:54.16:0,54,684 0/0:28,0:28:75.21:0,75,967 0/0:18,0:18:51.15:0,51,634 0/0:40,0:40:99:0,105,1317 0/0:45,0:45:99:0,126,1620 0/0:22,0:22:66.20:0,66,851 0/0:26,0:26:78.24:0,78,1002 0/0:28,0:28:84.22:0,84,1048 0/0:11,0:11:33.10:0,33,425 0/0:17,0:17:42.13:0,42,544 0/0:4,0:4:12.04:0,12,157 0/0:7,0:7:21.07:0,21,284 0/0:18,0:18:51.16:0,51,683 0/0:22,0:22:63.19:0,63,798 0/0:16,0:16:45.14:0,45,578 0/0:14,0:14:42.13:0,42,542 0/0:23,0:23:63.20:0,63,809 0/0:10,0:10:27.09:0,27,362 0/0:6,0:6:18.06:0,18,229 0/0:16,0:16:48.15:0,48,618 0/0:18,0:18:54.15:0,54,694 0/1:9,10:19:99:292,0,303 0/0:10,0:10:30.09:0,30,377 0/0:15,0:15:45.14:0,45,579 0/0:16,0:16:48.16:0,48,644 0/0:18,0:18:51.16:0,51,652 0/0:10,0:10:27.09:0,27,361 0/0:13,0:13:36.12:0,36,474 0/0:14,0:14:39.12:0,39,490 0/1:7,2:9:53.25:53,0,254 0/0:12,0:12:33.10:0,33,429 0/1:5,18:23:99:613,0,142 0/0:17,0:17:51.17:0,51,679 0/0:8,0:8:24.07:0,24,302 0/0:21,0:22:63.20:0,63,817 0/0:28,1:29:63.19:0,63,806 0/0:16,0:16:48.15:0,48,616 0/0:24,1:25:63.17:0,63,779 0/0:14,0:14:42.13:0,42,530 0/0:20,0:21:54.17:0,54,687 0/0:21,0:21:63.19:0,63,815 0/0:45,1:46:99:0,129,1649 0/0:17,0:17:42.11:0,42,543 0/0:16,0:16:39.10:0,39,503 0/0:34,0:34:84.22:0,84,1051 0/0:20,0:20:60.16:0,60,746 0/0:26,0:26:69.22:0,69,894 0/0:21,0:21:60.17:0,60,755 0/0:12,0:12:33.10:0,33,420 0/0:15,0:15:42.13:0,42,533 0/0:13,0:13:39.11:0,39,482 0/0:13,0:13:33.08:0,33,396 0/0:16,0:16:45.10:0,45,556 0/0:17,0:17:45.15:0,45,601 0/0:11,0:11:27.08:0,27,346 -chr1 883960 . G A 483.87 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.195;DP=3321;Dels=0.00;FS=1.899;HRun=0;HaplotypeScore=1.8090;InbreedingCoeff=-0.0084;MQ=57.94;MQ0=0;MQRankSum=2.447;QD=10.30;ReadPosRankSum=1.425;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|11),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N489|749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,synonymous_variant|aaC/aaT|N|ENSG00000188976|NOC2L|ENST00000327044|13/19|||489/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|11/17||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:32,0:32:90.25:0,90,1087 0/0:30,0:31:84.26:0,84,1062 0/0:34,0:34:99:0,102,1273 0/0:35,0:35:99:0,99,1235 0/0:57,0:57:99:0,169,2227 0/0:56,0:56:99:0,169,2213 0/0:91,0:91:99:0,268,3463 0/0:45,0:45:99:0,129,1683 0/0:113,0:113:99:0,334,4401 0/0:104,0:104:99:0,304,4014 0/0:66,0:66:99:0,193,2513 0/0:67,0:67:99:0,193,2471 0/0:88,0:88:99:0,256,3356 0/0:59,0:60:99:0,135,1824 0/0:64,0:64:99:0,169,2191 0/0:38,0:38:90.29:0,90,1213 0/0:63,0:64:99:0,141,1932 0/0:52,0:52:99:0,132,1717 0/0:54,0:56:99:0,129,1700 0/1:26,21:47:99:532,0,771 0/0:53,0:53:99:0,129,1727 0/0:68,0:68:99:0,165,2151 0/0:66,0:67:99:0,150,2046 0/0:47,0:47:99:0,120,1598 0/0:50,0:50:99:0,129,1708 0/0:47,0:47:99:0,108,1428 0/0:46,0:46:99:0,120,1609 0/0:52,1:53:99:0,129,1723 0/0:69,0:69:99:0,162,2129 0/0:61,2:64:99:0,115,2033 0/0:74,0:74:99:0,175,2279 0/0:47,0:47:99:0,123,1638 0/0:45,0:45:99:0,117,1561 0/0:65,0:65:99:0,147,1997 0/0:30,0:32:69.22:0,69,912 0/0:56,0:56:99:0,132,1759 0/0:75,0:77:99:0,184,2467 0/0:76,0:76:99:0,187,2511 0/0:37,0:37:81.26:0,81,1100 0/0:89,0:89:99:0,211,2748 0/0:59,0:59:99:0,138,1816 0/0:34,0:34:81.25:0,81,1062 0/0:42,0:42:99:0,102,1310 0/0:22,0:22:60.18:0,60,791 0/0:48,0:48:99:0,126,1673 0/0:60,0:60:99:0,150,1961 0/0:78,0:79:99:0,193,2533 0/0:23,0:24:57.17:0,57,743 0/0:52,0:53:99:0,120,1579 0/0:68,0:69:99:0,147,1902 0/0:60,0:60:99:0,141,1837 0/0:42,0:43:99:0,105,1367 0/0:58,0:58:99:0,135,1753 0/0:38,0:40:87.28:0,87,1155 0/0:45,0:45:99:0,114,1517 0/0:40,0:40:96.31:0,96,1277 0/0:28,0:28:66.21:0,66,876 0/0:51,0:51:99:0,111,1478 0/0:61,0:61:99:0,138,1842 0/0:42,0:42:93.27:0,93,1217 -chr1 884013 . G A 359.69 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.049;DP=1892;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.9736;InbreedingCoeff=-0.0084;MQ=57.09;MQ0=0;MQRankSum=2.918;QD=14.99;ReadPosRankSum=0.004;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:22,0:22:60.19:0,60,768 0/0:19,0:19:57.15:0,57,702 0/0:29,0:29:87.26:0,87,1104 0/0:23,0:23:69.19:0,69,870 0/0:43,0:43:99:0,129,1692 0/0:41,0:41:99:0,120,1629 0/0:60,0:60:99:0,175,2309 0/0:42,0:42:99:0,123,1648 0/0:73,0:74:99:0,217,2850 0/0:68,0:68:99:0,202,2673 0/0:34,0:34:99:0,99,1323 0/0:32,0:32:96.31:0,96,1278 0/0:57,0:57:99:0,172,2229 0/0:34,0:35:90.25:0,90,1145 0/0:48,0:48:99:0,126,1636 0/0:23,0:23:57.18:0,57,750 0/0:29,0:29:87.25:0,87,1098 0/0:29,0:29:78.24:0,78,1008 0/0:25,0:25:63.20:0,63,824 0/1:11,13:24:99:407,0,226 0/0:24,0:24:69.21:0,69,884 0/0:32,0:32:87.26:0,87,1097 0/0:31,0:31:81.26:0,81,1090 0/0:30,0:30:81.22:0,81,1027 0/0:25,0:25:72.23:0,72,943 0/0:19,0:19:57.17:0,57,721 0/0:21,0:21:60.17:0,60,758 0/0:21,0:21:57.18:0,57,731 0/0:40,0:41:99:0,105,1372 0/0:46,0:46:99:0,99,1336 0/0:36,0:36:96.29:0,96,1228 0/0:28,0:28:78.18:0,78,937 0/0:22,0:22:63.20:0,63,800 0/0:34,0:34:84.27:0,84,1097 0/0:15,0:15:39.13:0,39,518 0/0:23,0:23:57.19:0,57,773 0/0:41,0:41:99:0,108,1431 0/0:42,0:42:99:0,108,1426 0/0:21,0:21:51.15:0,51,665 0/0:51,0:51:99:0,129,1685 0/0:28,0:28:66.21:0,66,862 0/0:17,0:17:42.13:0,42,551 0/0:22,0:22:51.16:0,51,673 0/0:17,0:17:42.14:0,42,556 0/0:26,0:26:69.22:0,69,896 0/0:33,0:33:81.25:0,81,1031 0/0:32,0:34:81.26:0,81,1060 0/0:15,0:15:39.12:0,39,502 0/0:37,0:37:96.28:0,96,1238 0/0:40,0:40:93.24:0,93,1148 0/0:28,0:29:63.20:0,63,827 0/0:39,0:39:87.27:0,87,1154 0/0:26,0:26:57.19:0,57,771 0/0:27,0:28:51.17:0,51,694 0/0:21,0:21:51.15:0,51,652 0/0:18,0:18:48.15:0,48,623 0/0:13,0:14:30.10:0,30,392 0/0:26,0:26:69.22:0,69,908 0/0:40,0:42:99:0,99,1335 0/0:20,0:20:48.14:0,48,624 -chr1 884035 . G GCC 125.11 . AC=12;AF=0.1000;AN=120;BaseQRankSum=10.429;DP=1507;FS=5.790;HRun=1;HaplotypeScore=118.1286;InbreedingCoeff=-0.1150;MQ=55.10;MQ0=0;MQRankSum=-9.464;QD=0.53;ReadPosRankSum=-1.582;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:23,0:23:35.54:0,36,805 0/0:25,0:25:72.24:0,72,1076 0/0:29,0:29:57.57:0,58,1110 0/0:17,0:17:51.17:0,51,771 0/0:39,0:39:99:0,114,1746 0/0:34,0:34:77.57:0,78,1449 0/0:62,0:62:99:0,175,2629 0/0:39,0:39:99:0,108,1655 0/0:73,0:73:99:0,211,3171 0/0:63,0:63:99:0,175,2635 0/0:46,0:46:99:0,129,1967 0/0:18,0:18:51.17:0,51,781 0/0:53,0:53:99:0,160,2395 0/0:25,0:25:75.25:0,75,1149 0/0:29,1:30:23.62:0,24,1137 0/0:17,0:17:45.15:0,45,689 0/0:19,1:20:2.68:0,3,815 0/0:21,1:22:3.23:0,3,795 0/1:18,1:19:3.41:3,0,711 0/1:17,2:19:43.97:44,0,625 0/0:14,0:14:39.13:0,39,572 0/0:23,1:24:10.66:0,11,894 0/0:19,0:19:54.18:0,54,827 0/0:24,0:24:69.23:0,69,1042 0/0:15,1:16:3.53:0,4,632 0/1:13,2:15:66.13:66,0,509 0/0:15,0:15:42.14:0,42,628 0/0:16,1:17:1.76:0,2,621 0/0:25,1:26:17.41:0,17,1032 0/0:30,1:31:20.01:0,20,1174 0/0:28,1:29:29.60:0,30,1227 0/0:22,2:24:14.10:0,14,956 0/1:15,1:16:1.95:2,0,641 0/0:28,0:28:78.26:0,78,1183 0/1:10,1:11:24.85:25,0,426 0/0:12,0:12:36.12:0,36,538 0/1:30,2:32:12.88:13,0,1283 0/1:28,3:31:40.60:41,0,1101 0/0:15,0:15:45.15:0,45,689 0/0:34,1:35:63.65:0,64,1490 0/1:17,1:18:5.16:5,0,641 0/0:15,0:15:39.13:0,39,597 0/0:14,0:14:22.78:0,23,516 0/0:10,0:10:30.10:0,30,460 0/0:19,0:19:57.19:0,57,861 0/1:24,2:26:39.89:40,0,967 0/0:27,0:27:72.23:0,72,1081 0/0:12,0:12:30.10:0,30,459 0/0:25,0:25:53.88:0,54,975 0/0:27,1:28:19.95:0,20,1035 0/0:23,0:23:69.23:0,69,1042 0/0:34,0:34:96.30:0,96,1446 0/0:22,1:23:10.46:0,10,823 0/0:21,0:21:54.18:0,54,815 0/1:16,1:17:6.35:6,0,669 0/1:13,1:14:16.44:16,0,469 0/0:11,0:11:33.11:0,33,498 0/0:19,0:19:54.18:0,54,827 0/0:27,0:27:78.27:0,78,1197 0/1:16,1:17:12.37:12,0,585 -chr1 884040 . AC A 54.58 . AC=10;AF=0.0833;AN=120;BaseQRankSum=10.370;DP=1485;FS=5.837;HRun=3;HaplotypeScore=105.2143;InbreedingCoeff=-0.0972;MQ=54.77;MQ0=0;MQRankSum=-6.138;QD=0.29;ReadPosRankSum=-3.294;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/1:22,2:24:14.56:15,0,677 0/0:26,0:26:72.24:0,72,1025 0/0:29,1:30:13.49:0,13,1084 0/0:19,0:19:20.94:0,21,741 0/0:42,0:42:12.65:0,13,1456 0/0:31,2:33:21.88:0,22,1174 0/0:66,0:66:99:0,116,2452 0/0:42,0:42:77.88:0,78,1551 0/0:76,0:76:99:0,150,2771 0/0:64,1:65:99:0,147,2516 0/0:49,1:50:99:0,108,1975 0/1:21,0:21:5.96:6,0,717 0/0:53,0:53:77:0,77,1961 0/0:24,0:24:66.22:0,66,940 0/0:31,1:32:9.88:0,10,1037 0/0:17,0:17:14.50:0,15,655 0/0:18,1:19:20:0,20,730 0/1:22,1:23:10.85:11,0,716 0/0:15,1:16:7.96:0,8,568 0/1:18,2:20:40.10:40,0,580 0/0:12,0:12:30.10:0,30,432 0/0:22,1:23:27.46:0,27,792 0/0:18,0:18:48.16:0,48,692 0/0:22,0:22:60.20:0,60,864 0/0:14,1:15:15.18:0,15,565 0/1:14,2:16:61.57:62,0,433 0/0:15,0:15:27.14:0,27,547 0/0:14,1:15:4.67:0,5,524 0/0:24,1:25:35.05:0,35,957 0/0:30,1:31:50.09:0,50,1161 0/0:28,1:29:47.09:0,47,1117 0/1:22,2:24:6.69:7,0,798 0/1:16,1:17:25.33:25,0,557 0/0:28,0:28:78.26:0,78,1113 0/1:8,1:9:13.12:13,0,278 0/0:11,0:11:33.11:0,33,475 0/0:30,2:32:21.34:0,21,1140 0/0:26,3:29:5.93:0,6,1030 0/0:14,0:14:39.13:0,39,562 0/0:33,1:34:71.95:0,72,1332 0/0:15,1:16:12.63:0,13,572 0/0:14,0:14:39.13:0,39,549 0/0:14,0:14:1.92:0,2,481 0/0:9,0:9:27.09:0,27,389 0/0:18,0:18:42.14:0,42,604 0/1:21,2:23:8.18:8,0,763 0/0:22,0:22:57.19:0,57,820 0/0:10,0:10:27.09:0,27,389 0/0:23,0:23:66.21:0,66,933 0/0:25,1:26:38.83:0,39,969 0/0:20,0:20:57.19:0,57,821 0/0:34,0:34:84.28:0,84,1198 0/0:21,1:22:23.21:0,23,731 0/0:19,0:19:51.17:0,51,734 0/0:14,1:15:8.47:0,8,528 0/1:13,1:14:1.64:2,0,399 0/0:10,0:10:30.10:0,30,432 0/0:18,0:18:48.16:0,48,690 0/0:25,0:25:69.23:0,69,981 0/0:15,1:16:4.95:0,5,525 -chr1 884091 . C G 9412.98 . AC=59;AF=0.4917;AN=120;BaseQRankSum=0.144;DP=830;Dels=0.00;FS=3.690;HRun=1;HaplotypeScore=1.5824;InbreedingCoeff=-0.8297;MQ=49.85;MQ0=0;MQRankSum=3.025;QD=11.58;ReadPosRankSum=6.853;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/1:4,4:8:99:102,0,126 0/1:9,6:15:99:179,0,274 0/1:7,13:20:99:419,0,197 0/1:9,12:21:99:258,0,183 0/1:12,16:28:99:547,0,372 0/1:14,9:23:99:289,0,461 0/1:26,17:43:99:488,0,874 0/1:8,10:18:99:329,0,255 0/1:26,21:47:99:689,0,827 0/1:41,15:57:99:422,0,1268 0/1:5,10:15:99:277,0,126 0/1:11,19:30:99:650,0,289 0/1:22,14:36:99:364,0,678 0/1:5,2:7:45.81:46,0,156 0/1:9,4:13:68.59:69,0,266 0/1:4,1:5:24.96:25,0,137 0/1:5,5:10:99:103,0,117 0/1:8,7:15:99:172,0,231 0/1:6,3:9:84.95:85,0,159 0/1:9,7:16:99:183,0,271 1/1:0,4:4:12:119,12,0 0/1:8,4:12:94.79:95,0,252 0/1:4,4:8:99:106,0,117 0/1:9,5:14:99:147,0,242 0/1:5,3:8:82.25:82,0,83 0/1:2,5:7:42.97:152,0,43 1/1:1,8:9:21.07:272,21,0 0/1:6,2:8:45.81:46,0,154 0/1:7,1:8:9.36:9,0,226 0/1:11,6:17:99:153,0,329 0/1:7,7:14:99:171,0,209 0/1:10,6:17:99:154,0,276 0/1:9,5:14:99:113,0,256 0/1:6,9:15:99:309,0,152 0/1:4,2:6:18.42:18,0,119 0/1:2,4:6:46.94:119,0,47 0/1:5,5:10:99:150,0,147 0/1:10,5:15:99:135,0,314 0/1:5,1:6:21.95:22,0,181 0/1:11,5:16:72.33:72,0,271 0/1:7,3:10:80.13:80,0,212 0/1:8,1:9:9.36:9,0,243 0/1:4,4:8:99:117,0,116 0/1:2,1:3:28.77:29,0,69 0/1:2,5:7:47.62:184,0,48 0/1:8,5:13:99:99,0,252 0/1:6,6:12:99:187,0,183 0/0:5,0:5:15.03:0,15,163 0/0:8,0:8:24.07:0,24,301 0/1:12,5:17:99:114,0,371 0/1:13,3:16:46.42:46,0,421 0/1:10,2:12:43.21:43,0,332 0/1:11,3:14:58.22:58,0,329 0/1:6,3:9:50.66:51,0,190 0/1:4,3:7:53.18:53,0,116 0/1:4,4:8:99:113,0,110 0/1:3,1:4:22.32:22,0,94 0/0:4,0:4:12.04:0,12,144 0/1:5,2:7:53.17:53,0,134 0/1:6,1:7:12.37:12,0,204 -chr1 884101 . A C 9419.59 . AC=54;AF=0.4500;AN=120;BaseQRankSum=12.324;DP=697;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=1.3334;InbreedingCoeff=-0.7661;MQ=48.44;MQ0=0;MQRankSum=-6.895;QD=14.45;ReadPosRankSum=-14.010;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/1:5,4:9:19.31:138,0,19 0/1:5,8:13:79.32:263,0,79 0/1:13,7:20:99:139,0,338 0/1:12,6:18:99:170,0,253 0/1:10,9:19:99:280,0,304 0/1:9,11:20:99:349,0,270 0/1:13,18:31:99:557,0,294 0/1:11,3:14:83.35:83,0,334 0/1:17,17:34:99:543,0,476 0/1:31,19:51:99:471,0,929 0/0:11,1:12:27.08:0,27,328 0/1:14,8:22:99:231,0,403 0/1:10,9:19:99:213,0,248 0/1:3,3:6:59.62:85,0,60 0/1:4,7:11:75.38:195,0,75 0/1:1,4:5:21.93:133,0,22 0/1:4,5:9:78.57:92,0,79 0/1:7,7:14:99:201,0,171 0/1:4,4:8:66.62:117,0,67 0/1:7,7:14:99:165,0,203 0/0:5,0:5:12.03:0,12,134 0/1:2,8:10:35.85:255,0,36 0/0:6,0:6:18.03:0,18,205 0/1:5,9:14:99:275,0,128 0/1:5,3:9:48.82:49,0,116 0/1:5,2:7:45.81:46,0,150 0/0:8,1:9:15.05:0,15,190 0/1:2,6:8:42.80:177,0,43 0/1:1,5:6:15.38:157,0,15 0/1:5,7:12:99:201,0,117 0/1:6,6:12:99:171,0,155 0/1:5,7:12:99:168,0,146 0/1:5,7:12:96.84:220,0,97 0/1:8,6:15:99:161,0,251 0/1:2,1:3:24.41:24,0,56 0/1:6,2:8:48.98:49,0,98 0/1:5,3:8:76.24:76,0,146 0/1:5,9:14:99:284,0,128 0/1:1,3:4:26.54:105,0,27 0/1:4,11:15:63.30:295,0,63 0/1:3,7:10:45.67:220,0,46 0/0:7,0:7:15.04:0,15,169 0/1:5,3:8:79.24:79,0,120 0/0:1,0:1:3.01:0,3,41 0/1:7,1:8:12.37:12,0,213 0/1:6,7:13:99:211,0,141 0/1:6,6:12:99:147,0,177 0/0:5,0:5:12.03:0,12,132 0/1:1,4:5:22.75:127,0,23 0/1:6,10:16:99:311,0,115 0/1:11,2:13:41.57:42,0,290 0/1:2,9:11:45.11:284,0,45 0/1:3,6:9:73.22:185,0,73 0/1:3,4:7:57.14:118,0,57 0/1:3,4:7:59.62:85,0,60 0/1:4,4:8:99:102,0,109 0/1:3,1:4:23.48:23,0,61 1/1:0,3:3:9.03:105,9,0 0/1:3,3:6:77.47:91,0,77 0/1:2,4:6:48.81:134,0,49 -chr1 884111 . T C 106.0 . AC=12;AF=0.1017;AN=118;BaseQRankSum=-1.701;DP=405;Dels=0.00;FS=32.333;HRun=2;HaplotypeScore=0.1962;InbreedingCoeff=-0.1423;MQ=53.01;MQ0=0;MQRankSum=1.879;QD=1.39;ReadPosRankSum=-6.750;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:18.05:0,18,203 0/1:6,1:7:16.73:17,0,196 0/0:17,1:18:15.58:0,16,581 0/0:12,0:12:27.08:0,27,330 0/1:14,2:16:34.30:34,0,516 0/0:11,0:11:33.10:0,33,427 0/0:17,0:17:42.13:0,42,536 0/0:11,0:11:33.10:0,33,433 0/1:13,1:14:2.10:2,0,442 0/0:37,2:39:44.53:0,45,1272 0/0:9,0:9:27.07:0,27,326 0/0:14,1:15:4.49:0,4,494 0/0:14,0:14:36.11:0,36,461 0/0:3,0:3:9.03:0,9,109 0/0:4,0:4:12.04:0,12,144 0/1:1,1:2:31.78:32,0,36 0/0:4,0:4:12.04:0,12,146 0/0:7,0:7:18.06:0,18,233 0/0:4,0:4:9.03:0,9,112 0/0:6,0:6:18.05:0,18,217 0/0:6,0:6:18.04:0,18,205 0/0:3,0:3:3.01:0,3,33 0/0:6,0:6:18.06:0,18,230 0/0:5,0:5:15.05:0,15,193 0/0:6,0:6:12.03:0,12,139 0/0:5,0:5:15.04:0,15,175 0/0:8,0:8:18.06:0,18,225 0/0:1,0:1:3.01:0,3,33 0/1:1,1:2:27.42:32,0,27 0/0:5,0:5:15.04:0,15,183 0/0:7,0:7:21.06:0,21,261 0/1:5,1:6:22.75:23,0,134 0/1:7,1:8:12.37:12,0,206 0/0:9,1:10:24.07:0,24,314 0/0:2,0:2:6.02:0,6,66 0/0:6,0:6:12.03:0,12,134 0/0:5,0:5:12.04:0,12,145 0/0:5,0:5:15.05:0,15,184 0/0:1,0:1:3:0,3,29 0/1:4,1:5:24.41:24,0,58 0/1:3,1:4:21.42:21,0,85 0/0:5,0:5:15.04:0,15,178 0/0:5,0:5:15.05:0,15,179 0/0:1,0:1:3.01:0,3,42 0/0:7,0:7:21.07:0,21,279 0/0:7,0:7:21.06:0,21,240 0/0:7,0:7:21.06:0,21,255 0/0:5,0:5:15.05:0,15,196 0/0:1,0:1:3.01:0,3,38 0/0:5,0:5:15.05:0,15,184 0/0:7,0:7:18.06:0,18,229 0/0:3,0:3:9.03:0,9,124 0/1:3,1:4:23.22:23,0,88 0/0:4,0:4:9.03:0,9,107 0/0:3,0:3:6.02:0,6,73 0/0:4,0:4:9.03:0,9,106 0/0:3,0:3:9.03:0,9,112 ./. 0/1:4,1:5:0.29:0,0,94 0/1:2,1:3:28.77:29,0,53 -chr1 884426 . A AACAGCAAAG 1975.5 . AC=28;AF=1.000;AN=28;DP=24;FS=0.000;HRun=0;HaplotypeScore=8.5806;InbreedingCoeff=-0.1820;MQ=37.89;MQ0=0;QD=98.77;EFF=DOWNSTREAM(MODIFIER||||681|SAMD11|protein_coding|CODING|ENST00000342066|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000496938|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000455979||||-/541|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000496938|||||processed_transcript|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000342066||||-/681|protein_coding|1,intron_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000187634|SAMD11|ENST00000341065||||-/589|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:1,2:3:6.02:283,6,0 1/1:1,1:2:3.01:58,3,0 1/1:0,1:1:3.01:142,3,0 1/1:0,0:1:3.01:71,3,0 1/1:0,1:1:3.01:142,3,0 1/1:0,1:1:3.01:106,3,0 ./. ./. ./. ./. 1/1:0,0:1:3.01:99,3,0 ./. ./. ./. ./. ./. ./. 1/1:1,3:4:9.03:385,9,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:142,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:142,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:142,3,0 ./. ./. 1/1:0,0:1:3.01:71,3,0 ./. ./. ./. ./. ./. ./. ./. 1/1:1,0:1:3.01:102,3,0 1/1:0,1:1:3.01:142,3,0 ./. -chr1 886006 . T C 1030.61 . AC=32;AF=1.000;AN=32;DP=31;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=-0.1369;MQ=49.82;MQ0=0;QD=33.25;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,5:5:15.04:187,15,0 1/1:0,2:2:6.02:75,6,0 1/1:0,2:2:6.02:81,6,0 1/1:0,3:3:9.03:115,9,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:6.02:81,6,0 ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:45,3,0 1/1:0,1:1:3.01:36,3,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. 1/1:0,2:2:6.02:72,6,0 ./. 1/1:0,2:2:6.02:75,6,0 ./. 1/1:0,2:2:6.02:67,6,0 1/1:0,3:3:6.02:73,6,0 ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. 1/1:0,1:1:3.01:33,3,0 -chr1 886049 . ACAG A 1495.02 . AC=34;AF=0.944;AN=36;BaseQRankSum=1.722;DP=33;FS=2.691;HRun=0;HaplotypeScore=10.4318;InbreedingCoeff=0.1010;MQ=41.07;MQ0=0;MQRankSum=-2.098;QD=49.83;ReadPosRankSum=0.344;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3.01:42,3,0 1/1:0,7:8:24.08:433,24,0 1/1:0,5:5:15.05:237,15,0 ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:56,3,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:56,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:56,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:6.02:112,6,0 ./. ./. 1/1:0,1:1:3.01:56,3,0 ./. ./. 1/1:0,1:1:3.01:56,3,0 ./. 1/1:0,1:1:3.01:31,3,0 1/1:0,1:1:3.01:56,3,0 0/0:3,0:3:9.03:0,9,196 1/1:0,1:1:3.01:56,3,0 1/1:0,1:1:3.01:42,3,0 1/1:0,2:2:6.02:112,6,0 1/1:0,1:1:3.01:56,3,0 ./. ./. 1/1:0,1:1:3.01:53,3,0 ./. 1/1:0,1:1:3.01:56,3,0 -chr1 886179 . CA C 1612.0 . AC=47;AF=0.870;AN=54;BaseQRankSum=3.364;DP=49;FS=8.293;HRun=1;HaplotypeScore=18.7687;InbreedingCoeff=0.1732;MQ=36.71;MQ0=0;MQRankSum=-3.123;QD=36.64;ReadPosRankSum=0.259;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:1,4:5:12.04:167,12,0 1/1:0,5:5:15.04:193,15,0 1/1:0,4:4:12.03:153,12,0 ./. 1/1:1,2:3:9.03:114,9,0 1/1:1,2:3:9.03:126,9,0 ./. ./. 1/1:0,2:2:6.02:84,6,0 0/0:1,0:1:3.01:0,3,48 ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. 1/1:0,2:2:6.02:84,6,0 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 1/1:0,1:1:3.01:42,3,0 ./. ./. 1/1:0,1:1:3.01:42,3,0 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,2:2:6.02:84,6,0 0/0:1,0:1:3.01:0,3,48 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. 1/1:0,2:2:6.02:83,6,0 1/1:0,1:1:3.01:42,3,0 0/0:2,0:2:6.02:0,6,96 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. 0/1:1,1:2:35.97:36,0,42 ./. ./. ./. -chr1 886182 . TG T 1532.98 . AC=47;AF=0.870;AN=54;BaseQRankSum=3.246;DP=46;FS=5.278;HRun=1;HaplotypeScore=18.4565;InbreedingCoeff=0.1421;MQ=34.65;MQ0=0;MQRankSum=-2.960;QD=36.50;ReadPosRankSum=0.184;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:1,4:5:12.04:161,12,0 1/1:0,5:5:15.03:190,15,0 1/1:0,4:4:12.03:153,12,0 ./. 1/1:0,2:2:6.02:83,6,0 1/1:0,2:2:6.02:84,6,0 ./. ./. 1/1:0,2:2:6.02:84,6,0 0/0:1,0:1:3.01:0,3,48 ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. 1/1:0,2:2:6.02:84,6,0 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 1/1:0,1:1:3.01:42,3,0 ./. ./. 1/1:0,1:1:3.01:42,3,0 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,2:2:6.02:84,6,0 0/0:1,0:1:3.01:0,3,48 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. 1/1:0,2:2:6.02:83,6,0 1/1:0,1:1:3.01:42,3,0 0/0:1,0:1:3.01:0,3,48 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. 0/1:1,1:2:35.97:36,0,42 ./. ./. ./. -chr1 886186 . C CAG 2268.91 . AC=57;AF=0.891;AN=64;BaseQRankSum=3.232;DP=55;FS=6.052;HRun=0;HaplotypeScore=17.8027;InbreedingCoeff=0.1016;MQ=34.53;MQ0=0;MQRankSum=-3.122;QD=44.49;ReadPosRankSum=0.055;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:3,2:5:9.02:137,9,0 1/1:2,3:6:15.02:199,15,0 1/1:2,3:5:12.04:225,12,0 ./. 1/1:0,2:2:6.02:112,6,0 1/1:2,1:3:9.03:151,9,0 ./. ./. 1/1:1,1:2:3.01:32,3,0 0/0:1,0:1:3.01:0,3,31 ./. 1/1:1,0:1:3.01:56,3,0 1/1:0,1:1:3.01:56,3,0 ./. 1/1:0,1:1:3.01:56,3,0 ./. ./. 1/1:1,0:1:3.01:56,3,0 1/1:0,2:2:6.02:112,6,0 1/1:0,1:1:3.01:56,3,0 ./. 1/1:0,1:1:3.01:56,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:56,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:56,3,0 1/1:0,1:1:3.01:56,3,0 ./. ./. 1/1:0,1:1:3.01:56,3,0 1/1:0,1:1:3.01:56,3,0 ./. 1/1:0,1:1:3.01:56,3,0 ./. 1/1:0,2:2:6.02:112,6,0 0/0:1,0:1:3.01:0,3,44 1/1:0,1:1:3.01:56,3,0 1/1:0,1:1:3.01:56,3,0 1/1:0,1:1:3.01:56,3,0 ./. ./. ./. 1/1:0,2:2:6.02:112,6,0 1/1:1,1:2:6.02:112,6,0 0/0:1,0:1:3.01:0,3,44 ./. 1/1:0,1:1:3.01:56,3,0 ./. 1/1:1,0:1:3.01:57,3,0 ./. 0/1:1,1:2:38.18:50,0,38 ./. ./. 1/1:1,0:1:3.01:56,3,0 -chr1 886384 . G A 434.04 . AC=4;AF=0.0333;AN=120;BaseQRankSum=0.231;DP=475;Dels=0.00;FS=8.266;HRun=0;HaplotypeScore=0.2516;InbreedingCoeff=-0.0534;MQ=58.22;MQ0=0;MQRankSum=1.803;QD=11.42;ReadPosRankSum=-0.069;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:8,0:8:24.07:0,24,293 0/0:3,0:3:6.02:0,6,80 0/0:11,0:11:33.10:0,33,422 0/0:4,0:4:12.03:0,12,137 0/0:5,0:5:15.05:0,15,196 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,82 0/0:2,0:2:6.02:0,6,69 0/0:8,0:8:24.08:0,24,316 0/0:3,0:3:9.03:0,9,124 0/0:6,0:6:15.05:0,15,202 0/0:4,0:4:12.04:0,12,150 0/0:5,0:5:15.05:0,15,187 0/0:12,0:12:27.09:0,27,370 0/0:8,0:8:24.08:0,24,323 0/0:6,0:6:15.04:0,15,185 0/0:7,0:7:18.06:0,18,243 0/0:8,0:8:21.05:0,21,251 0/0:10,0:10:30.09:0,30,382 0/0:6,0:6:12.04:0,12,169 0/0:2,0:2:6.02:0,6,79 0/0:14,0:14:42.13:0,42,543 0/0:10,0:10:24.08:0,24,328 0/0:7,0:7:21.05:0,21,265 0/0:10,0:10:27.08:0,27,353 0/0:8,0:9:24.07:0,24,307 0/0:8,0:8:21.07:0,21,275 0/0:8,0:8:24.08:0,24,326 0/0:12,0:12:36.12:0,36,476 0/0:14,0:14:33.11:0,33,428 0/0:13,0:13:36.11:0,36,466 0/0:13,0:13:33.10:0,33,430 0/1:8,3:11:90.41:90,0,239 0/1:6,9:15:99:313,0,167 0/0:8,0:8:24.08:0,24,312 0/0:8,0:8:21.06:0,21,268 0/0:13,0:13:36.11:0,36,475 0/0:13,0:13:39.12:0,39,511 0/0:5,0:5:12.04:0,12,160 0/0:15,0:15:42.13:0,42,528 0/0:11,0:11:30.09:0,30,379 0/0:8,0:8:24.08:0,24,309 0/0:4,0:4:12.04:0,12,155 0/0:6,0:6:18.06:0,18,232 0/1:3,1:4:26.54:27,0,112 0/0:5,0:5:15.05:0,15,200 0/0:12,0:12:36.12:0,36,473 0/0:4,0:4:12.03:0,12,145 0/0:8,0:8:24.08:0,24,308 0/1:5,3:8:96.27:96,0,171 0/0:14,0:14:39.11:0,39,501 0/0:5,0:5:12.04:0,12,140 0/0:10,0:10:24.08:0,24,318 0/0:9,0:9:27.09:0,27,358 0/0:6,0:6:18.06:0,18,234 0/0:10,0:10:27.09:0,27,371 0/0:3,0:3:9.03:0,9,117 0/0:8,0:8:24.08:0,24,322 0/0:7,0:7:18.06:0,18,245 0/0:6,0:6:18.06:0,18,225 -chr1 886409 . G C 225.93 . AC=4;AF=0.0333;AN=120;BaseQRankSum=-0.047;DP=629;Dels=0.00;FS=1.803;HRun=2;HaplotypeScore=0.3393;InbreedingCoeff=-0.0500;MQ=58.47;MQ0=0;MQRankSum=0.500;QD=5.79;ReadPosRankSum=-0.845;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:5,0:5:9.03:0,9,114 0/0:2,0:2:3.01:0,3,33 0/0:9,0:9:27.09:0,27,347 0/0:3,0:3:9.03:0,9,107 0/0:2,0:2:6.02:0,6,73 0/0:4,0:4:12.04:0,12,152 0/1:2,3:5:65.50:106,0,65 0/0:2,0:2:6.02:0,6,71 0/0:6,0:6:18.06:0,18,239 0/0:4,0:4:12.04:0,12,164 0/0:7,0:7:18.04:0,18,217 0/0:3,0:3:9.03:0,9,109 0/1:1,3:4:29.55:64,0,30 0/0:13,0:13:33.11:0,33,437 0/0:14,0:14:39.13:0,39,528 0/0:10,0:10:24.08:0,24,308 0/0:9,0:9:24.08:0,24,315 0/1:7,5:12:76.06:76,0,236 0/0:19,0:19:57.18:0,57,732 0/0:9,0:9:21.07:0,21,290 0/0:4,0:4:12.04:0,12,167 0/0:14,0:14:42.13:0,42,529 0/0:15,0:15:39.13:0,39,524 0/0:9,0:9:24.08:0,24,309 0/0:16,0:16:48.15:0,48,611 0/0:11,0:11:24.08:0,24,313 0/0:9,0:9:27.08:0,27,346 0/0:12,0:12:30.10:0,30,411 0/0:20,0:20:48.15:0,48,623 0/0:14,0:14:36.11:0,36,462 0/0:16,0:16:39.13:0,39,514 0/0:12,1:13:33.09:0,33,403 0/0:18,0:18:51.16:0,51,656 0/0:20,0:20:54.16:0,54,703 0/0:13,0:13:39.08:0,39,461 0/0:11,0:11:30.10:0,30,398 0/0:21,0:21:63.19:0,63,796 0/0:19,0:19:51.15:0,51,645 0/0:4,0:4:9.03:0,9,123 0/0:17,0:17:51.15:0,51,634 0/0:11,0:11:24.08:0,24,311 0/0:14,0:14:42.13:0,42,529 0/0:8,0:8:21.06:0,21,265 0/0:9,0:9:24.07:0,24,301 0/0:11,0:11:27.08:0,27,352 0/0:7,0:7:21.07:0,21,272 0/1:15,3:18:73.10:73,0,463 0/0:7,0:7:18.06:0,18,242 0/0:11,0:12:30.09:0,30,382 0/0:13,0:13:30.09:0,30,386 0/0:14,0:14:36.12:0,36,472 0/0:5,0:5:15.04:0,15,178 0/0:19,0:19:45.14:0,45,590 0/0:14,0:14:36.11:0,36,461 0/0:11,0:11:33.11:0,33,435 0/0:10,0:10:30.10:0,30,378 0/0:2,0:2:6.02:0,6,81 0/0:14,0:14:39.13:0,39,516 0/0:7,0:7:18.06:0,18,232 0/0:5,0:5:12.03:0,12,152 -chr1 886477 . G A 1109.56 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.561;DP=1412;Dels=0.00;FS=5.360;HRun=0;HaplotypeScore=1.3637;InbreedingCoeff=-0.0325;MQ=58.75;MQ0=0;MQRankSum=0.602;QD=11.56;ReadPosRankSum=-1.213;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:6,0:6:15.02:0,15,167 0/0:9,0:9:24.07:0,24,300 0/0:5,0:5:15.05:0,15,190 0/0:4,0:4:9.03:0,9,118 0/0:2,0:2:6.02:0,6,81 0/0:6,0:6:18.06:0,18,239 0/0:7,0:7:21.07:0,21,267 0/0:2,0:2:6.02:0,6,73 0/0:9,0:9:27.09:0,27,356 0/0:10,0:10:27.09:0,27,359 0/0:5,0:5:15.05:0,15,198 0/0:3,0:3:9.03:0,9,107 0/0:7,0:7:18.06:0,18,228 0/0:29,0:29:75.24:0,75,999 0/0:37,0:37:93.30:0,93,1235 0/0:19,0:19:48.16:0,48,644 0/0:23,0:23:60.19:0,60,797 0/0:35,0:36:90.29:0,90,1183 0/0:41,0:41:99:0,102,1332 0/0:26,0:26:69.23:0,69,924 0/1:17,11:28:99:295,0,508 0/0:35,0:35:81.25:0,81,1063 0/0:37,0:37:90.28:0,90,1166 0/0:34,0:34:81.23:0,81,1054 0/0:32,0:33:84.27:0,84,1109 0/0:22,0:22:54.17:0,54,710 0/1:11,15:26:99:482,0,267 0/0:22,0:22:63.17:0,63,804 0/0:40,0:40:93.30:0,93,1244 0/0:37,0:37:93.30:0,93,1233 0/0:45,0:45:99:0,108,1410 0/0:33,0:34:69.22:0,69,930 0/0:38,0:38:96.30:0,96,1242 0/1:26,16:42:99:413,0,716 0/0:25,0:25:60.20:0,60,817 0/0:37,0:37:90.27:0,90,1189 0/0:45,0:45:99:0,99,1292 0/0:51,0:51:99:0,135,1758 0/0:13,0:13:33.11:0,33,439 0/0:23,0:23:63.20:0,63,821 0/0:24,0:24:60.19:0,60,766 0/0:23,0:23:54.15:0,54,674 0/0:19,0:19:51.16:0,51,669 0/0:14,0:14:36.11:0,36,443 0/0:23,0:23:45.14:0,45,588 0/0:14,0:14:36.12:0,36,470 0/0:44,0:44:99:0,99,1319 0/0:11,0:11:27.08:0,27,337 0/0:26,0:26:51.15:0,51,678 0/0:46,0:46:99:0,114,1465 0/0:30,1:31:46:0,46,1000 0/0:18,0:18:51.16:0,51,640 0/0:33,0:33:84.25:0,84,1079 0/0:27,0:27:60.17:0,60,770 0/0:27,0:27:66.20:0,66,853 0/0:15,0:15:42.13:0,42,535 0/0:9,0:9:21.07:0,21,274 0/0:22,1:23:22.83:0,23,688 0/0:12,0:12:36.10:0,36,455 0/0:20,0:20:42.11:0,42,526 -chr1 886492 . C T 237.45 . AC=2;AF=0.0167;AN=120;BaseQRankSum=0.074;DP=1595;Dels=0.00;FS=5.466;HRun=0;HaplotypeScore=0.8808;InbreedingCoeff=0.7925;MQ=58.78;MQ0=0;MQRankSum=0.397;QD=21.59;ReadPosRankSum=-0.482;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|12),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|10),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.05:0,15,186 0/0:7,0:7:15.05:0,15,186 0/0:5,0:5:12.03:0,12,143 0/0:4,0:4:12.03:0,12,146 0/0:7,0:7:21.07:0,21,286 0/0:5,0:5:12.04:0,12,164 0/0:7,0:7:21.06:0,21,269 0/0:2,0:2:6.02:0,6,77 0/0:7,0:7:21.07:0,21,285 0/0:7,0:7:21.07:0,21,282 0/0:8,0:8:24.08:0,24,311 0/0:6,0:6:18.06:0,18,242 0/0:8,0:8:21.05:0,21,250 0/0:35,0:35:87.27:0,87,1153 0/0:43,0:43:99:0,99,1319 0/0:26,0:26:57.18:0,57,761 0/0:25,0:25:69.21:0,69,894 0/0:42,0:42:96.29:0,96,1242 0/0:45,1:46:99:0,117,1546 0/0:27,0:27:72.23:0,72,946 0/0:28,0:28:66.22:0,66,910 0/0:45,0:45:99:0,105,1373 0/0:40,0:40:99:0,99,1304 0/0:35,0:35:87.27:0,87,1139 0/0:46,0:46:99:0,102,1371 0/0:31,0:31:75.22:0,75,970 0/0:29,0:29:72.21:0,72,950 0/0:26,0:26:69.22:0,69,905 0/0:42,0:42:99:0,99,1352 0/0:39,0:39:99:0,99,1311 0/0:47,0:47:99:0,105,1372 0/0:37,0:37:90.29:0,90,1191 0/0:43,0:43:99:0,102,1354 0/0:51,0:51:99:0,117,1504 0/0:30,0:30:78.25:0,78,1017 0/0:39,0:39:93.29:0,93,1248 0/0:52,0:52:99:0,105,1402 0/0:59,0:59:99:0,144,1939 0/0:15,0:15:42.13:0,42,538 0/0:31,0:31:78.25:0,78,1022 0/0:28,0:28:72.22:0,72,904 0/0:24,0:24:63.20:0,63,812 0/0:19,0:19:54.17:0,54,698 0/0:18,0:18:45.14:0,45,587 0/0:23,0:23:45.13:0,45,574 0/0:16,0:16:42.13:0,42,540 0/0:44,0:44:99:0,105,1377 1/1:0,11:11:24.08:306,24,0 0/0:26,0:26:60.15:0,60,763 0/0:55,0:55:99:0,132,1742 0/0:31,0:31:81.25:0,81,1057 0/0:24,0:24:60.18:0,60,746 0/0:32,0:32:75.22:0,75,944 0/0:34,0:34:78.24:0,78,1013 0/0:27,0:27:66.20:0,66,860 0/0:20,0:20:54.17:0,54,700 0/0:10,0:10:21.07:0,21,284 0/0:33,0:33:78.22:0,78,1030 0/0:12,0:12:33.08:0,33,413 0/0:21,0:21:51.15:0,51,654 -chr1 886653 . G A 558.63 . AC=2;AF=0.0169;AN=118;BaseQRankSum=1.368;DP=1520;Dels=0.00;FS=21.500;HRun=0;HaplotypeScore=1.1951;InbreedingCoeff=-0.0285;MQ=58.36;MQ0=0;MQRankSum=0.809;QD=15.52;ReadPosRankSum=-1.905;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|11),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|9),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.03:0,12,142 0/0:9,0:9:21.05:0,21,243 0/0:4,0:4:12.03:0,12,141 0/0:2,0:2:6.02:0,6,74 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,76 0/0:10,0:10:30.10:0,30,398 0/0:2,0:2:3.01:0,3,41 0/1:5,5:10:99:133,0,167 0/0:8,0:8:24.08:0,24,320 0/0:5,0:5:12.04:0,12,156 ./. 0/0:6,0:6:18.03:0,18,220 0/0:29,0:29:78.24:0,78,1004 0/0:34,0:34:75.20:0,75,956 0/0:25,0:25:66.20:0,66,844 0/0:35,0:35:81.21:0,81,1004 0/0:33,0:33:84.20:0,84,1037 0/0:28,0:28:60.18:0,60,781 0/0:30,0:30:72.22:0,72,932 0/0:28,1:29:66.20:0,66,856 0/0:33,0:33:72.22:0,72,920 0/0:30,0:32:75.24:0,75,971 0/0:27,0:27:63.19:0,63,823 0/0:29,0:29:75.21:0,75,948 0/0:27,0:27:63.20:0,63,823 0/0:32,0:32:78.25:0,78,1034 0/0:30,1:31:29.22:0,29,839 0/0:36,0:36:87.26:0,87,1120 0/0:28,0:28:63.20:0,63,820 0/0:41,0:41:99:0,102,1294 0/1:11,15:26:99:490,0,343 0/0:34,0:34:81.22:0,81,1017 0/0:42,0:42:99:0,105,1348 0/0:33,0:33:81.24:0,81,1034 0/0:30,0:30:69.21:0,69,896 0/0:41,0:41:99:0,102,1338 0/0:66,0:66:99:0,141,1839 0/0:14,0:14:33.10:0,33,411 0/0:36,0:36:81.24:0,81,1031 0/0:29,0:29:69.18:0,69,868 0/0:30,0:30:66.17:0,66,834 0/0:21,0:21:48.14:0,48,594 0/0:21,0:21:51.16:0,51,674 0/0:28,0:28:60.16:0,60,758 0/0:16,0:16:39.12:0,39,486 0/0:44,0:44:99:0,105,1313 0/0:26,0:26:57.18:0,57,744 0/0:21,0:21:51.15:0,51,650 0/0:59,0:59:99:0,144,1767 0/0:44,0:44:99:0,102,1288 0/0:38,0:38:78.24:0,78,1005 0/0:41,0:41:99:0,102,1226 0/0:18,0:18:39.12:0,39,497 0/0:24,1:25:69.20:0,69,860 0/0:26,0:26:48.12:0,48,619 0/0:17,0:17:39.12:0,39,496 0/0:22,0:22:48.12:0,48,617 0/0:21,0:22:54.17:0,54,703 0/0:27,0:28:60.16:0,60,748 -chr1 886788 . G A 9988.89 . AC=98;AF=0.8305;AN=118;BaseQRankSum=-1.367;DP=334;Dels=0.00;FS=18.012;HRun=1;HaplotypeScore=0.1988;InbreedingCoeff=0.2452;MQ=57.31;MQ0=0;MQRankSum=4.299;QD=32.86;ReadPosRankSum=-0.071;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|11),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|9),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,2:2:6.02:73,6,0 1/1:0,4:4:9.03:112,9,0 1/1:0,6:6:18.06:235,18,0 1/1:0,1:1:3.01:39,3,0 1/1:0,3:3:9.03:118,9,0 1/1:0,3:3:9.03:123,9,0 1/1:0,1:1:3.01:41,3,0 0/1:2,1:3:32.20:32,0,73 1/1:0,6:6:18.06:237,18,0 0/1:3,1:4:29.19:29,0,110 1/1:0,2:2:6.02:82,6,0 ./. 1/1:0,1:1:3.01:39,3,0 1/1:0,2:2:6.02:84,6,0 1/1:0,4:4:12.04:160,12,0 1/1:0,4:4:12.03:135,12,0 1/1:0,8:8:24.08:314,24,0 1/1:0,10:10:30.10:401,30,0 1/1:0,16:16:39.13:536,39,0 1/1:0,11:11:30.10:397,30,0 0/1:1,6:7:19.58:216,0,20 1/1:0,6:6:18.06:238,18,0 0/1:1,1:2:34.63:35,0,36 1/1:0,13:13:33.11:438,33,0 1/1:0,6:6:15.05:203,15,0 1/1:0,2:2:6.02:67,6,0 0/0:7,0:7:21.07:0,21,269 1/1:0,5:5:15.05:190,15,0 1/1:0,7:7:21.07:285,21,0 1/1:0,7:7:21.05:266,21,0 1/1:0,4:4:12.04:160,12,0 1/1:0,6:6:15.04:194,15,0 0/1:6,2:8:43.38:43,0,207 0/0:10,0:10:30.09:0,30,360 0/1:1,3:4:30.19:106,0,30 1/1:0,2:2:6.02:75,6,0 0/1:1,4:5:22.75:144,0,23 1/1:0,14:14:39.12:519,39,0 1/1:0,2:2:6.02:76,6,0 1/1:0,7:7:18.06:232,18,0 1/1:0,6:6:18.06:236,18,0 0/0:4,0:4:12.04:0,12,148 1/1:0,5:5:15.04:179,15,0 1/1:0,1:1:3.01:42,3,0 0/1:2,2:4:60.71:68,0,61 1/1:0,4:4:12.04:151,12,0 1/1:0,5:5:15.05:197,15,0 0/0:6,0:6:15.05:0,15,191 1/1:0,6:6:15.05:200,15,0 0/1:5,5:10:99:151,0,124 0/1:6,9:15:99:284,0,163 1/1:0,11:11:33.10:421,33,0 1/1:0,15:15:42.13:526,42,0 1/1:0,4:4:9.03:123,9,0 1/1:0,4:4:12.04:148,12,0 1/1:0,4:4:12.03:146,12,0 0/0:3,0:3:6.02:0,6,76 1/1:0,2:2:6.02:75,6,0 1/1:0,8:8:21.07:286,21,0 1/1:0,2:2:6.02:81,6,0 -chr1 886817 . C T 6332.01 . AC=90;AF=0.8182;AN=110;BaseQRankSum=-1.237;DP=216;Dels=0.00;FS=12.660;HRun=3;HaplotypeScore=0.3611;InbreedingCoeff=0.1623;MQ=57.12;MQ0=0;MQRankSum=2.897;QD=31.50;ReadPosRankSum=0.605;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|11),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|9),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,3:3:9.03:113,9,0 1/1:0,6:6:18.05:220,18,0 1/1:0,6:6:18.06:233,18,0 1/1:0,1:1:3.01:38,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:82,6,0 0/0:1,0:1:3.01:0,3,41 1/1:0,2:2:6.02:82,6,0 0/1:3,1:4:21.40:21,0,110 1/1:0,2:2:6.02:82,6,0 ./. ./. 1/1:0,2:2:6.02:78,6,0 1/1:0,4:4:9.03:125,9,0 1/1:0,2:2:6.02:72,6,0 1/1:0,4:4:12.03:145,12,0 1/1:0,8:8:21.07:277,21,0 1/1:0,8:8:24.08:317,24,0 0/1:1,7:8:13.29:220,0,13 0/1:1,4:5:23.21:110,0,23 1/1:0,4:4:12.04:163,12,0 ./. 1/1:0,7:7:21.06:267,21,0 1/1:0,5:5:12.04:161,12,0 1/1:0,3:3:9.03:118,9,0 0/1:6,1:7:12.37:12,0,205 1/1:0,3:3:9.03:107,9,0 1/1:0,4:4:12.04:154,12,0 1/1:0,8:8:18.05:234,18,0 1/1:0,4:4:12.04:166,12,0 1/1:0,3:3:9.03:124,9,0 0/1:2,3:5:51.83:92,0,52 0/0:4,0:4:12.03:0,12,134 0/1:1,1:2:33.99:34,0,35 1/1:0,2:2:6.02:78,6,0 0/1:1,1:2:32.56:35,0,33 1/1:0,11:11:30.10:409,30,0 1/1:0,4:4:12.04:148,12,0 1/1:0,4:4:12.04:145,12,0 1/1:0,3:3:9.03:123,9,0 0/0:3,0:3:9.03:0,9,109 1/1:0,2:2:3.01:33,3,0 ./. 0/1:2,1:3:27.10:27,0,59 1/1:0,2:2:6.02:76,6,0 1/1:0,3:3:9.03:124,9,0 0/0:5,0:5:12.04:0,12,150 1/1:0,3:3:9.01:105,9,0 0/1:2,2:4:54.83:58,0,55 0/1:4,2:7:64.35:64,0,142 1/1:0,8:8:24.08:309,24,0 1/1:0,7:7:18.06:232,18,0 1/1:0,3:3:9.03:119,9,0 1/1:0,3:3:9.02:102,9,0 1/1:0,1:1:3.01:37,3,0 0/0:2,0:2:3.01:0,3,41 1/1:0,2:2:6.02:73,6,0 1/1:0,3:3:9.02:107,9,0 ./. -chr1 886817 . C CATTTT 1195.05 . AC=14;AF=0.1296;AN=108;BaseQRankSum=-6.408;DP=215;FS=1.303;HRun=0;HaplotypeScore=40.0482;InbreedingCoeff=0.0654;MQ=57.03;MQ0=0;MQRankSum=-3.623;QD=23.43;ReadPosRankSum=-3.297;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|11),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|9),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/1:3,0:3:21.87:61,0,22 0/1:8,0:8:15.21:15,0,146 0/0:7,0:7:14.27:0,14,136 0/0:1,0:1:3:0,3,29 1/1:1,0:1:0.89:2,1,0 0/0:1,0:1:3:0,3,25 0/0:2,0:2:5.99:0,6,49 ./. 0/0:2,0:2:2.99:0,3,24 0/0:4,0:4:12.02:0,12,225 0/0:2,0:2:5.99:0,6,49 ./. ./. 0/0:2,0:2:6:0,6,54 0/0:4,0:4:11.98:0,12,126 0/0:1,0:1:3:0,3,27 0/0:4,0:4:12.01:0,12,121 0/0:8,0:8:17.94:0,18,151 0/0:7,0:7:20.98:0,21,179 0/0:8,0:8:20.58:0,21,224 0/0:4,0:4:11.99:0,12,105 0/0:4,0:4:11.98:0,12,99 ./. 0/1:7,0:7:12.35:12,0,147 0/0:5,0:5:11.97:0,12,101 0/0:3,0:3:6:0,6,52 0/1:5,2:7:99:238,0,240 0/0:3,0:3:9.01:0,9,93 0/0:4,0:4:12:0,12,107 0/1:8,0:8:30.32:30,0,124 0/0:4,0:4:11.96:0,12,94 0/0:3,0:3:8.98:0,9,72 0/1:4,1:5:44.95:249,0,45 1/1:1,3:4:12.04:388,12,0 0/0:2,0:2:6.01:0,6,93 0/0:2,0:2:6:0,6,54 0/0:2,0:2:6.01:0,6,92 0/0:11,0:11:32.97:0,33,284 0/0:4,0:4:12.02:0,12,120 0/0:4,0:4:12.01:0,12,121 0/0:3,0:3:8.97:0,9,73 0/0:3,0:3:9.03:0,9,165 0/0:2,0:2:3.01:0,3,34 ./. 0/1:2,1:3:21.95:144,0,22 0/0:2,0:2:6:0,6,56 0/0:3,0:3:8.97:0,9,71 0/0:5,0:5:15.05:0,15,334 0/0:3,0:3:9:0,9,93 0/1:2,2:4:51.96:182,0,52 0/0:7,0:7:21.03:0,21,345 0/0:8,0:8:23.97:0,24,210 0/0:7,0:7:14.80:0,15,136 0/0:3,0:3:8.99:0,9,78 0/0:3,0:3:9.01:0,9,92 1/1:1,0:1:3.01:32,3,0 0/0:2,0:2:3.01:0,3,67 0/0:2,0:2:5.99:0,6,49 0/0:3,0:3:9:0,9,92 ./. -chr1 887162 . T C 158.95 . AC=3;AF=0.0273;AN=110;BaseQRankSum=0.867;DP=242;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1059;InbreedingCoeff=-0.1008;MQ=57.95;MQ0=0;MQRankSum=1.543;QD=10.60;ReadPosRankSum=-1.064;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|11),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|9),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:6,0:6:15.05:0,15,186 0/0:12,0:12:24.05:0,24,288 0/0:6,0:7:15.05:0,15,189 0/0:5,0:5:15.05:0,15,194 0/0:6,0:6:18.05:0,18,224 0/0:11,0:11:27.09:0,27,355 0/0:4,0:4:12.04:0,12,163 0/0:8,0:8:21.06:0,21,257 0/0:9,0:9:27.09:0,27,365 0/0:9,0:9:21.06:0,21,264 0/0:8,0:8:21.06:0,21,266 0/0:6,0:6:15.05:0,15,196 0/0:10,0:10:27.09:0,27,359 0/0:6,0:6:18.04:0,18,223 0/0:3,0:3:6.02:0,6,73 0/0:2,0:2:3.01:0,3,42 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.02:0,6,80 0/0:4,0:4:12.01:0,12,126 ./. 0/1:2,3:5:67.52:68,0,70 0/0:4,0:4:9.03:0,9,119 0/0:2,0:2:3.01:0,3,42 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/1:3,2:5:61.94:62,0,98 0/0:1,0:1:3.01:0,3,35 0/0:2,0:2:6.02:0,6,69 0/0:2,0:2:3.01:0,3,37 0/0:4,0:5:9.03:0,9,120 0/0:1,0:1:3.01:0,3,32 0/0:3,0:3:6.02:0,6,72 0/1:2,3:5:61.32:106,0,61 0/0:3,0:3:9.03:0,9,116 ./. 0/0:6,0:6:15.05:0,15,190 0/0:4,0:4:12.04:0,12,160 0/0:3,0:3:9.03:0,9,106 0/0:7,0:7:21.06:0,21,262 0/0:6,0:6:15.05:0,15,189 0/0:3,0:3:9.03:0,9,117 0/0:6,0:6:15.05:0,15,185 0/0:3,0:3:6.02:0,6,71 0/0:2,0:2:6.02:0,6,78 0/0:3,0:3:9.03:0,9,125 0/0:3,0:3:9.03:0,9,111 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,31 0/0:5,0:5:15.05:0,15,188 0/0:7,0:7:12.03:0,12,147 0/0:7,0:7:18.06:0,18,226 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:3:0,3,29 0/0:2,0:2:6.02:0,6,75 0/0:2,0:2:6.02:0,6,75 0/0:3,0:3:9.01:0,9,99 0/0:2,0:2:3.01:0,3,42 0/0:3,0:3:6.02:0,6,77 ./. -chr1 887265 . C A 101.07 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.874;DP=895;Dels=0.00;FS=2.947;HRun=0;HaplotypeScore=0.4283;InbreedingCoeff=-0.0106;MQ=59.14;MQ0=0;MQRankSum=2.148;QD=6.74;ReadPosRankSum=-0.250;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|11),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|9),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000483767|);CSQ=upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000483767|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:11,0:11:30.07:0,30,337 0/0:14,0:14:42.13:0,42,522 0/0:18,0:18:51.16:0,51,642 0/0:11,0:12:30.09:0,30,379 0/0:21,0:21:63.20:0,63,820 0/0:24,1:26:34.01:0,34,898 0/0:38,0:38:99:0,111,1480 0/0:19,0:19:57.19:0,57,764 0/0:42,0:42:99:0,126,1688 0/0:45,1:46:99:0,132,1722 0/0:24,0:24:69.22:0,69,899 0/0:30,0:30:84.27:0,84,1105 0/0:23,0:23:69.22:0,69,899 0/0:11,0:11:33.09:0,33,424 0/0:15,0:15:42.14:0,42,556 0/0:7,0:7:18.06:0,18,248 0/0:7,0:7:21.07:0,21,287 0/0:9,0:9:24.07:0,24,299 0/0:7,0:7:18.06:0,18,242 0/0:10,0:10:30.10:0,30,401 0/0:11,0:11:30.10:0,30,391 0/0:10,0:10:30.10:0,30,396 0/0:9,0:9:27.09:0,27,369 0/0:7,0:7:21.07:0,21,276 0/0:11,0:11:33.11:0,33,442 0/0:12,0:12:30.09:0,30,386 0/0:5,0:5:12.04:0,12,163 0/0:12,0:12:30.10:0,30,389 0/0:7,0:7:21.07:0,21,270 0/0:17,0:17:42.14:0,42,564 0/0:15,0:15:39.13:0,39,538 0/0:9,0:9:24.08:0,24,318 0/0:7,0:7:18.06:0,18,244 0/0:16,0:16:45.15:0,45,594 0/0:6,0:6:18.05:0,18,227 0/0:9,0:9:27.09:0,27,354 0/0:17,0:17:51.16:0,51,662 0/0:15,0:15:42.14:0,42,569 0/1:9,6:15:99:149,0,236 0/0:14,0:14:39.11:0,39,493 0/0:12,0:12:27.09:0,27,362 0/0:8,0:8:21.07:0,21,276 0/0:13,0:13:33.11:0,33,430 0/0:11,0:11:27.09:0,27,368 0/0:9,0:9:21.07:0,21,278 0/0:11,0:11:27.09:0,27,353 0/0:31,0:31:66.21:0,66,886 0/0:9,0:9:24.08:0,24,313 0/0:12,0:12:30.10:0,30,400 0/0:30,0:30:78.24:0,78,1028 0/0:17,0:17:48.15:0,48,611 0/0:15,0:15:33.10:0,33,419 0/0:18,0:19:39.12:0,39,514 0/0:20,0:20:60.18:0,60,767 0/0:15,0:15:36.12:0,36,489 0/0:13,0:13:30.10:0,30,406 0/0:12,0:13:30.07:0,30,373 0/0:5,0:5:15.04:0,15,177 0/0:11,0:11:27.09:0,27,369 0/0:6,0:6:15.05:0,15,198 -chr1 887471 . G A 581.35 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.013;DP=3085;Dels=0.00;FS=3.856;HRun=1;HaplotypeScore=1.5844;InbreedingCoeff=-0.0084;MQ=59.14;MQ0=0;MQRankSum=3.944;QD=12.92;ReadPosRankSum=0.093;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|9),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L414|749|NOC2L|protein_coding|CODING|ENST00000327044|);CSQ=synonymous_variant|Ctg/Ttg|L|ENSG00000188976|NOC2L|ENST00000327044|11/19|||414/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|9/17||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:20,0:20:45.14:0,45,577 0/0:29,0:29:84.26:0,84,1047 0/0:32,0:32:93.30:0,93,1209 0/0:32,0:32:90.29:0,90,1165 0/0:59,0:59:99:0,175,2336 0/0:62,0:62:99:0,187,2510 0/0:87,0:87:99:0,259,3449 0/0:51,0:51:99:0,150,1981 0/0:96,0:96:99:0,283,3803 0/0:117,1:118:99:0,309,4599 0/0:70,0:70:99:0,208,2758 0/0:62,0:62:99:0,187,2452 0/0:83,1:84:99:0,247,3231 0/0:60,0:60:99:0,157,2096 0/0:49,0:49:99:0,135,1768 0/0:51,0:51:99:0,126,1691 0/0:66,0:66:99:0,153,2064 0/0:76,0:76:99:0,187,2512 0/0:78,0:78:99:0,187,2549 0/0:48,0:48:99:0,123,1634 0/0:54,0:54:99:0,126,1665 0/0:79,0:79:99:0,205,2746 0/0:53,0:53:99:0,132,1771 0/0:55,0:55:99:0,132,1762 0/0:64,0:64:99:0,157,2139 0/0:56,0:56:99:0,132,1818 0/1:22,23:45:99:629,0,715 0/0:41,0:41:99:0,108,1457 0/0:60,0:60:99:0,163,2168 0/0:64,0:64:99:0,153,2062 0/0:69,0:69:99:0,178,2381 0/0:45,0:45:99:0,117,1590 0/0:66,0:66:99:0,159,2125 0/0:68,0:68:99:0,160,2131 0/0:48,0:48:99:0,111,1514 0/0:67,0:67:99:0,157,2129 0/0:76,0:77:99:0,181,2465 0/0:96,0:96:99:0,247,3300 0/0:34,0:34:93.30:0,93,1250 0/0:45,0:45:99:0,108,1427 0/0:26,0:26:69.23:0,69,936 0/0:28,0:28:72.23:0,72,972 0/0:34,0:34:81.26:0,81,1087 0/0:22,0:22:57.18:0,57,747 0/0:25,0:25:66.19:0,66,833 0/0:29,0:29:78.24:0,78,1012 0/0:62,0:62:99:0,150,1992 0/0:20,0:20:54.16:0,54,693 0/0:46,0:46:99:0,105,1406 0/0:50,0:50:99:0,135,1804 0/0:56,0:56:99:0,135,1791 0/0:35,0:35:99:0,99,1317 0/0:38,0:38:99:0,99,1312 0/0:40,0:40:99:0,99,1336 0/0:30,0:30:66.22:0,66,927 0/0:24,0:24:69.22:0,69,907 0/0:26,0:26:69.23:0,69,947 0/0:24,0:24:63.20:0,63,821 0/0:27,0:27:63.21:0,63,874 0/0:27,0:27:63.19:0,63,850 -chr1 887537 . C T 1658.47 . AC=3;AF=0.0250;AN=120;BaseQRankSum=1.815;DP=2530;Dels=0.00;FS=6.149;HRun=0;HaplotypeScore=1.6593;InbreedingCoeff=-0.0258;MQ=59.28;MQ0=0;MQRankSum=2.238;QD=12.11;ReadPosRankSum=2.057;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|10),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|8);CSQ=intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:19,0:19:42.10:0,42,488 0/0:24,1:25:24.02:0,24,646 0/0:21,0:21:60.18:0,60,750 0/0:20,0:20:51.15:0,51,625 0/0:59,0:59:99:0,165,2131 0/0:71,0:71:99:0,199,2583 0/0:81,0:81:99:0,238,3103 0/0:50,0:50:99:0,147,1877 0/0:83,0:83:99:0,250,3268 0/0:104,0:104:99:0,301,3858 0/0:56,0:56:99:0,153,1987 0/0:50,0:50:99:0,147,1935 0/0:74,0:74:99:0,211,2724 0/0:42,0:42:99:0,117,1556 0/0:42,0:43:93.30:0,93,1220 0/0:45,0:45:99:0,105,1405 0/0:52,0:53:99:0,117,1570 0/0:55,0:55:99:0,135,1793 0/0:71,0:71:99:0,175,2301 0/0:45,1:46:99:0,117,1539 0/1:17,22:40:99:676,0,345 0/0:69,0:69:99:0,175,2299 0/0:32,0:33:87.28:0,87,1151 0/0:39,0:39:99:0,99,1318 0/0:50,0:51:99:0,123,1639 0/0:43,0:43:99:0,111,1521 0/1:21,22:43:99:551,0,560 0/0:41,0:41:99:0,99,1327 0/0:47,0:47:99:0,102,1362 0/0:61,0:61:99:0,150,1933 0/0:54,0:54:99:0,141,1829 0/0:35,0:35:78.25:0,78,1046 0/0:41,0:41:99:0,108,1442 0/1:36,18:54:99:512,0,926 0/0:40,0:41:99:0,102,1333 0/0:63,0:63:99:0,144,1963 0/0:57,0:57:99:0,141,1867 0/0:86,0:86:99:0,220,2908 0/0:34,0:34:81.26:0,81,1080 0/0:26,0:26:57.18:0,57,742 0/0:29,0:29:72.23:0,72,969 0/0:26,0:26:60.19:0,60,799 0/0:23,1:24:20.19:0,20,659 0/0:27,0:27:66.21:0,66,893 0/0:15,0:15:33.10:0,33,434 0/0:20,0:20:60.19:0,60,780 0/0:37,0:37:93.26:0,93,1206 0/0:21,0:21:51.15:0,51,643 0/0:32,0:32:72.22:0,72,966 0/0:37,0:37:90.29:0,90,1196 0/0:39,0:39:96.29:0,96,1256 0/0:29,0:30:66.20:0,66,879 0/0:23,0:23:57.18:0,57,753 0/0:30,0:30:66.20:0,66,860 0/0:17,0:17:45.15:0,45,610 0/0:20,0:20:51.17:0,51,683 0/0:17,0:17:39.13:0,39,530 0/0:18,0:18:48.15:0,48,633 0/0:18,0:18:39.13:0,39,537 0/0:24,0:24:48.16:0,48,658 -chr1 887560 . A C 70115.69 . AC=113;AF=0.9417;AN=120;BaseQRankSum=0.848;DP=2150;Dels=0.00;FS=10.744;HRun=1;HaplotypeScore=1.3105;InbreedingCoeff=0.2414;MQ=59.13;MQ0=0;MQRankSum=-0.778;QD=32.87;ReadPosRankSum=1.087;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|10),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|8);CSQ=intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,14:14:36.09:432,36,0 1/1:1,24:25:54.15:653,54,0 1/1:0,22:22:66.20:847,66,0 1/1:0,19:19:54.15:665,54,0 1/1:0,52:52:99:2044,156,0 1/1:0,57:57:99:1970,150,0 1/1:0,73:74:99:2717,208,0 1/1:0,43:43:99:1702,126,0 1/1:0,69:69:99:2762,208,0 0/1:52,46:98:99:1485,0,1536 1/1:0,63:63:99:2455,187,0 1/1:0,42:42:99:1630,123,0 1/1:0,67:67:99:2646,202,0 1/1:0,40:40:99:1458,111,0 1/1:0,34:34:81.26:1097,81,0 1/1:0,40:40:99:1381,102,0 1/1:0,48:49:99:1551,114,0 1/1:0,46:46:99:1595,117,0 1/1:0,53:53:99:1900,141,0 1/1:0,35:35:96.30:1251,96,0 1/1:0,30:30:72.23:957,72,0 1/1:0,57:57:99:1993,150,0 0/1:18,16:34:99:543,0,510 1/1:0,33:33:84.27:1142,84,0 1/1:1,41:42:99:1398,108,0 1/1:0,33:33:84.27:1133,84,0 1/1:0,34:34:84.27:1115,84,0 1/1:0,36:36:93.30:1247,93,0 1/1:1,39:40:90.29:1216,90,0 1/1:0,49:49:99:1576,120,0 1/1:0,50:50:99:1823,138,0 1/1:1,30:31:63.19:848,63,0 1/1:0,30:30:87.28:1151,87,0 1/1:0,40:40:96.29:1243,96,0 1/1:0,33:33:78.24:1032,78,0 1/1:0,49:49:99:1626,120,0 1/1:0,43:43:99:1363,102,0 1/1:0,73:73:99:2543,187,0 1/1:0,27:27:69.22:922,69,0 1/1:0,24:25:60.16:780,60,0 1/1:0,22:22:57.19:786,57,0 0/1:10,10:20:99:300,0,260 1/1:0,13:13:36.11:451,36,0 1/1:0,28:28:69.23:951,69,0 1/1:0,13:13:33.08:429,33,0 1/1:0,17:17:51.17:679,51,0 1/1:0,34:34:90.26:1166,90,0 0/0:17,0:17:51.16:0,51,661 1/1:0,22:22:54.18:722,54,0 1/1:0,31:31:84.24:1080,84,0 0/1:19,13:32:99:364,0,556 1/1:0,24:24:57.18:756,57,0 1/1:0,22:22:57.18:747,57,0 1/1:0,25:25:66.20:844,66,0 1/1:0,13:13:36.12:486,36,0 1/1:0,17:17:45.15:604,45,0 0/1:10,5:15:99:155,0,347 1/1:0,20:20:51.16:665,51,0 1/1:0,17:17:39.13:523,39,0 1/1:0,17:17:39.12:518,39,0 -chr1 887651 . C T 665.1 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.019;DP=1257;Dels=0.00;FS=1.751;HRun=0;HaplotypeScore=0.9128;InbreedingCoeff=-0.0177;MQ=58.63;MQ0=0;MQRankSum=3.510;QD=17.50;ReadPosRankSum=2.127;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|10),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|8);CSQ=intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12.04:0,12,153 0/0:15,0:15:39.07:0,39,439 0/0:17,0:17:45.13:0,45,561 0/0:14,0:14:39.13:0,39,515 0/0:29,0:29:87.28:0,87,1143 0/0:33,0:33:93.31:0,93,1251 0/0:34,0:34:99:0,99,1288 0/0:29,0:29:81.26:0,81,1075 0/0:47,0:47:99:0,141,1848 0/0:50,0:50:99:0,147,1973 0/0:28,0:28:81.27:0,81,1080 0/0:18,0:18:54.15:0,54,684 0/0:32,0:32:90.27:0,90,1164 0/0:12,0:12:36.12:0,36,478 0/0:21,0:21:57.16:0,57,757 0/0:15,0:16:45.15:0,45,597 0/0:23,0:23:60.20:0,60,829 0/0:22,0:22:60.19:0,60,792 0/0:21,0:21:54.18:0,54,719 0/0:18,0:18:54.17:0,54,698 0/0:25,0:26:63.19:0,63,805 0/0:22,0:22:60.17:0,60,772 0/0:23,0:23:60.19:0,60,790 0/0:16,0:16:45.14:0,45,604 0/1:8,13:21:99:422,0,266 0/0:16,0:16:45.15:0,45,617 0/0:26,0:26:78.22:0,78,1014 0/0:17,0:17:51.14:0,51,664 0/0:19,0:19:54.18:0,54,722 0/0:18,0:18:45.15:0,45,608 0/0:28,0:28:81.25:0,81,1039 0/0:16,0:16:45.15:0,45,604 0/0:18,0:18:39.12:0,39,517 0/0:26,0:26:63.20:0,63,841 0/0:11,0:11:27.09:0,27,368 0/0:17,0:17:42.14:0,42,565 0/0:25,0:25:75.22:0,75,964 0/0:29,0:29:78.25:0,78,1041 0/0:17,0:17:45.14:0,45,581 0/0:18,0:18:48.15:0,48,619 0/0:15,0:15:45.14:0,45,591 0/0:9,0:9:21.04:0,21,245 0/0:18,0:18:51.17:0,51,679 0/0:12,0:12:36.11:0,36,470 0/0:16,0:16:45.15:0,45,618 0/1:7,10:17:99:308,0,236 0/0:32,0:32:84.27:0,84,1092 0/0:6,0:6:18.06:0,18,236 0/0:13,0:13:33.11:0,33,434 0/0:35,0:35:99:0,102,1328 0/0:35,0:35:99:0,99,1296 0/0:19,0:19:48.16:0,48,639 0/0:27,0:27:72.23:0,72,963 0/0:18,0:18:54.17:0,54,720 0/0:17,0:17:51.16:0,51,660 0/0:15,0:15:45.14:0,45,585 0/0:15,0:15:42.14:0,42,575 0/0:20,0:20:51.16:0,51,674 0/0:13,0:13:39.13:0,39,515 0/0:12,0:12:33.09:0,33,426 -chr1 887801 . A G 116758.48 . AC=115;AF=0.9583;AN=120;BaseQRankSum=4.615;DP=3778;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=2.1571;InbreedingCoeff=-0.0435;MQ=57.90;MQ0=0;MQRankSum=2.145;QD=30.90;ReadPosRankSum=1.213;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|8),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T394|749|NOC2L|protein_coding|CODING|ENST00000327044|);CSQ=synonymous_variant|acT/acC|T|ENSG00000188976|NOC2L|ENST00000327044|10/19|||394/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|8/17||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,13:13:33.09:399,33,0 1/1:0,14:14:39.11:484,39,0 1/1:0,18:18:48.15:592,48,0 1/1:0,17:17:45.14:575,45,0 1/1:1,49:50:99:1746,116,0 1/1:0,34:34:99:1305,102,0 1/1:0,78:78:99:2993,232,0 1/1:0,48:48:99:1881,144,0 1/1:0,85:85:99:3210,250,0 0/1:42,48:90:99:1526,0,1258 1/1:0,49:49:99:1841,144,0 1/1:0,51:51:99:2000,153,0 1/1:0,55:55:99:1999,153,0 1/1:0,58:58:99:1967,147,0 1/1:0,70:71:99:2336,175,0 1/1:0,32:32:72.23:972,72,0 1/1:0,56:56:99:1890,141,0 1/1:0,37:37:99:1283,99,0 1/1:0,78:78:99:2666,202,0 1/1:0,52:52:99:1772,132,0 1/1:0,54:54:99:1749,132,0 1/1:0,74:74:99:2410,181,0 0/1:30,20:52:99:513,0,826 1/1:0,57:57:99:1825,132,0 1/1:0,50:51:99:1629,123,0 1/1:0,43:43:99:1484,108,0 1/1:0,60:62:99:1951,147,0 1/1:0,51:51:99:1619,120,0 1/1:0,57:57:99:1962,150,0 1/1:0,70:70:99:2239,169,0 1/1:0,57:57:99:1980,147,0 1/1:0,37:39:87.28:1162,87,0 1/1:0,62:62:99:1862,135,0 1/1:0,46:46:99:1591,120,0 1/1:0,48:48:99:1547,114,0 1/1:0,79:79:99:2484,181,0 1/1:0,81:81:99:2721,205,0 1/1:0,80:80:99:2491,187,0 1/1:0,69:69:99:2256,175,0 1/1:0,128:129:99:3775,292,0 1/1:0,85:85:99:2565,193,0 0/1:36,28:64:99:817,0,912 1/1:0,76:76:99:2326,178,0 1/1:0,72:72:99:2065,156,0 1/1:0,50:50:99:1758,135,0 1/1:0,64:64:99:2141,163,0 1/1:0,127:127:99:4017,310,0 1/1:0,42:42:99:1303,99,0 1/1:0,110:110:99:3313,250,0 1/1:1,117:119:99:3786,289,0 0/1:38,58:96:99:1493,0,1071 1/1:0,77:77:99:2458,193,0 1/1:0,96:96:99:3003,232,0 1/1:0,80:80:99:2275,172,0 1/1:0,79:79:99:2507,196,0 1/1:0,63:63:99:1938,147,0 0/1:18,20:39:99:439,0,503 1/1:0,50:50:99:1544,117,0 1/1:0,47:47:99:1600,120,0 1/1:0,94:95:99:2723,205,0 -chr1 888220 . G A 81.05 . AC=4;AF=0.044;AN=90;BaseQRankSum=-1.159;DP=137;Dels=0.00;FS=2.348;HRun=0;HaplotypeScore=0.1677;InbreedingCoeff=-0.0166;MQ=57.57;MQ0=0;MQRankSum=1.051;QD=7.37;ReadPosRankSum=1.796;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|9),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|7);CSQ=intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,80 0/0:4,0:4:12.04:0,12,158 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,78 0/0:4,0:4:12.04:0,12,154 0/0:9,0:9:24.08:0,24,326 0/0:7,0:7:21.07:0,21,272 0/0:2,0:2:6.01:0,6,70 0/0:10,0:10:30.10:0,30,394 0/0:12,0:12:33.09:0,33,408 0/0:2,0:2:6.02:0,6,81 0/0:4,0:4:12.03:0,12,140 0/0:3,0:3:9.03:0,9,117 0/0:2,0:2:6.02:0,6,81 0/0:2,0:2:6.02:0,6,84 ./. 0/0:2,0:2:6.02:0,6,80 0/0:2,0:2:6.02:0,6,73 ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:9.03:0,9,118 0/0:6,0:6:18.05:0,18,217 0/0:2,0:2:6.02:0,6,73 0/0:7,0:7:18.05:0,18,208 0/0:1,0:1:3.01:0,3,41 0/1:4,2:6:48.23:48,0,105 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,32 0/0:3,0:3:9.03:0,9,123 0/0:2,0:2:6.02:0,6,79 0/0:3,0:3:9.03:0,9,118 0/0:2,0:2:6.02:0,6,83 ./. 0/1:1,3:4:33.20:72,0,33 ./. 1/1:0,1:1:3.01:36,3,0 0/0:4,0:4:12.04:0,12,162 0/0:1,0:1:3.01:0,3,41 ./. 0/0:3,0:3:9.03:0,9,120 ./. 0/0:2,0:2:6.02:0,6,75 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,37 ./. 0/0:3,0:3:6.02:0,6,86 ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. 0/0:1,0:1:3.01:0,3,36 0/0:1,0:1:3.01:0,3,39 -chr1 888239 . C T 79.33 . AC=3;AF=0.034;AN=88;BaseQRankSum=0.324;DP=113;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0969;InbreedingCoeff=-0.0212;MQ=57.69;MQ0=0;MQRankSum=1.258;QD=13.22;ReadPosRankSum=-0.910;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|9),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|7);CSQ=intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.04:0,12,148 0/0:1,0:1:3:0,3,25 0/0:2,0:2:6.02:0,6,79 0/0:4,0:4:12.04:0,12,161 0/0:4,0:4:9.03:0,9,115 0/0:6,0:6:18.06:0,18,238 0/0:2,0:2:6.02:0,6,69 0/0:6,0:6:18.04:0,18,215 0/0:12,0:13:36.11:0,36,457 0/0:3,0:3:9.03:0,9,117 0/0:1,0:1:3.01:0,3,32 0/0:4,0:4:12.02:0,12,137 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,81 ./. 0/0:2,0:2:6.02:0,6,76 0/0:1,0:1:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,39 ./. 0/0:3,0:3:9.03:0,9,122 0/0:6,0:6:18.06:0,18,225 ./. 0/0:7,0:7:18.05:0,18,205 0/0:1,0:1:3.01:0,3,41 0/1:2,3:5:60.62:104,0,61 ./. 0/0:1,0:1:3.01:0,3,32 0/0:1,0:1:3.01:0,3,37 0/0:2,0:2:6.02:0,6,80 0/0:1,0:1:3.01:0,3,42 0/0:3,0:3:9.03:0,9,116 1/1:0,1:1:3.01:38,3,0 0/0:3,0:3:9.03:0,9,110 ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:6.02:0,6,78 ./. 0/0:3,0:3:9.03:0,9,115 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:6.02:0,6,87 ./. ./. ./. 0/0:2,0:2:6.02:0,6,75 ./. ./. ./. 0/0:1,0:1:3.01:0,3,35 ./. ./. ./. 0/0:1,0:1:3.01:0,3,36 0/0:1,0:1:3:0,3,29 -chr1 888639 . T C 94387.16 . AC=115;AF=0.9583;AN=120;BaseQRankSum=0.263;DP=3128;Dels=0.00;FS=2.314;HRun=1;HaplotypeScore=1.2974;InbreedingCoeff=-0.0435;MQ=54.95;MQ0=0;MQRankSum=0.465;QD=30.17;ReadPosRankSum=1.529;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|7),SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E306|749|NOC2L|protein_coding|CODING|ENST00000327044|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,synonymous_variant|gaA/gaG|E|ENSG00000188976|NOC2L|ENST00000327044|9/19|||306/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|7/17||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,14:14:39.11:459,39,0 1/1:0,17:18:42.10:495,42,0 1/1:0,22:22:60.19:762,60,0 1/1:0,18:18:45.14:567,45,0 1/1:0,38:39:99:1455,114,0 1/1:0,46:46:99:1656,132,0 1/1:0,66:66:99:2327,187,0 1/1:0,47:47:99:1689,132,0 1/1:0,79:79:99:2924,229,0 0/1:51,49:100:99:1507,0,1732 1/1:1,49:50:99:1815,144,0 1/1:0,38:38:99:1407,111,0 1/1:0,53:54:99:1912,153,0 1/1:0,47:47:99:1635,123,0 1/1:1,43:44:99:1337,102,0 1/1:0,27:27:69.22:895,69,0 1/1:0,29:30:69.20:900,69,0 1/1:0,27:27:66.20:854,66,0 1/1:0,44:44:99:1428,105,0 1/1:0,53:53:99:1750,135,0 1/1:0,39:39:96.31:1269,96,0 1/1:0,60:60:99:1828,135,0 0/1:23,21:44:99:520,0,671 1/1:0,31:31:69.22:912,69,0 1/1:0,41:41:99:1304,99,0 1/1:0,27:27:69.22:912,69,0 1/1:0,38:38:93.29:1220,93,0 1/1:0,36:36:93.30:1228,93,0 1/1:0,53:53:99:1801,138,0 1/1:0,36:36:90.27:1180,90,0 1/1:0,48:48:99:1605,123,0 1/1:0,36:36:72.23:977,72,0 1/1:0,44:44:99:1469,114,0 1/1:0,48:48:99:1410,108,0 1/1:0,43:43:99:1326,99,0 1/1:0,43:43:99:1390,108,0 1/1:0,56:56:99:1870,147,0 1/1:0,70:70:99:2347,178,0 1/1:0,61:61:99:2013,156,0 1/1:0,100:100:99:3224,253,0 1/1:0,80:80:99:2335,181,0 0/1:43,37:80:99:967,0,1260 1/1:0,49:49:99:1611,126,0 1/1:0,43:43:96.31:1296,96,0 1/1:0,60:60:99:1930,150,0 1/1:0,61:61:99:1885,144,0 1/1:0,99:99:99:3245,247,0 1/1:0,45:45:99:1384,108,0 1/1:0,76:76:99:2335,175,0 1/1:1,105:106:99:3518,241,0 0/1:44,43:88:99:1156,0,1184 1/1:1,68:69:99:1966,119,0 1/1:0,54:54:99:1728,132,0 1/1:1,74:75:99:2364,156,0 1/1:0,62:62:99:2040,156,0 1/1:0,48:48:99:1587,123,0 0/1:28,17:45:99:401,0,768 1/1:2,64:66:99:1894,117,0 1/1:0,52:52:99:1729,129,0 1/1:0,52:53:99:1435,105,0 -chr1 888659 . T C 80634.32 . AC=115;AF=0.9583;AN=120;BaseQRankSum=1.739;DP=2737;Dels=0.00;FS=2.276;HRun=1;HaplotypeScore=1.3379;InbreedingCoeff=-0.0436;MQ=54.78;MQ0=0;MQRankSum=-1.113;QD=29.46;ReadPosRankSum=4.132;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|7),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I300V|749|NOC2L|protein_coding|CODING|ENST00000327044|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,missense_variant|Atc/Gtc|I/V|ENSG00000188976|NOC2L|ENST00000327044|9/19|benign(0)|tolerated(0.98)|300/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|7/17||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,8:8:18.06:219,18,0 1/1:0,16:16:39.11:462,39,0 1/1:0,17:17:51.16:634,51,0 1/1:0,22:22:66.19:807,66,0 1/1:0,38:38:99:1442,114,0 1/1:0,37:37:99:1321,105,0 1/1:0,46:46:99:1611,132,0 1/1:0,41:41:99:1501,117,0 1/1:0,60:60:99:2262,178,0 0/1:41,35:76:99:1092,0,1316 1/1:0,35:35:99:1237,99,0 1/1:0,32:32:93.30:1208,93,0 1/1:0,40:41:99:1455,114,0 1/1:0,37:37:96.29:1236,96,0 1/1:0,34:34:72.23:959,72,0 1/1:0,27:27:66.20:849,66,0 1/1:0,27:27:63.20:820,63,0 1/1:0,27:27:60.19:769,60,0 1/1:0,38:38:81.26:1088,81,0 1/1:0,44:44:99:1440,111,0 1/1:0,45:45:99:1451,111,0 1/1:0,47:47:99:1469,111,0 0/1:22,19:41:99:433,0,545 1/1:0,28:29:63.20:842,63,0 1/1:0,36:36:87.25:1131,87,0 1/1:0,24:24:63.20:833,63,0 1/1:0,27:27:66.19:833,66,0 1/1:0,34:34:84.25:1073,84,0 1/1:0,48:48:99:1578,126,0 1/1:0,33:33:75.23:1003,75,0 1/1:0,35:35:90.28:1165,90,0 1/1:0,33:33:75.24:1010,75,0 1/1:0,40:40:99:1399,108,0 1/1:0,50:50:99:1441,111,0 1/1:0,39:39:90.29:1178,90,0 1/1:0,36:36:87.27:1128,87,0 1/1:0,47:47:99:1455,114,0 1/1:0,64:64:99:1998,150,0 1/1:0,53:53:99:1814,141,0 1/1:0,84:84:99:2672,211,0 1/1:0,69:69:99:2043,162,0 0/1:30,34:64:99:963,0,865 1/1:0,42:42:99:1281,102,0 1/1:0,39:39:99:1267,99,0 1/1:0,51:51:99:1620,129,0 1/1:0,63:63:99:1953,150,0 1/1:0,91:91:99:2809,214,0 1/1:0,38:39:84.26:1067,84,0 1/1:0,67:67:99:2003,150,0 1/1:1,93:94:99:2922,196,0 0/1:42,31:73:99:748,0,985 1/1:0,60:60:99:1716,132,0 1/1:0,56:57:99:1612,123,0 1/1:1,73:74:99:2241,138,0 1/1:0,64:64:99:1948,150,0 1/1:0,47:47:99:1450,114,0 0/1:26,13:41:99:280,0,693 1/1:1,58:59:99:1697,104,0 1/1:0,51:51:99:1432,111,0 1/1:0,43:43:99:1269,99,0 -chr1 889131 . A G 423.54 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-1.236;DP=1138;Dels=0.00;FS=7.564;HRun=1;HaplotypeScore=0.6841;InbreedingCoeff=-0.0300;MQ=57.89;MQ0=0;MQRankSum=0.858;QD=9.41;ReadPosRankSum=0.777;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|8),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|6);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.02:0,9,97 0/0:3,0:3:9.03:0,9,107 0/0:3,0:3:9.03:0,9,109 0/0:5,0:5:12.04:0,12,149 0/0:11,0:11:30.10:0,30,391 0/0:9,0:9:27.06:0,27,325 0/0:24,0:24:69.23:0,69,919 0/0:7,0:7:21.06:0,21,269 0/0:16,0:16:48.11:0,48,587 0/0:20,0:20:57.19:0,57,753 0/0:14,0:14:42.14:0,42,563 0/0:7,0:7:15.05:0,15,188 0/0:19,0:19:54.16:0,54,668 0/0:7,0:7:18.06:0,18,233 0/0:22,0:22:51.16:0,51,675 0/0:9,0:9:27.08:0,27,342 0/0:17,0:17:39.12:0,39,505 0/0:6,0:6:18.06:0,18,232 0/0:14,0:14:33.11:0,33,429 0/0:20,0:20:57.17:0,57,748 0/0:14,0:14:33.11:0,33,443 0/0:14,0:14:36.12:0,36,482 0/0:9,0:9:24.05:0,24,287 0/0:16,0:16:36.11:0,36,466 0/0:11,0:11:27.09:0,27,358 0/0:19,0:19:51.16:0,51,661 0/1:6,5:11:99:149,0,170 0/0:19,0:19:45.12:0,45,585 0/0:31,0:31:81.25:0,81,1053 0/0:17,0:17:45.14:0,45,586 0/0:11,0:11:30.09:0,30,382 0/0:19,0:19:42.11:0,42,547 0/0:20,0:20:54.17:0,54,701 0/0:10,0:10:27.09:0,27,349 0/1:8,3:11:63.42:63,0,275 0/0:13,0:13:33.08:0,33,411 0/1:14,9:23:99:291,0,368 0/0:30,0:30:81.26:0,81,1076 0/0:25,0:26:63.20:0,63,822 0/0:42,1:43:93.29:0,93,1219 0/0:35,0:35:84.26:0,84,1085 0/0:21,0:23:42.13:0,42,532 0/0:18,0:19:54.17:0,54,703 0/0:17,0:17:42.13:0,42,525 0/0:29,0:29:78.22:0,78,969 0/0:20,0:20:42.11:0,42,528 0/0:47,0:47:99:0,123,1558 0/0:11,0:11:21.07:0,21,282 0/0:36,0:36:87.23:0,87,1083 0/0:43,0:43:99:0,108,1338 0/0:44,0:45:99:0,108,1408 0/0:35,0:37:75.24:0,75,966 0/0:20,0:20:54.15:0,54,680 0/0:27,0:27:69.21:0,69,893 0/0:9,0:9:21.06:0,21,266 0/0:17,0:18:39.10:0,39,487 0/0:15,1:16:39.13:0,39,533 0/0:32,0:32:78.25:0,78,1022 0/0:25,0:25:69.21:0,69,878 0/0:23,0:23:54.17:0,54,697 -chr1 889158 . G C 40721.48 . AC=113;AF=0.9417;AN=120;BaseQRankSum=1.359;DP=1345;Dels=0.00;FS=0.512;HRun=1;HaplotypeScore=0.9432;InbreedingCoeff=0.2187;MQ=58.28;MQ0=0;MQRankSum=1.507;QD=30.55;ReadPosRankSum=0.613;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|8),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|6);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,5:5:12.04:151,12,0 1/1:0,2:2:3.01:39,3,0 1/1:0,4:4:12.03:145,12,0 1/1:0,8:8:21.06:262,21,0 1/1:0,14:14:42.13:539,42,0 1/1:0,9:9:24.08:325,24,0 1/1:0,22:22:66.22:877,66,0 1/1:0,8:8:24.08:324,24,0 1/1:0,15:15:45.14:596,45,0 0/1:10,13:23:99:447,0,327 1/1:0,22:22:66.21:872,66,0 1/1:0,8:8:24.05:284,24,0 1/1:0,19:20:57.18:749,57,0 1/1:0,18:18:42.13:558,42,0 1/1:0,29:29:63.19:839,63,0 1/1:0,14:14:39.13:524,39,0 1/1:0,24:24:51.17:710,51,0 1/1:0,15:15:39.13:521,39,0 1/1:0,16:16:33.11:455,33,0 1/1:0,29:29:81.25:1067,81,0 1/1:0,17:17:39.12:511,39,0 1/1:0,22:22:57.17:744,57,0 0/1:6,9:15:99:193,0,162 1/1:0,21:21:51.16:673,51,0 1/1:0,17:17:48.13:622,48,0 1/1:0,27:27:63.20:845,63,0 1/1:0,15:15:39.11:504,39,0 1/1:0,23:23:51.13:658,51,0 1/1:0,37:37:93.27:1169,93,0 1/1:0,22:22:48.16:647,48,0 1/1:0,21:21:48.15:633,48,0 1/1:0,21:21:48.16:650,48,0 1/1:0,26:26:63.19:812,63,0 1/1:0,20:20:48.16:637,48,0 1/1:0,12:13:33.11:425,33,0 1/1:0,16:16:42.13:549,42,0 1/1:0,29:29:72.23:944,72,0 1/1:0,43:43:99:1322,99,0 1/1:0,22:22:66.20:850,66,0 1/1:0,46:47:99:1562,120,0 1/1:0,34:34:75.24:979,75,0 0/1:13,12:25:99:293,0,358 1/1:0,20:20:57.16:718,57,0 1/1:0,17:17:45.13:567,45,0 1/1:0,29:29:66.21:863,66,0 1/1:0,22:22:57.15:729,57,0 1/1:1,43:44:99:1373,108,0 0/0:12,0:12:30.10:0,30,398 1/1:0,39:39:87.23:1092,87,0 1/1:0,54:54:99:1746,135,0 0/1:16,22:38:99:626,0,395 1/1:0,38:38:90.26:1126,90,0 1/1:0,28:28:63.20:813,63,0 1/1:0,26:26:54.17:712,54,0 1/1:0,10:10:27.07:334,27,0 1/1:0,21:21:51.15:644,51,0 0/1:11,7:18:99:165,0,300 1/1:0,36:36:78.25:1038,78,0 1/1:0,27:27:66.18:866,66,0 1/1:0,27:27:60.19:802,60,0 -chr1 889159 . A C 41244.53 . AC=113;AF=0.9417;AN=120;BaseQRankSum=1.309;DP=1361;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.8382;InbreedingCoeff=0.2198;MQ=58.26;MQ0=0;MQRankSum=1.567;QD=30.57;ReadPosRankSum=1.331;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|8),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|6);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,5:5:15.03:178,15,0 1/1:0,2:2:3.01:41,3,0 1/1:0,4:4:12.04:155,12,0 1/1:0,8:8:21.06:260,21,0 1/1:0,15:15:45.13:569,45,0 1/1:0,9:9:24.08:329,24,0 1/1:0,23:23:69.22:905,69,0 1/1:0,9:9:24.08:322,24,0 1/1:0,15:15:42.14:559,42,0 0/1:13,13:26:99:438,0,445 1/1:0,22:22:66.22:890,66,0 1/1:0,8:8:21.06:268,21,0 1/1:0,20:20:57.16:736,57,0 1/1:0,18:18:42.13:561,42,0 1/1:0,29:29:57.18:780,57,0 1/1:0,14:14:39.13:524,39,0 1/1:0,25:25:54.17:729,54,0 1/1:0,15:15:39.13:523,39,0 1/1:0,16:16:36.12:484,36,0 1/1:0,28:28:78.24:1028,78,0 1/1:0,17:17:36.10:470,36,0 1/1:0,22:22:57.19:761,57,0 0/1:6,9:15:99:187,0,191 1/1:0,21:21:51.15:661,51,0 1/1:1,17:18:48.15:636,48,0 1/1:0,28:28:63.20:848,63,0 1/1:0,16:16:42.13:543,42,0 1/1:0,22:22:48.15:647,48,0 1/1:0,38:38:90.28:1161,90,0 1/1:0,21:21:48.15:627,48,0 1/1:0,21:21:48.16:637,48,0 1/1:0,21:21:48.16:657,48,0 1/1:1,25:26:60.19:801,60,0 1/1:0,21:21:54.17:716,54,0 1/1:0,13:13:36.11:459,36,0 1/1:0,16:16:45.12:558,45,0 1/1:0,30:30:72.20:935,72,0 1/1:0,44:44:99:1320,99,0 1/1:0,24:24:66.21:858,66,0 1/1:0,48:48:99:1627,126,0 1/1:0,34:34:78.25:1028,78,0 0/1:12,12:25:99:293,0,354 1/1:0,21:21:57.17:725,57,0 1/1:0,17:17:45.14:579,45,0 1/1:0,29:29:72.21:913,72,0 1/1:0,22:22:54.17:697,54,0 1/1:0,44:44:99:1437,114,0 0/0:11,0:12:30.10:0,30,397 1/1:0,39:39:84.25:1073,84,0 1/1:0,54:54:99:1793,138,0 0/1:18,22:40:99:630,0,474 1/1:0,38:38:90.26:1128,90,0 1/1:1,27:28:66.21:859,66,0 1/1:0,26:26:54.18:730,54,0 1/1:0,11:11:27.08:346,27,0 1/1:0,21:21:51.16:664,51,0 0/1:10,7:17:99:163,0,279 1/1:0,36:36:84.23:1089,84,0 1/1:0,28:28:69.22:918,69,0 1/1:0,26:26:60.19:794,60,0 -chr1 889238 . G A 1672.71 . AC=5;AF=0.0417;AN=120;BaseQRankSum=-2.383;DP=1656;Dels=0.00;FS=10.199;HRun=0;HaplotypeScore=0.9421;InbreedingCoeff=-0.0479;MQ=58.37;MQ0=0;MQRankSum=0.456;QD=10.93;ReadPosRankSum=-1.085;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|6),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A271V|749|NOC2L|protein_coding|CODING|ENST00000327044|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,missense_variant|gCg/gTg|A/V|ENSG00000188976|NOC2L|ENST00000327044|8/19|benign(0.034)|deleterious(0.04)|271/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|6/17||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,39 0/0:6,0:6:15.05:0,15,193 0/0:7,0:7:21.06:0,21,253 0/0:5,0:5:9.03:0,9,114 0/0:11,0:11:30.09:0,30,367 0/0:11,0:11:33.11:0,33,428 0/0:21,0:21:57.18:0,57,734 0/0:12,0:12:24.07:0,24,302 0/0:27,0:28:78.25:0,78,1015 0/1:16,10:26:99:293,0,475 0/0:19,0:19:54.17:0,54,695 0/0:12,0:12:27.08:0,27,339 0/0:22,0:22:60.18:0,60,760 0/0:26,0:26:60.19:0,60,806 0/0:37,0:37:84.27:0,84,1124 0/0:19,0:19:51.15:0,51,683 0/0:32,0:32:75.24:0,75,1009 0/0:28,0:28:69.21:0,69,909 0/0:30,0:30:60.20:0,60,830 0/0:38,0:39:90.30:0,90,1233 0/0:19,0:19:51.15:0,51,640 0/0:26,0:26:72.20:0,72,917 0/1:10,15:25:99:400,0,264 0/0:25,0:25:63.19:0,63,828 0/0:31,0:31:75.24:0,75,993 0/0:23,0:23:57.17:0,57,719 0/0:26,1:27:30.48:0,30,879 0/0:18,0:18:51.17:0,51,682 0/0:41,0:41:99:0,108,1411 0/0:21,0:22:60.19:0,60,778 0/0:31,0:31:75.24:0,75,984 0/0:20,0:20:51.16:0,51,669 0/0:29,0:29:69.21:0,69,898 0/0:34,0:34:93.29:0,93,1192 0/0:25,0:25:60.20:0,60,811 0/0:20,0:21:45.11:0,45,581 0/0:39,0:39:96.32:0,96,1306 0/0:56,0:56:99:0,144,1907 0/0:28,0:28:63.21:0,63,856 0/0:48,0:49:99:0,111,1505 0/0:43,0:43:99:0,111,1468 0/1:23,16:39:99:432,0,660 0/0:30,0:30:72.19:0,72,898 0/0:19,0:19:45.14:0,45,595 0/0:36,0:36:99:0,102,1307 0/0:29,0:29:72.22:0,72,923 0/0:57,0:57:99:0,141,1842 0/0:18,0:18:45.15:0,45,603 0/0:37,0:37:99:0,99,1302 0/0:59,0:59:99:0,141,1858 0/1:30,19:49:99:404,0,800 0/0:44,0:44:99:0,117,1462 0/0:37,0:38:96.26:0,96,1188 0/0:27,0:27:72.23:0,72,932 0/0:19,0:19:48.15:0,48,622 0/0:22,0:23:45.15:0,45,606 0/1:4,10:14:99:248,0,120 0/0:35,0:35:84.26:0,84,1101 0/0:27,1:28:24.98:0,25,781 0/0:28,0:30:60.20:0,60,819 -chr1 889638 . G C 14363.41 . AC=105;AF=0.9211;AN=114;BaseQRankSum=-0.922;DP=427;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3035;InbreedingCoeff=0.0466;MQ=57.19;MQ0=0;MQRankSum=0.153;QD=34.12;ReadPosRankSum=1.663;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|5),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|6);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|5/17||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,2:2:3.01:39,3,0 1/1:0,4:4:12.04:156,12,0 ./. 1/1:0,3:3:9.03:105,9,0 ./. ./. 0/1:4,1:5:21.93:22,0,147 1/1:0,2:2:6.02:80,6,0 1/1:0,8:8:24.08:323,24,0 0/1:4,3:7:95.16:95,0,141 1/1:0,3:3:6.02:76,6,0 1/1:0,3:3:9.03:122,9,0 1/1:0,2:2:6.02:81,6,0 1/1:0,6:6:12.04:156,12,0 1/1:0,6:6:18.06:247,18,0 1/1:0,1:1:3.01:42,3,0 1/1:0,5:5:15.05:202,15,0 1/1:0,6:6:18.06:241,18,0 1/1:0,2:2:6.02:83,6,0 1/1:0,2:2:6.02:77,6,0 1/1:0,5:5:12.04:154,12,0 1/1:0,4:4:12.04:157,12,0 0/1:1,3:4:30.19:108,0,30 1/1:0,5:5:15.05:188,15,0 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:79,6,0 1/1:0,5:5:15.05:208,15,0 1/1:0,2:2:6.02:76,6,0 1/1:0,4:4:12.04:165,12,0 1/1:0,6:6:15.05:204,15,0 1/1:0,6:6:18.06:242,18,0 1/1:0,3:3:9.02:104,9,0 1/1:0,3:3:6.02:87,6,0 0/1:1,2:3:33.20:74,0,33 1/1:0,5:5:15.05:198,15,0 1/1:0,1:1:3.01:42,3,0 1/1:0,4:4:12.04:167,12,0 1/1:0,11:11:33.11:450,33,0 1/1:0,8:8:24.08:304,24,0 1/1:0,27:27:81.26:1070,81,0 1/1:0,15:15:39.11:489,39,0 0/1:3,6:9:97.40:193,0,97 1/1:0,10:10:27.09:357,27,0 1/1:0,10:10:24.07:308,24,0 1/1:0,11:11:30.10:392,30,0 1/1:0,15:15:42.13:548,42,0 1/1:0,21:21:60.19:780,60,0 0/0:6,0:6:18.06:0,18,238 1/1:0,15:15:42.13:550,42,0 1/1:0,17:18:51.15:646,51,0 0/1:6,8:14:99:250,0,199 1/1:0,12:12:36.12:464,36,0 1/1:0,18:18:48.15:618,48,0 1/1:0,13:13:36.08:441,36,0 1/1:0,9:9:27.09:357,27,0 1/1:0,11:11:27.09:369,27,0 0/1:7,7:14:99:223,0,149 1/1:0,16:16:48.15:628,48,0 1/1:0,7:7:18.06:241,18,0 1/1:0,7:7:18.06:243,18,0 -chr1 889713 . C A 5043.64 . AC=90;AF=0.918;AN=98;BaseQRankSum=-0.018;DP=155;Dels=0.00;FS=4.406;HRun=0;HaplotypeScore=0.0300;InbreedingCoeff=0.0572;MQ=56.80;MQ0=0;MQRankSum=1.329;QD=33.40;ReadPosRankSum=0.873;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|5),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|6);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|5/17||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6.02:75,6,0 1/1:0,1:1:3.01:41,3,0 1/1:0,6:6:18.03:215,18,0 ./. 1/1:0,2:2:6.01:67,6,0 0/1:1,1:2:33.29:35,0,33 1/1:0,1:1:3.01:40,3,0 1/1:0,1:1:3.01:39,3,0 0/1:2,2:4:33.30:34,0,33 1/1:0,1:1:3.01:41,3,0 ./. 1/1:0,2:2:6.02:81,6,0 1/1:0,5:5:9.03:113,9,0 1/1:0,1:1:3.01:40,3,0 1/1:0,1:1:3.01:39,3,0 ./. ./. 1/1:0,3:3:9.03:124,9,0 1/1:0,2:2:6.02:83,6,0 1/1:0,3:3:9.03:114,9,0 1/1:0,3:3:9.03:122,9,0 ./. 1/1:0,2:2:6.02:79,6,0 1/1:0,2:2:6.02:73,6,0 1/1:0,1:1:3.01:42,3,0 1/1:0,1:1:3.01:42,3,0 0/0:2,0:2:6.02:0,6,82 1/1:0,1:1:3.01:32,3,0 1/1:1,2:3:6.02:67,6,0 1/1:0,1:1:3.01:42,3,0 1/1:0,1:1:3.01:37,3,0 ./. 1/1:0,1:1:3.01:40,3,0 ./. ./. 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:80,6,0 1/1:0,10:10:27.09:362,27,0 1/1:0,7:7:21.06:259,21,0 ./. 1/1:0,3:3:9.03:123,9,0 1/1:0,3:3:9.03:115,9,0 1/1:0,5:5:15.05:202,15,0 1/1:0,5:5:12.03:145,12,0 1/1:0,9:9:24.08:328,24,0 0/0:2,0:2:6.02:0,6,70 1/1:0,1:1:3.01:40,3,0 1/1:0,5:5:15.05:202,15,0 0/1:2,2:4:69.51:70,0,70 1/1:0,7:7:21.07:269,21,0 1/1:0,9:9:27.07:319,27,0 1/1:0,4:4:12.04:155,12,0 1/1:0,4:4:12.01:141,12,0 1/1:0,2:2:6.01:66,6,0 0/1:4,2:6:64.40:64,0,141 1/1:0,5:5:12.04:167,12,0 1/1:0,5:5:9.03:107,9,0 ./. -chr1 891021 . G A 7780.97 . AC=101;AF=0.9182;AN=110;BaseQRankSum=0.260;DP=242;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1735;InbreedingCoeff=-0.0202;MQ=58.75;MQ0=0;MQRankSum=-0.704;QD=33.11;ReadPosRankSum=0.580;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|6),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|6),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|4),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,3:3:6.02:79,6,0 1/1:0,3:3:9.03:115,9,0 1/1:0,2:2:6.02:79,6,0 1/1:0,6:6:18.06:229,18,0 ./. 1/1:0,1:1:3.01:39,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:82,6,0 1/1:0,5:5:15.05:201,15,0 0/1:5,5:10:99:166,0,176 1/1:0,1:1:3.01:39,3,0 1/1:0,2:2:6.02:82,6,0 1/1:0,3:3:9.03:123,9,0 1/1:0,3:3:6.02:87,6,0 1/1:0,2:2:6.02:81,6,0 1/1:0,4:4:12.04:164,12,0 1/1:0,8:8:24.07:303,24,0 1/1:0,8:8:24.08:310,24,0 1/1:0,9:9:21.07:282,21,0 1/1:0,10:10:30.10:406,30,0 0/1:1,2:3:32.73:65,0,33 1/1:0,8:8:24.08:329,24,0 0/1:4,2:6:48.81:49,0,143 1/1:0,6:6:18.06:243,18,0 1/1:0,1:1:3.01:41,3,0 1/1:0,2:3:6.02:81,6,0 0/0:6,0:6:15.05:0,15,209 1/1:0,3:4:9.03:120,9,0 1/1:0,2:2:6.02:82,6,0 1/1:0,8:8:21.06:270,21,0 1/1:0,9:9:24.07:312,24,0 1/1:0,6:6:18.06:229,18,0 1/1:0,1:1:3.01:42,3,0 0/1:4,2:6:64.18:64,0,142 0/1:2,2:4:59.97:66,0,60 1/1:0,5:5:15.04:190,15,0 0/1:3,5:8:56.56:177,0,57 1/1:0,12:12:33.11:453,33,0 ./. 1/1:0,4:4:9.03:109,9,0 ./. ./. 1/1:0,2:2:6.02:79,6,0 1/1:0,2:2:3.01:42,3,0 1/1:0,3:3:9.03:110,9,0 1/1:0,4:4:12.04:154,12,0 1/1:0,6:6:18.06:238,18,0 1/1:0,2:2:6.02:84,6,0 1/1:0,2:2:6.02:82,6,0 1/1:0,5:5:12.04:171,12,0 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:82,6,0 1/1:0,10:10:27.09:364,27,0 ./. 1/1:0,1:1:3.01:34,3,0 1/1:0,3:3:6.02:86,6,0 0/1:2,1:3:32.73:33,0,62 1/1:0,3:3:9.03:117,9,0 1/1:0,5:5:15.05:193,15,0 1/1:0,1:1:3.01:42,3,0 -chr1 891059 . C T 8049.27 . AC=70;AF=0.5932;AN=118;BaseQRankSum=0.106;DP=392;Dels=0.00;FS=5.538;HRun=2;HaplotypeScore=0.1844;InbreedingCoeff=0.1314;MQ=58.93;MQ0=0;MQRankSum=-2.097;QD=26.74;ReadPosRankSum=0.989;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|6),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|6),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|4),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,7:7:21.06:257,21,0 1/1:0,6:6:18.05:220,18,0 0/1:2,5:7:55.07:168,0,55 0/1:1,3:4:28.61:103,0,29 0/1:2,3:5:67.41:106,0,67 0/1:2,3:5:60.16:60,0,66 0/0:2,0:2:6.02:0,6,77 1/1:0,1:1:3.01:41,3,0 0/0:4,0:4:12.04:0,12,161 0/0:5,0:5:12.04:0,12,161 0/1:1,1:2:32.56:35,0,33 1/1:0,1:1:3.01:40,3,0 1/1:0,2:2:6.02:82,6,0 0/0:9,0:9:24.08:0,24,317 0/1:5,3:8:99:103,0,177 1/1:0,8:8:24.08:329,24,0 0/1:4,6:10:99:172,0,138 0/1:6,3:9:99:101,0,129 0/1:3,7:10:85.15:208,0,85 0/1:7,8:15:99:269,0,219 0/1:5,4:9:99:125,0,135 1/1:0,15:15:42.14:559,42,0 0/1:4,6:10:99:175,0,133 0/1:5,7:12:99:235,0,156 1/1:0,11:11:33.11:444,33,0 0/1:2,2:4:52.89:53,0,65 0/0:12,0:12:30.10:0,30,409 0/1:2,3:5:66.83:107,0,67 1/1:0,8:8:21.07:287,21,0 1/1:0,9:9:27.09:352,27,0 1/1:0,10:10:27.09:362,27,0 1/1:0,9:9:24.08:316,24,0 0/1:4,1:5:24.96:25,0,135 0/0:10,0:10:30.10:0,30,402 0/0:6,0:6:15.05:0,15,190 0/1:1,5:6:9.61:182,0,10 0/1:5,7:12:99:211,0,126 0/0:24,0:24:69.23:0,69,935 ./. 1/1:0,8:8:21.07:277,21,0 0/1:4,1:5:33.20:33,0,74 0/0:2,0:2:6.02:0,6,82 1/1:0,3:3:9.03:120,9,0 1/1:0,4:4:12.04:163,12,0 0/1:2,4:6:64.18:137,0,64 1/1:0,5:5:15.04:191,15,0 0/1:5,3:8:99:101,0,145 0/0:3,0:3:9.03:0,9,123 1/1:0,3:3:9.03:115,9,0 0/0:9,0:9:27.06:0,27,327 0/0:3,0:3:9.03:0,9,126 1/1:0,4:4:12.04:163,12,0 1/1:0,9:9:24.08:316,24,0 1/1:0,1:1:3.01:35,3,0 1/1:0,2:2:6.02:84,6,0 1/1:0,4:4:12.04:165,12,0 0/1:2,3:5:41.20:110,0,41 1/1:0,4:4:12.04:153,12,0 1/1:0,5:5:12.04:158,12,0 0/0:2,0:2:6.02:0,6,81 -chr1 891401 . G A 2441.56 . AC=1;AF=0.0083;AN=120;BaseQRankSum=1.910;DP=6853;DS;Dels=0.00;FS=20.474;HRun=4;HaplotypeScore=2.8477;InbreedingCoeff=-0.0084;MQ=58.69;MQ0=0;MQRankSum=2.695;QD=14.45;ReadPosRankSum=2.367;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|5),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|5),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|3),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:71,1:72:99:0,202,2495 0/0:70,0:70:99:0,211,2702 0/0:84,0:84:99:0,250,3255 0/0:72,0:72:99:0,208,2637 0/0:155,0:155:99:0,464,6222 0/0:154,0:154:99:0,448,6002 0/0:250,0:250:99:0,749,10034 0/0:150,0:150:99:0,448,5978 0/0:250,0:250:99:0,749,10087 0/0:250,0:250:99:0,752,10049 0/0:151,0:151:99:0,451,6046 0/0:174,0:174:99:0,521,6898 0/0:216,0:216:99:0,644,8524 0/0:123,0:123:99:0,340,4452 0/0:156,0:156:99:0,424,5636 0/0:90,0:90:99:0,235,3116 0/0:140,0:141:99:0,370,4921 0/0:148,0:148:99:0,394,5313 0/0:162,0:164:99:0,421,5642 0/0:146,0:147:99:0,385,5202 0/0:142,0:142:99:0,388,5170 0/0:174,0:175:99:0,473,6284 0/0:131,0:131:99:0,346,4585 0/0:129,1:132:99:0,331,4416 0/0:138,1:139:99:0,361,4792 0/0:120,2:123:99:0,325,4398 0/1:81,88:169:99:2489,0,2384 0/0:122,0:123:99:0,331,4404 0/0:168,0:168:99:0,454,6108 0/0:166,0:166:99:0,439,5809 0/0:160,0:160:99:0,424,5659 0/0:111,0:112:99:0,301,4006 0/0:157,0:157:99:0,424,5656 0/0:159,0:161:99:0,415,5567 0/0:119,0:119:99:0,334,4387 0/0:124,1:126:99:0,334,4424 0/0:173,0:175:99:0,457,6086 0/0:198,0:199:99:0,518,6913 0/0:61,0:62:99:0,160,2114 0/0:91,0:91:99:0,253,3270 0/0:69,0:69:99:0,178,2401 0/0:43,0:43:99:0,120,1585 0/0:49,0:49:99:0,135,1796 0/0:39,1:40:99:0,114,1508 0/0:55,0:55:99:0,147,1931 0/0:49,0:49:99:0,135,1731 0/0:90,1:92:99:0,235,3039 0/0:30,0:30:75.24:0,75,1000 0/0:61,0:61:99:0,147,1946 0/0:54,0:54:99:0,144,1877 0/0:62,0:62:99:0,160,2108 0/0:39,0:39:99:0,102,1333 0/0:39,0:39:99:0,102,1346 0/0:60,0:60:99:0,144,1907 0/0:50,0:50:99:0,120,1613 0/0:40,0:40:99:0,102,1371 0/0:35,0:36:96.32:0,96,1305 0/0:41,0:41:99:0,111,1420 0/0:41,0:41:99:0,114,1523 0/0:52,0:52:99:0,132,1768 -chr1 891620 . C A 630.55 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.211;DP=3333;Dels=0.00;FS=17.146;HRun=0;HaplotypeScore=2.5646;InbreedingCoeff=-0.0084;MQ=59.15;MQ0=0;MQRankSum=0.979;QD=8.19;ReadPosRankSum=2.951;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|4),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|4),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|);CSQ=downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:28,0:28:78.20:0,78,924 0/0:27,0:27:75.22:0,75,951 0/0:38,0:38:99:0,105,1352 0/0:34,0:34:96.25:0,96,1168 0/0:64,0:64:99:0,187,2481 0/0:67,0:67:99:0,199,2599 0/0:121,0:122:99:0,361,4776 0/0:74,0:74:99:0,220,2902 0/0:148,0:149:99:0,436,5778 0/0:158,0:158:99:0,463,6030 0/0:72,0:72:99:0,211,2767 0/0:68,0:69:99:0,199,2630 0/0:95,0:95:99:0,274,3531 0/0:57,0:57:99:0,144,1946 0/0:62,0:62:99:0,169,2188 0/0:33,0:33:87.27:0,87,1141 0/0:44,0:44:99:0,111,1488 0/0:54,0:55:99:0,129,1693 0/0:54,0:54:99:0,138,1835 0/0:49,0:49:99:0,135,1787 0/0:67,0:67:99:0,144,1983 0/0:85,0:85:99:0,217,2909 0/0:47,0:47:99:0,123,1608 0/0:53,0:53:99:0,135,1809 0/0:64,0:64:99:0,150,2016 0/0:60,0:60:99:0,153,2012 0/0:32,0:32:78.25:0,78,1045 0/0:41,0:41:99:0,111,1458 0/0:52,0:52:99:0,141,1854 0/0:53,0:53:99:0,153,1987 0/0:84,0:84:99:0,196,2622 0/0:47,0:47:99:0,126,1623 0/0:44,0:44:99:0,108,1443 0/0:61,0:61:99:0,156,2066 0/0:48,0:49:99:0,123,1639 0/0:60,0:60:99:0,150,2017 0/0:84,0:84:99:0,193,2583 0/0:89,0:89:99:0,226,3007 0/0:33,0:33:87.28:0,87,1160 0/1:46,31:77:99:678,0,1280 0/0:41,0:41:99:0,105,1378 0/0:30,0:30:75.24:0,75,974 0/0:46,0:47:99:0,114,1467 0/0:25,0:25:69.20:0,69,886 0/0:32,0:32:78.24:0,78,1014 0/0:55,0:55:99:0,141,1842 0/0:82,0:82:99:0,196,2576 0/0:11,0:11:33.11:0,33,430 0/0:47,0:47:99:0,108,1419 0/0:63,0:63:99:0,159,2045 0/0:49,0:49:99:0,132,1669 0/0:27,0:27:54.17:0,54,698 0/0:37,0:38:78.23:0,78,1022 0/0:46,0:46:99:0,117,1534 0/0:42,0:42:99:0,105,1418 0/0:23,0:23:60.20:0,60,801 0/0:30,0:30:78.25:0,78,1006 0/0:31,0:31:63.21:0,63,880 0/0:51,0:51:99:0,120,1648 0/0:29,0:29:63.20:0,63,819 -chr1 891898 . T C 58.0 . AC=2;AF=0.026;AN=78;BaseQRankSum=-1.208;DP=130;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0256;InbreedingCoeff=-0.1375;MQ=58.94;MQ0=0;MQRankSum=0.462;QD=4.46;ReadPosRankSum=-1.373;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|4),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|4),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.03:0,12,145 0/0:5,0:5:9.03:0,9,119 0/0:6,0:6:18.06:0,18,232 0/0:3,0:3:9.03:0,9,112 0/0:3,0:3:9.03:0,9,120 0/0:8,0:8:21.07:0,21,277 0/1:6,3:9:92.14:92,0,215 0/0:5,0:5:15.05:0,15,202 0/0:7,0:7:21.07:0,21,286 0/0:20,0:20:60.19:0,60,780 0/0:7,0:7:21.07:0,21,274 0/0:2,0:2:6.02:0,6,82 0/0:6,0:6:18.06:0,18,226 ./. 0/0:3,0:3:9.03:0,9,124 ./. 0/0:2,0:2:3.01:0,3,36 0/0:1,0:1:3.01:0,3,41 0/1:3,1:4:24.41:24,0,73 ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:3,0:3:9.03:0,9,121 ./. ./. 0/0:1,0:1:3.01:0,3,36 0/0:1,0:1:3.01:0,3,32 0/0:2,0:2:6.02:0,6,84 0/0:2,0:2:3.01:0,3,42 ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,38 ./. 0/0:2,0:2:6.02:0,6,82 0/0:2,0:2:6.02:0,6,83 0/0:3,0:3:9.03:0,9,116 0/0:1,0:1:3.01:0,3,40 ./. 0/0:2,0:2:6.02:0,6,83 0/0:1,0:1:3.01:0,3,40 ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:3,0:3:9.03:0,9,121 ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:3.01:0,3,42 0/0:1,0:1:3.01:0,3,38 0/0:2,0:2:6.02:0,6,82 ./. ./. -chr1 891945 . A G 1861.84 . AC=44;AF=0.550;AN=80;BaseQRankSum=-1.331;DP=117;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.1025;InbreedingCoeff=0.1989;MQ=59.45;MQ0=0;MQRankSum=-0.841;QD=24.82;ReadPosRankSum=0.357;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|4),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|4),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3.01:39,3,0 1/1:0,7:7:15.05:190,15,0 ./. 0/1:1,4:5:28.61:85,0,29 0/0:1,0:1:3.01:0,3,41 0/1:2,5:7:60.22:181,0,60 0/1:2,2:4:65.07:65,0,66 0/1:3,1:4:27.28:27,0,110 1/1:0,3:3:9.03:122,9,0 0/0:19,0:19:57.18:0,57,746 0/1:2,2:4:61.40:61,0,65 1/1:0,7:7:21.07:274,21,0 1/1:0,1:1:3.01:41,3,0 0/0:2,1:3:6.01:0,6,65 ./. 1/1:0,1:1:3.01:42,3,0 0/0:1,0:1:3.01:0,3,42 1/1:0,1:1:3.01:42,3,0 0/0:3,0:3:6.02:0,6,78 ./. ./. 1/1:0,2:2:3.01:45,3,0 ./. 1/1:0,3:3:9.03:113,9,0 ./. 0/0:1,1:2:3.01:0,3,41 0/0:2,0:2:6.02:0,6,77 ./. 1/1:0,2:2:6.02:74,6,0 1/1:0,1:2:3.01:40,3,0 1/1:0,2:2:6.02:80,6,0 ./. 0/0:2,0:2:6.02:0,6,76 ./. 0/0:1,0:1:3.01:0,3,38 ./. 0/1:1,2:3:32.73:75,0,33 ./. ./. 1/1:0,1:1:3.01:38,3,0 0/1:1,3:4:30.19:111,0,30 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 1/1:1,1:2:3.01:37,3,0 ./. ./. ./. 0/0:2,0:2:6.02:0,6,82 1/1:0,1:1:3.01:42,3,0 1/1:0,2:2:6.02:80,6,0 ./. ./. 1/1:0,1:1:3.01:37,3,0 0/0:1,0:1:3.01:0,3,41 0/1:2,1:3:30.98:31,0,67 1/1:0,2:2:6.02:67,6,0 0/0:2,0:2:6.02:0,6,76 -chr1 892095 . C T 592.96 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.068;DP=1006;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5011;InbreedingCoeff=-0.0379;MQ=59.11;MQ0=0;MQRankSum=0.441;QD=14.82;ReadPosRankSum=1.641;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|4),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|4),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:10,0:10:24.07:0,24,302 0/0:20,0:20:60.19:0,60,766 0/0:16,0:16:39.13:0,39,505 0/0:15,0:15:45.11:0,45,534 0/0:36,0:36:99:0,108,1425 0/0:31,0:31:93.28:0,93,1198 0/0:68,0:68:99:0,199,2569 0/0:37,0:37:99:0,105,1373 0/0:73,0:74:99:0,217,2820 0/0:94,0:94:99:0,265,3409 0/0:40,0:40:99:0,111,1440 0/0:40,0:40:99:0,114,1481 0/0:52,0:52:99:0,150,1937 0/0:16,0:16:42.12:0,42,537 0/0:15,0:15:39.13:0,39,519 0/0:7,0:7:18.06:0,18,232 0/0:7,0:7:21.03:0,21,233 0/0:11,0:11:30.10:0,30,401 0/0:21,0:21:57.17:0,57,737 0/0:10,0:10:30.07:0,30,373 0/1:4,5:9:99:171,0,131 0/0:12,0:12:36.12:0,36,475 0/0:8,0:8:21.07:0,21,273 0/0:8,0:8:24.07:0,24,306 0/0:14,0:14:42.12:0,42,535 0/0:12,0:13:30.09:0,30,383 0/1:8,8:16:99:194,0,245 0/0:4,1:5:12.04:0,12,154 0/0:7,0:7:21.06:0,21,267 0/0:8,0:8:24.07:0,24,306 0/0:19,0:19:45.15:0,45,599 0/0:11,0:11:30.10:0,30,399 0/0:5,0:5:15.05:0,15,198 0/1:6,9:15:99:308,0,153 0/0:12,0:12:30.08:0,30,379 0/0:15,0:15:42.14:0,42,555 0/0:16,0:16:45.15:0,45,603 0/0:19,0:19:54.17:0,54,702 0/0:5,0:5:12.04:0,12,165 0/0:12,0:12:30.10:0,30,406 0/0:13,0:13:33.10:0,33,422 0/0:8,0:8:24.07:0,24,302 0/0:7,0:7:21.07:0,21,284 0/0:1,0:1:3.01:0,3,41 0/0:8,0:8:24.08:0,24,318 0/0:5,0:5:15.05:0,15,199 0/0:5,0:5:15.05:0,15,186 0/0:6,0:6:15.05:0,15,211 0/0:9,0:9:24.08:0,24,326 0/0:22,0:22:66.18:0,66,847 0/0:12,0:12:24.07:0,24,298 0/0:7,0:7:18.06:0,18,227 0/0:21,0:21:57.17:0,57,691 0/0:5,0:5:12.04:0,12,154 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.04:0,12,162 0/0:9,0:9:27.08:0,27,353 0/0:7,0:7:21.07:0,21,279 0/0:4,0:4:12.04:0,12,161 0/0:3,0:3:6.02:0,6,84 -chr1 892141 . C T 66.06 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-2.417;DP=1605;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.9164;InbreedingCoeff=-0.0175;MQ=59.28;MQ0=0;MQRankSum=0.188;QD=3.15;ReadPosRankSum=0.854;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|4),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|4),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:9,0:10:24.07:0,24,286 0/0:21,0:21:60.16:0,60,721 0/0:23,0:23:63.18:0,63,769 0/0:18,0:18:54.16:0,54,649 0/0:56,0:56:99:0,162,2106 0/0:57,0:57:99:0,162,2095 0/0:118,0:118:99:0,340,4357 0/0:56,0:56:99:0,165,2124 0/0:123,0:124:99:0,358,4633 0/0:122,0:122:99:0,364,4652 0/0:61,0:62:99:0,178,2308 0/0:62,0:62:99:0,180,2248 0/0:77,0:77:99:0,226,2741 0/0:17,0:17:48.14:0,48,590 0/0:17,0:17:48.14:0,48,592 0/0:19,0:19:51.16:0,51,687 0/0:13,0:14:39.12:0,39,504 0/0:18,0:18:51.16:0,51,657 0/0:25,0:25:69.22:0,69,898 0/0:19,0:19:51.14:0,51,639 0/0:15,0:15:42.12:0,42,557 0/0:30,0:30:90.29:0,90,1182 0/0:20,0:20:54.15:0,54,685 0/0:16,0:16:42.11:0,42,522 0/0:21,0:21:54.17:0,54,700 0/0:22,0:22:63.20:0,63,814 0/0:24,0:24:66.19:0,66,838 0/0:9,0:9:24.08:0,24,313 0/0:22,0:22:60.19:0,60,773 0/0:23,0:23:63.21:0,63,839 0/0:24,0:24:63.20:0,63,832 0/0:19,0:19:57.18:0,57,752 0/0:13,0:13:39.12:0,39,514 0/0:29,0:29:84.26:0,84,1038 0/0:17,0:18:51.16:0,51,649 0/0:19,0:19:51.16:0,51,654 0/0:25,0:25:69.21:0,69,858 0/0:37,0:37:99:0,105,1400 0/0:6,0:7:15.05:0,15,199 0/0:21,0:21:51.16:0,51,657 0/0:17,0:17:45.14:0,45,571 0/0:14,0:14:42.10:0,42,510 0/0:16,0:16:45.13:0,45,580 0/1:9,1:10:12.05:12,0,240 0/0:12,0:12:30.10:0,30,401 0/0:6,0:6:15.02:0,15,161 0/0:11,0:11:27.09:0,27,359 0/1:6,5:11:99:113,0,172 0/0:11,0:11:21.07:0,21,283 0/0:24,0:24:66.21:0,66,853 0/0:22,0:22:57.18:0,57,752 0/0:14,0:14:33.09:0,33,424 0/0:25,0:25:69.17:0,69,833 0/0:10,0:10:24.07:0,24,317 0/0:7,0:7:21.07:0,21,274 0/0:9,0:9:18.06:0,18,238 0/0:8,0:8:24.08:0,24,308 0/0:10,0:10:27.06:0,27,333 0/0:10,0:10:30.09:0,30,388 0/0:9,0:9:21.07:0,21,275 -chr1 892237 . C A 5045.9 . AC=2;AF=0.0167;AN=120;BaseQRankSum=2.206;DP=4638;DS;Dels=0.00;FS=16.397;HRun=0;HaplotypeScore=2.4024;InbreedingCoeff=-0.0170;MQ=59.24;MQ0=0;MQRankSum=2.024;QD=16.22;ReadPosRankSum=-3.730;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|4),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|4),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:49,0:49:99:0,135,1691 0/0:61,1:62:99:0,159,1991 0/0:59,0:59:99:0,163,2106 0/0:49,0:49:99:0,129,1624 0/0:176,0:176:99:0,515,6919 0/0:141,0:141:99:0,415,5589 0/0:250,0:250:99:0,749,9938 0/0:136,0:136:99:0,397,5310 0/1:119,130:250:99:4389,0,4053 0/0:244,0:244:99:0,716,9535 0/0:198,0:198:99:0,578,7719 0/0:149,0:150:99:0,442,5884 0/0:205,0:205:99:0,608,8058 0/0:53,0:53:99:0,141,1837 0/0:100,0:100:99:0,271,3591 0/0:50,0:50:99:0,135,1752 0/0:65,0:65:99:0,160,2132 0/0:75,0:75:99:0,199,2591 0/0:80,0:80:99:0,211,2776 0/0:62,0:62:99:0,169,2232 0/0:63,0:63:99:0,172,2258 0/0:93,0:93:99:0,226,2985 0/0:71,0:71:99:0,184,2426 0/0:62,0:62:99:0,172,2274 0/0:55,0:56:99:0,150,1994 0/0:72,0:72:99:0,181,2430 0/0:75,0:75:99:0,208,2746 0/0:56,0:56:99:0,150,1995 0/0:88,0:89:99:0,226,2977 0/0:95,0:95:99:0,247,3272 0/0:105,0:105:99:0,274,3703 0/1:37,23:61:99:657,0,1210 0/0:73,1:75:99:0,199,2642 0/0:100,0:100:99:0,256,3401 0/0:63,0:63:99:0,157,2091 0/0:74,0:74:99:0,169,2286 0/0:80,0:80:99:0,211,2793 0/0:117,0:117:99:0,289,3816 0/0:25,0:25:51.15:0,51,659 0/0:43,0:44:96.26:0,96,1199 0/0:50,0:50:99:0,117,1541 0/0:43,0:43:99:0,102,1310 0/0:26,0:27:69.22:0,69,871 0/0:30,0:30:66.18:0,66,867 0/0:25,0:25:60.19:0,60,765 0/0:27,0:27:69.22:0,69,910 0/0:50,0:50:99:0,111,1450 0/0:18,0:18:42.13:0,42,514 0/0:46,0:46:99:0,99,1295 0/0:60,0:60:99:0,138,1812 0/0:49,0:49:99:0,123,1602 0/0:34,0:34:78.25:0,78,1017 0/0:49,0:49:99:0,120,1527 0/0:42,0:42:87.28:0,87,1149 0/0:25,0:25:54.14:0,54,687 0/0:34,0:34:78.25:0,78,1033 0/0:20,0:20:51.14:0,51,658 0/0:31,0:31:78.24:0,78,1010 0/0:19,0:19:39.12:0,39,512 0/0:27,0:27:60.18:0,60,782 -chr1 892460 . G C 4504.79 . AC=5;AF=0.0417;AN=120;BaseQRankSum=2.877;DP=3730;Dels=0.00;FS=1.037;HRun=0;HaplotypeScore=2.4668;InbreedingCoeff=-0.0435;MQ=59.20;MQ0=0;MQRankSum=1.411;QD=15.17;ReadPosRankSum=0.828;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|3),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|3),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|1),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:44,0:44:99:0,123,1472 0/0:49,0:49:99:0,141,1748 0/0:59,0:59:99:0,169,2182 0/0:39,0:39:99:0,108,1378 0/0:76,0:76:99:0,223,2979 0/0:84,0:84:99:0,250,3350 0/0:134,0:134:99:0,400,5387 0/1:49,38:88:99:1271,0,1657 0/0:173,0:173:99:0,515,6885 0/0:185,0:185:99:0,542,7233 0/0:74,0:74:99:0,220,2931 0/0:79,0:79:99:0,235,3037 0/0:123,0:124:99:0,367,4725 0/0:65,1:66:99:0,172,2263 0/0:96,0:96:99:0,262,3485 0/0:44,0:44:99:0,123,1578 0/0:73,0:73:99:0,202,2603 0/0:63,0:63:99:0,172,2256 0/0:71,0:71:99:0,199,2628 0/0:63,0:63:99:0,175,2256 0/0:68,0:70:99:0,193,2523 0/0:74,0:74:99:0,214,2747 0/0:55,0:55:99:0,150,1985 0/0:65,0:66:99:0,184,2409 0/0:61,0:61:99:0,169,2190 0/0:64,0:64:99:0,172,2279 0/0:62,1:63:99:0,144,2218 0/0:63,0:63:99:0,181,2346 0/0:79,0:79:99:0,214,2773 0/0:79,0:80:99:0,214,2809 0/0:92,0:92:99:0,235,3070 0/0:58,0:59:99:0,166,2122 0/1:43,37:80:99:1242,0,1301 0/1:35,37:72:99:1177,0,1076 0/0:61,0:62:99:0,169,2185 0/0:74,0:74:99:0,208,2733 0/0:79,0:80:99:0,226,2961 0/0:116,0:118:99:0,325,4357 0/0:28,0:28:78.25:0,78,1028 0/0:58,0:58:99:0,153,2005 0/0:43,0:44:99:0,123,1619 0/0:45,1:46:99:0,117,1558 0/0:35,0:35:96.26:0,96,1214 0/0:38,0:38:99:0,99,1247 0/1:14,18:33:99:608,0,388 0/0:37,0:37:99:0,99,1314 0/0:53,2:56:99:0,99,1754 0/0:24,0:24:60.15:0,60,783 0/0:26,0:26:72.23:0,72,936 0/1:15,9:24:99:206,0,463 0/0:25,0:26:57.15:0,57,725 0/0:31,0:31:72.22:0,72,939 0/0:20,1:21:54.17:0,54,710 0/0:28,0:28:75.22:0,75,959 0/0:38,0:38:99:0,102,1340 0/0:26,0:26:69.22:0,69,904 0/0:29,0:29:78.25:0,78,1028 0/0:27,0:27:78.24:0,78,1028 0/0:25,0:25:63.20:0,63,827 0/0:30,0:30:69.21:0,69,895 -chr1 892470 . C T 571.4 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.526;DP=3581;Dels=0.00;FS=5.690;HRun=0;HaplotypeScore=4.5258;InbreedingCoeff=-0.0084;MQ=59.15;MQ0=0;MQRankSum=0.418;QD=11.90;ReadPosRankSum=0.317;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|3),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|3),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|1),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:37,0:38:99:0,99,1160 0/0:42,0:42:99:0,102,1236 0/0:51,0:51:99:0,150,1894 0/0:27,0:27:78.21:0,78,992 0/0:58,0:58:99:0,166,2241 0/0:74,0:74:99:0,217,2873 0/0:112,0:112:99:0,337,4434 0/0:79,0:79:99:0,229,3044 0/0:146,0:146:99:0,436,5838 0/0:169,0:169:99:0,485,6402 0/0:68,0:68:99:0,199,2663 0/0:69,0:69:99:0,205,2701 0/0:111,0:111:99:0,325,4313 0/0:61,0:61:99:0,166,2179 0/0:89,0:89:99:0,238,3171 0/1:27,20:48:99:619,0,806 0/0:72,0:72:99:0,205,2620 0/0:58,0:58:99:0,162,2099 0/0:75,0:75:99:0,211,2744 0/0:60,0:60:99:0,166,2188 0/0:73,0:73:99:0,205,2660 0/0:67,1:68:99:0,187,2412 0/0:57,0:57:99:0,141,1845 0/0:65,0:65:99:0,175,2282 0/0:55,0:56:99:0,147,1913 0/0:64,0:64:99:0,169,2191 0/0:60,0:60:99:0,166,2161 0/0:57,0:57:99:0,160,2065 0/0:80,0:80:99:0,223,2896 0/0:81,0:81:99:0,214,2795 0/0:90,0:90:99:0,241,3142 0/0:53,0:53:99:0,153,1986 0/0:83,0:83:99:0,223,2943 0/0:64,1:65:99:0,145,2373 0/0:71,0:71:99:0,187,2491 0/0:75,1:77:99:0,205,2675 0/0:71,1:72:99:0,165,2607 0/0:119,0:119:99:0,334,4400 0/0:30,0:30:75.24:0,75,1007 0/0:53,0:53:99:0,144,1863 0/0:50,0:50:99:0,135,1804 0/0:49,0:49:99:0,123,1634 0/0:36,0:36:93.30:0,93,1212 0/0:35,0:35:90.29:0,90,1177 0/0:35,0:35:96.31:0,96,1287 0/0:41,0:41:99:0,105,1394 0/0:58,0:59:99:0,135,1754 0/0:26,0:26:60.19:0,60,775 0/0:31,0:31:75.24:0,75,1004 0/0:30,0:30:78.25:0,78,1019 0/0:27,0:27:63.20:0,63,816 0/0:32,0:32:69.21:0,69,916 0/0:24,0:24:60.18:0,60,761 0/0:28,0:28:72.22:0,72,909 0/0:42,0:42:99:0,114,1499 0/0:28,0:28:72.23:0,72,937 0/0:31,0:31:75.24:0,75,1006 0/0:27,0:27:69.21:0,69,905 0/0:31,0:31:75.21:0,75,980 0/0:36,0:36:81.25:0,81,1066 -chr1 892471 . G A 2720.48 . AC=4;AF=0.0333;AN=120;BaseQRankSum=-7.069;DP=3602;Dels=0.00;FS=2.243;HRun=0;HaplotypeScore=2.7847;InbreedingCoeff=0.4828;MQ=59.14;MQ0=0;MQRankSum=-0.017;QD=13.95;ReadPosRankSum=-0.355;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|3),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|3),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|1),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:37,0:37:96.26:0,96,1141 0/0:40,0:42:99:0,102,1257 0/0:52,0:52:99:0,153,1876 0/0:26,0:27:72.20:0,72,906 0/0:58,0:58:99:0,166,2233 0/0:74,0:74:99:0,214,2818 0/1:59,51:110:99:1407,0,1961 0/0:78,0:78:99:0,223,2903 0/0:141,1:142:99:0,384,5560 0/0:160,0:160:99:0,448,5870 0/0:66,1:67:99:0,163,2446 0/0:67,0:67:99:0,199,2549 0/0:111,1:112:99:0,284,4072 0/0:60,0:61:99:0,165,2118 0/0:89,0:89:99:0,235,3108 0/0:49,0:49:99:0,135,1738 0/0:75,0:75:99:0,199,2585 0/0:59,0:59:99:0,153,2003 0/0:78,0:78:99:0,217,2813 0/0:62,0:63:99:0,159,2079 0/0:74,1:75:99:0,199,2585 0/0:69,0:70:99:0,196,2527 0/0:57,0:57:99:0,144,1915 0/0:65,0:65:99:0,163,2121 0/0:53,0:53:99:0,138,1773 0/0:62,0:62:99:0,160,2113 0/0:61,0:61:99:0,160,2079 0/1:33,26:59:99:705,0,941 0/0:82,0:83:99:0,223,2925 0/0:83,0:83:99:0,217,2793 0/0:90,0:91:99:0,241,3112 0/0:55,0:55:99:0,156,2004 0/0:85,0:85:99:0,220,2915 0/0:67,0:67:99:0,190,2505 0/0:71,0:71:99:0,187,2465 0/0:77,0:77:99:0,199,2612 0/0:72,0:73:99:0,202,2685 0/0:117,0:117:99:0,319,4207 0/0:30,0:30:75.24:0,75,999 0/0:53,0:54:99:0,141,1848 0/0:50,0:50:99:0,135,1798 0/0:50,0:50:99:0,129,1695 0/0:38,0:38:93.28:0,93,1198 0/0:35,0:35:90.28:0,90,1178 0/0:38,0:38:96.30:0,96,1274 0/0:41,0:41:99:0,102,1338 0/0:58,0:60:99:0,138,1798 1/1:2,21:26:57.17:708,57,0 0/0:31,0:31:72.23:0,72,958 0/0:31,0:32:81.25:0,81,1050 0/0:27,0:27:60.16:0,60,746 0/0:34,0:34:75.24:0,75,990 0/0:24,0:25:60.17:0,60,747 0/0:26,0:26:63.19:0,63,811 0/0:42,0:43:99:0,117,1540 0/0:29,0:29:72.22:0,72,941 0/0:30,0:31:78.24:0,78,1029 0/0:29,0:29:75.23:0,75,981 0/0:31,0:31:72.23:0,72,958 0/0:37,0:38:87.26:0,87,1131 -chr1 892724 . C T 85.66 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.766;DP=1274;Dels=0.00;FS=3.424;HRun=1;HaplotypeScore=0.8538;InbreedingCoeff=-0.0064;MQ=58.33;MQ0=0;MQRankSum=0.065;QD=14.28;ReadPosRankSum=-0.872;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|1),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|2),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|1/17||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.05:0,15,201 0/0:3,0:3:9.02:0,9,103 0/0:8,0:8:24.08:0,24,313 0/0:6,0:6:18.06:0,18,232 0/0:10,0:10:30.10:0,30,411 0/0:8,0:8:24.08:0,24,327 0/0:15,0:15:45.14:0,45,581 0/0:6,0:6:18.06:0,18,245 0/0:26,0:26:78.25:0,78,1027 0/0:34,0:34:99:0,102,1347 0/0:9,0:9:27.09:0,27,352 0/0:9,0:9:27.09:0,27,359 0/0:14,0:14:42.13:0,42,546 0/0:21,0:21:57.18:0,57,752 0/0:37,0:37:99:0,99,1304 0/0:18,0:18:51.14:0,51,657 0/0:36,0:36:96.30:0,96,1251 0/0:21,0:21:54.17:0,54,705 0/0:33,0:33:90.25:0,90,1157 0/0:27,0:27:75.24:0,75,980 0/0:22,0:22:57.18:0,57,760 0/0:27,0:27:72.23:0,72,964 0/0:29,0:29:72.23:0,72,960 0/0:28,0:28:78.24:0,78,1018 0/0:22,0:22:63.21:0,63,846 0/0:26,0:26:69.21:0,69,910 0/0:16,0:16:45.13:0,45,585 0/0:22,0:23:63.20:0,63,815 0/0:27,0:27:78.25:0,78,1020 0/0:27,0:27:81.22:0,81,1029 0/0:22,0:22:60.16:0,60,786 0/0:9,0:9:24.08:0,24,330 0/0:27,0:27:63.20:0,63,816 0/0:28,0:28:75.18:0,75,961 0/0:16,0:16:48.16:0,48,654 0/0:14,0:14:30.08:0,30,387 0/0:16,0:16:42.14:0,42,568 0/0:34,0:34:93.29:0,93,1221 0/0:19,0:19:51.14:0,51,646 0/0:26,0:26:72.15:0,72,886 0/0:27,0:27:75.23:0,75,969 0/0:29,0:29:75.23:0,75,973 0/0:23,0:23:66.19:0,66,843 0/0:22,0:22:57.18:0,57,750 0/0:14,0:14:42.13:0,42,550 0/0:18,0:18:54.15:0,54,684 0/0:48,0:49:99:0,111,1488 0/1:2,4:6:26.71:133,0,27 0/0:21,0:21:48.15:0,48,634 0/0:18,0:18:42.13:0,42,529 0/0:32,0:32:75.24:0,75,1000 0/0:21,0:21:54.12:0,54,653 0/0:22,0:22:54.14:0,54,672 0/0:18,0:18:45.15:0,45,615 0/0:26,0:26:72.21:0,72,934 0/0:24,0:24:63.20:0,63,838 0/0:23,0:23:54.17:0,54,705 0/0:31,0:31:72.23:0,72,951 0/0:20,0:20:45.15:0,45,612 0/0:24,0:24:60.19:0,60,798 -chr1 892745 . G A 33455.23 . AC=115;AF=0.9583;AN=120;BaseQRankSum=-1.159;DP=989;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3493;InbreedingCoeff=-0.0478;MQ=58.30;MQ0=0;MQRankSum=0.300;QD=33.83;ReadPosRankSum=-0.595;EFF=DOWNSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|1),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|2),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,downstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|1/17||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,5:5:15.05:187,15,0 1/1:0,4:4:9.03:120,9,0 1/1:0,5:5:15.05:200,15,0 1/1:0,5:5:15.03:178,15,0 1/1:0,5:5:15.05:202,15,0 1/1:0,11:11:33.11:449,33,0 1/1:0,13:13:39.13:522,39,0 1/1:0,5:5:15.05:204,15,0 1/1:0,20:20:60.20:813,60,0 0/1:8,16:24:99:562,0,257 1/1:0,8:8:24.08:320,24,0 1/1:0,6:6:18.06:231,18,0 1/1:0,16:16:45.14:590,45,0 1/1:0,18:18:48.14:637,48,0 1/1:0,32:33:84.27:1131,84,0 1/1:0,15:15:42.13:557,42,0 1/1:0,26:26:72.23:958,72,0 1/1:0,12:12:33.11:445,33,0 1/1:0,26:26:72.22:940,72,0 1/1:0,19:19:57.18:752,57,0 1/1:0,17:17:48.15:628,48,0 1/1:0,18:18:48.16:647,48,0 0/1:10,12:22:99:409,0,299 1/1:0,22:22:57.19:769,57,0 1/1:0,17:17:45.14:591,45,0 1/1:0,22:22:60.19:797,60,0 1/1:0,15:15:36.12:487,36,0 1/1:0,15:15:42.13:547,42,0 1/1:0,23:23:63.17:805,63,0 1/1:0,17:17:51.17:681,51,0 1/1:0,14:14:42.13:534,42,0 1/1:0,6:6:15.05:203,15,0 1/1:0,23:23:57.16:747,57,0 1/1:0,19:19:51.15:664,51,0 1/1:0,14:14:42.14:559,42,0 1/1:0,12:12:33.08:417,33,0 1/1:0,13:13:33.09:432,33,0 1/1:0,23:23:60.20:829,60,0 1/1:0,17:17:45.15:605,45,0 1/1:0,18:18:51.16:664,51,0 1/1:0,22:22:63.18:809,63,0 0/1:15,9:24:99:274,0,445 1/1:0,22:22:60.18:767,60,0 1/1:0,17:17:51.15:655,51,0 1/1:0,13:13:33.11:442,33,0 1/1:0,12:12:36.11:452,36,0 1/1:0,34:34:96.31:1257,96,0 1/1:0,6:6:12.04:157,12,0 1/1:0,16:16:39.12:496,39,0 1/1:0,17:17:36.11:455,36,0 0/1:14,12:26:99:344,0,411 1/1:1,17:18:9.49:443,9,0 1/1:0,16:16:42.13:551,42,0 1/1:0,12:12:33.11:437,33,0 1/1:0,17:17:51.16:677,51,0 1/1:0,17:17:51.16:677,51,0 0/1:5,10:15:99:347,0,109 1/1:0,27:27:72.23:940,72,0 1/1:0,22:22:57.17:752,57,0 1/1:0,13:13:39.13:509,39,0 -chr1 893719 . G A 126.7 . AC=10;AF=0.833;AN=12;BaseQRankSum=-0.198;DP=10;Dels=0.00;FS=3.680;HRun=0;HaplotypeScore=0.1223;MQ=57.66;MQ0=0;MQRankSum=-1.495;QD=21.12;ReadPosRankSum=0.198;EFF=EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|2),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|1),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|2),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000469563|2/2||||retained_intron|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000477976|1/17||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3:25,3,0 ./. 1/1:0,1:1:3.01:35,3,0 1/1:0,1:1:3.01:42,3,0 ./. ./. 1/1:0,2:2:3.01:31,3,0 ./. ./. ./. ./. ./. 0/0:3,0:3:6.02:0,6,79 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 894027 . G A 256.69 . AC=1;AF=0.012;AN=82;BaseQRankSum=-0.446;DP=427;Dels=0.00;FS=4.334;HRun=2;HaplotypeScore=0.2194;InbreedingCoeff=-0.0706;MQ=57.55;MQ0=0;MQRankSum=0.775;QD=18.34;ReadPosRankSum=-0.924;EFF=EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|2),INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|2),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|2),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000469563|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,78 0/0:7,0:7:21.07:0,21,276 0/0:9,0:9:27.09:0,27,354 0/0:10,0:10:30.10:0,30,389 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,79 0/0:4,0:4:12.04:0,12,165 0/0:6,0:6:18.06:0,18,235 0/0:2,0:2:6.02:0,6,80 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. 0/0:1,0:1:3.01:0,3,35 ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,32 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 0/0:14,0:15:42.14:0,42,559 0/0:35,0:35:93.29:0,93,1220 0/0:24,0:24:72.22:0,72,911 0/1:5,9:14:99:302,0,146 0/0:20,0:20:57.15:0,57,692 0/0:14,0:14:39.13:0,39,528 0/0:15,0:16:45.15:0,45,593 0/0:17,0:17:45.14:0,45,591 0/0:34,0:34:90.27:0,90,1167 0/0:12,0:13:27.08:0,27,340 0/0:18,0:18:39.12:0,39,509 0/0:6,0:6:12.04:0,12,156 0/0:17,0:18:42.11:0,42,518 0/0:9,0:9:24.05:0,24,275 0/0:8,0:8:18.06:0,18,226 0/0:22,0:22:60.19:0,60,781 0/0:11,0:11:27.09:0,27,364 0/0:16,0:16:48.16:0,48,640 0/0:15,0:15:39.10:0,39,495 0/0:19,0:19:45.12:0,45,575 0/0:16,0:16:39.11:0,39,495 0/0:13,0:13:36.09:0,36,449 -chr1 894330 . G A 79.5 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.248;DP=1450;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7814;InbreedingCoeff=-0.0087;MQ=58.82;MQ0=0;MQRankSum=0.499;QD=7.23;ReadPosRankSum=0.368;EFF=EXON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|2),EXON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P53L|749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,missense_variant|cCg/cTg|P/L|ENSG00000188976|NOC2L|ENST00000327044|2/19|benign(0.001)|tolerated(0.41)|53/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000469563|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|2/7||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:13,0:14:30.06:0,30,328 0/0:15,0:16:42.09:0,42,473 0/0:15,0:15:39.11:0,39,460 0/0:13,0:13:27.05:0,27,310 0/0:29,0:29:81.24:0,81,1018 0/0:18,0:18:48.15:0,48,620 0/0:50,0:51:99:0,150,1840 0/0:31,0:31:81.24:0,81,1021 0/0:64,0:64:99:0,187,2348 0/0:60,1:61:99:0,168,2121 0/0:38,0:38:99:0,108,1367 0/0:36,0:36:99:0,99,1279 0/0:41,0:41:99:0,114,1452 0/0:19,0:19:45.14:0,45,586 0/0:15,0:15:39.13:0,39,510 0/0:11,0:11:30.09:0,30,372 0/0:11,0:11:27.09:0,27,372 0/0:24,0:24:60.18:0,60,779 0/0:17,0:17:45.15:0,45,593 0/0:15,0:15:42.12:0,42,525 0/0:25,0:25:66.20:0,66,850 0/0:20,0:20:60.19:0,60,786 0/0:22,0:22:54.17:0,54,714 0/0:22,0:23:54.17:0,54,718 0/0:21,0:21:51.16:0,51,660 0/0:18,0:18:42.14:0,42,562 0/0:27,0:27:66.21:0,66,871 0/0:15,0:15:36.12:0,36,475 0/0:24,0:24:60.19:0,60,795 0/0:16,1:17:39.12:0,39,513 0/0:25,0:25:66.21:0,66,868 0/0:11,0:11:21.05:0,21,263 0/0:24,0:24:63.20:0,63,819 0/0:18,0:18:42.14:0,42,561 0/1:7,4:11:99:127,0,215 0/0:21,0:21:48.16:0,48,642 0/0:31,2:34:39.49:0,39,1011 0/0:33,0:33:81.25:0,81,1066 0/0:20,0:21:54.17:0,54,693 0/0:28,0:29:72.20:0,72,887 0/0:26,0:26:69.20:0,69,883 0/0:20,0:20:48.14:0,48,586 0/0:15,0:15:42.13:0,42,524 0/0:19,0:19:45.14:0,45,594 0/0:21,0:22:57.19:0,57,762 0/0:22,0:22:63.20:0,63,805 0/0:40,0:40:99:0,102,1331 0/0:16,0:16:36.12:0,36,490 0/0:25,0:25:54.17:0,54,704 0/0:42,0:42:99:0,99,1280 0/0:31,0:31:84.27:0,84,1102 0/0:25,0:25:66.20:0,66,844 0/0:37,0:37:93.29:0,93,1224 0/0:23,0:23:54.17:0,54,705 0/0:23,0:23:60.18:0,60,770 0/0:18,0:18:42.12:0,42,529 0/0:20,0:20:54.16:0,54,672 0/0:18,0:18:42.11:0,42,523 0/0:22,0:22:45.14:0,45,573 0/0:8,0:8:18.06:0,18,241 -chr1 894519 . G A 127.69 . AC=2;AF=0.0167;AN=120;BaseQRankSum=0.782;DP=1334;Dels=0.00;FS=1.737;HRun=1;HaplotypeScore=0.3864;InbreedingCoeff=-0.0205;MQ=58.98;MQ0=0;MQRankSum=0.710;QD=6.72;ReadPosRankSum=0.813;EFF=INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|1),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|1),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|1),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12.04:0,12,161 0/0:12,0:12:33.10:0,33,413 0/0:15,0:15:45.14:0,45,587 0/0:13,0:13:39.11:0,39,477 0/0:31,0:31:90.29:0,90,1199 0/0:19,0:19:57.19:0,57,772 0/0:53,0:53:99:0,160,2131 0/0:22,0:22:63.21:0,63,847 0/0:73,0:73:99:0,220,2897 0/0:76,0:76:99:0,223,2978 0/0:30,0:30:84.27:0,84,1121 0/0:30,0:30:90.29:0,90,1203 0/0:38,0:38:99:0,111,1479 0/0:26,0:26:72.23:0,72,952 0/0:29,0:29:81.24:0,81,1081 0/0:14,0:14:33.11:0,33,433 0/0:24,0:24:63.20:0,63,844 0/0:27,0:27:72.21:0,72,907 0/0:31,0:31:78.26:0,78,1050 0/0:28,0:28:72.23:0,72,955 0/0:24,0:24:66.21:0,66,858 0/0:37,0:37:90.26:0,90,1182 0/0:29,0:29:72.22:0,72,938 0/0:29,0:29:69.20:0,69,927 0/0:23,0:23:57.16:0,57,744 0/0:27,0:27:60.20:0,60,818 0/0:25,0:25:66.21:0,66,856 0/0:19,0:19:54.17:0,54,703 0/0:40,0:40:99:0,99,1331 0/0:27,0:27:66.22:0,66,900 0/0:41,0:41:99:0,114,1522 0/0:36,0:36:96.30:0,96,1258 0/0:28,0:28:78.25:0,78,1009 0/0:31,0:31:75.24:0,75,987 0/0:17,0:17:45.14:0,45,576 0/0:18,0:18:51.16:0,51,673 0/0:30,0:30:78.25:0,78,1032 0/0:48,0:48:99:0,123,1637 0/0:9,0:9:24.08:0,24,311 0/0:14,0:14:36.11:0,36,461 0/0:12,0:12:24.07:0,24,314 0/1:5,3:8:97.65:98,0,131 0/0:8,0:8:24.07:0,24,301 0/0:5,0:5:12.03:0,12,153 0/0:6,0:6:15.05:0,15,198 0/0:6,0:6:18.05:0,18,219 0/0:13,0:13:39.11:0,39,477 0/0:4,0:4:12.04:0,12,147 0/0:8,0:8:21.06:0,21,264 0/0:24,0:25:57.18:0,57,755 0/0:17,0:17:45.14:0,45,566 0/0:9,0:9:24.06:0,24,288 0/0:10,0:10:27.09:0,27,355 0/0:6,0:6:15.04:0,15,182 0/0:14,0:14:36.12:0,36,475 0/0:5,0:5:15.04:0,15,188 0/1:6,5:11:95.48:95,0,212 0/0:5,0:5:12.04:0,12,162 0/0:8,0:8:18.06:0,18,237 0/0:6,0:6:15.05:0,15,190 -chr1 894573 . G A 31559.56 . AC=101;AF=0.8417;AN=120;BaseQRankSum=-0.317;DP=1219;Dels=0.00;FS=2.978;HRun=0;HaplotypeScore=0.8111;InbreedingCoeff=0.1756;MQ=58.45;MQ0=0;MQRankSum=-0.591;QD=27.47;ReadPosRankSum=-0.806;EFF=INTRON(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|1),INTRON(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|1),INTRON(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|1),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,intron_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,5:5:15.03:170,15,0 1/1:0,11:11:27.05:304,27,0 1/1:0,12:12:33.07:390,33,0 1/1:0,11:11:24.08:315,24,0 1/1:0,14:14:42.13:535,42,0 1/1:0,19:19:57.19:759,57,0 1/1:0,37:37:99:1384,105,0 0/1:8,11:19:99:341,0,255 1/1:0,44:44:99:1670,129,0 0/1:27,19:46:99:580,0,873 1/1:0,33:33:96.30:1244,96,0 1/1:0,17:18:51.16:675,51,0 1/1:2,24:27:34.58:873,35,0 1/1:0,25:25:60.20:803,60,0 1/1:0,25:26:60.20:800,60,0 1/1:0,16:16:33.09:426,33,0 1/1:0,20:20:51.15:657,51,0 1/1:0,31:32:81.22:1026,81,0 1/1:0,30:30:75.23:962,75,0 1/1:0,35:36:78.24:1033,78,0 0/1:11,10:22:99:295,0,267 1/1:0,39:39:90.26:1156,90,0 0/1:12,19:31:99:410,0,264 1/1:0,22:22:57.16:745,57,0 1/1:0,17:17:45.07:526,45,0 1/1:0,30:30:72.22:917,72,0 0/0:29,0:29:78.25:0,78,1017 0/1:6,17:23:99:459,0,137 1/1:0,33:33:78.24:1026,78,0 1/1:0,23:24:60.15:741,60,0 1/1:0,44:44:99:1378,105,0 1/1:0,33:33:63.20:833,63,0 0/1:21,17:38:99:422,0,606 0/0:36,0:36:78.25:0,78,1041 0/1:11,7:18:99:150,0,360 1/1:0,29:29:63.20:840,63,0 0/1:15,18:33:99:489,0,414 1/1:0,32:32:81.24:1053,81,0 1/1:0,13:13:36.07:434,36,0 1/1:0,6:6:15.05:186,15,0 1/1:0,8:8:21.07:271,21,0 0/1:1,6:7:20.52:167,0,21 1/1:0,11:11:21.07:282,21,0 1/1:0,8:8:18.05:224,18,0 0/1:1,3:4:17.59:101,0,18 1/1:0,9:9:27.05:314,27,0 1/1:0,9:10:21.07:262,21,0 0/0:5,0:5:15.04:0,15,178 1/1:0,6:6:15.05:190,15,0 0/1:6,10:16:99:185,0,190 0/1:10,9:19:99:234,0,254 1/1:0,13:13:33.09:391,33,0 1/1:0,16:16:30.10:388,30,0 1/1:0,9:9:21.06:267,21,0 1/1:0,11:11:30.10:396,30,0 1/1:0,6:6:12.04:159,12,0 0/1:2,6:8:15.38:180,0,15 1/1:0,5:5:9.03:131,9,0 1/1:0,7:7:18.05:216,18,0 1/1:0,7:7:15.04:193,15,0 -chr1 894719 . C T 134.46 . AC=5;AF=0.0463;AN=108;BaseQRankSum=-1.930;DP=230;Dels=0.00;FS=6.502;HRun=0;HaplotypeScore=0.2397;InbreedingCoeff=0.1830;MQ=54.07;MQ0=0;MQRankSum=-0.173;QD=8.40;ReadPosRankSum=1.316;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:3.01:0,3,33 0/0:3,0:3:9.03:0,9,102 ./. ./. 0/0:3,0:3:9.03:0,9,121 0/0:4,0:4:9.03:0,9,116 0/0:4,0:4:9.03:0,9,117 0/0:10,0:10:18.06:0,18,233 0/0:13,0:13:33.08:0,33,398 0/0:2,0:2:6.02:0,6,78 0/0:3,0:3:9.03:0,9,116 0/0:2,0:2:6.02:0,6,70 0/0:1,0:1:3.01:0,3,40 0/0:3,0:3:9.03:0,9,124 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,73 0/0:4,0:4:12.04:0,12,149 0/0:12,0:12:33.10:0,33,426 ./. 1/1:0,3:3:6.02:68,6,0 0/0:3,0:3:9.03:0,9,117 0/0:6,0:6:15.05:0,15,186 0/0:5,0:5:15.05:0,15,189 0/0:6,0:6:12.02:0,12,138 0/0:9,0:9:21.07:0,21,283 1/1:0,4:4:12.04:145,12,0 0/0:3,0:3:6.02:0,6,74 0/0:6,0:6:18.06:0,18,240 0/0:3,0:3:9.02:0,9,103 0/0:11,0:11:30.08:0,30,375 0/0:4,0:4:12.03:0,12,150 0/0:13,0:13:36.10:0,36,460 0/1:7,2:9:9.37:9,0,214 0/0:5,0:5:15.05:0,15,184 0/0:11,0:11:24.07:0,24,298 0/0:9,0:10:24.08:0,24,312 0/0:2,0:2:6.02:0,6,73 0/0:5,0:5:12.04:0,12,164 0/0:3,0:3:9.02:0,9,100 0/0:4,0:4:12.04:0,12,155 ./. 0/0:2,0:2:6.02:0,6,80 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:6.02:0,6,82 0/0:2,0:2:3.01:0,3,40 0/0:6,0:6:15.05:0,15,198 0/0:1,0:1:3.01:0,3,41 ./. 0/0:2,0:2:6.02:0,6,78 0/0:5,0:5:12.04:0,12,156 0/0:1,0:1:3.01:0,3,42 0/0:3,0:3:9.03:0,9,112 0/0:1,0:1:3.01:0,3,37 0/0:2,0:2:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 -chr1 894890 . A AAGAC 433.26 . AC=10;AF=1.00;AN=10;DP=6;FS=0.000;HRun=0;HaplotypeScore=9.9355;MQ=29.00;MQ0=0;QD=72.21;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:1,0:1:3.01:80,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:80,3,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:80,3,0 1/1:0,2:2:6.02:160,6,0 ./. ./. 1/1:0,1:1:3.01:80,3,0 ./. ./. ./. ./. -chr1 895706 . G A 654.83 . AC=24;AF=0.857;AN=28;BaseQRankSum=-0.382;DP=28;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.1332;InbreedingCoeff=0.2034;MQ=55.74;MQ0=0;MQRankSum=1.582;QD=26.19;ReadPosRankSum=1.255;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3.01:41,3,0 1/1:0,3:3:6.02:79,6,0 1/1:0,10:10:18.06:233,18,0 1/1:0,2:2:3:29,3,0 1/1:0,1:1:3.01:40,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,41 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 ./. ./. 1/1:0,2:2:6.02:77,6,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3:28,3,0 ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:36,3,0 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 ./. -chr1 895755 . A AG 836.52 . AC=32;AF=0.941;AN=34;BaseQRankSum=-1.595;DP=39;FS=0.000;HRun=6;HaplotypeScore=8.1200;InbreedingCoeff=0.0511;MQ=54.87;MQ0=0;MQRankSum=1.595;QD=24.60;ReadPosRankSum=-1.456;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:1,3:4:6.02:75,6,0 1/1:0,2:2:3.01:38,3,0 1/1:2,3:5:6.02:76,6,0 1/1:1,3:4:6.02:75,6,0 1/1:0,1:1:3.01:38,3,0 1/1:0,2:2:6.02:76,6,0 1/1:0,1:1:3.01:38,3,0 ./. 1/1:0,1:1:3.01:38,3,0 1/1:2,1:3:3.01:38,3,0 1/1:0,4:4:12.04:151,12,0 ./. 1/1:0,2:2:6.02:75,6,0 1/1:1,0:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 1/1:0,1:1:3.01:38,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,31 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 ./. ./. ./. ./. ./. ./. ./. -chr1 896476 . A G 230.97 . AC=14;AF=1.000;AN=14;DP=11;Dels=0.00;FS=0.000;HRun=4;HaplotypeScore=0.0000;MQ=57.87;MQ0=0;QD=21.00;EFF=INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|1),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|1),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 1/1:0,2:2:3.01:45,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:33,3,0 ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:39,3,0 ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:37,3,0 ./. ./. ./. ./. ./. -chr1 896950 . C A 1565.88 . AC=3;AF=0.0273;AN=110;BaseQRankSum=-1.726;DP=1397;Dels=0.00;FS=5.899;HRun=0;HaplotypeScore=0.8800;InbreedingCoeff=-0.0557;MQ=59.13;MQ0=0;MQRankSum=0.483;QD=13.27;ReadPosRankSum=2.665;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|1),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|1),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|2),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|1/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,79 0/0:5,0:5:12.04:0,12,145 0/0:5,0:5:15.03:0,15,172 0/0:13,0:13:33.11:0,33,423 0/0:31,0:31:87.29:0,87,1173 0/0:25,0:25:72.23:0,72,933 0/0:48,0:48:99:0,144,1906 0/0:25,0:25:75.23:0,75,968 0/0:54,0:54:99:0,160,2072 0/0:52,0:52:99:0,156,2017 0/0:23,0:23:63.20:0,63,815 0/0:24,0:25:69.22:0,69,877 0/0:39,0:39:99:0,111,1448 0/0:41,0:41:99:0,114,1450 0/0:32,0:32:90.29:0,90,1186 0/0:26,0:26:66.21:0,66,867 0/0:31,0:31:81.25:0,81,1064 0/0:40,0:42:96.30:0,96,1264 0/0:54,0:54:99:0,135,1788 0/0:32,0:32:81.23:0,81,1050 0/1:19,22:41:99:578,0,606 0/0:47,0:47:99:0,126,1668 0/0:44,0:45:99:0,102,1381 0/0:30,0:30:75.21:0,75,974 0/0:46,0:47:99:0,120,1602 0/0:34,0:34:87.27:0,87,1152 0/1:13,21:34:99:635,0,380 0/0:32,0:32:90.28:0,90,1164 0/0:50,0:50:99:0,126,1610 0/0:31,0:32:72.23:0,72,934 0/0:50,0:50:99:0,129,1705 0/0:32,0:32:78.24:0,78,1027 0/0:36,1:38:93.28:0,93,1211 0/1:26,16:43:99:431,0,774 0/0:31,0:31:75.24:0,75,997 0/0:34,0:34:99:0,102,1321 0/0:33,0:34:96.30:0,96,1248 0/0:67,0:67:99:0,178,2351 0/0:3,0:3:9.03:0,9,118 0/0:9,0:9:21.07:0,21,285 0/0:5,0:5:15.05:0,15,197 0/0:4,0:4:12.04:0,12,147 ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. 0/0:4,0:4:6.02:0,6,83 0/0:1,0:1:3:0,3,28 ./. 0/0:8,0:8:21.07:0,21,266 0/0:2,0:2:6.02:0,6,81 0/0:5,0:5:12.04:0,12,160 0/0:6,0:6:12.04:0,12,152 ./. 0/0:11,0:11:24.08:0,24,319 0/0:4,0:4:12.04:0,12,162 0/0:3,0:3:9.03:0,9,111 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,41 -chr1 896977 . G C 992.92 . AC=1;AF=0.0086;AN=116;BaseQRankSum=3.226;DP=1654;Dels=0.00;FS=64.681;HRun=1;HaplotypeScore=1.1124;InbreedingCoeff=-0.0302;MQ=59.13;MQ0=0;MQRankSum=0.693;QD=19.09;ReadPosRankSum=-3.945;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|1),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|1),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|2),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|1/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.04:0,12,146 0/0:5,0:5:15.05:0,15,184 0/0:8,0:8:18.06:0,18,226 0/0:5,0:5:15.04:0,15,176 0/0:24,0:24:69.23:0,69,935 0/0:17,0:17:48.16:0,48,639 0/0:39,0:39:99:0,117,1515 0/0:17,0:17:51.15:0,51,650 0/0:48,0:48:99:0,141,1890 0/1:21,31:52:99:1040,0,689 0/0:27,0:27:75.23:0,75,971 0/0:21,0:21:57.18:0,57,753 0/0:30,0:30:78.25:0,78,1013 0/0:46,0:46:99:0,126,1543 0/0:44,0:44:99:0,114,1477 0/0:31,0:31:78.21:0,78,980 0/0:41,0:41:99:0,99,1307 0/0:56,0:56:99:0,132,1736 0/0:64,0:64:99:0,156,2036 0/0:47,0:47:99:0,114,1470 0/0:53,0:53:99:0,135,1741 0/0:71,0:71:99:0,187,2415 0/0:50,0:50:99:0,129,1647 0/0:41,0:41:93.29:0,93,1238 0/0:56,0:57:99:0,147,1885 0/0:41,0:41:99:0,114,1498 0/0:53,0:53:99:0,138,1804 0/0:31,0:31:78.24:0,78,1015 0/0:58,0:58:99:0,144,1786 0/0:41,0:41:96.29:0,96,1253 0/0:64,0:64:99:0,163,2098 0/0:47,0:48:99:0,111,1477 0/0:55,0:55:99:0,138,1783 0/0:56,0:56:99:0,135,1763 0/0:46,0:46:99:0,111,1452 0/0:40,0:40:99:0,108,1346 0/0:41,0:41:99:0,102,1338 0/0:85,0:85:99:0,220,2841 0/0:4,0:4:12.04:0,12,149 0/0:7,0:7:18.05:0,18,226 0/0:9,0:9:21.07:0,21,272 0/0:4,0:4:9.03:0,9,126 ./. ./. 0/0:2,0:2:6.02:0,6,76 0/0:3,0:3:6.02:0,6,85 0/0:8,0:8:21.05:0,21,262 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,40 0/0:11,0:11:27.08:0,27,332 0/0:3,0:3:9.03:0,9,112 0/0:4,0:4:12.04:0,12,144 0/0:9,0:9:21.07:0,21,274 0/0:5,0:5:15.05:0,15,192 0/0:8,0:8:15.05:0,15,197 0/0:3,0:3:9.03:0,9,117 0/0:5,0:5:15.04:0,15,188 0/0:3,0:3:9.02:0,9,105 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:6.02:0,6,83 -chr1 897325 . G C 125121.37 . AC=109;AF=0.9083;AN=120;BaseQRankSum=2.562;DP=4268;Dels=0.00;FS=6.072;HRun=1;HaplotypeScore=2.5759;InbreedingCoeff=0.0992;MQ=58.65;MQ0=0;MQRankSum=-0.923;QD=29.72;ReadPosRankSum=-2.769;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A203|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|),UTR_5_PRIME(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|3);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,synonymous_variant|gcG/gcC|A|ENSG00000187961|KLHL17|ENST00000338591|4/12|||203/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,13:13:36.10:429,36,0 1/1:0,13:13:33.08:400,33,0 1/1:0,19:19:57.15:703,57,0 1/1:0,14:15:36.10:423,36,0 1/1:0,37:37:99:1450,111,0 1/1:0,35:35:99:1326,102,0 1/1:0,67:67:99:2587,196,0 1/1:0,37:37:99:1483,111,0 1/1:0,88:88:99:3464,262,0 0/1:36,48:84:99:1625,0,1101 1/1:0,44:44:99:1715,129,0 1/1:0,52:52:99:1840,147,0 1/1:0,55:55:99:2063,162,0 1/1:0,67:67:99:2126,163,0 1/1:0,48:48:99:1503,117,0 1/1:0,29:29:72.21:900,72,0 1/1:0,53:53:99:1802,135,0 1/1:1,68:69:99:2134,166,0 1/1:0,56:56:99:1639,123,0 1/1:0,44:44:93.28:1211,93,0 0/1:24,27:51:99:638,0,502 1/1:0,52:52:99:1743,138,0 0/1:26,22:48:99:549,0,698 1/1:0,44:44:99:1474,111,0 1/1:0,57:57:99:1871,141,0 1/1:0,44:44:99:1351,102,0 0/1:38,42:81:99:1189,0,954 0/1:26,21:47:99:546,0,661 1/1:0,56:57:99:1572,117,0 1/1:0,59:59:99:1896,144,0 1/1:0,83:83:99:2650,202,0 1/1:0,45:45:99:1455,111,0 1/1:0,48:48:99:1444,111,0 0/1:31,20:51:99:589,0,726 1/1:0,40:40:99:1289,99,0 1/1:0,43:43:99:1312,99,0 1/1:0,74:74:99:2328,184,0 1/1:0,86:86:99:2741,211,0 1/1:0,92:92:99:2924,226,0 1/1:0,136:138:99:4396,340,0 1/1:1,102:103:99:3346,259,0 0/1:46,59:105:99:1633,0,1181 1/1:0,90:90:99:3201,247,0 1/1:1,79:80:99:2518,196,0 1/1:0,85:85:99:2946,229,0 1/1:0,125:125:99:4051,313,0 1/1:3,172:175:99:5550,364,0 0/0:58,0:58:99:0,138,1767 1/1:0,133:133:99:3978,310,0 1/1:0,154:154:99:5088,400,0 0/1:75,74:149:99:2111,0,2148 1/1:0,123:123:99:4054,322,0 1/1:0,126:126:99:4315,334,0 1/1:0,96:96:99:2916,232,0 1/1:0,107:107:99:3545,274,0 1/1:1,77:78:99:2497,199,0 0/1:38,29:67:99:734,0,975 1/1:1,88:90:99:2816,188,0 1/1:0,73:74:99:2361,184,0 1/1:0,84:84:99:2679,202,0 -chr1 897337 . C T 1277.99 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.453;DP=4287;Dels=0.00;FS=8.422;HRun=0;HaplotypeScore=2.3521;InbreedingCoeff=-0.0084;MQ=58.59;MQ0=0;MQRankSum=0.646;QD=14.36;ReadPosRankSum=0.556;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),START_GAINED(LOW||||412|KLHL17|protein_coding|CODING|ENST00000455747|3),SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S207|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,synonymous_variant|agC/agT|S|ENSG00000187961|KLHL17|ENST00000338591|4/12|||207/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:11,0:11:30.07:0,30,345 0/0:14,0:14:39.10:0,39,482 0/0:19,0:19:54.17:0,54,702 0/0:15,0:15:45.10:0,45,522 0/0:41,0:41:99:0,117,1565 0/0:45,0:45:99:0,135,1787 0/0:68,0:68:99:0,202,2635 0/0:32,0:32:96.32:0,96,1297 0/0:71,0:71:99:0,214,2867 0/0:92,0:92:99:0,265,3522 0/0:35,0:35:99:0,102,1339 0/0:51,0:51:99:0,147,1942 0/0:55,0:55:99:0,163,2122 0/0:57,0:57:99:0,141,1866 0/0:49,0:49:99:0,114,1487 0/0:31,0:31:78.23:0,78,974 0/0:53,0:53:99:0,135,1804 0/0:65,0:65:99:0,153,1992 0/0:53,0:54:99:0,120,1579 0/0:40,0:40:90.25:0,90,1134 0/0:50,0:50:99:0,108,1395 0/0:48,0:48:99:0,120,1562 0/0:48,0:48:99:0,111,1469 0/0:43,0:44:99:0,99,1321 0/0:55,0:55:99:0,123,1651 0/0:41,0:41:93.30:0,93,1261 0/0:77,0:77:99:0,181,2383 0/0:42,0:42:99:0,105,1339 0/0:53,0:53:99:0,102,1379 0/0:55,0:55:99:0,135,1770 0/0:78,0:78:99:0,187,2460 0/0:40,0:40:96.31:0,96,1273 0/0:44,0:44:99:0,105,1351 0/0:55,0:55:99:0,129,1642 0/0:39,0:39:93.27:0,93,1220 0/0:46,0:46:96.31:0,96,1302 0/0:71,0:71:99:0,166,2170 0/0:87,0:87:99:0,214,2791 0/0:97,0:97:99:0,229,3009 0/0:152,2:154:99:0,306,4901 0/0:99,0:99:99:0,250,3229 0/0:109,0:110:99:0,277,3568 0/0:87,0:87:99:0,238,3099 0/0:85,0:85:99:0,220,2811 0/1:39,50:89:99:1326,0,1233 0/0:129,0:129:99:0,310,4012 0/0:179,0:180:99:0,469,6030 0/0:57,0:57:99:0,135,1790 0/0:141,0:141:99:0,337,4332 0/0:159,0:159:99:0,403,5177 0/0:160,0:160:99:0,412,5315 0/0:125,0:125:99:0,310,3911 0/0:121,0:121:99:0,307,3951 0/0:106,0:106:99:0,253,3339 0/0:102,0:102:99:0,250,3243 0/0:82,0:82:99:0,196,2514 0/0:71,0:71:99:0,172,2208 0/0:100,0:100:99:0,247,3204 0/0:75,0:75:99:0,184,2385 0/0:87,0:87:99:0,196,2601 -chr1 897460 . A C 4476.36 . AC=24;AF=0.2069;AN=116;BaseQRankSum=-6.649;DP=4306;DS;Dels=0.00;FS=1182.881;HRun=6;HaplotypeScore=18.5719;InbreedingCoeff=-0.2955;MQ=53.12;MQ0=0;MQRankSum=-6.585;QD=1.27;ReadPosRankSum=-5.387;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|3),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|4),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 0/0:4,0:4:9.02:0,9,102 0/0:3,1:4:3:0,3,28 ./. 0/0:7,1:8:12.03:0,12,138 0/0:10,0:11:18:0,18,185 0/0:21,1:22:5.63:0,6,350 0/0:4,0:4:12.02:0,12,131 0/0:15,0:15:39.06:0,39,415 0/0:34,2:36:81.12:0,81,866 0/0:6,0:6:15.01:0,15,158 0/0:9,1:10:24.03:0,24,256 0/0:6,0:6:9.02:0,9,96 0/0:7,2:9:18.02:0,18,191 0/1:4,2:7:17.67:18,0,45 0/0:8,0:9:21.03:0,21,221 0/0:11,2:13:21.04:0,21,218 0/0:12,1:13:24.03:0,24,247 0/0:10,1:11:24.03:0,24,246 0/0:9,0:9:15.02:0,15,152 0/0:12,1:14:30.06:0,30,334 0/1:11,2:13:16.65:17,0,79 0/0:10,3:13:24.05:0,24,251 0/1:5,2:7:11.65:12,0,113 0/0:17,2:20:39.03:0,39,396 0/0:5,0:5:6.01:0,6,65 0/0:10,0:10:21.04:0,21,227 0/1:10,3:14:24.29:24,0,223 0/0:7,0:7:15:0,15,146 0/0:8,0:8:12.04:0,12,140 0/0:14,0:14:30.05:0,30,339 0/0:9,1:10:24.05:0,24,261 0/0:9,0:9:21.05:0,21,234 0/0:12,2:14:30.09:0,30,348 0/0:5,0:5:6.02:0,6,71 0/0:7,0:7:6.02:0,6,70 0/1:11,2:13:5.22:5,0,229 0/0:20,6:27:23.34:0,23,483 0/1:116,43:160:99:143,0,1588 0/1:179,60:241:99:149,0,2388 0/0:138,59:198:1.52:0,2,2031 0/1:102,46:152:99:191,0,1486 0/1:109,41:152:99:196,0,1686 0/1:99,41:143:99:221,0,1726 0/1:93,33:126:16.74:17,0,1349 0/1:166,48:221:99:191,0,2244 0/1:151,89:243:99:504,0,1889 0/0:87,28:116:6.15:0,6,1232 0/1:132,46:178:99:123,0,1682 0/1:169,63:236:99:316,0,2223 0/1:166,75:244:99:333,0,2291 0/1:128,49:180:99:259,0,1869 0/1:158,65:228:99:408,0,2033 0/1:117,52:172:99:315,0,1414 0/1:127,55:185:99:172,0,1974 0/1:100,45:147:99:285,0,1264 0/1:72,37:110:99:359,0,942 0/1:143,39:183:57.91:58,0,2162 0/1:91,53:145:99:161,0,1311 0/0:90,30:121:0.23:0,0,1350 -chr1 897465 . A C 207.3 . AC=8;AF=0.0678;AN=118;BaseQRankSum=-6.006;DP=4323;DS;Dels=0.00;FS=207.986;HRun=4;HaplotypeScore=15.9325;InbreedingCoeff=-0.0865;MQ=53.13;MQ0=0;MQRankSum=-13.595;QD=0.15;ReadPosRankSum=-11.475;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|3),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|4),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 0/0:4,0:4:9:0,9,91 0/0:5,0:5:9:0,9,99 0/0:2,0:2:3.01:0,3,41 0/0:10,0:10:21.06:0,21,250 0/1:9,1:10:7.66:8,0,163 0/0:15,3:19:17.37:0,17,405 0/0:4,0:4:12:0,12,117 0/0:18,0:18:48.04:0,48,509 0/0:31,1:32:69.06:0,69,700 0/0:8,0:8:18.03:0,18,190 0/0:8,0:8:18.05:0,18,209 0/0:7,0:7:12.02:0,12,137 0/0:9,0:9:24.03:0,24,266 0/0:4,3:7:9.01:0,9,98 0/0:8,1:9:21.03:0,21,224 0/0:12,0:12:24.01:0,24,234 0/0:13,1:14:24.05:0,24,263 0/0:10,0:10:21.02:0,21,213 0/0:8,1:9:18.03:0,18,199 0/0:12,1:13:24.03:0,24,249 0/0:14,1:15:24.01:0,24,244 0/0:12,1:13:24.04:0,24,257 0/0:5,2:7:12.02:0,12,122 0/0:16,1:18:27.03:0,27,279 0/0:2,1:4:3:0,3,29 0/0:10,0:10:15.01:0,15,149 0/0:12,2:14:24.06:0,24,276 0/0:5,1:6:12.03:0,12,134 0/0:5,2:7:15.02:0,15,157 0/0:14,0:14:33.05:0,33,341 0/0:9,1:10:15.04:0,15,171 0/0:5,1:7:9.02:0,9,102 0/0:8,4:12:21.05:0,21,222 0/0:4,0:4:6:0,6,54 0/0:6,0:6:11.99:0,12,106 0/0:10,3:13:21.05:0,21,236 0/0:23,2:26:39.02:0,39,379 0/0:144,20:167:99:0,106,2432 0/1:186,45:240:32.80:33,0,3160 0/0:165,38:204:76.81:0,77,2749 0/0:126,25:154:26.27:0,26,2127 0/1:118,37:158:55.08:55,0,1972 0/0:117,28:148:77.35:0,77,2320 0/0:113,19:135:99:0,117,2054 0/0:190,32:227:45.99:0,46,3098 0/1:193,45:240:46.73:47,0,2551 0/0:101,20:121:8.73:0,9,1399 0/0:140,32:177:17.48:0,17,2404 0/1:184,49:236:1.33:1,0,2695 0/0:187,53:245:99:0,119,3128 0/1:142,37:181:33.27:33,0,2181 0/0:179,46:227:21.02:0,21,2912 0/0:139,29:172:55.06:0,55,2164 0/1:147,41:190:41.64:42,0,2259 0/0:112,27:140:71.53:0,72,2066 0/1:85,20:109:99:109,0,1243 0/0:160,22:185:99:0,195,2685 0/0:112,31:145:28.71:0,29,1725 0/0:104,15:119:21.81:0,22,1762 -chr1 897470 . A C 60.04 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-10.911;DP=4336;DS;Dels=0.00;FS=267.922;HRun=4;HaplotypeScore=16.3920;InbreedingCoeff=-0.0465;MQ=53.18;MQ0=0;MQRankSum=-11.192;QD=0.22;ReadPosRankSum=-11.844;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|3),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|4),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,32 0/0:3,0:4:6.02:0,6,70 0/0:5,1:6:12.04:0,12,153 0/0:2,0:2:6.02:0,6,70 0/0:7,0:8:18.05:0,18,215 0/0:9,0:11:24.03:0,24,262 0/0:14,3:17:9.63:0,10,452 0/0:4,0:4:12.04:0,12,151 0/0:21,0:22:57.11:0,57,644 0/0:29,1:30:72.18:0,72,848 0/0:6,0:6:18.03:0,18,187 0/0:6,0:6:12.04:0,12,149 0/0:8,0:8:24.07:0,24,298 0/0:8,1:9:24.02:0,24,251 0/0:5,2:7:9.03:0,9,106 0/0:8,0:9:18.04:0,18,196 0/0:10,2:12:18.05:0,18,204 0/1:10,3:13:6.36:6,0,255 0/0:8,2:10:21.05:0,21,228 0/0:8,1:9:18.04:0,18,194 0/0:10,0:10:18.01:0,18,177 0/0:13,3:16:21.02:0,21,227 0/0:9,1:10:18.04:0,18,198 0/0:5,2:7:8.99:0,9,84 0/0:14,1:16:30.05:0,30,331 0/0:4,0:4:9.02:0,9,100 0/0:9,1:10:21.06:0,21,239 0/0:12,0:13:24.01:0,24,253 0/0:5,1:6:12.02:0,12,129 0/0:7,0:7:12.02:0,12,126 0/0:12,0:13:33.02:0,33,327 0/0:7,1:8:12:0,12,119 0/0:5,0:6:9:0,9,94 0/0:7,4:11:21.06:0,21,244 0/0:4,0:4:8.99:0,9,85 0/0:4,1:5:8.97:0,9,71 0/0:9,2:11:21.05:0,21,222 0/0:23,1:24:51.06:0,51,527 0/0:135,27:164:99:0,145,2778 0/0:197,40:243:9.04:0,9,3914 0/0:168,35:205:99:0,101,2962 0/0:130,24:155:55.18:0,55,2447 0/0:136,30:168:99:0,148,2654 0/0:112,35:150:40.10:0,40,2110 0/0:116,17:135:84.96:0,85,2090 0/0:189,36:228:99:0,176,3506 0/0:194,41:240:23.79:0,24,2927 0/0:101,24:125:99:0,144,2077 0/0:152,29:185:1.84:0,2,2595 0/0:192,39:239:99:0,104,3149 0/0:198,44:246:99:0,147,3618 0/0:151,25:180:99:0,115,2708 0/0:179,39:223:25.55:0,26,3121 0/0:145,32:182:69:0,69,2752 0/0:149,32:181:99:0,116,2569 0/1:119,26:147:40.22:40,0,2120 0/1:81,29:112:84.22:84,0,1404 0/0:165,20:186:99:0,211,3186 0/0:113,27:142:87.91:0,88,2072 0/0:102,18:120:61.38:0,61,1959 -chr1 897564 . T C 105645.82 . AC=111;AF=0.9407;AN=118;BaseQRankSum=-0.165;DP=3668;DS;Dels=0.00;FS=4.440;HRun=1;HaplotypeScore=1.8075;InbreedingCoeff=0.1915;MQ=54.46;MQ0=0;MQRankSum=3.570;QD=29.65;ReadPosRankSum=-1.056;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|3),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|4),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,7:7:18.06:229,18,0 1/1:0,3:3:9.03:115,9,0 1/1:0,2:2:6.02:77,6,0 1/1:0,8:8:21.07:262,21,0 1/1:0,15:16:45.14:588,45,0 1/1:0,21:21:63.21:858,63,0 1/1:0,20:20:57.19:757,57,0 1/1:0,8:8:24.08:327,24,0 1/1:0,43:43:99:1652,123,0 0/1:20,18:38:99:610,0,651 1/1:0,18:18:54.15:698,54,0 1/1:0,18:19:54.18:733,54,0 1/1:0,21:21:60.19:792,60,0 1/1:0,7:7:21.07:270,21,0 1/1:0,11:11:33.11:439,33,0 1/1:0,8:8:24.08:312,24,0 1/1:0,8:8:24.07:304,24,0 1/1:0,9:9:27.08:337,27,0 1/1:0,6:6:18.06:249,18,0 1/1:0,7:7:21.07:288,21,0 1/1:0,2:2:6.02:80,6,0 1/1:0,7:7:21.07:262,21,0 0/1:5,3:8:96.54:97,0,144 1/1:0,3:3:9.03:118,9,0 1/1:0,7:7:21.06:260,21,0 1/1:0,7:8:18.06:246,18,0 1/1:0,7:7:21.07:277,21,0 ./. 1/1:0,10:10:30.10:414,30,0 1/1:0,9:9:27.08:342,27,0 1/1:0,9:9:27.08:348,27,0 1/1:0,11:11:27.09:380,27,0 1/1:0,2:2:6.02:80,6,0 1/1:0,9:9:24.07:295,24,0 1/1:0,3:3:9.03:115,9,0 1/1:0,6:6:15.05:204,15,0 1/1:0,6:6:18.05:226,18,0 1/1:0,10:10:30.09:389,30,0 1/1:0,115:115:99:3723,301,0 1/1:0,211:212:99:6608,533,0 1/1:0,180:180:99:5771,466,0 0/1:68,73:142:99:1897,0,1949 1/1:1,149:150:99:4862,391,0 1/1:0,131:131:99:4235,340,0 1/1:1,133:134:99:4295,334,0 1/1:2,154:156:99:4787,388,0 1/1:1,233:235:99:7437,602,0 0/0:100,4:104:99:0,184,2959 1/1:0,161:161:99:5008,403,0 1/1:2,185:187:99:5785,472,0 0/1:93,122:215:99:3316,0,2483 1/1:1,110:112:99:3384,241,0 1/1:0,172:172:99:5397,433,0 1/1:2,165:167:99:5068,374,0 1/1:0,143:143:99:4729,376,0 1/1:0,125:125:99:3982,313,0 0/1:54,42:96:99:968,0,1449 1/1:0,123:125:99:3910,313,0 1/1:1,103:104:99:3136,250,0 1/1:0,103:103:99:3321,259,0 -chr1 897641 . C T 42.61 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.313;DP=2743;DS;Dels=0.00;FS=9.036;HRun=0;HaplotypeScore=1.2616;InbreedingCoeff=-0.0088;MQ=55.91;MQ0=0;MQRankSum=0.432;QD=3.87;ReadPosRankSum=0.049;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|3),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|4),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:12,0:12:30.10:0,30,390 0/0:10,0:10:24.08:0,24,307 0/0:9,0:10:24.08:0,24,318 0/0:17,0:17:42.13:0,42,539 0/0:19,0:19:54.16:0,54,719 0/0:34,0:34:99:0,99,1325 0/0:52,0:52:99:0,154,2053 0/0:16,0:16:48.16:0,48,654 0/0:88,0:88:99:0,256,3403 0/0:83,0:83:99:0,241,3157 0/0:31,0:31:93.30:0,93,1243 0/0:36,0:36:99:0,102,1355 0/0:44,1:45:99:0,132,1739 0/0:18,0:18:54.17:0,54,723 0/0:17,0:17:51.15:0,51,656 0/0:8,0:8:24.06:0,24,296 0/0:17,1:18:15.91:0,16,605 0/0:20,0:20:60.19:0,60,788 0/0:12,0:12:30.09:0,30,390 0/0:14,0:14:42.14:0,42,561 0/0:10,0:11:27.09:0,27,355 0/0:17,0:17:51.17:0,51,687 0/0:17,0:17:51.15:0,51,647 0/0:12,0:12:36.12:0,36,477 0/0:15,0:15:42.14:0,42,572 0/0:11,0:11:33.11:0,33,434 0/0:17,0:17:45.15:0,45,607 0/1:8,3:11:90.36:90,0,287 0/0:15,0:15:36.12:0,36,480 0/0:22,0:22:63.20:0,63,835 0/0:33,0:33:93.29:0,93,1223 0/0:11,0:11:33.10:0,33,422 0/0:15,0:15:42.13:0,42,540 0/0:17,0:17:51.16:0,51,664 0/0:9,0:9:27.08:0,27,354 0/0:18,0:18:54.18:0,54,727 0/0:21,0:21:57.18:0,57,748 0/0:35,0:35:99:0,102,1325 0/0:70,0:70:99:0,178,2223 0/0:127,0:127:99:0,328,4185 0/0:84,0:84:99:0,217,2757 0/0:74,0:74:99:0,193,2448 0/0:83,0:83:99:0,214,2704 0/0:73,0:73:99:0,196,2479 0/0:85,0:85:99:0,226,2918 0/0:88,0:88:99:0,244,3102 0/0:172,0:172:99:0,439,5468 0/0:43,0:44:99:0,120,1529 0/0:79,0:79:99:0,208,2669 0/0:113,0:113:99:0,298,3731 0/0:117,0:117:99:0,307,3911 0/0:70,0:70:99:0,184,2366 0/0:94,0:94:99:0,259,3291 0/0:87,1:89:99:0,229,2843 0/0:79,0:79:99:0,217,2742 0/0:80,0:80:99:0,214,2713 0/0:62,0:62:99:0,159,2060 0/0:72,0:72:99:0,181,2294 0/0:57,0:57:99:0,150,1903 0/0:64,0:64:99:0,175,2248 -chr1 897730 . C T 1850.25 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.726;DP=3106;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=3.1479;InbreedingCoeff=-0.0256;MQ=58.41;MQ0=0;MQRankSum=-0.353;QD=12.94;ReadPosRankSum=-0.223;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|3),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|4),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:17,0:17:42.12:0,42,522 0/0:20,0:20:57.17:0,57,713 0/0:27,0:28:75.22:0,75,926 0/0:27,0:27:78.20:0,78,954 0/0:39,0:39:99:0,114,1518 0/0:50,0:50:99:0,147,1950 0/0:82,0:82:99:0,244,3253 0/1:15,13:28:99:433,0,512 0/0:104,0:104:99:0,301,3968 0/0:115,0:115:99:0,337,4474 0/0:36,0:36:99:0,105,1383 0/0:52,0:52:99:0,153,1999 0/0:61,0:61:99:0,178,2347 0/0:65,0:65:99:0,144,1986 0/0:50,0:50:99:0,105,1448 0/0:25,0:26:54.17:0,54,711 0/0:59,0:59:99:0,138,1883 0/0:50,0:50:99:0,114,1538 0/0:43,0:43:99:0,105,1393 0/0:58,0:58:99:0,126,1752 0/0:36,0:36:84.27:0,84,1125 0/0:74,2:76:99:0,130,2272 0/0:51,0:51:99:0,123,1608 0/0:46,0:46:99:0,111,1481 0/0:64,0:64:99:0,150,2057 0/0:55,0:55:99:0,129,1759 0/0:58,0:58:99:0,135,1804 0/0:36,0:37:87.28:0,87,1152 0/0:53,0:53:99:0,129,1747 0/0:43,0:43:99:0,105,1391 0/0:78,0:78:99:0,190,2562 0/0:45,0:45:99:0,108,1450 0/1:26,28:54:99:736,0,711 0/0:57,0:57:99:0,129,1756 0/0:33,0:33:72.24:0,72,1006 0/0:66,0:66:99:0,144,1972 0/0:82,0:82:99:0,190,2541 0/0:84,0:84:99:0,214,2878 0/0:49,0:49:99:0,111,1482 0/0:82,0:82:99:0,199,2612 0/0:51,0:51:99:0,132,1712 0/0:51,0:51:99:0,126,1621 0/0:42,0:42:99:0,114,1453 0/0:42,0:42:99:0,108,1415 0/0:40,0:40:99:0,99,1316 0/0:57,0:57:99:0,147,1907 0/0:81,0:81:99:0,208,2709 0/0:28,0:28:69.22:0,69,910 0/0:45,1:46:87.74:0,88,1432 0/1:32,29:61:99:762,0,874 0/0:52,0:52:99:0,141,1816 0/0:42,0:42:99:0,102,1328 0/0:50,0:50:99:0,129,1673 0/0:54,0:54:99:0,144,1877 0/0:50,0:50:99:0,120,1557 0/0:47,0:47:99:0,114,1526 0/0:39,0:39:87.28:0,87,1157 0/0:45,0:45:99:0,117,1529 0/0:36,0:37:84.28:0,84,1160 0/0:31,0:32:75.24:0,75,996 -chr1 897738 . C T 5799.05 . AC=8;AF=0.0667;AN=120;BaseQRankSum=1.153;DP=3157;Dels=0.00;FS=6.498;HRun=2;HaplotypeScore=2.6795;InbreedingCoeff=0.1964;MQ=58.52;MQ0=0;MQRankSum=1.044;QD=16.11;ReadPosRankSum=-1.772;EFF=EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|2),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L239|642|KLHL17|protein_coding|CODING|ENST00000338591|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L9|412|KLHL17|protein_coding|CODING|ENST00000455747|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,synonymous_variant|Ctg/Ttg|L|ENSG00000187961|KLHL17|ENST00000338591|5/12|||239/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000463212|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:19,0:19:51.14:0,51,614 0/0:23,0:23:60.18:0,60,752 0/0:30,0:30:87.24:0,87,1057 0/0:29,0:29:84.26:0,84,1061 0/0:38,0:38:99:0,114,1483 0/0:49,0:49:99:0,147,1917 0/0:81,0:81:99:0,238,3170 0/0:31,0:31:93.30:0,93,1236 0/0:114,0:114:99:0,337,4417 0/1:53,60:113:99:2051,0,1690 0/0:36,0:36:99:0,105,1369 0/0:49,0:49:99:0,147,1923 0/0:63,0:63:99:0,187,2420 0/0:67,0:67:99:0,160,2125 0/0:56,0:57:99:0,123,1639 0/0:30,0:30:63.20:0,63,823 0/0:63,0:63:99:0,147,2008 0/0:55,0:55:99:0,120,1625 0/0:51,0:51:99:0,123,1637 0/0:62,0:62:99:0,135,1863 0/0:40,0:40:90.28:0,90,1183 0/0:76,0:76:99:0,172,2314 0/1:20,31:51:99:848,0,542 0/0:48,0:48:99:0,111,1483 0/0:67,0:67:99:0,160,2156 0/0:56,0:56:99:0,129,1756 0/0:58,0:58:99:0,144,1937 0/1:23,17:40:99:493,0,611 0/0:56,0:56:99:0,144,1951 0/0:45,0:45:99:0,111,1478 0/0:84,1:85:99:0,202,2715 0/0:48,0:48:99:0,114,1523 0/0:59,0:59:99:0,132,1769 0/0:65,0:65:99:0,150,2001 0/0:35,0:35:75.25:0,75,1045 0/0:67,0:67:99:0,153,2061 0/0:84,1:85:99:0,190,2544 0/0:88,0:88:99:0,220,2937 0/0:48,0:48:99:0,117,1501 0/0:74,0:74:99:0,184,2380 0/0:46,0:46:99:0,120,1535 0/1:24,23:47:99:671,0,618 0/0:41,0:41:99:0,117,1471 0/0:44,0:44:99:0,111,1469 0/0:39,0:39:90.27:0,90,1186 0/0:57,0:57:99:0,144,1881 0/0:78,0:78:99:0,205,2649 1/1:0,26:26:66.21:879,66,0 0/0:42,0:43:99:0,114,1456 0/0:57,1:58:99:0,144,1802 0/1:31,17:48:99:445,0,903 0/0:41,0:41:99:0,105,1343 0/0:45,0:46:99:0,120,1570 0/0:49,0:49:99:0,129,1687 0/0:53,0:53:99:0,129,1654 0/0:48,0:48:99:0,120,1571 0/1:19,16:35:99:412,0,577 0/0:45,0:45:99:0,111,1462 0/0:31,0:33:78.25:0,78,1057 0/0:29,0:29:72.21:0,72,933 -chr1 897879 . C T 1100.72 . AC=4;AF=0.0333;AN=120;BaseQRankSum=-0.411;DP=1081;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7665;InbreedingCoeff=-0.0357;MQ=58.62;MQ0=0;MQRankSum=0.745;QD=12.80;ReadPosRankSum=2.064;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|4),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|5),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:9,0:9:18.05:0,18,216 0/0:12,0:12:30.09:0,30,375 0/0:4,0:4:12.04:0,12,149 0/0:10,0:10:30.07:0,30,348 0/0:14,0:14:39.13:0,39,519 0/0:15,0:15:45.15:0,45,599 0/0:33,0:33:93.29:0,93,1207 0/0:15,0:15:45.14:0,45,578 0/0:44,0:44:99:0,126,1671 0/0:56,1:57:99:0,117,1904 0/0:21,0:22:63.20:0,63,842 0/0:17,0:17:39.13:0,39,516 0/0:23,0:23:69.22:0,69,913 0/0:15,0:15:45.15:0,45,592 0/0:20,0:20:60.19:0,60,781 0/0:15,0:15:36.11:0,36,466 0/0:25,0:25:72.23:0,72,941 0/0:18,0:18:51.17:0,51,683 0/0:23,0:23:57.18:0,57,749 0/0:15,0:15:42.14:0,42,562 0/0:11,0:11:27.09:0,27,357 0/0:19,0:19:51.17:0,51,673 0/0:18,0:18:48.14:0,48,632 0/0:18,0:18:54.17:0,54,704 0/0:27,0:27:66.22:0,66,896 0/0:15,0:15:42.14:0,42,567 0/1:13,5:18:99:152,0,421 0/0:17,0:17:48.15:0,48,616 0/0:20,0:20:60.19:0,60,763 0/0:13,0:13:39.12:0,39,517 0/0:33,0:33:93.29:0,93,1226 0/0:13,0:13:36.11:0,36,472 0/0:28,0:28:75.24:0,75,983 0/0:24,0:24:69.21:0,69,904 0/1:8,6:14:99:205,0,231 0/0:22,0:22:57.18:0,57,723 0/1:13,6:19:99:140,0,423 0/0:35,0:35:99:0,99,1312 0/0:11,0:11:27.04:0,27,316 0/0:19,0:19:57.18:0,57,733 0/0:29,0:29:72.22:0,72,921 0/0:12,0:12:30.07:0,30,353 0/0:11,0:11:33.08:0,33,416 0/0:13,0:13:33.11:0,33,430 0/0:11,0:11:33.11:0,33,432 0/0:15,0:15:45.14:0,45,587 0/0:21,0:21:63.19:0,63,782 0/0:6,0:6:18.06:0,18,245 0/0:16,0:16:42.14:0,42,559 0/1:13,22:35:99:696,0,329 0/0:11,0:11:33.10:0,33,404 0/0:12,0:12:33.11:0,33,430 0/0:16,0:16:33.10:0,33,415 0/0:13,0:13:36.11:0,36,461 0/0:14,0:14:33.11:0,33,450 0/0:10,0:11:24.08:0,24,322 0/0:6,0:6:18.06:0,18,231 0/0:12,0:12:30.10:0,30,395 0/0:7,0:7:21.07:0,21,267 0/0:10,0:10:27.08:0,27,343 -chr1 898068 . G C 79.28 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.132;DP=1385;Dels=0.00;FS=2.990;HRun=1;HaplotypeScore=0.9318;InbreedingCoeff=0.8872;MQ=57.94;MQ0=0;MQRankSum=0.935;QD=19.82;ReadPosRankSum=-0.735;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|4),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|5),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,4:4:12.02:139,12,0 0/0:6,0:6:18.06:0,18,233 0/0:4,0:4:12.04:0,12,148 0/0:5,0:5:15.05:0,15,187 0/0:16,0:16:48.16:0,48,635 0/0:12,0:12:36.12:0,36,482 0/0:14,0:14:39.12:0,39,506 0/0:8,0:8:24.07:0,24,306 0/0:23,0:23:69.22:0,69,915 0/0:33,0:33:96.31:0,96,1280 0/0:16,0:16:48.13:0,48,604 0/0:15,0:15:45.15:0,45,605 0/0:12,0:12:36.12:0,36,484 0/0:9,0:9:27.08:0,27,334 0/0:17,0:17:45.13:0,45,556 0/0:12,0:12:30.10:0,30,398 0/0:15,0:15:36.11:0,36,461 0/0:15,0:15:36.12:0,36,474 0/0:17,0:17:36.12:0,36,485 0/0:18,0:18:48.15:0,48,632 0/0:20,0:20:45.14:0,45,590 0/0:15,0:15:36.11:0,36,469 0/0:14,0:14:27.09:0,27,367 0/0:12,0:12:33.07:0,33,392 0/0:8,0:8:24.08:0,24,312 0/0:15,0:15:36.12:0,36,481 0/0:5,0:5:15.04:0,15,188 0/0:10,0:10:24.08:0,24,321 0/0:19,0:19:45.15:0,45,616 0/0:16,0:16:45.14:0,45,589 0/0:13,0:13:27.08:0,27,359 0/0:7,0:7:18.06:0,18,239 0/0:16,0:16:45.14:0,45,588 0/0:17,0:17:45.14:0,45,596 0/0:10,0:10:24.08:0,24,333 0/0:16,0:17:39.10:0,39,512 0/0:18,0:18:48.16:0,48,638 0/0:29,0:29:78.25:0,78,1050 0/0:34,0:34:90.29:0,90,1187 0/0:43,0:43:99:0,129,1669 0/0:36,0:36:99:0,102,1298 0/0:38,0:38:96.31:0,96,1272 0/0:40,0:40:99:0,111,1421 0/0:25,0:25:66.21:0,66,848 0/0:35,0:35:99:0,99,1263 0/0:33,0:33:96.30:0,96,1236 0/0:66,0:66:99:0,178,2208 0/0:23,0:23:66.20:0,66,841 0/0:42,0:42:99:0,105,1336 0/0:61,0:61:99:0,165,2077 0/0:67,0:67:99:0,178,2321 0/0:42,0:43:99:0,123,1562 0/0:43,0:43:99:0,117,1494 0/0:39,0:40:99:0,105,1323 0/0:38,1:39:99:0,114,1456 0/0:27,0:27:75.24:0,75,975 0/0:31,0:31:87.24:0,87,1075 0/0:38,0:38:99:0,108,1428 0/0:24,0:24:66.22:0,66,886 0/0:24,0:24:69.22:0,69,892 -chr1 898323 . T C 52014.58 . AC=115;AF=0.9583;AN=120;BaseQRankSum=-0.884;DP=1603;Dels=0.00;FS=3.229;HRun=1;HaplotypeScore=0.9054;InbreedingCoeff=-0.0448;MQ=58.52;MQ0=0;MQRankSum=-0.998;QD=32.45;ReadPosRankSum=2.785;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|5),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|6),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,10:10:27.08:341,27,0 1/1:0,5:5:12.04:149,12,0 1/1:0,5:5:12.04:155,12,0 1/1:0,6:6:18.05:220,18,0 1/1:0,13:13:39.13:522,39,0 1/1:0,9:9:24.08:327,24,0 1/1:0,24:24:60.19:793,60,0 1/1:0,11:11:33.11:440,33,0 1/1:0,40:40:99:1565,117,0 0/1:23,18:41:99:575,0,723 1/1:0,17:17:51.16:656,51,0 1/1:0,15:15:42.13:546,42,0 1/1:0,14:14:42.14:557,42,0 1/1:0,34:34:87.27:1115,87,0 1/1:0,35:36:81.25:1059,81,0 1/1:0,25:25:63.20:836,63,0 1/1:0,33:33:87.25:1134,87,0 1/1:0,18:18:48.14:594,48,0 1/1:0,41:41:96.30:1263,96,0 1/1:0,31:31:69.22:931,69,0 1/1:0,31:32:81.25:1037,81,0 1/1:0,33:33:84.25:1068,84,0 0/1:13,16:29:99:414,0,399 1/1:0,30:30:75.23:982,75,0 1/1:0,15:15:39.13:524,39,0 1/1:0,34:34:93.30:1200,93,0 1/1:0,22:22:51.15:675,51,0 1/1:0,27:27:75.24:995,75,0 1/1:0,28:28:66.21:873,66,0 1/1:0,37:37:99:1308,102,0 1/1:0,46:46:99:1457,108,0 1/1:0,26:26:57.19:772,57,0 1/1:0,30:30:81.24:1010,81,0 1/1:0,59:59:99:1839,144,0 1/1:0,29:29:75.22:973,75,0 1/1:0,26:26:60.20:826,60,0 1/1:0,41:41:99:1350,102,0 1/1:0,56:56:99:1844,138,0 1/1:0,17:17:51.16:662,51,0 1/1:0,39:39:99:1246,102,0 1/1:0,22:22:66.19:827,66,0 0/1:9,7:16:99:226,0,292 1/1:0,37:37:99:1308,105,0 1/1:0,25:25:66.21:865,66,0 1/1:0,15:15:42.12:526,42,0 1/1:0,28:28:78.23:972,78,0 1/1:0,49:49:99:1821,144,0 1/1:0,14:14:39.12:477,39,0 1/1:0,23:23:69.22:908,69,0 1/1:0,48:48:99:1627,135,0 0/1:15,20:35:99:515,0,436 1/1:0,45:45:99:1523,117,0 1/1:0,43:43:99:1537,120,0 1/1:0,23:23:57.18:731,57,0 1/1:0,22:22:66.20:827,66,0 1/1:0,12:12:36.12:481,36,0 0/1:5,9:14:99:265,0,166 1/1:0,19:19:57.18:736,57,0 1/1:0,10:10:24.08:310,24,0 1/1:0,19:19:54.17:701,54,0 -chr1 898467 . C T 1510.84 . AC=5;AF=0.0417;AN=120;BaseQRankSum=-0.034;DP=1255;Dels=0.00;FS=4.507;HRun=0;HaplotypeScore=0.8357;InbreedingCoeff=-0.0475;MQ=58.85;MQ0=0;MQRankSum=-1.026;QD=13.49;ReadPosRankSum=-1.131;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|5),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|6),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=synonymous_variant&NMD_transcript_variant|ccC/ccT|P|ENSG00000187961|KLHL17|ENST00000466300|2/6|||83/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.03:0,12,142 0/0:5,0:5:15.03:0,15,182 0/0:8,0:8:15.04:0,15,177 0/0:6,0:6:15.05:0,15,192 0/0:20,0:20:54.17:0,54,724 0/0:8,0:8:18.06:0,18,240 0/0:22,0:22:66.21:0,66,869 0/0:5,0:5:12.04:0,12,161 0/0:20,0:20:57.19:0,57,765 0/1:22,16:38:99:495,0,680 0/0:10,0:10:30.06:0,30,365 0/0:11,0:11:33.11:0,33,430 0/0:11,0:11:33.11:0,33,424 0/0:33,0:33:84.26:0,84,1076 0/0:54,0:54:99:0,132,1743 0/0:20,0:20:48.15:0,48,630 0/0:44,0:44:99:0,111,1449 0/0:35,0:35:84.28:0,84,1139 0/0:30,0:30:75.24:0,75,966 0/0:31,0:31:78.24:0,78,1010 0/0:35,0:35:90.29:0,90,1181 0/0:49,1:50:99:0,135,1750 0/1:17,20:37:99:529,0,494 0/0:22,0:22:48.16:0,48,648 0/0:27,0:27:69.21:0,69,888 0/0:30,0:30:78.25:0,78,1020 0/0:30,0:30:78.24:0,78,1002 0/0:26,0:26:63.18:0,63,793 0/0:44,0:44:99:0,114,1424 0/0:35,0:35:90.28:0,90,1154 0/0:35,0:35:90.28:0,90,1164 0/0:23,0:23:69.22:0,69,889 0/0:30,0:30:81.26:0,81,1048 0/0:28,0:28:75.24:0,75,974 0/0:44,0:45:99:0,99,1328 0/0:21,0:21:42.14:0,42,572 0/0:41,0:41:93.31:0,93,1268 0/0:44,0:45:99:0,120,1586 0/0:5,0:5:15.05:0,15,194 0/0:15,0:15:42.13:0,42,506 0/0:10,0:10:24.07:0,24,308 0/1:4,8:12:99:160,0,116 0/0:12,0:12:36.12:0,36,475 0/0:8,0:8:24.08:0,24,305 0/0:8,0:8:24.08:0,24,325 0/0:12,0:12:30.08:0,30,378 0/0:20,0:20:54.17:0,54,712 0/0:5,0:6:12.04:0,12,149 0/0:5,0:5:12.04:0,12,163 0/0:15,0:15:36.11:0,36,465 0/1:6,12:18:99:373,0,148 0/0:11,0:11:30.10:0,30,398 0/0:13,0:13:39.13:0,39,513 0/0:9,0:9:24.07:0,24,296 0/0:15,0:15:36.11:0,36,469 0/0:12,0:12:33.11:0,33,455 0/1:5,2:7:57.54:58,0,134 0/0:6,0:6:18.05:0,18,219 0/0:5,0:5:15.05:0,15,192 0/0:11,0:11:27.09:0,27,361 -chr1 898603 . C G 116.84 . AC=8;AF=0.0667;AN=120;BaseQRankSum=-8.523;DP=3456;Dels=0.00;FS=28.932;HRun=2;HaplotypeScore=4.3555;InbreedingCoeff=-0.0746;MQ=57.81;MQ0=0;MQRankSum=-3.388;QD=0.70;ReadPosRankSum=-5.743;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gGg|A156G|412|KLHL17|protein_coding|CODING|ENST00000455747|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gGg|A386G|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=missense_variant&NMD_transcript_variant|Cgg/Ggg|R/G|ENSG00000187961|KLHL17|ENST00000466300|2/6|unknown(0)|deleterious(0)|129/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,missense_variant|gCg/gGg|A/G|ENSG00000187961|KLHL17|ENST00000338591|7/12|possibly_damaging(0.8)|tolerated(0.13)|386/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:2,5:7:5.97:0,6,45 0/1:3,2:6:24.41:24,0,54 0/1:4,4:8:49.90:50,0,93 0/0:6,0:6:15.03:0,15,171 0/1:17,7:24:16.86:17,0,488 0/1:7,6:13:36.95:37,0,238 0/1:21,7:28:38.06:38,0,602 0/0:10,1:11:12.04:0,12,150 0/1:21,12:33:1.58:2,0,719 0/1:22,16:38:46.41:46,0,538 0/0:12,6:18:0.38:0,0,251 0/0:10,2:13:27.07:0,27,304 0/1:12,5:17:27.02:27,0,311 0/0:69,0:69:99:0,168,2126 0/0:116,2:119:99:0,268,3461 0/0:54,0:54:99:0,114,1441 0/0:87,0:87:99:0,208,2699 0/0:89,1:90:99:0,208,2648 0/0:84,0:84:99:0,217,2688 0/0:67,0:67:99:0,171,2150 0/0:86,0:86:99:0,202,2530 0/0:108,2:110:99:0,259,3369 0/0:88,2:90:99:0,211,2680 0/0:68,1:70:99:0,150,1907 0/0:74,2:76:99:0,187,2372 0/0:80,0:81:99:0,184,2302 0/0:72,1:73:99:0,175,2228 0/0:54,0:54:99:0,135,1663 0/0:93,0:93:99:0,229,2872 0/0:62,0:64:99:0,162,2030 0/0:93,1:94:99:0,214,2788 0/0:78,0:78:99:0,178,2269 0/0:81,0:82:99:0,181,2351 0/0:93,0:93:99:0,235,2956 0/0:81,0:81:99:0,199,2609 0/0:83,0:83:99:0,184,2336 0/0:96,0:96:99:0,241,2995 0/0:144,2:146:99:0,340,4440 0/0:33,0:34:87.25:0,87,1075 0/0:80,1:81:99:0,205,2584 0/0:59,1:60:99:0,150,1880 0/0:49,0:51:99:0,117,1495 0/0:53,1:54:99:0,138,1782 0/0:41,0:41:99:0,105,1318 0/0:36,0:36:96.29:0,96,1193 0/0:50,0:51:99:0,132,1646 0/0:65,1:66:99:0,156,1824 0/0:34,2:36:87.25:0,87,1074 0/0:56,2:59:99:0,144,1736 0/0:82,2:84:99:0,208,2551 0/0:93,0:93:99:0,232,2913 0/0:60,1:61:99:0,159,1980 0/0:32,1:33:78.22:0,78,934 0/0:45,0:45:99:0,111,1376 0/0:53,0:53:99:0,132,1636 0/0:41,1:42:99:0,102,1275 0/0:22,0:22:45.14:0,45,574 0/0:45,0:45:99:0,117,1490 0/0:32,1:34:69.22:0,69,900 0/0:28,3:31:63.17:0,63,788 -chr1 898604 . G A 684.72 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.572;DP=3527;Dels=0.00;FS=8.272;HRun=0;HaplotypeScore=4.4131;InbreedingCoeff=-0.0111;MQ=57.83;MQ0=0;MQRankSum=0.825;QD=9.92;ReadPosRankSum=-0.003;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A156|412|KLHL17|protein_coding|CODING|ENST00000455747|),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A386|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000477976|);CSQ=missense_variant&NMD_transcript_variant|cGg/cAg|R/Q|ENSG00000187961|KLHL17|ENST00000466300|2/6|unknown(0)|deleterious(0)|129/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,synonymous_variant|gcG/gcA|A|ENSG00000187961|KLHL17|ENST00000338591|7/12|||386/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000477976|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:7,0:7:5.99:0,6,50 0/0:7,0:7:12.04:0,12,141 0/0:8,0:8:18.06:0,18,223 0/0:6,0:6:15.04:0,15,174 0/0:24,0:24:48.15:0,48,623 0/0:14,0:14:27.08:0,27,346 0/0:27,0:27:66.21:0,66,841 0/0:10,0:10:21.07:0,21,264 0/0:34,0:34:81.24:0,81,1035 0/0:40,0:40:87.26:0,87,1067 0/0:19,0:19:42.11:0,42,515 0/0:15,0:15:30.09:0,30,375 0/0:17,0:17:42.12:0,42,518 0/0:70,0:70:99:0,162,2107 0/0:122,0:122:99:0,277,3531 0/0:55,0:55:99:0,120,1508 0/0:92,0:92:99:0,220,2895 0/0:89,0:91:99:0,208,2655 0/0:86,0:86:99:0,229,2853 0/0:70,0:70:99:0,178,2260 0/0:85,0:85:99:0,208,2621 0/0:109,2:111:99:0,214,3224 0/0:89,0:89:99:0,211,2681 0/0:70,0:70:99:0,150,1923 0/0:74,1:75:99:0,147,2272 0/0:80,0:82:99:0,190,2361 0/0:76,0:76:99:0,178,2308 0/0:54,0:54:99:0,135,1713 0/0:93,0:94:99:0,229,2937 0/0:66,0:66:99:0,165,2096 0/0:96,0:96:99:0,223,2906 0/0:77,0:77:99:0,172,2215 0/0:85,0:85:99:0,202,2556 0/0:92,1:93:99:0,229,2934 0/0:81,0:81:99:0,196,2571 0/0:84,0:84:99:0,184,2353 0/0:96,0:96:99:0,241,3048 0/0:144,0:146:99:0,352,4559 0/0:37,0:37:90.27:0,90,1118 0/0:82,0:84:99:0,208,2563 0/0:62,0:62:99:0,162,1973 0/0:51,0:51:99:0,126,1594 0/0:55,0:55:99:0,144,1824 0/0:42,0:42:99:0,108,1328 0/0:37,0:37:96.28:0,96,1178 0/0:51,0:52:99:0,135,1691 0/1:34,35:69:99:732,0,781 0/0:36,0:36:87.26:0,87,1071 0/0:61,0:62:99:0,150,1791 0/0:86,0:87:99:0,220,2676 0/0:100,0:100:99:0,241,2989 0/0:62,0:62:99:0,156,1976 0/0:34,0:34:81.23:0,81,977 0/0:49,0:49:99:0,126,1552 0/0:54,0:54:99:0,132,1620 0/0:43,0:43:99:0,105,1323 0/0:22,0:22:51.12:0,51,622 0/0:47,0:47:99:0,123,1564 0/0:34,0:34:72.23:0,72,925 0/0:33,0:33:69.19:0,69,857 -chr1 898893 . G C 345.84 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.109;DP=2327;Dels=0.00;FS=1.347;HRun=0;HaplotypeScore=1.8649;InbreedingCoeff=-0.0084;MQ=58.71;MQ0=0;MQRankSum=0.616;QD=12.81;ReadPosRankSum=0.720;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|7),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|8),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,upstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:8,0:8:24.07:0,24,280 0/0:13,0:13:30.08:0,30,364 0/0:16,0:16:48.08:0,48,561 0/0:22,0:22:63.20:0,63,824 0/0:32,0:32:93.29:0,93,1214 0/0:30,0:30:81.26:0,81,1066 0/0:62,0:62:99:0,172,2283 0/0:27,0:27:78.23:0,78,1019 0/0:85,0:85:99:0,244,3231 0/0:86,0:87:99:0,253,3303 0/0:35,0:35:93.30:0,93,1243 0/0:22,0:22:63.19:0,63,789 0/0:41,0:41:99:0,120,1530 0/0:32,0:32:78.25:0,78,1044 0/0:35,0:35:90.29:0,90,1209 0/0:24,0:24:63.20:0,63,836 0/0:33,0:33:84.25:0,84,1111 0/0:29,0:29:81.26:0,81,1081 0/0:37,0:37:99:0,102,1372 0/0:23,0:24:66.21:0,66,854 0/0:34,0:34:87.28:0,87,1145 0/0:50,0:50:99:0,126,1654 0/0:18,0:18:51.16:0,51,671 0/0:30,0:30:84.27:0,84,1123 0/0:25,0:25:72.23:0,72,946 0/0:29,0:29:75.20:0,75,962 0/0:26,0:26:69.21:0,69,882 0/0:19,0:19:48.14:0,48,625 0/0:25,0:25:66.19:0,66,870 0/0:27,0:27:72.23:0,72,954 0/0:35,0:35:84.27:0,84,1129 0/0:16,0:16:39.13:0,39,530 0/0:31,0:31:81.24:0,81,1063 0/0:34,0:34:90.29:0,90,1212 0/0:21,0:21:48.15:0,48,643 0/0:30,0:30:72.23:0,72,956 0/0:45,0:45:99:0,117,1607 0/0:42,0:42:99:0,108,1443 0/0:35,0:35:90.27:0,90,1182 0/0:70,0:71:99:0,178,2265 0/0:44,0:44:99:0,123,1569 0/0:59,0:59:99:0,153,1974 0/0:53,0:53:99:0,138,1849 0/0:30,0:30:75.24:0,75,980 0/0:36,0:36:99:0,99,1274 0/0:40,0:40:99:0,108,1405 0/0:72,0:72:99:0,193,2503 0/1:15,12:27:99:394,0,393 0/0:48,0:48:99:0,111,1457 0/0:80,0:80:99:0,193,2499 0/0:95,0:95:99:0,259,3423 0/0:48,0:48:99:0,123,1600 0/0:55,0:55:99:0,141,1838 0/0:44,0:44:99:0,102,1324 0/0:44,0:44:99:0,108,1435 0/0:48,0:48:99:0,126,1679 0/0:34,0:34:96.29:0,96,1232 0/0:41,0:41:99:0,111,1510 0/0:51,0:51:99:0,120,1612 0/0:41,0:41:99:0,105,1410 -chr1 898934 . G A 47.08 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.111;DP=1477;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6015;InbreedingCoeff=-0.0091;MQ=58.84;MQ0=0;MQRankSum=0.087;QD=5.89;ReadPosRankSum=-1.045;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|1),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|7),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|8),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000481067|1/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.03:0,12,136 0/0:10,0:10:30.10:0,30,393 0/0:8,0:8:24.07:0,24,295 0/0:10,0:10:30.09:0,30,378 0/0:32,0:32:96.31:0,96,1290 0/0:20,0:20:60.19:0,60,795 0/0:40,0:40:99:0,120,1608 0/0:24,0:24:72.21:0,72,918 0/0:51,0:51:99:0,150,2020 0/0:60,0:60:99:0,181,2380 0/0:26,0:26:78.23:0,78,1026 0/0:22,0:22:63.20:0,63,834 0/0:34,0:34:96.29:0,96,1235 0/0:17,0:17:45.14:0,45,578 0/0:23,0:23:69.22:0,69,918 0/0:9,0:9:24.08:0,24,329 0/0:16,0:16:48.13:0,48,606 0/0:21,0:21:63.20:0,63,814 0/0:19,0:19:54.17:0,54,707 0/0:15,0:15:45.15:0,45,601 0/0:22,0:22:63.20:0,63,835 0/0:40,0:40:99:0,108,1442 0/0:6,0:6:18.06:0,18,251 0/0:26,0:26:69.21:0,69,917 0/0:16,0:16:45.15:0,45,605 0/0:16,0:16:42.13:0,42,559 0/0:19,0:19:54.16:0,54,698 0/0:11,0:11:33.11:0,33,446 0/0:13,0:13:39.13:0,39,522 0/0:16,0:16:45.15:0,45,601 0/0:19,0:19:54.18:0,54,717 0/1:5,3:8:94.84:95,0,172 0/0:13,0:13:33.11:0,33,441 0/0:23,0:23:57.19:0,57,769 0/0:10,0:10:30.10:0,30,402 0/0:12,0:12:30.10:0,30,398 0/0:25,0:25:69.22:0,69,916 0/0:34,0:34:93.30:0,93,1235 0/0:20,0:20:54.17:0,54,714 0/0:51,0:51:99:0,144,1877 0/0:33,0:33:93.30:0,93,1244 0/0:38,0:38:99:0,105,1376 0/0:31,0:31:87.27:0,87,1134 0/0:14,0:15:42.13:0,42,527 0/0:24,0:24:66.21:0,66,874 0/0:23,0:23:60.19:0,60,801 0/0:54,0:54:99:0,135,1734 0/0:19,0:19:51.16:0,51,666 0/0:35,0:35:75.22:0,75,1010 0/0:61,0:61:99:0,138,1795 0/0:50,0:50:99:0,138,1763 0/0:33,0:34:84.22:0,84,1071 0/0:36,0:37:90.29:0,90,1200 0/0:26,0:27:60.19:0,60,793 0/0:31,0:31:81.22:0,81,1045 0/0:21,0:21:51.16:0,51,680 0/0:17,0:17:45.15:0,45,616 0/0:23,0:23:57.19:0,57,798 0/0:23,0:23:63.20:0,63,849 0/0:20,0:20:45.14:0,45,596 -chr1 899000 . C T 654.34 . AC=8;AF=0.0667;AN=120;BaseQRankSum=-0.932;DP=651;Dels=0.00;FS=1.229;HRun=0;HaplotypeScore=0.5946;InbreedingCoeff=0.3177;MQ=58.35;MQ0=0;MQRankSum=0.454;QD=16.36;ReadPosRankSum=0.885;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|1),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|7),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|8),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000481067|1/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:8,0:8:24.06:0,24,279 0/0:4,0:4:6.02:0,6,71 0/0:7,0:7:15.02:0,15,183 0/0:6,0:6:18.06:0,18,220 0/0:11,0:11:33.11:0,33,432 0/0:16,0:17:45.13:0,45,566 0/0:20,0:20:60.20:0,60,799 0/0:13,0:13:39.11:0,39,471 0/0:33,0:33:99:0,99,1301 0/0:35,0:35:99:0,99,1278 0/0:11,0:11:33.10:0,33,417 0/0:5,0:5:12.04:0,12,158 0/0:22,0:22:63.19:0,63,800 0/0:7,0:7:21.07:0,21,286 0/0:8,0:8:21.04:0,21,262 0/0:2,0:2:6.02:0,6,79 0/0:6,0:6:18.06:0,18,234 0/0:10,0:10:30.10:0,30,402 0/1:5,1:6:21.95:22,0,179 0/0:6,0:6:18.06:0,18,241 0/1:2,7:9:44.74:233,0,45 0/0:8,0:8:21.07:0,21,282 0/0:1,0:1:3.01:0,3,41 0/0:12,0:12:27.09:0,27,368 0/0:8,0:8:21.06:0,21,262 0/0:9,0:9:24.08:0,24,323 1/1:0,6:6:18.04:218,18,0 0/0:5,0:5:12.04:0,12,162 0/0:7,0:7:21.05:0,21,247 0/0:6,0:6:18.06:0,18,228 0/0:7,0:7:21.06:0,21,262 0/0:7,0:7:21.06:0,21,276 0/0:9,0:9:21.06:0,21,255 0/1:2,5:7:58.94:180,0,59 1/1:2,2:4:3.01:35,3,0 0/0:4,0:4:6.02:0,6,90 0/1:5,3:8:96.83:97,0,140 0/0:14,0:14:42.14:0,42,555 0/0:9,0:9:27.08:0,27,328 0/0:19,0:19:57.18:0,57,718 0/0:12,0:13:33.11:0,33,445 0/0:17,0:17:51.13:0,51,632 0/0:12,0:12:33.10:0,33,429 0/0:7,0:7:21.07:0,21,274 0/0:8,0:8:21.06:0,21,259 0/0:14,0:14:39.13:0,39,529 0/0:18,0:18:39.12:0,39,496 0/0:7,0:7:21.07:0,21,264 0/0:16,0:16:39.11:0,39,481 0/0:30,0:30:81.25:0,81,1053 0/0:19,0:19:54.17:0,54,685 0/0:15,0:15:42.14:0,42,555 0/0:20,0:20:54.16:0,54,673 0/0:6,0:6:18.06:0,18,232 0/0:10,0:10:30.10:0,30,396 0/0:11,0:11:30.10:0,30,395 0/0:8,0:8:24.07:0,24,301 0/0:6,0:6:15.05:0,15,194 0/0:11,0:11:27.08:0,27,348 0/0:7,0:7:18.06:0,18,240 -chr1 899318 . C T 428.77 . AC=1;AF=0.0083;AN=120;BaseQRankSum=1.231;DP=2100;Dels=0.00;FS=29.933;HRun=0;HaplotypeScore=1.6653;InbreedingCoeff=-0.0087;MQ=58.94;MQ0=0;MQRankSum=-0.016;QD=10.99;ReadPosRankSum=-1.614;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P228|412|KLHL17|protein_coding|CODING|ENST00000455747|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P458|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|);CSQ=3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300|4/6|||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,synonymous_variant|ccC/ccT|P|ENSG00000187961|KLHL17|ENST00000338591|9/12|||458/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000481067|1/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:9,0:9:21.04:0,21,255 0/0:10,0:10:21.06:0,21,259 0/0:9,0:9:18.05:0,18,223 0/0:9,0:9:24.04:0,24,276 0/0:27,0:27:78.26:0,78,1053 0/0:22,0:22:66.19:0,66,843 0/0:42,0:42:99:0,123,1633 0/0:22,0:22:60.20:0,60,810 0/0:59,1:60:99:0,175,2310 0/0:57,0:58:99:0,169,2215 0/1:24,15:39:99:477,0,826 0/0:25,0:25:72.24:0,72,968 0/0:34,0:34:99:0,99,1290 0/0:45,0:45:99:0,114,1500 0/0:64,0:64:99:0,138,1840 0/0:30,0:30:78.25:0,78,1025 0/0:46,0:46:99:0,105,1417 0/0:40,0:40:93.30:0,93,1248 0/0:57,0:57:99:0,135,1785 0/0:49,0:49:99:0,117,1558 0/0:51,0:51:99:0,123,1654 0/0:67,0:67:99:0,160,2145 0/0:50,0:50:99:0,129,1715 0/0:31,0:31:78.22:0,78,1001 0/0:48,0:48:99:0,114,1510 0/0:54,0:54:99:0,120,1634 0/0:42,0:43:99:0,105,1391 0/0:43,0:43:99:0,111,1484 0/0:44,0:44:99:0,105,1387 0/0:40,0:40:96.30:0,96,1249 0/0:53,0:53:99:0,114,1507 0/0:43,0:43:99:0,105,1408 0/0:32,0:32:81.26:0,81,1086 0/0:67,0:67:99:0,160,2119 0/0:56,0:56:99:0,138,1826 0/0:52,0:52:99:0,135,1795 0/0:66,0:66:99:0,150,2011 0/0:75,0:75:99:0,184,2485 0/0:15,0:15:39.13:0,39,519 0/0:39,0:39:90.29:0,90,1213 0/0:27,0:27:69.22:0,69,901 0/0:24,0:24:57.17:0,57,735 0/0:23,0:23:60.19:0,60,779 0/0:15,0:15:36.11:0,36,472 0/0:18,0:18:51.16:0,51,675 0/0:29,0:29:66.20:0,66,861 0/0:26,0:26:60.19:0,60,782 0/0:13,0:13:33.11:0,33,446 0/0:19,0:19:39.13:0,39,522 0/0:24,0:24:51.16:0,51,667 0/0:31,0:31:84.24:0,84,1063 0/0:16,0:16:48.15:0,48,634 0/0:29,0:29:78.21:0,78,969 0/0:17,0:17:45.12:0,45,581 0/0:23,0:23:57.18:0,57,765 0/0:21,1:22:24.94:0,25,720 0/0:19,0:19:45.15:0,45,624 0/0:26,0:26:66.21:0,66,875 0/0:15,0:15:33.11:0,33,435 0/0:17,0:17:45.15:0,45,613 -chr1 899374 . G A 298.41 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.204;DP=2588;Dels=0.00;FS=1.169;HRun=1;HaplotypeScore=1.4609;InbreedingCoeff=-0.0084;MQ=58.81;MQ0=0;MQRankSum=0.082;QD=10.29;ReadPosRankSum=2.022;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R247Q|412|KLHL17|protein_coding|CODING|ENST00000455747|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGa/cAa|R477Q|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|);CSQ=3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300|4/6|||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,missense_variant|cGa/cAa|R/Q|ENSG00000187961|KLHL17|ENST00000338591|9/12|possibly_damaging(0.886)|deleterious(0.03)|477/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000481067|1/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:21,0:21:54.16:0,54,689 0/0:17,0:17:45.14:0,45,571 0/0:14,0:14:33.11:0,33,424 0/0:11,0:11:27.08:0,27,338 0/0:49,0:49:99:0,144,1891 0/0:61,0:61:99:0,175,2287 0/0:109,0:109:99:0,304,4020 0/0:42,0:42:99:0,123,1612 0/0:121,0:121:99:0,349,4581 0/0:145,0:145:99:0,406,5379 0/0:49,0:49:99:0,138,1802 0/0:55,0:55:99:0,159,2038 0/0:60,0:60:99:0,181,2351 0/0:48,0:49:99:0,105,1373 0/0:61,0:61:99:0,147,1925 0/0:25,0:25:63.20:0,63,834 0/0:48,0:48:99:0,126,1652 0/0:42,0:43:99:0,111,1439 0/0:43,0:43:99:0,114,1476 0/0:42,0:42:99:0,108,1407 0/0:45,0:45:99:0,117,1526 0/0:55,0:56:99:0,144,1866 0/0:37,0:37:99:0,99,1272 0/0:38,1:39:64.68:0,65,1277 0/0:60,0:60:99:0,150,1974 0/0:39,0:39:96.31:0,96,1285 0/0:33,0:33:75.25:0,75,1015 0/0:48,0:48:99:0,129,1697 0/0:38,0:38:99:0,105,1350 0/0:34,0:34:90.29:0,90,1173 0/0:46,0:46:99:0,129,1675 0/0:38,0:38:99:0,99,1267 0/1:18,11:29:99:346,0,569 0/0:54,0:54:99:0,132,1690 0/0:43,0:43:99:0,117,1496 0/0:54,0:54:99:0,138,1815 0/0:53,0:54:99:0,138,1780 0/0:66,0:66:99:0,181,2389 0/0:20,0:20:54.15:0,54,680 0/0:50,0:50:99:0,126,1648 0/0:46,0:46:99:0,120,1552 0/0:23,0:23:60.20:0,60,807 0/0:37,0:38:75.24:0,75,1007 0/0:18,0:18:45.14:0,45,585 0/0:27,0:27:75.22:0,75,949 0/0:27,0:27:69.21:0,69,900 0/0:47,0:47:99:0,120,1519 0/0:15,0:15:45.14:0,45,579 0/0:23,0:23:63.20:0,63,810 0/0:54,0:54:99:0,132,1712 0/0:48,0:48:99:0,126,1607 0/0:29,0:29:78.23:0,78,980 0/0:37,0:37:93.28:0,93,1192 0/0:39,0:39:99:0,99,1302 0/0:31,0:31:72.22:0,72,947 0/0:32,0:32:84.27:0,84,1125 0/0:18,0:18:42.14:0,42,558 0/0:37,0:37:87.27:0,87,1143 0/0:25,0:25:60.16:0,60,775 0/0:25,0:25:63.19:0,63,815 -chr1 899515 . C T 554.46 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.826;DP=4376;Dels=0.00;FS=0.766;HRun=0;HaplotypeScore=2.1786;InbreedingCoeff=-0.0084;MQ=58.98;MQ0=0;MQRankSum=-0.199;QD=13.86;ReadPosRankSum=2.919;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),EXON(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|2),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y261|412|KLHL17|protein_coding|CODING|ENST00000455747|),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y491|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|),UPSTREAM(MODIFIER|||||NOC2L|retained_intron|CODING|ENST00000469563|);CSQ=3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300|5/6|||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,synonymous_variant|taC/taT|Y|ENSG00000187961|KLHL17|ENST00000338591|10/12|||491/642|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000469563|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187961|KLHL17|ENST00000481067|2/2||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:28,0:29:66.20:0,66,819 0/0:30,0:30:87.22:0,87,1062 0/0:46,1:47:99:0,123,1525 0/0:22,0:22:51.15:0,51,611 0/0:100,0:100:99:0,286,3773 0/0:87,0:87:99:0,247,3221 0/0:190,0:190:99:0,530,6810 0/0:63,0:63:99:0,156,2003 0/0:214,0:214:99:0,608,7938 0/0:223,1:226:99:0,650,8445 0/0:97,0:98:99:0,280,3587 0/0:83,0:84:99:0,223,2836 0/0:132,0:132:99:0,361,4567 0/0:75,0:76:99:0,169,2266 0/0:90,0:90:99:0,220,2918 0/0:56,0:56:99:0,135,1804 0/0:85,0:85:99:0,202,2650 0/0:85,0:85:99:0,196,2620 0/0:71,1:72:99:0,163,2181 0/0:75,0:75:99:0,190,2497 0/0:65,0:65:99:0,157,2103 0/0:107,0:107:99:0,247,3300 0/0:72,0:72:99:0,169,2219 0/0:75,0:75:99:0,172,2229 0/0:75,0:75:99:0,181,2425 0/0:61,0:61:99:0,141,1858 0/0:70,0:70:99:0,162,2125 0/0:58,0:58:99:0,147,1963 0/0:71,0:71:99:0,172,2268 0/0:57,0:57:99:0,132,1767 0/0:116,0:116:99:0,265,3522 0/0:49,0:49:99:0,123,1622 0/0:95,0:95:99:0,229,3053 0/0:88,0:88:99:0,217,2862 0/0:72,0:72:99:0,172,2257 0/0:74,0:74:99:0,175,2373 0/0:89,0:89:99:0,217,2904 0/0:102,2:105:99:0,206,3164 0/0:40,0:40:99:0,99,1298 0/0:68,0:68:99:0,175,2284 0/0:64,1:65:99:0,146,2203 0/0:51,0:51:99:0,123,1598 0/0:47,0:47:99:0,114,1465 0/0:36,0:36:78.25:0,78,1021 0/1:16,24:40:99:602,0,434 0/0:44,0:44:99:0,120,1555 0/0:79,0:79:99:0,211,2716 0/0:38,1:39:99:0,102,1267 0/0:41,0:41:99:0,111,1451 0/0:64,0:64:99:0,168,2151 0/0:84,0:84:99:0,220,2873 0/0:44,1:45:99:0,123,1576 0/0:75,0:75:99:0,205,2549 0/0:52,0:52:99:0,129,1712 0/0:47,0:48:99:0,117,1536 0/0:44,0:44:99:0,105,1368 0/0:36,0:36:87.26:0,87,1135 0/0:53,0:53:99:0,117,1560 0/0:42,0:42:99:0,114,1475 0/0:23,0:23:63.20:0,63,818 -chr1 899648 . C T 506.51 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.603;DP=2206;Dels=0.00;FS=1.040;HRun=0;HaplotypeScore=2.2848;InbreedingCoeff=-0.0084;MQ=57.02;MQ0=0;MQRankSum=0.240;QD=14.90;ReadPosRankSum=1.277;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|9),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|10),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||749|NOC2L|protein_coding|CODING|ENST00000327044|),UPSTREAM(MODIFIER|||||NOC2L|processed_transcript|CODING|ENST00000487214|);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000327044||||-/749|protein_coding|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,upstream_gene_variant|||ENSG00000188976|NOC2L|ENST00000487214|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:16,0:16:39.12:0,39,478 0/0:19,0:19:42.08:0,42,483 0/0:15,0:15:33.11:0,33,424 0/0:11,0:11:27.08:0,27,332 0/0:49,0:49:99:0,135,1685 0/0:32,0:32:90.27:0,90,1141 0/0:77,0:77:99:0,214,2676 0/0:32,0:32:84.27:0,84,1076 0/0:95,0:95:99:0,265,3397 0/0:105,0:105:99:0,295,3736 0/0:43,0:43:99:0,117,1468 0/0:38,0:38:99:0,102,1297 0/0:60,0:60:99:0,172,2187 0/0:18,0:18:54.11:0,54,608 0/0:36,0:36:99:0,102,1164 0/0:21,0:21:57.17:0,57,691 0/0:30,0:30:84.22:0,84,984 0/0:24,0:24:60.15:0,60,700 0/0:29,0:29:69.17:0,69,796 0/0:33,1:34:90.21:0,90,1052 0/0:26,1:27:38.73:0,39,728 0/0:32,0:32:90.25:0,90,1074 0/0:24,0:24:57.15:0,57,674 0/0:25,0:25:69.13:0,69,771 0/0:29,0:29:84.22:0,84,969 0/0:22,0:22:66.17:0,66,765 0/0:20,0:20:54.15:0,54,639 0/0:18,0:18:48.11:0,48,548 0/0:31,0:31:84.20:0,84,985 0/0:28,0:28:81.22:0,81,952 0/0:35,0:35:96.24:0,96,1131 0/0:23,0:23:60.18:0,60,735 0/0:31,0:31:81.20:0,81,912 0/1:12,22:34:99:554,0,283 0/0:27,0:27:75.17:0,75,861 0/0:22,0:22:63.17:0,63,745 0/0:29,0:29:72.21:0,72,885 0/0:37,0:37:99:0,102,1211 0/0:32,0:33:84.20:0,84,990 0/0:64,0:64:99:0,153,1878 0/0:46,0:46:99:0,114,1370 0/0:36,0:36:78.20:0,78,946 0/0:34,0:34:78.16:0,78,889 0/0:35,0:35:78.19:0,78,962 0/0:34,0:34:81.22:0,81,970 0/0:45,0:45:99:0,105,1277 0/0:70,0:70:99:0,168,1980 0/0:36,0:36:90.22:0,90,1052 0/0:38,0:38:93.26:0,93,1159 0/0:54,0:54:99:0,129,1475 0/0:62,0:62:99:0,153,1807 0/0:41,0:41:99:0,105,1125 0/0:61,0:61:99:0,129,1473 0/0:28,0:28:72.20:0,72,847 0/0:35,0:35:87.22:0,87,1026 0/0:34,0:34:87.22:0,87,1022 0/0:13,0:13:30.06:0,30,338 0/0:49,0:49:99:0,111,1314 0/0:39,0:39:81.20:0,81,932 0/0:39,0:39:81.21:0,81,983 -chr1 899824 . C T 386.57 . AC=2;AF=0.0169;AN=118;BaseQRankSum=-1.360;DP=1027;Dels=0.00;FS=0.938;HRun=0;HaplotypeScore=0.7940;InbreedingCoeff=-0.0327;MQ=52.55;MQ0=0;MQRankSum=2.078;QD=10.17;ReadPosRankSum=-2.959;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N308|412|KLHL17|protein_coding|CODING|ENST00000455747|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N538|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000187961|KLHL17|ENST00000466300|6/6|||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,synonymous_variant|aaC/aaT|N|ENSG00000187961|KLHL17|ENST00000338591|11/12|||538/642|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,30 ./. 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.02:0,6,76 0/0:7,0:7:15.03:0,15,165 0/0:6,0:6:15.05:0,15,192 0/0:7,0:7:15.04:0,15,166 0/0:5,0:5:12.04:0,12,142 0/1:6,7:13:99:192,0,182 0/0:17,0:17:45.08:0,45,531 0/0:6,0:6:15.04:0,15,184 0/0:2,0:2:3.01:0,3,32 0/0:6,0:6:9.01:0,9,99 0/0:24,0:24:51.15:0,51,651 0/0:42,0:42:99:0,99,1228 0/0:22,0:22:48.14:0,48,608 0/0:20,0:20:51.15:0,51,662 0/0:28,0:28:72.19:0,72,872 0/0:28,0:29:66.18:0,66,785 0/0:29,0:29:66.20:0,66,813 0/0:29,1:30:72.22:0,72,900 0/0:40,1:42:54.69:0,55,1097 0/0:21,0:22:54.15:0,54,651 0/0:14,0:14:33.10:0,33,432 0/0:28,0:28:69.20:0,69,833 0/0:27,0:27:54.16:0,54,695 0/0:20,1:21:48.12:0,48,588 0/0:14,0:14:30.09:0,30,391 0/0:30,0:30:75.22:0,75,923 0/0:23,0:24:63.19:0,63,795 0/0:35,0:36:87.27:0,87,1096 0/1:13,11:25:99:259,0,299 0/0:23,0:23:48.14:0,48,600 0/0:34,0:34:81.23:0,81,1005 0/0:27,0:27:57.17:0,57,719 0/0:24,0:24:57.18:0,57,725 0/0:29,0:29:72.22:0,72,891 0/0:48,0:48:99:0,108,1377 0/0:6,0:6:15.05:0,15,184 0/0:23,0:23:48.15:0,48,596 0/0:14,0:14:42.12:0,42,495 0/0:7,0:7:21.07:0,21,274 0/0:6,0:6:12.04:0,12,155 0/0:5,0:5:12.04:0,12,156 0/0:11,0:12:33.10:0,33,417 0/0:12,0:12:36.10:0,36,428 0/0:26,0:26:66.18:0,66,798 0/0:3,0:3:6.02:0,6,77 0/0:14,0:14:30.09:0,30,384 0/0:13,0:13:33.10:0,33,407 0/0:22,0:22:66.15:0,66,748 0/0:11,0:11:30.09:0,30,386 0/0:14,0:14:36.11:0,36,435 0/0:8,0:8:24.07:0,24,277 0/0:11,0:11:30.10:0,30,394 0/0:10,0:10:24.07:0,24,307 0/0:5,0:5:12.04:0,12,153 0/0:17,0:17:39.11:0,39,456 0/0:8,0:8:18.06:0,18,226 0/0:12,0:12:33.10:0,33,419 -chr1 899926 . GC G 146.78 . AC=3;AF=0.0273;AN=110;BaseQRankSum=-1.149;DP=401;FS=8.501;HRun=1;HaplotypeScore=98.5276;InbreedingCoeff=-0.0768;MQ=46.11;MQ0=0;MQRankSum=-4.025;QD=4.32;ReadPosRankSum=-1.794;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,44 ./. ./. ./. 0/0:1,0:1:3.01:0,3,34 0/0:6,0:6:18.06:0,18,266 0/0:2,0:2:6.02:0,6,70 0/0:2,0:2:6.02:0,6,88 0/0:5,0:5:12.04:0,12,174 0/0:1,0:1:3.01:0,3,44 0/0:1,0:1:3.01:0,3,43 ./. 0/0:16,0:16:48.15:0,48,684 0/0:8,0:8:21.07:0,21,298 0/0:7,0:7:18.06:0,18,256 0/0:11,0:11:32.91:0,33,414 0/0:19,0:19:48.12:0,48,646 0/0:6,0:6:15.05:0,15,220 0/0:14,0:14:39.12:0,39,542 0/1:13,5:18:96.91:97,0,389 0/0:12,0:12:33.09:0,33,437 0/0:12,0:12:36.12:0,36,539 0/0:6,0:6:17.96:0,18,217 0/0:8,0:8:21.07:0,21,291 0/0:10,0:10:30.09:0,30,398 0/1:5,2:7:51.91:52,0,134 0/0:10,0:10:30.08:0,30,410 0/0:12,0:12:36.12:0,36,516 0/0:15,0:15:45.15:0,45,635 0/0:11,0:11:27.09:0,27,387 0/0:6,0:6:15.05:0,15,198 0/0:7,0:7:18.06:0,18,257 0/1:7,2:9:84.39:84,0,171 0/0:19,0:19:54.17:0,54,750 0/0:12,1:13:4.10:0,4,483 0/0:17,0:17:48.15:0,48,679 0/0:11,0:11:33.11:0,33,489 0/0:3,0:3:6.02:0,6,88 0/0:4,1:5:6.11:0,6,73 0/0:9,0:9:24.08:0,24,333 0/0:6,0:6:15.04:0,15,199 0/0:4,0:4:9.03:0,9,136 0/0:4,0:4:12.03:0,12,159 0/0:3,0:3:9.03:0,9,130 0/0:6,0:6:15.05:0,15,215 0/0:9,0:9:21.07:0,21,309 0/0:2,0:2:6.02:0,6,94 0/0:5,0:5:12.04:0,12,176 0/0:11,0:11:27.09:0,27,375 0/0:7,0:7:18.06:0,18,267 0/0:3,0:3:9.03:0,9,133 0/0:2,0:2:6.02:0,6,87 0/0:2,0:2:6.02:0,6,87 0/0:4,0:4:9.03:0,9,131 0/0:2,0:2:6.01:0,6,68 0/0:1,0:1:3.01:0,3,44 0/0:3,0:3:9.03:0,9,127 0/0:1,0:1:3.01:0,3,37 0/0:6,0:6:18.03:0,18,226 -chr1 899928 . G C 10304.35 . AC=95;AF=0.8636;AN=110;BaseQRankSum=-2.647;DP=394;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.9435;InbreedingCoeff=-0.0052;MQ=45.90;MQ0=0;MQRankSum=-1.207;QD=26.35;ReadPosRankSum=1.974;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,6:6:18.03:191,18,0 1/1:0,1:1:3.01:33,3,0 1/1:0,2:2:6.01:61,6,0 0/1:1,4:5:32.20:65,0,32 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:33,3,0 ./. 1/1:0,15:15:42.11:479,42,0 1/1:0,8:8:21.05:233,21,0 1/1:0,7:7:15.05:185,15,0 1/1:0,11:11:30.07:346,30,0 1/1:0,19:19:39.10:466,39,0 1/1:0,6:6:15.05:185,15,0 1/1:0,14:14:33.09:377,33,0 0/1:2,11:18:38.14:289,0,38 1/1:0,11:12:27.08:315,27,0 0/1:6,6:12:99:166,0,142 1/1:0,6:6:18.05:216,18,0 1/1:0,8:8:21.05:237,21,0 0/1:1,7:8:9.36:225,0,9 1/1:0,5:7:12.03:125,12,0 0/1:4,6:10:99:132,0,135 1/1:0,12:12:36.11:430,36,0 1/1:0,15:15:39.12:479,39,0 1/1:1,10:11:27.08:329,27,0 1/1:0,6:6:15.04:169,15,0 1/1:0,6:6:18.05:208,18,0 0/1:1,6:9:15.39:143,0,15 1/1:1,16:17:45.14:552,45,0 1/1:0,12:13:33.07:370,33,0 1/1:0,17:17:42.10:485,42,0 1/1:0,11:11:30.09:377,30,0 1/1:0,3:3:6.02:73,6,0 0/1:4,1:5:21.40:21,0,92 1/1:1,8:9:24.07:289,24,0 0/1:5,1:6:21.08:21,0,140 1/1:0,4:4:6.02:74,6,0 0/1:1,3:4:21.40:94,0,21 1/1:0,3:3:9.03:106,9,0 1/1:0,5:5:9.01:89,9,0 1/1:0,9:9:21.06:243,21,0 0/0:2,0:2:6.02:0,6,75 1/1:0,5:5:12.04:152,12,0 1/1:0,11:11:27.07:315,27,0 0/1:3,5:8:21.98:136,0,22 0/1:1,2:3:24.41:58,0,24 1/1:0,2:2:6:62,6,0 1/1:0,2:2:6.02:67,6,0 1/1:0,4:4:9.02:100,9,0 1/1:0,2:2:6.02:78,6,0 1/1:0,1:1:3.01:33,3,0 1/1:0,3:3:9.02:100,9,0 1/1:0,1:1:3.01:36,3,0 1/1:0,6:6:15.05:187,15,0 -chr1 899937 . G T 7323.3 . AC=86;AF=0.860;AN=100;BaseQRankSum=-1.886;DP=301;Dels=0.00;FS=4.882;HRun=0;HaplotypeScore=1.0717;InbreedingCoeff=0.2201;MQ=45.04;MQ0=0;MQRankSum=-1.460;QD=25.61;ReadPosRankSum=2.493;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,4:4:9.02:100,9,0 ./. ./. 0/1:1,2:3:24.57:25,0,35 1/1:0,1:1:3.01:33,3,0 ./. ./. 1/1:0,13:13:36.10:425,36,0 1/1:0,7:7:15.04:170,15,0 1/1:1,5:6:15.04:181,15,0 1/1:1,7:8:15.04:174,15,0 1/1:0,10:11:27.08:313,27,0 1/1:0,4:4:6.02:72,6,0 1/1:0,11:11:30.06:338,30,0 1/1:0,14:14:30.07:332,30,0 1/1:0,10:10:18.05:209,18,0 0/1:4,5:9:99:121,0,131 1/1:1,1:2:3.01:33,3,0 1/1:1,6:7:18.05:200,18,0 0/1:1,4:5:18.39:124,0,18 1/1:0,4:4:6.01:64,6,0 0/1:3,3:6:71.44:71,0,103 1/1:0,12:12:33.07:362,33,0 1/1:0,13:13:33.09:396,33,0 1/1:0,8:8:21.06:246,21,0 1/1:0,5:5:9.02:99,9,0 1/1:0,6:6:18.04:205,18,0 1/1:1,4:5:9.02:96,9,0 1/1:0,13:13:33.10:419,33,0 1/1:0,9:9:24.06:277,24,0 1/1:0,16:17:36.10:429,36,0 1/1:0,9:9:24.06:285,24,0 1/1:0,3:3:6.01:71,6,0 0/0:3,1:4:9.02:0,9,100 1/1:0,6:6:12.02:129,12,0 0/0:5,0:5:12.02:0,12,132 1/1:1,3:4:6.02:75,6,0 0/1:1,2:3:27.42:33,0,27 1/1:0,2:2:3.01:33,3,0 1/1:0,4:4:12.03:132,12,0 1/1:0,7:7:18.04:203,18,0 0/0:2,0:2:6.02:0,6,74 1/1:0,2:2:6.02:73,6,0 1/1:0,9:9:21.05:240,21,0 0/1:3,5:8:24.18:149,0,24 1/1:1,1:2:3.01:33,3,0 1/1:0,2:2:3.01:41,3,0 1/1:0,2:2:3.01:33,3,0 1/1:0,2:2:3.01:33,3,0 1/1:0,1:1:3.01:39,3,0 ./. 1/1:0,2:2:6.02:67,6,0 ./. 1/1:0,4:4:9.02:105,9,0 -chr1 899938 . G C 7723.52 . AC=86;AF=0.860;AN=100;BaseQRankSum=-1.269;DP=292;Dels=0.00;FS=6.709;HRun=1;HaplotypeScore=0.9273;InbreedingCoeff=0.2346;MQ=45.14;MQ0=0;MQRankSum=-2.046;QD=27.78;ReadPosRankSum=2.689;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,4:4:9.02:100,9,0 ./. ./. 0/1:1,2:3:32.21:53,0,32 1/1:0,1:1:3.01:33,3,0 ./. ./. 1/1:0,12:12:36.10:433,36,0 1/1:0,7:7:18.04:198,18,0 1/1:0,6:6:15.04:180,15,0 1/1:0,8:8:18.05:204,18,0 1/1:1,9:10:27.08:322,27,0 1/1:0,4:4:9.01:97,9,0 1/1:0,10:10:27.05:301,27,0 1/1:0,14:14:33.08:381,33,0 1/1:0,10:10:21.05:234,21,0 0/1:4,5:9:99:130,0,127 1/1:0,2:2:6.01:62,6,0 1/1:0,7:7:18.04:198,18,0 0/1:1,4:5:18.39:123,0,18 1/1:0,4:4:9.01:95,9,0 0/1:3,3:6:67.97:75,0,68 1/1:0,12:12:33.08:368,33,0 1/1:0,13:13:36.11:438,36,0 1/1:0,8:8:18.05:219,18,0 1/1:0,5:5:9.03:109,9,0 1/1:0,6:6:18.04:205,18,0 1/1:0,5:5:12.03:134,12,0 1/1:0,13:13:36.10:442,36,0 1/1:0,9:9:24.07:284,24,0 1/1:0,15:15:36.10:439,36,0 1/1:0,9:9:24.07:300,24,0 1/1:0,3:3:6.02:75,6,0 0/0:3,1:4:9.02:0,9,100 1/1:0,6:6:15.02:150,15,0 0/0:5,0:5:9.03:0,9,114 1/1:1,3:4:6.02:78,6,0 0/1:1,1:2:27.42:33,0,27 1/1:0,2:2:3.01:33,3,0 1/1:0,4:4:12.03:134,12,0 1/1:0,7:7:18.04:202,18,0 0/0:2,0:2:6.02:0,6,75 1/1:0,2:2:6.02:75,6,0 1/1:0,8:8:15.05:179,15,0 0/1:2,6:8:21.19:170,0,21 1/1:1,1:2:3.01:33,3,0 1/1:0,2:2:3.01:37,3,0 1/1:0,2:2:6:58,6,0 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:39,3,0 ./. 1/1:0,2:2:6.02:67,6,0 ./. 1/1:0,4:4:12.02:134,12,0 -chr1 899942 . G A 9223.42 . AC=87;AF=0.8529;AN=102;BaseQRankSum=-0.795;DP=333;Dels=0.00;FS=4.035;HRun=0;HaplotypeScore=0.7409;InbreedingCoeff=0.1074;MQ=43.28;MQ0=0;MQRankSum=-1.361;QD=28.38;ReadPosRankSum=1.851;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,4:4:9.02:100,9,0 ./. ./. 0/1:1,2:3:32.21:59,0,32 1/1:0,1:1:3.01:33,3,0 ./. ./. 1/1:0,13:13:39.12:483,39,0 1/1:0,7:7:21.06:244,21,0 1/1:0,7:7:15.02:177,15,0 1/1:0,8:8:21.06:245,21,0 1/1:0,11:11:33.10:394,33,0 1/1:0,7:7:18.05:206,18,0 1/1:0,11:11:30.08:337,30,0 0/1:4,13:17:58.18:348,0,58 1/1:0,14:14:36.06:388,36,0 0/1:4,4:8:99:127,0,135 1/1:0,3:3:9.02:98,9,0 1/1:0,8:8:18.05:201,18,0 1/1:0,4:4:12.03:141,12,0 1/1:1,6:7:18.04:198,18,0 0/1:3,3:6:71.48:71,0,101 1/1:0,12:12:33.09:385,33,0 1/1:0,14:14:36.11:439,36,0 1/1:1,8:9:24.05:274,24,0 1/1:0,5:5:9.03:109,9,0 1/1:0,6:6:18.05:212,18,0 0/1:4,4:8:99:110,0,110 1/1:0,15:15:45.13:550,45,0 0/1:1,8:9:1.62:228,0,2 1/1:0,16:16:45.11:532,45,0 1/1:0,9:9:24.08:302,24,0 1/1:0,3:3:6.02:76,6,0 0/0:3,1:4:9.02:0,9,100 1/1:0,9:9:27.06:300,27,0 0/1:5,1:6:18.39:18,0,140 1/1:0,4:4:12.04:143,12,0 0/1:1,2:3:24.41:61,0,24 1/1:1,1:2:3.01:33,3,0 1/1:0,5:5:12.03:138,12,0 1/1:0,7:7:18.05:209,18,0 0/0:2,0:2:3.01:0,3,42 1/1:0,3:3:9.03:109,9,0 1/1:0,10:10:24.06:273,24,0 0/1:2,8:10:48.59:207,0,49 1/1:1,2:3:6.02:67,6,0 1/1:0,2:2:6.02:76,6,0 1/1:0,2:2:6.02:67,6,0 1/1:0,3:3:9.02:100,9,0 1/1:0,1:1:3.01:39,3,0 ./. 1/1:0,2:2:6.02:67,6,0 1/1:0,2:2:6.02:69,6,0 1/1:0,4:4:12.04:145,12,0 -chr1 899943 . G C 99.41 . AC=3;AF=0.0294;AN=102;BaseQRankSum=-1.668;DP=334;Dels=0.00;FS=4.946;HRun=0;HaplotypeScore=0.6513;InbreedingCoeff=-0.0759;MQ=42.96;MQ0=0;MQRankSum=-3.741;QD=2.76;ReadPosRankSum=-1.346;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:4,0:4:12.01:0,12,123 ./. ./. 0/0:3,0:3:9.03:0,9,114 0/0:2,0:2:6.02:0,6,70 ./. ./. 0/0:13,0:13:39.12:0,39,478 0/0:7,0:7:21.06:0,21,242 0/0:7,0:7:18.04:0,18,212 0/0:8,0:8:21.06:0,21,245 0/0:11,0:11:33.10:0,33,392 0/0:7,0:7:15.04:0,15,174 0/0:11,0:11:30.08:0,30,339 0/1:13,4:17:58.20:58,0,330 0/0:14,0:14:36.08:0,36,391 0/0:8,0:8:24.08:0,24,306 0/0:3,0:3:9.02:0,9,100 0/0:8,0:8:18.05:0,18,206 0/0:5,0:5:15.03:0,15,158 0/0:6,1:7:18.05:0,18,201 0/0:5,0:5:12.04:0,12,162 0/0:12,0:12:33.10:0,33,385 0/0:14,0:14:39.12:0,39,471 0/0:9,0:9:24.07:0,24,282 0/0:5,0:5:9.03:0,9,109 0/0:6,0:6:18.06:0,18,221 0/1:6,4:10:99:103,0,140 0/0:15,0:15:45.14:0,45,554 0/1:8,1:9:9.36:9,0,228 0/0:16,0:16:45.13:0,45,542 0/0:8,0:8:24.08:0,24,307 0/0:3,0:3:6.02:0,6,76 0/0:4,0:4:9.02:0,9,100 0/0:10,0:10:30.06:0,30,320 0/0:5,0:5:15.05:0,15,186 0/0:4,0:4:12.04:0,12,143 0/0:3,0:3:9.03:0,9,105 0/0:1,0:1:3.01:0,3,33 0/0:6,0:6:15.04:0,15,172 0/0:7,0:7:15.04:0,15,182 0/0:2,0:2:6.02:0,6,73 0/0:3,0:3:9.03:0,9,109 0/0:10,0:10:27.08:0,27,310 0/0:10,0:10:27.07:0,27,309 0/0:3,0:3:6.02:0,6,67 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:6.02:0,6,67 0/0:3,0:3:9.02:0,9,100 0/0:1,0:1:3.01:0,3,39 ./. 0/0:2,0:2:6.02:0,6,67 0/0:2,0:2:3.01:0,3,33 0/0:4,0:4:12.03:0,12,137 -chr1 899959 . G GC 686.45 . AC=19;AF=0.190;AN=100;BaseQRankSum=-3.215;DP=298;FS=12.605;HRun=0;HaplotypeScore=100.2656;InbreedingCoeff=-0.1846;MQ=45.28;MQ0=0;MQRankSum=-5.322;QD=4.40;ReadPosRankSum=0.742;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:2,0:2:3.48:0,3,43 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,84 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:4,0:4:12.04:0,12,168 0/0:3,0:3:9.03:0,9,126 ./. ./. 0/1:11,1:12:8.87:9,0,426 0/0:6,0:6:18.06:0,18,240 0/1:4,1:5:28.83:29,0,153 0/0:6,0:6:18.05:0,18,237 0/1:8,1:9:17.90:18,0,309 0/1:4,3:7:94.91:117,0,95 0/1:7,1:8:23.92:24,0,231 0/1:12,2:14:5.86:6,0,464 0/1:12,2:14:56.82:57,0,383 0/0:8,0:8:21.07:0,21,294 0/0:2,1:3:9.03:0,9,126 0/1:5,1:6:26.41:26,0,192 0/0:5,0:5:15.05:0,15,210 0/1:7,1:8:23.92:24,0,230 0/0:2,0:2:6.02:0,6,84 0/0:9,0:9:24.08:0,24,330 0/1:11,1:12:11.88:12,0,387 0/0:8,0:8:24.08:0,24,335 0/0:4,0:4:12.04:0,12,168 0/0:5,0:5:15.05:0,15,210 0/1:7,6:13:99:225,0,217 0/1:14,2:16:44.89:45,0,501 0/0:7,0:7:21.07:0,21,285 0/1:13,1:14:2.86:3,0,503 0/0:10,0:10:30.10:0,30,420 0/0:3,0:3:6.02:0,6,84 0/0:3,0:3:9.03:0,9,126 0/1:6,2:8:67.16:67,0,189 0/0:4,0:4:12.04:0,12,168 0/1:2,1:3:35.96:36,0,75 0/0:3,0:3:9.03:0,9,126 ./. 0/0:6,0:6:15.05:0,15,210 0/0:7,0:7:21.07:0,21,294 ./. 0/1:1,1:2:35.97:41,0,36 0/0:7,0:7:21.07:0,21,293 0/0:10,0:10:30.10:0,30,419 0/1:2,1:3:35.97:40,0,36 0/0:3,0:3:6.02:0,6,84 0/0:2,0:2:6.02:0,6,84 1/1:0,2:2:6.02:88,6,0 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:2,0:2:6.02:0,6,81 0/0:3,0:3:9.03:0,9,126 -chr1 899960 . T C 416.06 . AC=19;AF=0.190;AN=100;BaseQRankSum=3.474;DP=298;Dels=0.00;FS=12.762;HRun=0;HaplotypeScore=0.3615;InbreedingCoeff=-0.1710;MQ=45.28;MQ0=0;MQRankSum=-6.659;QD=2.87;ReadPosRankSum=-1.194;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:2,0:2:3.01:0,3,38 0/0:1,0:1:3:0,3,28 0/0:1,0:1:2.99:0,3,24 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:2.99:0,3,23 ./. ./. 0/0:4,0:4:12.04:0,12,144 0/0:3,0:3:8.99:0,9,82 ./. ./. 0/1:11,1:12:0.34:0,0,352 0/0:6,0:6:18.05:0,18,204 0/1:4,1:5:18.39:18,0,131 0/0:6,0:6:12.04:0,12,145 0/1:8,1:9:6.35:6,0,266 0/1:4,3:7:60.15:85,0,60 0/1:7,1:8:12.38:12,0,189 0/1:12,2:14:26.96:27,0,309 0/1:12,2:14:0.39:0,0,287 0/0:8,0:8:21.07:0,21,272 0/1:2,1:3:24.43:24,0,47 0/1:5,1:6:15.38:15,0,167 0/0:5,0:5:15.02:0,15,170 0/1:7,1:8:12.37:12,0,189 0/0:2,0:2:6.02:0,6,83 0/0:9,0:9:24.05:0,24,270 0/1:11,1:12:0.33:0,0,334 0/0:8,0:8:21.06:0,21,259 0/0:4,0:4:9.03:0,9,108 0/0:5,0:5:15.05:0,15,186 0/1:7,6:13:99:159,0,143 0/1:13,2:16:21.73:22,0,457 0/0:7,0:7:18.05:0,18,210 0/0:13,1:14:5.66:0,6,386 0/0:10,0:10:27.06:0,27,338 0/0:3,0:3:6.01:0,6,70 0/0:3,0:3:9.02:0,9,97 0/1:6,2:8:45.81:46,0,150 0/0:4,0:4:12.04:0,12,144 0/1:2,1:3:24.41:24,0,67 0/0:3,0:3:9.03:0,9,109 ./. 0/0:6,0:6:15.04:0,15,172 0/0:7,0:7:18.05:0,18,222 ./. 0/1:1,1:2:27.42:27,0,36 0/0:7,0:7:18.05:0,18,219 0/0:10,0:10:30.07:0,30,330 0/1:1,1:3:27.42:27,0,27 0/0:3,0:3:6.02:0,6,81 0/0:2,0:2:6:0,6,56 1/1:0,2:2:6.02:67,6,0 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/0:1,0:2:3.01:0,3,38 0/0:3,0:3:9.02:0,9,104 -chr1 899974 . G A 175.25 . AC=17;AF=0.170;AN=100;BaseQRankSum=1.366;DP=246;Dels=0.00;FS=8.615;HRun=0;HaplotypeScore=0.2560;InbreedingCoeff=-0.1500;MQ=45.05;MQ0=0;MQRankSum=-5.035;QD=1.79;ReadPosRankSum=-2.296;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:2,0:2:3.01:0,3,30 0/0:1,0:1:3.01:0,3,40 0/1:1,1:2:27.42:27,0,34 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:1,0:1:2.99:0,3,24 0/0:5,0:5:15.05:0,15,185 0/0:2,0:2:6.02:0,6,71 ./. ./. 0/1:11,1:12:0.33:0,0,334 0/0:5,0:5:15.04:0,15,175 0/1:2,1:3:24.41:24,0,67 0/0:5,0:5:12.03:0,12,137 0/0:7,0:7:18.04:0,18,207 0/1:1,1:3:27.42:27,0,34 0/0:5,0:5:9.03:0,9,112 0/1:10,1:11:3.36:3,0,272 0/1:9,1:10:7.61:8,0,171 0/0:8,0:8:24.07:0,24,298 0/1:1,1:2:22.63:27,0,23 0/1:5,1:6:15.39:15,0,155 0/1:4,1:5:18.39:18,0,137 0/1:7,1:8:15.40:15,0,150 0/1:1,1:2:22.63:23,0,34 0/0:7,0:7:18.05:0,18,208 0/0:9,0:9:24.07:0,24,298 0/0:5,0:5:12.03:0,12,140 0/0:4,0:4:9:0,9,90 0/0:4,0:4:12.04:0,12,159 0/0:11,0:11:30.05:0,30,313 0/1:9,1:10:6.35:6,0,280 0/0:3,0:3:9.03:0,9,105 0/1:10,1:11:0.36:0,0,315 0/0:11,0:11:30.09:0,30,372 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,67 0/1:5,2:7:34.08:34,0,146 0/0:4,0:4:12.04:0,12,152 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:6.02:0,6,72 ./. 0/0:5,0:5:12.04:0,12,143 0/0:5,0:5:15.04:0,15,180 ./. 0/0:1,0:1:3.01:0,3,38 0/0:8,0:8:24.06:0,24,278 0/0:9,1:11:27.07:0,27,306 0/1:2,1:3:27.42:27,0,27 0/0:2,0:2:3.01:0,3,40 0/0:2,0:2:6.02:0,6,67 1/1:1,2:3:6.02:67,6,0 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/0:2,0:2:6.02:0,6,69 0/0:2,0:2:6.02:0,6,73 -chr1 899975 . C G 161.84 . AC=18;AF=0.180;AN=100;BaseQRankSum=1.074;DP=239;Dels=0.00;FS=8.632;HRun=1;HaplotypeScore=0.2414;InbreedingCoeff=-0.1746;MQ=44.67;MQ0=0;MQRankSum=-6.140;QD=1.54;ReadPosRankSum=-2.132;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:2,0:2:3.01:0,3,39 0/0:1,0:1:3.01:0,3,39 0/1:1,1:2:27.42:27,0,34 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:1,0:1:2.99:0,3,23 0/0:5,0:5:15.05:0,15,189 0/0:2,0:2:6.01:0,6,63 ./. ./. 0/1:9,1:10:6.35:6,0,272 0/0:5,0:5:15.03:0,15,173 0/1:2,1:3:24.41:24,0,67 0/0:5,0:5:15.03:0,15,165 0/0:7,0:7:18.05:0,18,217 0/1:1,2:3:27.42:27,0,34 0/0:5,0:5:12.03:0,12,141 0/1:10,1:11:3.35:3,0,277 0/1:9,1:10:6.63:7,0,171 0/0:8,0:8:24.07:0,24,291 0/1:1,1:2:25.53:27,0,26 0/1:5,1:6:15.38:15,0,165 0/1:4,1:5:18.39:18,0,135 0/1:6,1:7:18.39:18,0,120 0/1:1,1:2:18.68:19,0,34 0/0:7,0:7:18.04:0,18,204 0/0:8,1:9:24.07:0,24,290 0/0:5,0:5:12.03:0,12,140 0/0:4,0:4:9.03:0,9,107 0/0:4,0:4:12.04:0,12,154 0/1:10,1:11:3.36:3,0,259 0/1:8,2:10:6.35:6,0,279 0/0:2,0:2:6.02:0,6,67 0/1:9,1:10:3.35:3,0,291 0/0:10,0:10:27.08:0,27,337 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/1:5,2:7:15.39:15,0,149 0/0:4,0:4:12.03:0,12,143 0/0:1,0:1:3.01:0,3,33 0/0:2,1:3:6.02:0,6,75 ./. 0/0:5,0:5:12.04:0,12,143 0/0:5,0:5:12.04:0,12,142 ./. 0/0:1,0:1:3.01:0,3,38 0/0:8,0:8:24.07:0,24,284 0/0:10,0:11:27.06:0,27,309 0/1:2,1:3:25.53:27,0,26 0/0:2,0:2:3.01:0,3,39 0/0:2,0:2:6.02:0,6,67 1/1:1,2:3:6.02:67,6,0 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/0:2,0:2:6.02:0,6,67 0/0:2,0:2:6:0,6,57 -chr1 899987 . GGATGT G 805.24 . AC=10;AF=0.102;AN=98;BaseQRankSum=-2.007;DP=183;FS=4.301;HRun=0;HaplotypeScore=71.0169;InbreedingCoeff=0.1259;MQ=41.55;MQ0=0;MQRankSum=-2.599;QD=19.64;ReadPosRankSum=-2.063;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:2,0:2:6:0,6,54 0/0:1,0:1:3.01:0,3,56 0/0:2,0:2:6.02:0,6,148 0/0:1,0:1:3.01:0,3,57 ./. ./. 0/0:1,0:1:3.01:0,3,82 0/0:5,0:5:15.01:0,15,325 0/0:2,0:2:5.61:0,6,66 0/0:1,0:1:3.01:0,3,53 ./. 0/0:3,0:3:9.03:0,9,164 0/0:4,0:4:12.04:0,12,274 0/0:2,0:2:3.01:0,3,55 0/0:4,0:4:12.04:0,12,219 0/0:7,0:7:4.10:0,4,211 0/0:2,0:2:6.02:0,6,121 0/0:3,0:3:9.03:0,9,193 0/1:8,3:11:99:270,0,225 0/0:8,0:8:14.87:0,15,236 0/0:4,0:4:12.04:0,12,266 0/0:2,0:2:6.02:0,6,111 0/0:3,0:3:9.03:0,9,183 0/1:4,0:4:18.96:19,0,169 0/1:3,2:5:54.88:55,0,173 1/1:0,1:1:3.01:67,3,0 0/0:7,0:7:18.06:0,18,359 0/0:8,0:8:11.08:0,11,261 0/0:4,0:4:12.04:0,12,240 0/0:3,0:3:6.02:0,6,111 0/0:3,0:3:8.98:0,9,125 1/1:4,6:10:25.32:499,25,0 0/1:8,0:8:9.96:10,0,288 0/0:2,0:2:6.02:0,6,106 0/0:4,0:4:12.04:0,12,238 0/0:7,0:7:15.60:0,16,331 0/0:1,0:1:3.01:0,3,56 ./. 0/0:2,0:2:6.02:0,6,123 0/0:4,0:4:12.04:0,12,349 0/0:1,0:1:3.01:0,3,58 0/0:2,0:2:3.01:0,3,58 ./. 0/0:4,0:4:4.26:0,4,110 0/0:4,0:4:9.03:0,9,169 ./. ./. 0/0:4,0:4:12.04:0,12,231 0/0:9,1:10:24.08:0,24,516 ./. 0/0:2,0:2:3:0,3,53 0/0:3,0:3:9.03:0,9,164 0/0:2,0:2:3.01:0,3,80 1/1:2,0:2:2.98:22,3,0 ./. 0/0:1,0:1:3.01:0,3,82 0/0:2,0:2:6.02:0,6,117 0/0:1,0:1:3.01:0,3,45 -chr1 899998 . G C 172.67 . AC=3;AF=0.0288;AN=104;BaseQRankSum=-3.045;DP=165;Dels=0.01;FS=6.898;HRun=1;HaplotypeScore=3.2446;InbreedingCoeff=-0.1274;MQ=38.58;MQ0=0;MQRankSum=-2.770;QD=7.85;ReadPosRankSum=2.697;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,32 0/0:2,0:2:6:0,6,57 ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:5,0:5:12.04:0,12,157 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:2.99:0,3,23 ./. 0/0:3,0:3:9.03:0,9,105 0/0:4,0:4:12.03:0,12,138 0/0:1,0:1:3.01:0,3,33 0/0:4,0:4:12.03:0,12,134 0/0:4,0:4:12.03:0,12,138 0/0:2,0:2:6.02:0,6,67 0/0:3,0:3:9.03:0,9,104 0/1:6,4:10:70.51:71,0,115 0/0:6,0:6:12.04:0,12,143 0/0:3,0:3:9.03:0,9,112 0/0:2,0:2:3.01:0,3,39 0/0:3,0:3:9.03:0,9,105 0/0:3,0:3:9.03:0,9,105 0/1:3,2:5:42.10:42,0,83 0/0:1,0:1:3:0,3,25 0/0:5,0:5:15.04:0,15,172 0/0:5,0:5:12.03:0,12,134 0/0:4,0:4:12.03:0,12,134 0/0:3,0:3:6.02:0,6,72 0/0:2,0:2:6.02:0,6,71 0/1:1,6:7:15.40:135,0,15 0/0:6,0:6:15.04:0,15,172 0/0:2,0:2:6.02:0,6,67 0/0:4,0:4:12.03:0,12,134 0/0:6,0:6:18.05:0,18,219 0/0:1,0:1:3.01:0,3,33 ./. 0/0:2,0:2:6.01:0,6,60 0/0:4,0:4:12.04:0,12,158 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:3.01:0,3,33 ./. 0/0:3,0:3:9.02:0,9,100 0/0:4,0:4:9.01:0,9,92 0/0:2,0:2:6.02:0,6,67 ./. 0/0:6,0:6:15.04:0,15,176 0/0:13,0:13:33.09:0,33,382 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:3.01:0,3,33 0/0:4,0:4:12.03:0,12,133 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,68 ./. -chr1 900000 . G GAA 4516.13 . AC=82;AF=0.8039;AN=102;BaseQRankSum=-0.011;DP=158;FS=8.933;HRun=0;HaplotypeScore=53.7512;InbreedingCoeff=0.0958;MQ=37.58;MQ0=0;MQRankSum=-2.778;QD=29.91;ReadPosRankSum=0.180;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:1,0:1:2.99:23,3,0 1/1:0,1:1:3.01:61,3,0 ./. 0/0:1,0:1:3.01:0,3,37 1/1:2,0:2:5.93:54,6,0 ./. ./. 1/1:1,0:1:3.01:40,3,0 0/1:4,1:5:83.88:84,0,120 ./. 0/0:1,0:1:1.55:0,2,4 ./. 1/1:0,3:3:9.03:183,9,0 1/1:3,0:3:8.97:86,9,0 1/1:1,0:1:3:28,3,0 1/1:2,1:3:8.98:111,9,0 1/1:2,2:4:10.85:167,11,0 1/1:1,1:2:5.93:78,6,0 1/1:0,2:2:6.02:112,6,0 0/1:9,0:9:61.05:61,0,174 1/1:6,0:6:11.81:163,12,0 0/1:3,0:3:39.95:56,0,40 1/1:2,1:3:3.01:61,3,0 1/1:3,0:3:8.98:92,9,0 0/1:2,1:3:31.51:87,0,32 0/1:5,0:5:75.40:75,0,82 0/0:1,0:1:3.01:0,3,49 1/1:5,0:5:9.17:117,9,0 1/1:5,0:5:10.58:115,11,0 1/1:3,0:3:9.03:118,9,0 1/1:3,0:3:4.56:37,5,0 1/1:0,1:1:3.01:61,3,0 0/1:7,0:7:3.32:3,0,226 1/1:3,3:6:15.05:253,15,0 1/1:0,2:2:6.02:122,6,0 1/1:4,0:4:12.03:145,12,0 1/1:0,6:6:18.06:366,18,0 1/1:0,1:1:3.01:61,3,0 0/0:1,0:1:0:0,0,0 1/1:1,1:2:5.97:79,6,0 0/1:3,1:4:48.96:49,0,119 1/1:1,0:1:3.01:36,3,0 1/1:2,0:2:3.48:40,3,0 ./. 1/1:3,0:3:6.91:79,7,0 1/1:3,2:5:10.28:164,10,0 0/0:2,0:2:6.02:0,6,79 ./. 1/1:2,4:6:13.60:247,14,0 0/1:4,9:13:64.77:516,0,65 1/1:1,0:1:3:29,3,0 1/1:2,0:2:3:29,3,0 1/1:2,1:3:7.84:101,8,0 1/1:1,0:1:2.80:13,3,0 0/0:1,0:1:3.01:0,3,39 1/1:2,0:2:3.46:25,3,0 1/1:1,0:1:3.01:40,3,0 1/1:2,0:2:5.69:49,6,0 ./. -chr1 900001 . G A 1769.07 . AC=55;AF=0.561;AN=98;BaseQRankSum=-1.838;DP=158;Dels=0.00;FS=12.659;HRun=1;HaplotypeScore=4.3165;InbreedingCoeff=0.0703;MQ=37.58;MQ0=0;MQRankSum=-1.578;QD=15.38;ReadPosRankSum=-0.873;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:29,3,0 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,2:2:5.99:55,6,0 ./. ./. 1/1:0,1:1:3.01:33,3,0 0/1:4,1:5:25.60:26,0,141 ./. 1/1:0,1:1:2.99:23,3,0 ./. 0/0:3,0:3:9.03:0,9,105 1/1:0,3:3:9:89,9,0 1/1:0,1:1:3.01:32,3,0 0/1:1,2:3:24.41:58,0,24 0/1:2,2:4:43.09:43,0,55 0/1:1,1:2:21.65:22,0,27 0/0:2,0:2:3:0,3,28 0/1:5,4:9:79.26:79,0,104 1/1:0,6:6:12.04:144,12,0 0/1:1,2:3:30.98:59,0,31 0/0:2,1:3:6.02:0,6,72 1/1:0,3:3:9.03:105,9,0 0/1:2,1:3:24.41:24,0,63 0/1:2,3:5:49.01:68,0,49 0/0:1,0:1:3.01:0,3,31 1/1:0,5:5:15.04:170,15,0 1/1:1,4:5:12.03:134,12,0 1/1:0,3:3:9.02:100,9,0 1/1:0,3:3:6.02:70,6,0 0/0:1,0:1:3.01:0,3,33 0/1:6,1:7:15.40:15,0,140 0/1:3,3:6:51.82:52,0,90 0/0:2,0:2:6.02:0,6,67 1/1:0,4:4:12.03:134,12,0 0/0:6,0:6:18.05:0,18,218 0/0:1,0:1:3.01:0,3,33 ./. 0/1:1,1:2:25.53:27,0,26 0/0:4,0:4:12.04:0,12,154 1/1:0,1:1:3.01:33,3,0 1/1:1,1:2:3.01:33,3,0 ./. 1/1:0,3:3:9.02:99,9,0 0/1:4,1:5:21.40:21,0,90 0/0:2,0:2:3:0,3,29 ./. 0/1:5,1:6:18.39:18,0,124 0/0:13,0:13:33.09:0,33,368 1/1:0,1:1:3.01:33,3,0 1/1:0,2:2:3.01:33,3,0 0/1:1,2:3:27.42:27,0,27 ./. 0/0:1,0:1:3.01:0,3,33 0/1:1,1:2:27.42:27,0,27 1/1:0,1:1:3:28,3,0 1/1:0,2:2:3.01:37,3,0 ./. -chr1 900009 . C G 1460.59 . AC=51;AF=0.510;AN=100;BaseQRankSum=1.557;DP=154;Dels=0.00;FS=5.254;HRun=6;HaplotypeScore=3.7869;InbreedingCoeff=0.1584;MQ=37.06;MQ0=0;MQRankSum=-2.397;QD=14.75;ReadPosRankSum=1.027;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 ./. ./. 1/1:1,1:2:3.01:33,3,0 0/0:3,0:3:9.03:0,9,112 ./. 1/1:0,1:1:3.01:33,3,0 ./. 0/0:3,0:3:9.03:0,9,108 1/1:0,3:3:9.02:96,9,0 ./. 1/1:0,2:2:6.02:65,6,0 0/1:3,2:5:43.09:43,0,85 0/1:3,1:4:14.66:15,0,81 0/0:2,0:2:5.99:0,6,55 0/1:5,3:8:48.82:49,0,116 1/1:1,5:6:15.04:175,15,0 0/1:1,1:2:29.23:29,0,32 0/0:2,1:3:6.02:0,6,72 1/1:0,3:3:9.03:108,9,0 0/0:2,0:2:6.02:0,6,75 0/1:3,3:6:82.25:91,0,82 0/0:1,0:1:3:0,3,27 1/1:0,3:3:9.02:100,9,0 1/1:1,2:3:6.02:67,6,0 1/1:0,3:3:9.02:100,9,0 0/1:1,2:3:27.42:31,0,27 ./. 0/1:6,1:7:12.38:12,0,175 0/1:3,1:4:21.40:21,0,92 0/0:2,0:2:6.02:0,6,67 1/1:0,4:4:12.03:128,12,0 0/0:6,0:6:18.05:0,18,205 0/0:1,0:1:3.01:0,3,32 0/0:1,1:2:3.01:0,3,33 0/1:2,1:3:18.68:19,0,23 0/0:3,0:3:9.03:0,9,113 1/1:0,1:1:3.01:33,3,0 0/1:2,1:3:24.43:24,0,48 ./. 1/1:0,3:3:6.02:67,6,0 0/1:5,1:6:18.41:18,0,109 0/0:3,0:3:3:0,3,25 ./. 0/0:6,0:6:15.03:0,15,161 0/0:12,1:13:33.09:0,33,370 1/1:0,1:1:3.01:33,3,0 1/1:0,2:2:3.01:33,3,0 0/1:1,2:3:27.42:27,0,27 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,33 0/1:1,1:2:24.58:27,0,25 1/1:0,1:1:3.01:33,3,0 1/1:0,2:2:6.02:70,6,0 0/0:1,0:1:3.01:0,3,33 -chr1 900009 . CG C 3423.69 . AC=75;AF=0.765;AN=98;BaseQRankSum=-1.591;DP=149;FS=3.362;HRun=6;HaplotypeScore=53.0225;InbreedingCoeff=-0.0140;MQ=37.05;MQ0=0;MQRankSum=0.377;QD=24.45;ReadPosRankSum=3.509;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:1,0:1:3:26,3,0 1/1:0,1:1:3.01:42,3,0 ./. 0/0:1,0:1:3.01:0,3,41 1/1:1,0:1:3:29,3,0 ./. ./. 1/1:2,0:2:3.01:31,3,0 0/1:2,1:3:32.93:33,0,87 ./. 1/1:1,0:1:1.55:4,2,0 ./. 1/1:0,2:2:6.02:84,6,0 1/1:3,0:3:8.96:80,9,0 ./. 0/1:2,0:2:10.01:15,0,10 1/1:3,2:5:13.91:137,14,0 0/1:3,1:4:11.57:47,0,12 1/1:0,2:2:6.02:74,6,0 1/1:4,4:8:5.60:187,6,0 1/1:6,0:6:14.88:169,15,0 1/1:1,0:1:3:25,3,0 1/1:2,1:3:3.01:42,3,0 0/1:3,0:3:5.10:60,0,5 0/1:1,1:2:35.97:36,0,42 1/1:4,2:6:15.89:168,16,0 0/0:1,0:1:3.01:0,3,47 1/1:3,0:3:9.01:87,9,0 0/1:3,0:3:7.69:29,0,8 1/1:3,0:3:9.02:94,9,0 0/1:3,0:3:19.84:21,0,20 ./. 0/1:2,5:7:27:202,0,27 1/1:1,3:4:12.04:165,12,0 1/1:0,1:1:3.01:42,3,0 1/1:4,0:4:11.97:117,12,0 1/1:0,6:6:18.06:252,18,0 ./. 0/0:2,0:2:1.25:0,1,3 1/1:1,2:3:5.85:55,6,0 0/1:2,1:3:32.94:33,0,87 1/1:1,0:1:3:29,3,0 0/1:2,1:3:28.16:65,0,28 ./. 0/1:3,0:3:5.06:37,0,5 0/1:4,2:6:1.90:105,0,2 0/0:3,0:3:6.02:0,6,78 ./. 1/1:1,5:6:12.04:167,12,0 0/1:4,8:12:76.06:303,0,76 1/1:1,0:1:3.01:38,3,0 1/1:2,0:2:6.01:66,6,0 1/1:2,1:3:6.01:71,6,0 1/1:1,0:1:2.99:23,3,0 0/0:1,0:1:3.01:0,3,48 1/1:1,1:2:5.98:46,6,0 1/1:1,0:1:3.01:30,3,0 1/1:2,0:2:5.97:50,6,0 1/1:1,0:1:2.04:6,2,0 -chr1 900010 . G GC 2274.92 . AC=67;AF=0.684;AN=98;BaseQRankSum=-2.660;DP=149;FS=0.000;HRun=1;HaplotypeScore=58.6576;InbreedingCoeff=0.1712;MQ=37.05;MQ0=0;MQRankSum=0.765;QD=18.35;ReadPosRankSum=2.099;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3.01:42,3,0 0/0:1,0:1:0:0,0,0 ./. 0/0:1,0:1:3.01:0,3,38 1/1:0,1:1:3.01:45,3,0 ./. ./. 1/1:1,1:2:3.01:45,3,0 0/1:3,0:3:12:12,0,69 ./. 1/1:0,1:1:3:25,3,0 ./. 0/0:2,0:2:0.47:0,0,1 1/1:0,3:3:9.03:132,9,0 ./. 1/1:1,1:2:6.01:73,6,0 0/1:3,2:5:19.78:79,0,20 0/1:3,1:4:20.14:42,0,20 1/1:2,0:2:4.26:46,4,0 1/1:6,2:8:1.78:68,2,0 1/1:1,4:6:14.43:164,14,0 1/1:0,1:1:3.01:45,3,0 1/1:2,1:3:0.47:1,0,0 1/1:1,1:3:9:96,9,0 0/0:2,0:2:2.59:0,3,38 1/1:3,3:6:7.15:122,7,0 0/0:1,0:1:3.01:0,3,39 1/1:0,3:3:9.03:133,9,0 1/1:1,1:3:6.02:75,6,0 1/1:0,3:3:9.03:133,9,0 1/1:1,2:3:2.76:44,3,0 ./. 0/1:6,1:7:32.05:32,0,34 1/1:3,1:4:3.74:10,4,0 0/0:1,0:1:0.47:0,0,1 1/1:0,4:4:12.04:178,12,0 1/1:6,0:6:4.27:40,4,0 ./. 0/0:2,0:2:1.25:0,1,3 1/1:2,1:3:6.01:73,6,0 0/0:3,0:3:3.97:0,4,68 1/1:0,1:1:3.01:45,3,0 0/1:2,1:3:15.33:47,0,15 ./. 1/1:1,2:3:9.03:110,9,0 0/1:5,1:6:12.77:56,0,13 0/0:3,0:3:6.02:0,6,69 ./. 0/0:6,0:6:0.36:0,0,2 0/1:12,0:12:9.23:9,0,70 1/1:0,1:1:3.01:36,3,0 1/1:0,2:2:6.02:82,6,0 1/1:1,2:3:2.25:44,2,0 1/1:0,1:1:3.01:45,3,0 0/0:1,0:1:3.01:0,3,39 1/1:1,1:2:6.02:81,6,0 1/1:0,1:1:3.01:45,3,0 1/1:0,2:2:6.02:89,6,0 0/0:1,0:1:2.04:0,2,6 -chr1 900012 . G A 52.89 . AC=9;AF=0.092;AN=98;BaseQRankSum=-1.584;DP=144;Dels=0.00;FS=9.518;HRun=0;HaplotypeScore=1.9499;InbreedingCoeff=-0.1191;MQ=37.30;MQ0=0;MQRankSum=-1.274;QD=1.56;ReadPosRankSum=-3.899;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,31 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,32 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:2,0:2:6.02:0,6,67 0/0:3,0:3:9.03:0,9,115 ./. 0/0:1,0:1:3.01:0,3,30 ./. 0/0:2,0:2:6.02:0,6,74 0/1:2,1:3:24.41:24,0,58 ./. 0/0:1,0:1:3.01:0,3,33 0/1:4,1:5:18.39:18,0,122 0/1:3,1:4:13.66:14,0,88 0/0:2,0:2:6.02:0,6,71 0/0:7,0:7:15.04:0,15,167 0/0:5,1:6:15.05:0,15,190 0/0:1,0:1:3.01:0,3,37 0/0:3,0:3:6.02:0,6,73 0/0:2,0:2:6.02:0,6,74 0/0:2,0:2:6.02:0,6,75 0/1:5,1:6:15.39:15,0,146 0/0:1,0:1:3:0,3,28 0/0:3,0:3:9.03:0,9,109 0/0:2,0:2:3.01:0,3,33 0/0:3,0:3:9.02:0,9,100 0/1:2,1:3:27.42:27,0,35 ./. 0/0:7,0:7:21.06:0,21,234 0/0:4,0:4:12.03:0,12,137 0/0:1,0:1:3.01:0,3,33 0/0:4,0:4:12.03:0,12,134 0/0:6,0:6:18.05:0,18,214 ./. 0/0:2,0:2:3.01:0,3,33 0/0:3,0:3:6:0,6,58 0/0:3,0:3:9.03:0,9,112 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:9.02:0,9,100 ./. 0/0:2,0:2:6.02:0,6,67 0/1:5,1:6:18.40:18,0,114 0/0:2,0:3:6.02:0,6,65 ./. 0/1:5,1:6:18.39:18,0,122 0/0:12,0:12:30.06:0,30,332 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.01:0,6,57 0/0:3,0:3:6.02:0,6,67 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.01:0,6,59 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,75 1/1:0,1:1:3.01:33,3,0 -chr1 900018 . G A 202.57 . AC=3;AF=0.033;AN=90;BaseQRankSum=-0.005;DP=138;Dels=0.00;FS=14.921;HRun=0;HaplotypeScore=2.7642;InbreedingCoeff=-0.1390;MQ=37.35;MQ0=0;MQRankSum=-2.631;QD=11.25;ReadPosRankSum=-0.202;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,31 0/0:3,0:3:9.03:0,9,115 ./. ./. ./. 0/0:2,0:2:6.02:0,6,75 0/0:3,0:3:9.02:0,9,100 ./. 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,71 0/0:4,0:4:12.03:0,12,134 0/0:2,0:2:6.02:0,6,73 0/1:3,4:7:48.82:113,0,49 0/0:6,0:6:15.05:0,15,189 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:6.02:0,6,76 0/0:2,0:2:6.02:0,6,70 0/0:2,0:2:6.02:0,6,75 0/1:4,1:5:13.62:14,0,114 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:9.03:0,9,109 0/0:2,0:2:3.01:0,3,33 0/0:3,0:3:9.02:0,9,100 0/0:3,0:3:6.02:0,6,74 ./. 0/1:1,5:6:15.39:146,0,15 0/0:4,0:4:12:0,12,119 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,67 0/0:5,0:5:15.05:0,15,186 ./. 0/0:3,0:3:6.02:0,6,67 0/0:3,0:3:6.02:0,6,67 0/0:2,0:2:6.02:0,6,71 ./. 0/0:3,0:3:9.01:0,9,87 ./. 0/0:3,0:3:9.02:0,9,99 0/0:6,0:6:15.03:0,15,158 0/0:3,0:3:3.01:0,3,33 ./. 0/0:7,0:7:18.01:0,18,184 0/0:11,0:11:27.05:0,27,288 0/0:3,0:3:6.02:0,6,67 0/0:2,0:2:6:0,6,56 0/0:3,0:3:6.02:0,6,67 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,67 0/0:2,0:2:6.01:0,6,61 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:3.01:0,3,42 0/0:1,0:1:3.01:0,3,33 -chr1 900025 . GGATGT G 524.76 . AC=16;AF=0.174;AN=92;BaseQRankSum=3.838;DP=133;FS=8.461;HRun=0;HaplotypeScore=57.1337;InbreedingCoeff=-0.0789;MQ=37.07;MQ0=0;MQRankSum=-2.025;QD=12.49;ReadPosRankSum=0.267;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,82 0/0:1,0:1:3.01:0,3,55 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,96 0/0:1,0:1:3.01:0,3,53 ./. ./. ./. 0/1:2,1:3:21.06:21,0,185 0/0:2,0:2:6.02:0,6,128 ./. 0/0:1,0:1:3.01:0,3,97 0/1:1,1:2:60.90:61,0,91 0/1:3,1:4:54.87:55,0,211 0/0:2,0:2:6.02:0,6,194 0/0:7,0:7:9.93:0,10,343 0/0:5,1:6:13.29:0,13,366 0/0:1,0:1:3.01:0,3,97 0/0:3,0:3:3.01:0,3,97 0/0:2,0:2:3.01:0,3,97 0/0:2,0:2:6.02:0,6,194 0/1:3,1:4:32.50:33,0,129 1/1:0,1:1:3.01:67,3,0 0/0:2,0:2:6.02:0,6,128 0/0:2,0:2:4.26:0,4,100 0/0:2,0:2:6.02:0,6,188 0/1:2,1:3:60.90:61,0,91 ./. 0/0:6,0:6:15.05:0,15,485 0/0:4,0:4:10.27:0,10,228 1/1:0,1:1:3.01:67,3,0 ./. 0/0:4,0:4:12.04:0,12,388 ./. 0/0:3,0:3:3.92:0,4,14 0/0:3,0:3:6.02:0,6,194 0/0:1,0:1:3.01:0,3,78 0/0:1,0:1:3.01:0,3,97 0/1:3,0:3:38.87:39,0,42 0/0:1,0:1:3.01:0,3,48 0/0:3,0:3:6.02:0,6,194 0/1:6,0:6:18.83:19,0,266 1/1:0,2:3:6.02:114,6,0 ./. 0/1:6,1:7:30.44:30,0,288 0/0:12,0:12:30.10:0,30,806 0/1:2,1:3:14.33:54,0,14 0/0:2,0:2:4.26:0,4,100 0/0:3,0:3:6.02:0,6,188 0/0:1,0:1:3.01:0,3,95 0/0:2,0:2:6.02:0,6,162 0/0:3,0:3:6.02:0,6,189 0/0:1,0:1:3.01:0,3,97 0/0:2,0:2:3.01:0,3,97 0/1:1,1:2:43.33:61,0,43 -chr1 900036 . C G 56.0 . AC=8;AF=0.095;AN=84;BaseQRankSum=-0.360;DP=115;Dels=0.02;FS=4.181;HRun=3;HaplotypeScore=2.4570;InbreedingCoeff=0.0759;MQ=37.96;MQ0=0;MQRankSum=-2.183;QD=3.73;ReadPosRankSum=1.383;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,30 ./. ./. ./. ./. 0/0:3,0:3:9.03:0,9,107 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:2,0:2:6.02:0,6,75 0/1:3,1:4:24.41:24,0,58 0/0:2,0:2:6.02:0,6,79 0/0:5,1:6:12.03:0,12,134 0/0:6,0:6:15.04:0,15,178 0/0:1,0:1:3.01:0,3,42 0/0:1,1:2:3.01:0,3,42 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:9.02:0,9,98 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,36 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:6.02:0,6,75 ./. 0/0:4,0:4:12.03:0,12,134 0/0:3,0:3:6.02:0,6,72 0/0:1,0:1:3.01:0,3,33 ./. 0/0:4,0:4:12.04:0,12,154 ./. 0/0:3,0:4:9.02:0,9,95 0/0:3,0:3:3.01:0,3,33 ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:2,0:3:3.01:0,3,33 0/1:3,1:4:27.42:27,0,27 1/1:1,2:3:3.01:33,3,0 ./. 0/0:7,0:7:21.05:0,21,235 0/0:10,1:11:24.04:0,24,264 0/0:2,0:2:6:0,6,58 0/0:2,0:2:3.01:0,3,33 0/0:2,0:2:3.01:0,3,33 0/0:1,0:1:3.01:0,3,32 0/0:2,0:2:6.02:0,6,67 0/0:3,0:3:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:6.02:0,6,70 1/1:1,1:2:3.01:33,3,0 -chr1 900045 . G T 197.92 . AC=12;AF=0.158;AN=76;BaseQRankSum=-0.033;DP=97;Dels=0.00;FS=9.602;HRun=0;HaplotypeScore=0.8494;InbreedingCoeff=-0.1283;MQ=36.39;MQ0=0;MQRankSum=-3.050;QD=6.60;ReadPosRankSum=0.794;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. 0/1:1,1:2:27.42:27,0,27 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/1:1,1:2:27.42:27,0,36 0/1:3,1:4:21.40:21,0,88 0/0:2,0:2:6.02:0,6,82 0/0:5,0:5:15.04:0,15,163 0/0:2,1:3:6.02:0,6,77 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:3.01:0,3,40 ./. 0/0:1,0:1:3.01:0,3,38 1/1:1,1:2:3.01:33,3,0 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,33 ./. 0/1:1,1:2:20.67:27,0,21 ./. 0/0:3,0:3:9.02:0,9,98 0/0:3,0:3:9.03:0,9,105 1/1:0,1:1:3.01:33,3,0 ./. 0/0:4,0:4:12.04:0,12,152 ./. 0/0:4,0:4:6.02:0,6,67 0/0:2,0:2:6.01:0,6,60 ./. ./. 0/0:2,0:2:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:1,1:2:3.01:0,3,33 0/1:3,1:4:14.65:15,0,88 0/0:3,0:3:3.01:0,3,33 ./. 0/1:5,2:7:48.82:49,0,124 0/0:10,0:10:27.07:0,27,306 0/1:2,1:3:24.41:24,0,58 0/0:2,0:2:6.01:0,6,63 0/0:2,0:2:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:6.02:0,6,65 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/1:1,2:3:24.41:58,0,24 -chr1 900046 . G C 221.18 . AC=14;AF=0.194;AN=72;BaseQRankSum=0.606;DP=95;Dels=0.00;FS=15.119;HRun=1;HaplotypeScore=0.8152;InbreedingCoeff=-0.0844;MQ=36.53;MQ0=0;MQRankSum=-3.254;QD=6.91;ReadPosRankSum=0.931;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1:1,1:2:27.42:27,0,27 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/1:1,1:2:27.42:27,0,36 0/1:3,1:4:21.40:21,0,88 0/0:2,0:2:6.02:0,6,80 0/0:5,0:5:15.03:0,15,159 0/0:2,1:3:6.01:0,6,69 0/0:1,0:1:3.01:0,3,40 0/0:1,1:2:3.01:0,3,40 ./. 0/0:1,0:1:3.01:0,3,38 1/1:1,1:2:3.01:33,3,0 ./. 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,30 ./. 1/1:1,1:2:3.01:33,3,0 ./. 0/0:3,0:3:6.02:0,6,67 0/0:3,0:3:9.03:0,9,105 1/1:0,1:1:3.01:33,3,0 ./. 0/0:4,0:4:12.04:0,12,150 ./. 0/0:4,0:4:6.02:0,6,67 0/0:2,0:2:3.01:0,3,33 ./. ./. 0/0:1,1:2:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/1:1,1:2:18.68:19,0,27 0/1:3,1:4:21.40:21,0,86 0/0:3,0:3:3.01:0,3,33 ./. 0/1:5,2:7:48.82:49,0,124 0/0:9,0:9:21.06:0,21,241 0/1:2,1:3:19.63:20,0,58 0/0:2,0:2:6.01:0,6,60 0/0:1,0:2:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:6.02:0,6,67 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/1:1,2:3:24.41:58,0,24 -chr1 900047 . CG C 209.92 . AC=15;AF=0.208;AN=72;BaseQRankSum=1.707;DP=88;FS=0.000;HRun=6;HaplotypeScore=49.2935;InbreedingCoeff=-0.1925;MQ=36.21;MQ0=0;MQRankSum=-2.511;QD=4.47;ReadPosRankSum=0.230;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. 0/1:1,0:1:0:0,0,0 ./. ./. ./. ./. ./. ./. ./. 0/1:2,0:2:8.50:8,0,42 0/0:1,0:1:3.01:0,3,48 ./. ./. 0/1:2,0:2:0.61:1,0,43 0/1:3,1:4:29.94:30,0,121 0/0:2,0:2:6.02:0,6,96 0/0:5,0:5:8.84:0,9,144 0/1:3,0:3:29.76:30,0,56 0/0:1,0:1:3.01:0,3,48 0/0:2,0:2:3.01:0,3,47 ./. ./. 1/1:2,0:2:2.50:9,2,0 0/0:1,0:1:3.01:0,3,48 ./. 0/0:1,0:1:1.25:0,1,3 ./. 0/0:2,0:2:3.92:0,4,14 ./. 0/1:2,0:2:31.74:32,0,42 0/1:3,0:3:29.85:30,0,71 0/0:1,0:1:2.94:0,3,18 ./. 0/0:4,0:4:12.04:0,12,191 ./. 0/0:4,0:4:4.99:0,5,15 0/1:1,1:2:35.97:36,0,41 ./. 0/0:1,0:1:0.47:0,0,1 0/0:1,0:1:3:0,3,25 0/0:1,0:1:3.01:0,3,45 0/0:2,0:2:6.02:0,6,72 0/1:3,1:4:33.39:33,0,42 0/0:2,0:2:3.01:0,3,48 ./. 0/1:7,0:7:39.83:40,0,72 0/1:8,1:9:9.64:10,0,186 0/1:2,1:3:33.03:33,0,36 0/0:1,0:1:3.01:0,3,48 0/0:2,0:2:3.01:0,3,48 0/0:1,0:1:3.01:0,3,48 0/0:1,0:1:3.01:0,3,48 0/0:3,0:3:6.02:0,6,96 ./. 0/0:1,0:1:2.99:0,3,24 0/1:2,1:3:4.50:40,0,4 -chr1 900050 . G A 240.82 . AC=14;AF=0.226;AN=62;BaseQRankSum=1.097;DP=84;Dels=0.00;FS=15.435;HRun=0;HaplotypeScore=0.6581;InbreedingCoeff=-0.0898;MQ=34.67;MQ0=0;MQRankSum=-1.036;QD=8.03;ReadPosRankSum=0.391;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1:1,1:2:27.42:27,0,27 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/1:1,1:2:27.42:27,0,33 0/1:3,1:4:18.56:19,0,88 0/0:2,0:2:6.02:0,6,82 0/0:5,0:5:12.03:0,12,134 0/1:2,1:3:24.41:24,0,66 0/0:1,0:1:3.01:0,3,40 ./. ./. 0/0:1,0:1:3:0,3,28 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. 0/1:1,1:2:27.42:27,0,27 ./. 0/0:2,0:2:6.02:0,6,67 0/0:2,0:2:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 ./. 0/0:3,0:3:9.02:0,9,100 ./. 0/0:4,0:4:6.02:0,6,67 0/0:2,0:2:6.02:0,6,67 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 1/1:1,1:2:3.01:33,3,0 0/0:4,0:4:12.03:0,12,130 0/0:2,0:2:3.01:0,3,33 ./. 0/1:5,2:7:48.82:49,0,123 0/0:9,0:9:18.04:0,18,194 0/1:2,1:3:24.41:24,0,57 ./. 0/0:2,0:2:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3:0,3,27 0/0:3,0:3:6.02:0,6,67 ./. 0/0:1,0:1:3:0,3,25 0/1:1,2:3:24.41:58,0,24 -chr1 900065 . A C 247.12 . AC=17;AF=0.304;AN=56;BaseQRankSum=1.516;DP=63;Dels=0.00;FS=9.830;HRun=0;HaplotypeScore=2.1490;InbreedingCoeff=-0.0549;MQ=32.56;MQ0=0;MQRankSum=-0.918;QD=7.06;ReadPosRankSum=2.224;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3:0,3,25 ./. ./. ./. 1/1:1,1:2:3.01:33,3,0 ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 0/0:2,0:2:6.02:0,6,65 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,65 0/0:1,1:2:3.01:0,3,40 ./. 0/0:1,0:1:3.01:0,3,32 ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. 0/1:1,1:2:27.42:27,0,27 ./. ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 0/1:2,1:4:21.65:27,0,22 0/0:2,0:2:3.01:0,3,33 ./. ./. 1/1:0,1:1:3:25,3,0 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3:28,3,0 0/1:3,1:4:21.41:21,0,80 0/0:2,0:2:3.01:0,3,33 ./. 0/1:2,1:4:27.42:27,0,27 0/1:6,1:9:15.42:15,0,128 0/1:2,1:3:25.53:27,0,26 ./. 0/0:2,0:2:3:0,3,27 0/0:1,0:1:3.01:0,3,33 ./. 0/0:2,0:2:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,33 0/1:1,2:3:24.41:58,0,24 -chr1 900068 . TGCTGCC T 518.39 . AC=13;AF=0.217;AN=60;BaseQRankSum=4.713;DP=59;FS=14.526;HRun=0;HaplotypeScore=44.2811;InbreedingCoeff=0.0509;MQ=31.33;MQ0=0;MQRankSum=-0.386;QD=28.80;ReadPosRankSum=4.120;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. 0/0:0,0:1:0:0,0,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,64 ./. ./. ./. 0/1:1,1:2:36.89:58,0,37 ./. ./. 0/0:1,0:1:3.01:0,3,64 1/1:0,1:1:3.01:74,3,0 0/0:2,0:2:6.02:0,6,133 0/0:1,0:1:3.01:0,3,60 0/0:2,0:2:6.02:0,6,139 0/1:1,1:2:54.51:68,0,55 ./. 0/0:1,0:1:1.25:0,1,3 ./. 0/0:1,0:1:1.25:0,1,3 ./. ./. ./. ./. ./. 0/0:2,0:2:1.25:0,1,3 ./. ./. 0/0:1,0:1:3.01:0,3,100 1/1:0,1:1:3.01:74,3,0 ./. ./. ./. 0/0:3,0:3:4.26:0,4,113 0/0:2,0:2:6.02:0,6,181 ./. ./. 1/1:1,0:1:2.60:10,3,0 0/0:1,0:1:3.01:0,3,110 1/1:0,1:1:3.01:74,3,0 0/0:4,0:4:2.65:0,3,52 0/0:2,0:2:3.01:0,3,49 ./. 0/1:3,1:4:67.89:68,0,104 0/0:6,0:6:7.27:0,7,221 0/1:2,1:3:64.76:65,0,204 ./. 0/0:2,0:2:3.01:0,3,110 0/0:1,0:1:3.01:0,3,61 0/0:1,0:1:3.01:0,3,119 0/0:2,0:2:6.02:0,6,167 ./. 0/0:1,0:1:3.01:0,3,94 0/1:1,2:3:99:139,0,102 -chr1 900083 . G T 196.8 . AC=12;AF=0.286;AN=42;BaseQRankSum=-2.303;DP=46;Dels=0.00;FS=9.918;HRun=0;HaplotypeScore=1.2000;InbreedingCoeff=0.0257;MQ=29.00;MQ0=0;MQRankSum=0.317;QD=10.36;ReadPosRankSum=1.627;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 0/0:2,0:2:3.01:0,3,33 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 0/0:3,0:3:3.01:0,3,33 0/0:2,1:3:6.02:0,6,67 ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:32,3,0 0/1:2,1:3:23.61:24,0,27 0/0:2,0:2:3.01:0,3,33 ./. 0/1:3,2:5:24.41:58,0,24 0/0:5,0:5:9.02:0,9,100 0/1:3,1:4:24.41:24,0,58 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,33 0/1:1,2:3:24.43:48,0,24 -chr1 900084 . G C 236.51 . AC=14;AF=0.350;AN=40;BaseQRankSum=-0.904;DP=46;Dels=0.00;FS=12.035;HRun=1;HaplotypeScore=1.2233;InbreedingCoeff=0.0591;MQ=29.00;MQ0=0;MQRankSum=-0.215;QD=11.83;ReadPosRankSum=1.420;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 0/0:2,0:2:3.01:0,3,33 ./. ./. 1/1:0,1:1:3.01:32,3,0 ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 0/0:3,0:3:3.01:0,3,33 0/0:2,1:3:6.02:0,6,67 ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3:29,3,0 0/1:2,1:3:27.42:27,0,27 0/0:2,0:2:3.01:0,3,33 ./. 0/1:3,2:5:24.41:58,0,24 0/0:5,0:5:9.02:0,9,100 0/1:3,1:4:24.41:24,0,58 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,33 0/1:1,2:3:24.41:57,0,24 -chr1 900085 . C G 54.45 . AC=7;AF=0.175;AN=40;BaseQRankSum=1.312;DP=45;Dels=0.00;FS=0.000;HRun=6;HaplotypeScore=0.9242;InbreedingCoeff=0.1696;MQ=29.00;MQ0=0;MQRankSum=0.641;QD=7.78;ReadPosRankSum=-1.373;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. 0/0:1,0:1:3:0,3,28 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:3:0,3,29 ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3:0,3,29 ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. 0/0:3,0:3:6.02:0,6,67 ./. ./. 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3:0,3,27 0/0:1,0:1:3:0,3,25 0/1:2,1:3:27.42:27,0,27 1/1:0,2:2:3.01:33,3,0 ./. 0/0:4,1:5:9.02:0,9,100 0/0:4,1:5:6:0,6,53 0/0:3,1:4:9.02:0,9,92 ./. ./. ./. ./. 0/0:1,0:1:3:0,3,27 ./. ./. 0/0:3,0:3:9.02:0,9,100 -chr1 900086 . G GC 66.18 . AC=9;AF=0.265;AN=34;BaseQRankSum=-0.405;DP=42;FS=3.909;HRun=1;HaplotypeScore=46.6346;InbreedingCoeff=0.0729;MQ=29.00;MQ0=0;MQRankSum=0.231;QD=4.41;ReadPosRankSum=-0.925;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:2.99:0,3,24 ./. ./. 1/1:0,1:1:3.01:44,3,0 0/0:1,0:1:3.01:0,3,30 ./. ./. ./. 0/0:1,0:1:2.84:0,3,14 ./. 0/0:1,0:1:1.25:0,1,3 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:2.97:0,3,20 ./. ./. ./. 1/1:1,1:2:2.60:10,3,0 0/0:3,0:3:6.91:0,7,80 ./. ./. 0/0:0,1:1:0:0,0,0 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,37 0/1:2,1:3:20.68:34,0,21 1/1:2,0:2:3:27,3,0 ./. 0/0:5,0:5:7.73:0,8,67 0/1:4,0:4:19.77:23,0,20 0/0:4,0:4:0.08:0,0,48 ./. ./. ./. ./. ./. ./. ./. 0/1:3,0:3:7.64:8,0,59 -chr1 900089 . G C 230.72 . AC=14;AF=0.500;AN=28;BaseQRankSum=0.692;DP=39;Dels=0.00;FS=10.780;HRun=0;HaplotypeScore=0.8484;InbreedingCoeff=0.2201;MQ=29.00;MQ0=0;MQRankSum=0.165;QD=14.42;ReadPosRankSum=0.495;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 0/0:2,0:2:3.01:0,3,33 0/0:2,1:3:6.01:0,6,62 ./. ./. ./. ./. 1/1:0,1:1:3.01:30,3,0 0/0:3,0:3:6.02:0,6,67 ./. ./. 1/1:2,2:4:6.02:67,6,0 0/0:4,0:4:6.01:0,6,62 0/1:3,1:4:21.57:22,0,56 ./. ./. ./. ./. ./. ./. ./. 0/1:1,2:3:24.41:58,0,24 -chr1 900103 . A C 245.84 . AC=13;AF=0.650;AN=20;BaseQRankSum=2.098;DP=29;Dels=0.00;FS=4.393;HRun=0;HaplotypeScore=1.1682;InbreedingCoeff=-0.0533;MQ=29.00;MQ0=0;MQRankSum=2.098;QD=15.37;ReadPosRankSum=0.146;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. 0/0:2,1:3:6.02:0,6,67 ./. ./. ./. ./. 1/1:0,1:1:3.01:32,3,0 0/1:2,1:3:27.42:27,0,27 ./. ./. 1/1:0,2:2:6.02:67,6,0 ./. 0/1:2,1:4:24.43:24,0,45 ./. ./. ./. ./. ./. ./. ./. 0/1:1,2:3:24.41:58,0,24 -chr1 900112 . C G 149.58 . AC=10;AF=0.556;AN=18;BaseQRankSum=1.027;DP=24;Dels=0.04;FS=2.276;HRun=3;HaplotypeScore=0.9865;MQ=29.00;MQ0=0;MQRankSum=1.027;QD=12.47;ReadPosRankSum=0.201;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. 0/0:1,1:2:3.01:0,3,33 ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 1/1:0,2:2:6.02:67,6,0 ./. 0/1:3,1:4:24.41:24,0,58 ./. ./. ./. ./. ./. ./. ./. 0/1:2,1:3:17.66:18,0,58 -chr1 900115 . G A 35.09 . AC=5;AF=0.227;AN=22;BaseQRankSum=2.382;DP=23;Dels=0.00;FS=13.570;HRun=1;HaplotypeScore=1.7631;InbreedingCoeff=0.1307;MQ=29.00;MQ0=0;MQRankSum=-0.361;QD=7.02;ReadPosRankSum=-1.083;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:1,0:1:3:0,3,27 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. 0/0:1,1:2:3.01:0,3,33 ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:2,0:2:6.02:0,6,65 ./. 0/1:2,1:3:24.41:24,0,58 ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3:0,3,25 0/0:3,0:3:6.01:0,6,61 -chr1 900123 . C G 41.39 . AC=5;AF=0.357;AN=14;BaseQRankSum=1.931;DP=20;Dels=0.00;FS=14.771;HRun=6;HaplotypeScore=1.5461;MQ=29.00;MQ0=0;MQRankSum=0.000;QD=5.17;ReadPosRankSum=-0.382;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:1,1:2:3.01:33,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 0/0:2,0:2:6.02:0,6,65 ./. 0/1:4,1:5:24.41:24,0,56 ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3:0,3,29 -chr1 900123 . CG C 239.86 . AC=12;AF=0.600;AN=20;BaseQRankSum=0.715;DP=20;FS=2.363;HRun=6;HaplotypeScore=37.1615;InbreedingCoeff=0.0592;MQ=29.00;MQ0=0;MQRankSum=-0.965;QD=17.13;ReadPosRankSum=0.627;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,48 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:1.25:0,1,3 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1:2,0:2:31.90:32,0,36 ./. ./. ./. ./. 1/1:1,0:1:3.01:41,3,0 0/0:1,0:1:3:0,3,27 ./. ./. 1/1:1,2:3:6.02:84,6,0 1/1:1,0:1:3.01:35,3,0 0/1:4,1:5:33.46:33,0,48 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 -chr1 900161 . C G 95.96 . AC=3;AF=0.041;AN=74;BaseQRankSum=-0.808;DP=152;Dels=0.00;FS=0.000;HRun=6;HaplotypeScore=0.5011;InbreedingCoeff=-0.1315;MQ=55.56;MQ0=0;MQRankSum=1.024;QD=4.17;ReadPosRankSum=-2.738;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,76 ./. 0/0:3,0:3:6.01:0,6,64 0/0:1,0:1:3.01:0,3,37 ./. 0/0:1,0:1:3.01:0,3,37 0/0:3,0:3:9.03:0,9,113 0/0:2,0:2:6.01:0,6,63 0/0:1,0:1:3.01:0,3,37 ./. ./. ./. ./. 0/0:3,0:3:6.02:0,6,74 ./. 0/0:1,0:1:3:0,3,26 0/0:2,0:2:6.02:0,6,76 0/0:3,0:3:6.02:0,6,72 0/0:1,0:1:3.01:0,3,39 ./. 0/1:1,1:2:27.42:27,0,33 0/0:3,0:3:6.01:0,6,61 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:9.01:0,9,98 0/0:10,0:10:30.10:0,30,382 0/0:11,0:11:30.08:0,30,357 0/0:6,0:6:15.05:0,15,194 0/0:2,0:2:6.02:0,6,76 0/0:5,0:5:9.03:0,9,113 0/0:4,0:4:9.03:0,9,111 0/0:6,0:6:15.05:0,15,185 0/0:9,0:9:21.05:0,21,249 0/0:1,0:1:3.01:0,3,33 0/0:3,1:4:9.03:0,9,111 0/1:4,7:11:99:125,0,120 0/0:9,0:9:24.04:0,24,272 0/0:9,0:9:15.03:0,15,179 0/1:9,1:10:9.37:9,0,233 0/0:3,0:3:9.01:0,9,92 0/0:5,0:5:12.04:0,12,151 ./. 0/0:2,0:2:6.02:0,6,77 0/0:2,0:3:3.01:0,3,39 0/0:4,0:4:12.04:0,12,155 0/0:4,0:4:12.04:0,12,154 -chr1 900188 . C G 109.47 . AC=2;AF=0.021;AN=96;BaseQRankSum=0.425;DP=319;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=0.5571;InbreedingCoeff=-0.0765;MQ=55.58;MQ0=0;MQRankSum=-4.308;QD=9.95;ReadPosRankSum=-1.562;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,37 ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. 0/0:2,0:2:6.02:0,6,80 0/0:3,0:3:9.03:0,9,117 0/0:4,0:4:12.04:0,12,162 0/0:3,0:3:5.99:0,6,60 0/0:3,0:3:6.02:0,6,76 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,39 0/0:7,0:7:15.05:0,15,199 0/0:6,0:6:18.06:0,18,217 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:6.02:0,6,83 0/0:1,0:1:3.01:0,3,42 ./. 0/0:3,0:3:9.03:0,9,118 0/1:3,2:5:21.40:21,0,99 0/0:2,0:2:6.02:0,6,78 0/0:1,0:1:3:0,3,28 0/0:4,0:4:12.04:0,12,157 0/0:4,0:4:12.04:0,12,149 0/0:2,0:2:6.02:0,6,72 ./. 0/0:4,0:4:9.03:0,9,114 0/0:4,0:4:12.03:0,12,143 0/0:1,0:1:3.01:0,3,37 0/0:4,0:4:12.04:0,12,151 0/0:9,0:9:24.07:0,24,295 0/0:16,0:16:39.12:0,39,500 0/0:18,0:18:51.15:0,51,639 0/0:12,0:13:36.09:0,36,451 0/0:9,0:9:27.08:0,27,339 0/0:8,0:8:24.07:0,24,295 0/0:8,0:8:21.06:0,21,259 0/0:7,0:7:18.06:0,18,228 0/0:15,0:15:39.12:0,39,509 0/1:1,5:6:19.75:149,0,20 0/0:5,0:5:12.04:0,12,143 0/0:23,1:24:57.17:0,57,713 0/0:23,0:23:60.19:0,60,759 0/0:16,0:16:39.12:0,39,508 0/0:14,0:14:39.12:0,39,490 0/0:6,0:6:18.05:0,18,206 0/0:12,0:12:30.09:0,30,378 0/0:6,0:6:18.06:0,18,241 0/0:4,0:5:9.03:0,9,118 0/0:8,0:8:21.07:0,21,275 0/0:9,1:10:27.09:0,27,361 0/0:8,0:8:24.08:0,24,318 -chr1 900191 . G A 78.75 . AC=2;AF=0.020;AN=98;BaseQRankSum=0.169;DP=359;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.6619;InbreedingCoeff=-0.0713;MQ=55.88;MQ0=0;MQRankSum=-3.973;QD=7.16;ReadPosRankSum=-0.841;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,40 ./. 0/0:1,0:1:3.01:0,3,34 ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:2,0:2:6.02:0,6,75 ./. ./. ./. 0/0:2,0:2:6.02:0,6,82 0/0:4,0:4:12.04:0,12,156 0/0:6,0:6:18.06:0,18,239 0/0:4,0:4:9.03:0,9,109 0/0:5,0:5:12.04:0,12,154 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,39 0/0:7,0:7:15.05:0,15,203 0/0:6,0:6:18.06:0,18,238 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:9.03:0,9,117 0/0:1,0:1:3.01:0,3,33 ./. 0/0:3,0:3:9.03:0,9,113 0/1:3,2:5:21.41:21,0,90 0/0:3,0:3:9.03:0,9,106 0/0:1,0:1:3.01:0,3,35 0/0:4,0:4:12.04:0,12,160 0/0:4,0:4:9.03:0,9,114 0/0:3,0:3:9.02:0,9,106 ./. 0/0:4,0:4:9.03:0,9,114 0/0:4,0:4:12.04:0,12,151 0/0:1,0:1:3.01:0,3,39 0/0:6,0:6:18.06:0,18,225 0/0:9,0:9:21.07:0,21,269 0/0:18,0:18:48.14:0,48,597 0/0:19,0:19:54.17:0,54,686 0/0:13,0:13:39.11:0,39,495 0/0:10,0:10:30.09:0,30,380 0/0:9,0:9:27.07:0,27,324 0/0:8,0:8:21.06:0,21,256 0/0:11,0:11:30.09:0,30,373 0/0:17,0:17:45.12:0,45,555 0/1:1,5:6:24.96:119,0,25 0/0:5,0:5:12.04:0,12,143 0/0:25,0:25:60.17:0,60,740 0/0:26,0:26:66.20:0,66,832 0/0:18,0:18:45.14:0,45,586 0/0:17,0:17:48.12:0,48,587 0/0:8,0:8:21.06:0,21,255 0/0:14,0:14:39.12:0,39,485 0/0:9,0:9:27.09:0,27,357 0/0:5,0:5:12.04:0,12,162 0/0:8,0:8:21.06:0,21,268 0/0:11,0:11:33.10:0,33,427 0/0:7,0:8:21.07:0,21,267 -chr1 900199 . C G 122.69 . AC=2;AF=0.0196;AN=102;BaseQRankSum=-0.625;DP=419;Dels=0.00;FS=5.991;HRun=6;HaplotypeScore=0.9712;InbreedingCoeff=-0.0705;MQ=55.82;MQ0=0;MQRankSum=-4.226;QD=11.15;ReadPosRankSum=-0.138;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:2.99:0,3,23 0/0:1,0:1:3.01:0,3,38 ./. ./. 0/0:2,0:2:3.01:0,3,41 ./. ./. 0/0:2,0:2:6.02:0,6,73 ./. ./. ./. 0/0:2,0:2:6.02:0,6,76 0/0:5,0:5:15.05:0,15,191 0/0:6,0:6:18.06:0,18,228 0/0:6,0:6:12.03:0,12,131 0/0:7,0:7:15.05:0,15,197 0/0:1,0:1:3:0,3,26 0/0:1,0:1:3.01:0,3,37 0/0:9,0:9:21.06:0,21,263 0/0:6,0:6:18.04:0,18,202 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:9.02:0,9,102 0/0:2,0:2:6.02:0,6,71 0/0:1,0:1:3.01:0,3,38 0/0:4,0:4:6.02:0,6,72 0/1:3,2:5:51.85:52,0,78 0/0:4,0:4:6.02:0,6,79 0/0:1,0:1:3.01:0,3,31 0/0:4,0:4:12.01:0,12,125 0/0:4,0:4:6.02:0,6,76 0/0:4,0:4:9.03:0,9,111 ./. 0/0:4,0:4:12.03:0,12,136 0/0:4,0:4:9.03:0,9,108 0/0:2,0:2:6.01:0,6,66 0/0:10,0:10:24.07:0,24,298 0/0:11,0:11:27.07:0,27,314 0/0:22,0:22:63.14:0,63,726 0/0:23,0:23:57.16:0,57,703 0/0:14,0:14:39.11:0,39,464 0/0:12,0:12:33.07:0,33,385 0/0:10,0:10:24.07:0,24,295 0/0:8,0:8:21.06:0,21,258 0/0:12,0:12:33.10:0,33,403 0/0:21,0:21:48.12:0,48,566 0/1:1,5:6:20.54:134,0,21 0/0:7,0:7:18.04:0,18,210 0/0:27,0:27:63.10:0,63,694 0/0:33,1:34:78.18:0,78,935 0/0:22,0:22:51.14:0,51,612 0/0:20,0:20:51.12:0,51,606 0/0:8,0:8:18.06:0,18,218 0/0:14,0:14:36.07:0,36,417 0/0:9,0:9:27.08:0,27,331 0/0:6,0:6:15.03:0,15,175 0/0:8,0:9:21.06:0,21,251 0/0:12,0:12:36.11:0,36,453 0/0:8,0:8:24.06:0,24,283 -chr1 900200 . G GC 138.36 . AC=2;AF=0.0192;AN=104;BaseQRankSum=4.004;DP=447;FS=5.745;HRun=1;HaplotypeScore=63.8129;InbreedingCoeff=-0.0683;MQ=55.87;MQ0=0;MQRankSum=-4.054;QD=10.64;ReadPosRankSum=-0.688;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/0:3,0:3:6.02:0,6,74 ./. ./. 0/0:2,0:2:6.02:0,6,76 0/0:1,0:1:3.01:0,3,34 ./. ./. 0/0:2,0:2:6.02:0,6,78 0/0:7,0:7:18.05:0,18,225 0/0:6,0:6:18.06:0,18,234 0/0:6,0:6:12.04:0,12,155 0/0:7,0:7:21.07:0,21,272 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:3.01:0,3,39 0/0:9,0:9:24.08:0,24,312 0/0:7,0:7:21.07:0,21,266 0/0:1,0:1:3.01:0,3,39 0/0:5,0:5:12.04:0,12,148 0/0:2,0:2:6.02:0,6,77 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:9.03:0,9,117 0/1:3,2:5:65.39:65,0,102 0/0:4,0:4:12.04:0,12,154 0/0:1,0:1:3.01:0,3,33 0/0:5,0:5:12.04:0,12,154 0/0:4,0:4:9.03:0,9,117 0/0:4,0:4:9.03:0,9,116 ./. 0/0:4,0:4:12.04:0,12,156 0/0:4,0:4:12.04:0,12,156 0/0:2,0:2:6.02:0,6,78 0/0:10,0:10:27.09:0,27,351 0/0:12,0:12:33.10:0,33,419 0/0:23,0:23:69.22:0,69,886 0/0:23,0:23:60.19:0,60,779 0/0:16,0:16:42:0,42,520 0/0:13,0:13:39.13:0,39,500 0/0:10,0:10:27.09:0,27,345 0/0:8,0:8:21:0,21,252 0/0:14,0:14:39.11:0,39,487 0/0:22,0:22:63.20:0,63,808 0/1:4,4:8:24.12:145,0,24 0/0:8,0:8:21.07:0,21,273 0/0:29,0:29:69.22:0,69,883 0/0:34,0:34:87.15:0,87,1121 0/0:23,0:23:58.43:0,58,740 0/0:21,0:21:54.17:0,54,699 0/0:8,0:7:24.08:0,24,309 0/0:14,0:14:39.13:0,39,504 0/0:10,0:10:30.09:0,30,381 0/0:7,0:7:18.06:0,18,227 0/0:11,0:11:27.08:0,27,341 0/0:13,0:13:39.12:0,39,498 0/0:8,0:8:24.08:0,24,312 -chr1 900205 . T C 3848.55 . AC=28;AF=0.2642;AN=106;BaseQRankSum=3.976;DP=500;Dels=0.00;FS=4.311;HRun=2;HaplotypeScore=0.8450;InbreedingCoeff=-0.0127;MQ=56.04;MQ0=0;MQRankSum=2.371;QD=15.21;ReadPosRankSum=0.624;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3:0,3,27 0/0:1,0:1:3.01:0,3,40 1/1:0,1:1:3.01:34,3,0 ./. ./. 0/0:3,0:3:6.02:0,6,72 ./. ./. 0/1:1,2:3:30.98:65,0,31 0/0:1,0:1:3.01:0,3,40 ./. 0/0:1,0:1:3.01:0,3,41 1/1:0,3:3:9.03:117,9,0 0/1:6,3:9:92.32:92,0,149 0/0:6,0:6:15.01:0,15,157 0/1:3,3:6:52.20:83,0,52 0/1:5,3:8:46.22:46,0,135 1/1:0,2:2:6:58,6,0 0/1:1,1:2:30.11:33,0,30 0/0:9,0:9:21.04:0,21,237 0/0:7,0:7:12.03:0,12,132 0/0:1,0:1:3.01:0,3,31 0/1:4,2:6:58.78:59,0,95 0/0:2,0:2:3.01:0,3,39 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:6.01:0,6,59 0/0:5,0:5:9.01:0,9,87 0/0:4,0:5:12.01:0,12,124 0/0:1,0:2:3.01:0,3,38 0/0:6,0:6:15.04:0,15,178 0/1:1,3:4:15.69:41,0,16 0/1:2,2:4:29.56:30,0,52 ./. 0/1:2,2:4:49.08:51,0,49 0/1:1,1:4:29.23:31,0,29 0/0:2,0:3:3.01:0,3,37 1/1:0,12:12:36.11:446,36,0 0/1:7,5:13:44.62:45,0,189 0/0:26,0:26:69.11:0,69,752 1/1:1,24:25:39.55:747,40,0 0/1:11,6:17:99:157,0,237 0/0:14,0:14:33.08:0,33,380 0/0:11,0:12:24.07:0,24,285 0/0:8,1:9:18.05:0,18,205 0/0:16,0:16:36.09:0,36,414 0/1:12,12:24:99:346,0,264 0/0:8,0:9:21.02:0,21,215 0/0:12,0:12:33.07:0,33,383 0/1:16,15:31:99:343,0,241 0/1:18,22:40:99:556,0,337 0/0:26,0:26:63.16:0,63,732 0/0:21,0:24:57.13:0,57,664 0/0:8,0:8:24.01:0,24,237 0/0:15,0:15:33.03:0,33,338 0/0:11,0:11:30.06:0,30,322 0/0:7,0:7:18.05:0,18,211 0/1:8,3:12:57.53:58,0,145 0/1:9,5:14:99:152,0,253 0/1:1,8:9:11.50:259,0,11 -chr1 900208 . G A 196.8 . AC=3;AF=0.0278;AN=108;BaseQRankSum=-1.850;DP=545;Dels=0.00;FS=3.034;HRun=0;HaplotypeScore=0.9217;InbreedingCoeff=-0.0711;MQ=55.89;MQ0=0;MQRankSum=-1.612;QD=8.56;ReadPosRankSum=-1.195;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,40 ./. ./. 0/0:3,0:3:6.02:0,6,75 0/0:1,0:1:3.01:0,3,33 ./. 0/0:3,0:3:9.03:0,9,116 0/0:1,0:1:3.01:0,3,35 ./. 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:6.02:0,6,77 0/0:10,0:10:27.09:0,27,350 0/0:6,0:6:18.04:0,18,216 0/0:7,0:7:15.04:0,15,180 0/1:7,1:8:15.92:16,0,197 0/0:2,0:2:6.02:0,6,77 0/0:2,0:2:6.01:0,6,63 0/0:9,0:9:21.07:0,21,276 0/0:8,0:8:24.06:0,24,281 0/0:2,0:2:6.02:0,6,74 0/0:8,0:8:21.06:0,21,258 0/0:4,0:4:12.04:0,12,146 0/0:2,0:2:6.02:0,6,79 0/0:4,0:4:9.01:0,9,85 0/1:3,3:6:66.60:86,0,67 0/0:6,0:6:15.05:0,15,188 0/0:3,0:3:6.02:0,6,77 0/0:6,0:6:15.04:0,15,173 0/0:4,0:4:9.01:0,9,89 0/0:5,0:5:12.04:0,12,147 ./. 0/0:4,0:4:12.03:0,12,140 0/0:4,0:4:9.01:0,9,99 0/0:5,0:5:15.04:0,15,173 0/0:12,0:12:36.09:0,36,427 0/0:14,1:15:0.81:0,1,334 0/0:28,0:28:81.21:0,81,968 0/0:29,0:29:81.18:0,81,961 0/0:19,0:19:51.15:0,51,631 0/0:15,0:15:39.12:0,39,485 0/0:12,0:12:30.07:0,30,354 0/0:9,0:9:24.06:0,24,274 0/0:19,0:19:51.15:0,51,616 0/0:24,0:24:63.18:0,63,774 0/1:1,7:9:17.54:170,0,18 0/0:15,0:15:42.11:0,42,502 0/0:31,0:32:81.19:0,81,935 0/0:42,0:43:99:0,117,1415 0/0:27,0:27:72.21:0,72,884 0/0:25,0:25:72.21:0,72,873 0/0:8,0:8:21.05:0,21,244 0/0:16,0:16:42.13:0,42,515 0/0:11,0:11:33.10:0,33,415 0/0:8,0:9:21.06:0,21,261 0/0:11,0:12:27.07:0,27,320 0/0:15,0:15:42.13:0,42,530 0/0:11,0:11:33.09:0,33,393 -chr1 900252 . G A 2492.99 . AC=7;AF=0.0593;AN=118;BaseQRankSum=0.859;DP=1112;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.6311;InbreedingCoeff=-0.0857;MQ=55.70;MQ0=0;MQRankSum=2.953;QD=13.33;ReadPosRankSum=-0.555;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,38 ./. 0/0:3,0:3:9.03:0,9,115 0/0:1,0:1:3.01:0,3,41 0/1:1,2:3:31.62:73,0,32 0/0:4,0:4:12.04:0,12,152 0/0:4,0:4:12.04:0,12,159 0/0:2,0:2:6.02:0,6,73 0/0:2,0:2:6.02:0,6,81 0/0:9,0:9:27.09:0,27,367 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.02:0,9,106 0/0:1,0:1:3.01:0,3,32 0/0:11,0:11:33.10:0,33,413 0/0:16,0:16:45.13:0,45,587 0/0:11,0:11:30.10:0,30,402 0/0:10,0:10:27.07:0,27,348 0/0:14,0:14:39.12:0,39,511 0/0:8,0:8:21.06:0,21,269 0/0:6,0:6:18.06:0,18,238 0/0:15,0:15:45.14:0,45,583 0/0:16,0:16:42.14:0,42,556 0/0:4,0:4:12.04:0,12,154 0/0:13,0:13:33.09:0,33,429 0/0:14,0:14:42.13:0,42,549 0/1:4,5:9:99:178,0,139 0/0:13,0:13:30.09:0,30,386 0/0:6,0:6:15.05:0,15,193 0/0:13,0:13:36.12:0,36,482 0/0:5,0:5:15.05:0,15,195 0/0:10,0:10:30.10:0,30,397 0/0:11,0:11:33.11:0,33,440 0/0:11,0:11:30.09:0,30,379 0/0:4,0:4:12.04:0,12,168 0/0:6,0:6:15.05:0,15,197 0/0:5,0:5:15.05:0,15,201 0/0:11,0:11:33.08:0,33,407 0/0:22,0:22:60.18:0,60,753 0/0:33,0:33:87.26:0,87,1091 0/1:24,25:50:99:803,0,710 0/0:45,0:45:99:0,126,1597 0/0:34,0:34:99:0,99,1256 0/0:28,0:29:78.24:0,78,1014 0/1:16,11:27:99:327,0,520 0/0:23,0:23:63.20:0,63,789 0/0:36,0:36:99:0,99,1254 0/0:48,0:48:99:0,141,1765 0/0:22,0:22:63.19:0,63,774 0/0:35,0:35:99:0,102,1303 0/0:69,0:71:99:0,187,2398 0/0:79,0:79:99:0,214,2719 0/1:23,17:40:99:488,0,650 0/0:54,0:55:99:0,150,1875 0/1:15,17:32:99:543,0,394 0/0:28,0:29:78.23:0,78,988 0/1:19,7:26:99:204,0,581 0/0:25,0:25:69.20:0,69,878 0/0:26,0:26:72.22:0,72,928 0/0:27,0:27:78.24:0,78,988 0/0:21,0:21:60.19:0,60,752 -chr1 900285 . C T 49972.75 . AC=105;AF=0.9052;AN=116;BaseQRankSum=-3.461;DP=1713;Dels=0.00;FS=2.048;HRun=0;HaplotypeScore=2.6694;InbreedingCoeff=0.0387;MQ=55.27;MQ0=0;MQRankSum=-1.138;QD=29.80;ReadPosRankSum=-0.012;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,2:2:6.02:73,6,0 ./. 1/1:0,1:1:3.01:40,3,0 1/1:0,1:1:3:25,3,0 1/1:0,1:1:3.01:39,3,0 1/1:0,3:3:9.01:96,9,0 1/1:0,6:6:18.05:213,18,0 1/1:0,1:1:3.01:39,3,0 1/1:0,4:4:12.04:152,12,0 0/1:3,3:6:64.76:65,0,96 1/1:0,1:1:3.01:34,3,0 ./. 1/1:0,1:1:3.01:39,3,0 1/1:0,18:18:54.16:652,54,0 1/1:0,23:24:57.13:678,57,0 1/1:0,15:15:39.12:506,39,0 1/1:0,15:15:33.11:442,33,0 1/1:0,21:22:54.16:689,54,0 1/1:0,15:15:42.13:529,42,0 1/1:0,9:9:24.08:312,24,0 0/1:9,6:15:99:159,0,235 1/1:0,31:31:87.27:1110,87,0 0/1:4,6:10:99:203,0,104 1/1:0,16:16:45.10:536,45,0 1/1:1,20:21:51.12:601,51,0 1/1:0,15:15:42.12:513,42,0 0/1:16,8:24:99:240,0,442 0/1:4,8:12:99:231,0,127 1/1:0,21:21:57.16:703,57,0 1/1:0,16:16:45.14:559,45,0 1/1:0,19:19:57.18:729,57,0 1/1:0,14:14:36.11:458,36,0 1/1:0,17:17:45.14:571,45,0 0/1:6,5:11:99:163,0,178 1/1:0,10:10:30.09:374,30,0 1/1:0,15:15:39.13:511,39,0 1/1:0,25:25:63.17:784,63,0 1/1:0,36:37:96.26:1176,96,0 1/1:0,44:44:99:1428,117,0 1/1:1,84:85:99:2792,226,0 1/1:0,61:61:99:2032,165,0 0/1:20,21:41:99:653,0,615 1/1:0,46:47:99:1672,135,0 1/1:0,37:38:96.24:1159,96,0 1/1:0,36:38:96.24:1159,96,0 1/1:1,62:64:99:1984,162,0 1/1:0,79:79:99:2520,208,0 0/0:34,2:36:48.53:0,49,1102 1/1:0,52:54:99:1707,144,0 1/1:0,89:91:99:2878,235,0 0/1:51,57:108:99:1662,0,1492 1/1:2,67:69:99:2045,146,0 1/1:1,73:75:99:2351,190,0 1/1:0,58:58:99:1867,153,0 1/1:0,43:44:99:1477,120,0 1/1:0,43:43:99:1518,120,0 0/1:14,21:35:99:647,0,348 1/1:0,42:42:99:1456,120,0 1/1:0,43:43:99:1578,129,0 1/1:0,37:37:87.27:1143,87,0 -chr1 900286 . A G 53795.91 . AC=111;AF=0.9569;AN=116;BaseQRankSum=-1.271;DP=1744;Dels=0.00;FS=6.893;HRun=1;HaplotypeScore=2.7132;InbreedingCoeff=-0.0679;MQ=55.34;MQ0=0;MQRankSum=0.681;QD=30.85;ReadPosRankSum=0.607;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,2:2:6.02:78,6,0 ./. 1/1:0,1:1:3.01:38,3,0 1/1:0,1:1:3.01:37,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,3:3:9.03:104,9,0 1/1:0,6:6:18.06:228,18,0 1/1:0,1:1:3.01:41,3,0 1/1:0,4:4:12.03:146,12,0 0/1:3,3:6:64.27:64,0,96 1/1:0,1:1:3.01:36,3,0 ./. 1/1:0,1:1:3.01:36,3,0 1/1:0,18:18:54.16:655,54,0 1/1:0,24:25:63.18:766,63,0 1/1:0,15:15:39.12:504,39,0 1/1:0,15:15:33.11:450,33,0 1/1:0,20:21:51.15:659,51,0 1/1:0,18:18:48.15:607,48,0 1/1:0,10:10:27.09:361,27,0 1/1:0,15:15:39.12:498,39,0 1/1:0,31:31:84.26:1096,84,0 0/1:6,6:12:99:195,0,145 1/1:0,16:16:45.13:562,45,0 1/1:0,21:22:51.15:608,51,0 1/1:0,16:16:45.14:568,45,0 1/1:0,24:24:63.20:824,63,0 1/1:0,13:13:36.12:473,36,0 1/1:0,22:22:60.18:763,60,0 1/1:0,16:16:45.14:571,45,0 1/1:0,19:19:54.17:695,54,0 1/1:0,14:14:42.12:524,42,0 1/1:0,17:17:45.13:577,45,0 1/1:0,11:11:30.10:402,30,0 1/1:0,10:10:30.09:377,30,0 1/1:0,15:15:39.12:499,39,0 1/1:0,25:25:63.19:794,63,0 1/1:0,37:38:96.24:1194,96,0 1/1:0,43:43:99:1465,117,0 1/1:0,87:87:99:2949,238,0 1/1:0,61:61:99:2105,169,0 0/1:21,21:42:99:646,0,667 1/1:0,47:47:99:1622,129,0 1/1:0,37:38:99:1204,99,0 1/1:0,40:40:99:1274,102,0 1/1:0,63:63:99:1966,156,0 1/1:0,81:82:99:2696,220,0 1/1:0,36:36:93.28:1179,93,0 1/1:0,55:55:99:1754,144,0 1/1:0,93:94:99:2911,241,0 0/1:51,58:110:99:1718,0,1485 1/1:1,68:69:99:2026,138,0 1/1:0,78:78:99:2420,193,0 1/1:0,58:59:99:1907,156,0 1/1:0,45:45:99:1513,123,0 1/1:0,44:44:99:1573,123,0 0/1:15,22:37:99:676,0,342 1/1:0,44:44:99:1465,120,0 1/1:1,42:43:88.56:1478,89,0 1/1:0,37:37:93.25:1174,93,0 -chr1 900298 . C G 1312.84 . AC=5;AF=0.0417;AN=120;BaseQRankSum=-2.430;DP=2069;Dels=0.00;FS=2.014;HRun=1;HaplotypeScore=1.8253;InbreedingCoeff=0.1410;MQ=55.23;MQ0=0;MQRankSum=1.938;QD=10.67;ReadPosRankSum=-0.720;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.01:0,6,63 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:3.01:0,3,41 0/0:2,0:2:6.02:0,6,71 0/0:2,0:2:6.02:0,6,82 0/0:2,0:2:3.01:0,3,39 0/0:7,0:7:21.06:0,21,262 0/0:1,0:1:3.01:0,3,41 0/0:5,0:5:12.04:0,12,165 0/0:14,0:14:39.11:0,39,499 0/0:2,0:2:6.02:0,6,82 1/1:0,1:1:3.01:32,3,0 0/0:3,0:3:9.03:0,9,112 0/0:22,0:22:66.19:0,66,810 0/0:30,0:30:78.24:0,78,987 0/0:14,0:14:39.12:0,39,487 0/0:15,0:15:39.13:0,39,523 0/0:18,0:18:48.15:0,48,636 0/0:23,0:23:63.19:0,63,812 0/0:16,0:16:42.14:0,42,553 0/0:20,0:20:57.17:0,57,707 0/0:37,0:37:99:0,102,1338 0/0:14,0:14:36.12:0,36,479 0/0:20,0:20:54.17:0,54,708 0/1:15,11:26:99:245,0,350 0/0:19,0:19:51.16:0,51,665 0/0:26,0:26:72.21:0,72,957 0/0:16,0:16:45.14:0,45,588 0/1:12,19:31:99:567,0,268 0/0:20,0:20:57.18:0,57,740 0/0:26,0:26:72.23:0,72,957 0/0:19,0:19:57.16:0,57,712 0/0:19,0:19:57.17:0,57,722 0/0:13,0:13:36.12:0,36,485 0/0:11,0:11:33.11:0,33,436 0/0:19,0:19:54.15:0,54,689 0/0:29,0:29:72.22:0,72,932 0/0:37,0:37:99:0,105,1363 0/0:52,0:52:99:0,147,1803 0/0:95,0:95:99:0,256,3232 0/0:70,0:70:99:0,181,2336 0/0:61,0:61:99:0,166,2093 0/0:62,0:62:99:0,172,2187 0/0:43,0:43:99:0,114,1437 0/0:57,0:57:99:0,144,1829 0/0:72,0:72:99:0,175,2253 0/0:96,0:96:99:0,244,3059 0/0:39,0:40:96.29:0,96,1206 0/0:71,0:71:99:0,172,2143 0/0:109,0:109:99:0,286,3645 0/0:114,0:114:99:0,307,3857 0/0:75,0:75:99:0,178,2229 0/0:82,0:82:99:0,205,2582 0/0:66,0:68:99:0,184,2257 0/0:53,0:53:99:0,135,1731 0/0:52,0:52:99:0,144,1875 0/0:52,0:52:99:0,147,1830 0/1:43,22:65:99:564,0,1227 0/0:46,0:46:99:0,135,1710 0/0:49,0:49:99:0,120,1556 -chr1 900319 . G A 830.69 . AC=3;AF=0.0250;AN=120;BaseQRankSum=0.864;DP=2658;Dels=0.00;FS=5.182;HRun=0;HaplotypeScore=1.8883;InbreedingCoeff=-0.0417;MQ=56.04;MQ0=0;MQRankSum=2.734;QD=10.93;ReadPosRankSum=1.705;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|10),INTRON(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|11),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:6.02:0,6,76 0/0:4,0:4:12.04:0,12,150 0/0:1,0:1:3.01:0,3,36 0/0:2,0:2:6.02:0,6,77 0/0:1,0:1:3.01:0,3,40 0/0:3,0:3:9.03:0,9,117 0/0:8,0:8:24.07:0,24,308 0/0:5,0:5:15.05:0,15,198 0/0:6,0:6:18.06:0,18,247 0/0:14,0:14:42.13:0,42,551 0/0:2,0:2:6.02:0,6,82 0/0:2,0:2:3.01:0,3,39 0/0:8,0:8:24.08:0,24,306 0/0:29,0:29:81.24:0,81,1012 0/0:31,0:31:84.23:0,84,1039 0/0:20,0:20:57.18:0,57,726 0/0:21,0:21:57.18:0,57,746 0/0:20,0:20:57.18:0,57,746 0/0:29,0:29:84.21:0,84,1047 0/0:22,0:22:63.15:0,63,781 0/0:28,0:28:75.22:0,75,935 0/0:43,0:43:99:0,111,1425 0/0:16,0:16:39.13:0,39,508 0/0:17,0:17:45.15:0,45,595 0/0:26,0:26:69.18:0,69,840 0/0:22,0:22:57.18:0,57,755 0/1:21,9:30:99:203,0,653 0/0:19,0:19:45.14:0,45,594 0/0:38,0:38:96.29:0,96,1254 0/0:27,0:27:81.26:0,81,1047 0/0:37,0:37:99:0,105,1319 0/0:21,0:21:57.17:0,57,730 0/0:34,0:34:90.27:0,90,1163 0/0:20,0:20:57.18:0,57,741 0/1:8,8:16:99:223,0,238 0/0:28,0:28:72.22:0,72,907 0/1:14,16:30:99:485,0,302 0/0:52,0:52:99:0,135,1781 0/0:73,0:75:99:0,183,2238 0/0:121,0:123:99:0,304,3780 0/0:100,0:100:99:0,259,3284 0/0:79,0:80:99:0,199,2463 0/0:74,0:74:99:0,178,2289 0/0:58,1:59:99:0,144,1847 0/0:73,0:75:99:0,172,2199 0/0:88,0:88:99:0,208,2540 0/0:114,0:114:99:0,253,3179 0/0:56,0:56:99:0,126,1586 0/0:93,0:93:99:0,223,2766 0/0:142,0:142:99:0,346,4293 0/0:145,0:146:99:0,352,4306 0/0:92,0:92:99:0,214,2539 0/0:92,1:93:99:0,238,2942 0/0:81,0:81:99:0,186,2230 0/0:71,0:71:99:0,177,2182 0/0:71,0:71:99:0,181,2282 0/0:58,0:58:99:0,156,1931 0/0:105,0:105:99:0,265,3355 0/0:62,0:62:99:0,156,2016 0/0:63,0:64:99:0,162,2017 -chr1 900397 . C T 2009.84 . AC=2;AF=0.0167;AN=120;BaseQRankSum=1.145;DP=5436;DS;Dels=0.00;FS=0.454;HRun=0;HaplotypeScore=4.5718;InbreedingCoeff=-0.0195;MQ=57.26;MQ0=0;MQRankSum=1.619;QD=12.72;ReadPosRankSum=-0.157;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N355|412|KLHL17|protein_coding|CODING|ENST00000455747|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N585|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,synonymous_variant|aaC/aaT|N|ENSG00000187961|KLHL17|ENST00000338591|12/12|||585/642|protein_coding|1 GT:AD:DP:GQ:PL 0/0:10,0:10:18.05:0,18,199 0/0:5,0:5:15.04:0,15,175 0/0:5,0:5:12.02:0,12,126 0/0:6,0:6:15.05:0,15,195 0/0:3,0:3:9.03:0,9,121 0/0:9,0:9:27.09:0,27,346 0/0:9,0:9:27.08:0,27,347 0/0:9,0:9:27.09:0,27,351 0/0:20,0:20:60.17:0,60,736 0/0:18,0:18:51.17:0,51,680 0/0:6,0:6:18.06:0,18,236 0/0:7,0:7:21.07:0,21,280 0/0:6,0:6:18.06:0,18,237 0/0:74,0:75:99:0,175,2206 0/0:62,0:62:99:0,141,1724 0/0:39,0:40:87.24:0,87,1125 0/0:52,0:52:99:0,132,1695 0/0:63,0:63:99:0,153,1929 0/0:65,0:65:99:0,168,2086 0/0:57,0:57:99:0,135,1739 0/0:57,0:57:99:0,138,1767 0/0:78,0:78:99:0,190,2401 0/0:38,0:38:96.30:0,96,1238 0/0:63,0:63:99:0,153,1931 0/0:59,0:59:99:0,144,1826 0/0:40,0:40:93.26:0,93,1188 0/0:59,0:59:99:0,147,1865 0/1:24,25:50:99:669,0,666 0/0:58,0:58:99:0,144,1791 0/0:64,0:64:99:0,159,2006 0/0:76,0:76:99:0,187,2344 0/0:38,0:38:93.29:0,93,1179 0/0:74,0:75:99:0,165,2080 0/0:54,0:54:99:0,132,1678 0/0:46,0:46:99:0,99,1286 0/0:54,0:54:99:0,132,1672 0/0:54,0:54:99:0,138,1733 0/0:97,0:97:99:0,253,3154 0/0:142,0:142:99:0,346,4384 0/0:250,0:250:99:0,623,7807 0/0:181,0:181:99:0,457,5803 0/0:169,0:169:99:0,421,5347 0/0:123,0:124:99:0,307,3903 0/0:134,0:134:99:0,322,4057 0/0:138,1:139:99:0,317,4403 0/0:154,0:154:99:0,385,4794 0/0:247,0:249:99:0,623,7584 0/1:56,51:108:99:1407,0,1247 0/0:219,0:219:99:0,518,6501 0/0:250,0:250:99:0,632,7815 0/0:247,0:247:99:0,632,7853 0/0:199,1:201:99:0,490,6078 0/0:213,0:214:99:0,536,6683 0/0:171,0:172:99:0,385,4783 0/0:166,0:166:99:0,382,4863 0/0:149,0:149:99:0,385,4880 0/0:101,0:103:99:0,250,3117 0/0:198,0:198:99:0,463,5881 0/0:135,0:135:99:0,313,3989 0/0:143,1:145:99:0,306,4057 -chr1 900505 . G C 36708.31 . AC=34;AF=0.2881;AN=118;BaseQRankSum=3.779;DP=6012;DS;Dels=0.00;FS=16.118;HRun=1;HaplotypeScore=4.6415;InbreedingCoeff=-0.1592;MQ=56.94;MQ0=0;MQRankSum=2.324;QD=13.04;ReadPosRankSum=-1.518;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V391|412|KLHL17|protein_coding|CODING|ENST00000455747|),SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V621|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,synonymous_variant|gtG/gtC|V|ENSG00000187961|KLHL17|ENST00000338591|12/12|||621/642|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:9.03:0,9,107 ./. 0/1:3,6:9:50.09:50,0,60 0/1:2,6:8:30.98:70,0,31 0/1:5,6:11:99:162,0,153 0/1:7,6:13:99:104,0,241 0/1:16,16:33:99:213,0,395 0/1:8,7:15:99:195,0,149 0/1:30,15:45:99:236,0,551 0/1:22,10:32:99:196,0,462 0/1:6,12:18:72.11:302,0,72 0/0:12,0:12:24.08:0,24,312 0/1:10,9:19:99:200,0,175 1/1:1,63:64:99:1790,144,0 0/1:34,43:77:99:908,0,824 0/0:36,0:36:81.22:0,81,988 0/1:24,28:52:99:563,0,593 0/1:23,41:64:99:1075,0,427 0/1:42,26:68:99:627,0,1008 0/1:26,30:56:99:654,0,571 0/0:48,0:48:99:0,120,1483 0/0:88,0:88:99:0,199,2505 0/0:53,0:53:99:0,132,1615 0/1:37,32:69:99:853,0,927 0/0:67,0:68:99:0,150,1923 0/1:27,16:43:99:369,0,665 0/0:77,0:77:99:0,178,2216 0/0:51,0:51:99:0,111,1408 0/0:71,0:71:99:0,144,1810 0/0:58,0:58:99:0,120,1501 0/0:86,3:89:99:0,187,2341 0/0:50,0:50:96.20:0,96,1147 0/1:37,23:60:99:486,0,921 0/0:51,0:51:99:0,129,1579 0/1:22,27:49:99:577,0,451 0/1:28,25:53:99:638,0,562 0/0:72,0:72:99:0,172,2198 1/1:0,77:77:99:2382,193,0 0/1:75,95:170:99:2382,0,1647 0/1:131,103:234:99:2393,0,3096 0/1:102,81:183:99:2163,0,2669 0/1:112,91:204:99:2323,0,2620 0/0:187,2:189:99:0,427,5295 0/0:173,0:175:99:0,415,5068 0/0:162,0:162:99:0,391,4887 0/0:202,0:204:99:0,460,5711 0/1:126,117:243:99:2697,0,3112 0/0:120,1:122:99:0,227,3223 0/0:214,2:218:99:0,484,5987 0/0:237,1:239:99:0,511,6206 0/1:120,127:248:99:2859,0,2857 0/0:205,2:207:99:0,469,5600 0/0:201,4:205:99:0,448,5354 0/1:128,96:224:99:2277,0,2787 0/0:210,1:213:99:0,460,5635 0/0:137,1:138:99:0,301,3737 0/0:132,1:133:99:0,328,4059 0/1:107,102:209:99:2472,0,2417 0/0:151,5:156:99:0,265,4148 1/1:1,161:162:99:4492,328,0 -chr1 900560 . A C 336.55 . AC=11;AF=0.0917;AN=120;BaseQRankSum=-16.919;DP=3961;DS;Dels=0.00;FS=94.082;HRun=2;HaplotypeScore=2.4690;InbreedingCoeff=-0.1027;MQ=56.02;MQ0=0;MQRankSum=-0.133;QD=2.37;ReadPosRankSum=-4.673;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T410P|412|KLHL17|protein_coding|CODING|ENST00000455747|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T640P|642|KLHL17|protein_coding|CODING|ENST00000338591|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,missense_variant|Acc/Ccc|T/P|ENSG00000187961|KLHL17|ENST00000338591|12/12|unknown(0)|deleterious(0.02)|640/642|protein_coding|1 GT:AD:DP:GQ:PL 0/1:8,5:13:0.64:1,0,222 0/0:3,3:6:9.03:0,9,105 0/1:8,5:13:44.55:45,0,207 0/1:3,1:4:22.52:23,0,71 0/1:5,2:7:41.43:41,0,133 0/1:6,3:9:38.74:39,0,204 0/1:8,3:11:71.79:72,0,211 0/1:5,4:9:35.14:35,0,165 0/1:18,8:26:13.96:14,0,501 0/1:16,14:30:99:139,0,474 0/1:5,5:10:42.09:42,0,106 0/1:7,3:10:35.19:35,0,187 0/0:7,4:11:0.37:0,0,235 0/0:32,4:36:66.17:0,66,777 0/0:44,7:51:99:0,108,1222 0/0:11,2:13:27.08:0,27,317 0/0:24,2:26:25.57:0,26,585 0/0:31,3:35:63.10:0,63,722 0/0:33,10:43:69.12:0,69,776 0/0:31,3:35:10.12:0,10,664 0/0:22,5:27:51.11:0,51,584 0/0:47,7:54:76.96:0,77,1267 0/0:24,3:27:54.11:0,54,617 0/0:25,6:31:57.11:0,57,639 0/0:32,4:36:50.88:0,51,852 0/0:23,3:26:57.14:0,57,672 0/0:33,5:39:75.16:0,75,849 0/0:25,2:27:29.47:0,29,635 0/0:33,1:34:72.12:0,72,829 0/0:33,4:39:78.16:0,78,885 0/0:44,3:48:99:0,108,1227 0/0:26,2:28:26.52:0,27,588 0/0:27,2:29:54.15:0,54,639 0/0:30,3:33:63.13:0,63,744 0/0:24,0:25:48.10:0,48,548 0/0:29,1:31:54.11:0,54,623 0/0:37,2:39:78.21:0,78,943 0/0:35,9:45:40.29:0,40,719 0/0:105,10:117:99:0,222,2828 0/0:177,16:193:99:0,382,4686 0/0:107,8:116:99:0,265,3166 0/0:113,13:126:99:0,229,2981 0/0:124,12:136:99:0,269,3411 0/0:93,10:104:99:0,226,2699 0/0:98,5:103:99:0,201,2638 0/0:125,19:145:99:0,260,3306 0/0:187,14:201:99:0,374,4953 0/0:75,4:80:99:0,147,2013 0/0:125,16:141:99:0,292,3413 0/0:164,25:191:99:0,304,3852 0/0:164,22:186:99:0,276,3972 0/0:138,13:152:99:0,292,3532 0/0:136,17:154:99:0,278,3592 0/0:136,13:149:99:0,264,3260 0/0:117,16:133:99:0,274,3159 0/0:80,9:89:99:0,167,1944 0/0:92,11:103:99:0,202,2433 0/0:127,6:133:99:0,290,3787 0/0:76,10:86:99:0,131,1803 0/0:93,11:105:99:0,217,2590 -chr1 900717 . CTTAT C 9074.2 . AC=69;AF=0.6053;AN=114;BaseQRankSum=10.277;DP=412;FS=7.468;HRun=0;HaplotypeScore=48.3915;InbreedingCoeff=0.0298;MQ=48.25;MQ0=0;MQRankSum=-9.614;QD=26.85;ReadPosRankSum=3.811;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UTR_3_PRIME(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|11),UTR_3_PRIME(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|12);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,3_prime_UTR_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591|12/12|||-/642|protein_coding|1 GT:AD:DP:GQ:PL 1/1:2,1:3:3.01:55,3,0 1/1:1,6:7:18.06:331,18,0 0/1:6,2:8:92.38:92,0,284 0/1:7,0:7:22.86:23,0,301 ./. 0/1:5,0:5:43.14:43,0,222 0/1:7,1:8:72.07:72,0,294 0/1:6,0:6:43.16:43,0,226 0/1:12,2:14:99:131,0,432 0/0:17,0:17:39.13:0,39,887 0/1:6,1:7:82.07:82,0,138 1/1:3,2:5:9.03:149,9,0 0/1:2,2:4:70.27:101,0,70 0/0:2,0:2:3.01:0,3,79 0/1:4,0:4:24.94:25,0,101 1/1:1,2:3:6.02:110,6,0 1/1:2,2:4:9.02:138,9,0 0/1:3,3:6:99:148,0,220 0/1:5,3:8:99:200,0,217 0/1:2,2:4:70.27:101,0,70 0/1:2,0:2:41.22:41,0,73 1/1:1,2:3:6.02:110,6,0 0/1:2,1:3:24.97:93,0,25 0/1:2,2:4:70.96:101,0,71 1/1:2,3:5:15.05:248,15,0 1/1:2,1:3:3.01:55,3,0 0/0:1,0:1:3.01:0,3,79 0/1:4,1:5:27.65:49,0,28 1/1:2,2:4:6.02:110,6,0 1/1:0,3:3:9.03:166,9,0 1/1:4,6:10:21.07:379,21,0 1/1:0,2:2:3.01:55,3,0 0/1:2,1:3:46.19:46,0,150 0/0:4,0:4:12.04:0,12,317 ./. ./. 0/0:5,0:5:9.03:0,9,238 0/0:7,0:7:18.06:0,18,435 0/1:10,0:10:26.17:26,0,315 1/1:5,11:16:30.10:552,30,0 0/1:9,4:13:99:246,0,275 0/0:15,0:15:36.12:0,36,886 1/1:6,6:12:24.08:399,24,0 1/1:5,8:13:27.09:489,27,0 0/1:7,3:10:99:142,0,283 1/1:2,8:10:24.08:442,24,0 0/1:18,4:22:99:419,0,351 0/0:2,0:2:6.02:0,6,159 1/1:0,3:3:9.03:166,9,0 0/0:7,0:7:6.02:0,6,159 0/0:4,0:4:12.04:0,12,316 1/1:1,8:9:27.09:497,27,0 1/1:1,5:6:15.05:276,15,0 1/1:3,11:14:33.11:607,33,0 1/1:2,8:10:24.08:441,24,0 1/1:4,4:8:15.05:276,15,0 0/1:7,6:13:99:350,0,360 0/1:6,6:12:99:301,0,287 1/1:5,2:7:9.03:144,9,0 0/0:5,0:5:15.05:0,15,382 -chr1 900723 . T G 285.98 . AC=14;AF=0.1228;AN=114;BaseQRankSum=-3.773;DP=321;Dels=0.00;FS=2.147;HRun=0;HaplotypeScore=11.3195;InbreedingCoeff=-0.1788;MQ=46.06;MQ0=0;MQRankSum=4.705;QD=2.95;ReadPosRankSum=-6.059;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UTR_3_PRIME(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|11),UTR_3_PRIME(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|12);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187961|KLHL17|ENST00000338591|12/12|||-/642|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,33 0/0:7,0:7:21.06:0,21,238 0/0:6,0:6:18.06:0,18,227 0/1:4,1:5:25.62:26,0,111 0/0:2,0:2:6.02:0,6,78 0/0:4,0:4:12.04:0,12,161 0/1:6,1:7:19.58:20,0,211 0/1:3,1:4:21.40:21,0,110 0/0:9,0:9:27.08:0,27,340 0/0:15,0:15:45.15:0,45,599 0/1:3,1:4:29.19:29,0,101 0/1:3,1:4:29.20:29,0,88 0/0:4,0:4:12.03:0,12,136 ./. 0/1:3,1:4:31.78:32,0,39 0/0:2,0:2:6.02:0,6,67 0/1:2,1:3:23.47:23,0,58 0/0:6,0:6:18.05:0,18,223 0/0:7,0:7:18.05:0,18,214 0/0:3,0:3:9.03:0,9,109 0/0:3,0:3:9.03:0,9,116 0/0:2,0:2:6.02:0,6,67 0/0:3,0:3:9.03:0,9,111 0/0:3,0:3:9.03:0,9,107 0/1:4,1:5:22.75:23,0,119 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,71 0/0:2,0:2:6.02:0,6,67 0/0:3,0:3:9.02:0,9,100 0/0:7,0:7:21.06:0,21,239 0/0:2,0:2:3.01:0,3,33 0/0:3,0:3:9.02:0,9,100 0/0:4,0:4:12.04:0,12,156 ./. ./. 0/0:3,0:3:9.03:0,9,120 0/0:6,0:6:18.04:0,18,226 0/0:7,0:7:21.07:0,21,270 0/1:12,1:13:7.71:8,0,271 0/0:10,0:10:30.09:0,30,355 0/0:12,0:12:36.11:0,36,462 0/1:6,2:8:51.54:52,0,167 0/0:9,0:9:27.08:0,27,306 0/0:9,0:9:24.07:0,24,276 0/0:8,0:8:24.07:0,24,266 0/1:10,6:16:99:141,0,319 0/0:3,0:3:9.03:0,9,110 0/0:3,0:3:9.02:0,9,100 0/0:2,0:2:6.02:0,6,75 0/0:4,0:4:12.02:0,12,136 0/1:8,1:9:10.72:11,0,240 0/0:5,0:5:15.04:0,15,167 0/0:11,0:11:33.09:0,33,364 0/0:8,0:8:24.06:0,24,265 0/0:5,0:5:15.04:0,15,169 0/1:11,1:12:1.69:2,0,369 0/0:10,0:10:27.08:0,27,324 0/1:2,1:3:28.77:29,0,58 0/0:5,0:5:15.05:0,15,196 -chr1 900730 . G A 7842.1 . AC=100;AF=0.8621;AN=116;BaseQRankSum=-0.675;DP=275;Dels=0.00;FS=1.534;HRun=0;HaplotypeScore=5.4770;InbreedingCoeff=0.2758;MQ=43.76;MQ0=0;MQRankSum=-4.770;QD=29.93;ReadPosRankSum=-1.794;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UTR_3_PRIME(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|11),UTR_3_PRIME(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|12);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187961|KLHL17|ENST00000338591|12/12|||-/642|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,2:2:6.01:64,6,0 1/1:0,9:9:27.08:316,27,0 1/1:0,5:5:12.04:149,12,0 1/1:0,4:4:9.02:103,9,0 1/1:0,2:2:6.02:81,6,0 1/1:0,3:3:9.03:122,9,0 1/1:0,2:2:6.02:75,6,0 0/0:2,0:2:6.02:0,6,81 1/1:0,7:7:21.06:256,21,0 0/1:6,4:10:99:134,0,210 1/1:0,3:3:9.03:109,9,0 1/1:0,3:3:9.01:91,9,0 1/1:0,3:3:9.03:104,9,0 1/1:0,1:1:3:29,3,0 1/1:0,2:2:3.01:38,3,0 1/1:0,2:2:6.02:67,6,0 1/1:0,2:2:6.02:67,6,0 1/1:0,6:6:18.05:222,18,0 1/1:0,7:7:18.05:215,18,0 1/1:0,3:3:9.03:109,9,0 0/1:2,1:3:28.77:29,0,65 1/1:1,2:3:6.02:67,6,0 1/1:0,2:2:6.02:71,6,0 1/1:0,2:2:6.02:67,6,0 1/1:0,4:4:12.03:134,12,0 1/1:0,1:1:3.01:33,3,0 ./. 1/1:0,1:1:3.01:33,3,0 1/1:0,3:3:9.03:107,9,0 1/1:0,3:3:9.02:100,9,0 1/1:0,7:7:18.05:203,18,0 1/1:1,1:2:3.01:33,3,0 1/1:0,3:3:9.03:103,9,0 0/0:4,0:4:12.04:0,12,163 0/0:1,0:1:3.01:0,3,39 ./. 0/0:2,0:2:6.02:0,6,81 1/1:0,6:6:18.05:222,18,0 1/1:0,3:3:9.03:122,9,0 1/1:0,12:12:33.08:356,33,0 1/1:0,6:6:18.05:201,18,0 0/1:5,5:10:99:162,0,172 1/1:0,6:6:18.05:201,18,0 1/1:0,9:9:27.07:301,27,0 0/1:4,4:8:99:106,0,121 1/1:0,8:8:24.07:267,24,0 1/1:1,11:12:30.09:358,30,0 0/0:3,0:3:9.02:0,9,103 1/1:0,3:3:9.02:100,9,0 1/1:0,2:2:6.02:76,6,0 0/1:1,2:3:31.63:54,0,32 1/1:0,8:8:24.07:267,24,0 1/1:0,5:5:15.04:167,15,0 1/1:0,12:12:36.08:395,36,0 1/1:0,8:8:21.06:234,21,0 1/1:0,5:5:15.04:172,15,0 0/1:4,6:10:99:171,0,134 1/1:0,10:10:30.09:359,30,0 1/1:0,2:2:6.02:67,6,0 1/1:0,4:4:12.04:155,12,0 -chr1 900972 . T G 837.46 . AC=38;AF=0.950;AN=40;BaseQRankSum=1.091;DP=28;Dels=0.00;FS=5.863;HRun=1;HaplotypeScore=0.0000;InbreedingCoeff=-0.0011;MQ=56.62;MQ0=0;MQRankSum=1.091;QD=32.21;ReadPosRankSum=1.348;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UTR_3_PRIME(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|11),UTR_3_PRIME(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|12);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187961|KLHL17|ENST00000338591|12/12|||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:27,3,0 1/1:0,2:2:6.02:73,6,0 1/1:0,2:2:6.02:81,6,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:31,3,0 ./. ./. 1/1:0,1:1:3.01:30,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:3.01:45,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. 1/1:0,3:3:6.02:78,6,0 ./. ./. ./. 1/1:0,2:2:6.02:78,6,0 ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 1/1:0,2:2:6.02:76,6,0 0/0:1,0:1:3.01:0,3,32 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:39,3,0 ./. 1/1:0,1:1:3.01:40,3,0 ./. 1/1:0,1:1:3.01:37,3,0 ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. -chr1 901023 . T C 668.0 . AC=30;AF=0.882;AN=34;BaseQRankSum=0.039;DP=25;Dels=0.00;FS=13.318;HRun=0;HaplotypeScore=0.1562;InbreedingCoeff=-0.0502;MQ=59.07;MQ0=0;MQRankSum=-1.123;QD=29.04;ReadPosRankSum=-2.053;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UTR_3_PRIME(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|11),UTR_3_PRIME(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|12);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187961|KLHL17|ENST00000338591|12/12|||-/642|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3.01:36,3,0 1/1:0,1:1:3.01:32,3,0 1/1:0,3:3:6.02:79,6,0 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. 1/1:0,2:2:6.02:78,6,0 0/1:1,1:2:33.99:34,0,35 1/1:0,1:1:3.01:40,3,0 ./. ./. 1/1:0,2:2:3.01:45,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:6.02:84,6,0 0/1:1,1:2:27.42:27,0,31 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 0/0:2,0:2:6.02:0,6,82 1/1:0,1:1:3.01:38,3,0 ./. ./. ./. ./. ./. ./. ./. ./. -chr1 901046 . ACC A 367.24 . AC=14;AF=0.368;AN=38;BaseQRankSum=3.349;DP=34;FS=3.319;HRun=4;HaplotypeScore=8.5629;InbreedingCoeff=0.2418;MQ=57.94;MQ0=0;MQRankSum=-0.562;QD=26.23;ReadPosRankSum=0.832;EFF=DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UTR_3_PRIME(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|11),UTR_3_PRIME(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|12);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,3_prime_UTR_variant&feature_truncation|||ENSG00000187961|KLHL17|ENST00000338591|12/12|||-/642|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,112 0/0:2,0:2:6.02:0,6,112 1/1:0,2:2:6.02:88,6,0 0/1:1,2:3:47.21:79,0,47 1/1:1,1:2:3.01:44,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,56 0/1:1,2:3:47.16:79,0,47 0/0:2,0:2:3.01:0,3,39 1/1:0,1:1:3.01:44,3,0 ./. ./. 1/1:0,1:1:3.01:44,3,0 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,55 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,56 ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,112 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:44,3,0 0/0:1,1:2:3.01:0,3,56 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:44,3,0 0/0:3,0:3:9.03:0,9,169 0/0:1,0:1:3.01:0,3,56 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,56 ./. -chr1 901460 . C T 32.18 . AC=2;AF=0.045;AN=44;BaseQRankSum=0.046;DP=29;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0879;InbreedingCoeff=-0.0076;MQ=59.20;MQ0=0;MQRankSum=0.231;QD=16.09;ReadPosRankSum=-1.435;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:2:3.01:0,3,36 0/0:3,0:3:6.02:0,6,75 0/0:1,0:1:3.01:0,3,38 0/0:2,0:2:3.01:0,3,38 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,30 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,75 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,40 ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:6.02:79,6,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 0/0:1,0:1:3.01:0,3,33 -chr1 901559 . G A 1182.94 . AC=46;AF=0.920;AN=50;BaseQRankSum=0.433;DP=38;Dels=0.00;FS=2.501;HRun=0;HaplotypeScore=0.1286;InbreedingCoeff=-0.0789;MQ=56.89;MQ0=0;MQRankSum=-0.974;QD=31.97;ReadPosRankSum=-0.704;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3.01:31,3,0 1/1:0,2:2:6.02:77,6,0 ./. 1/1:0,1:1:3.01:32,3,0 ./. 1/1:0,2:2:6.02:82,6,0 1/1:0,2:2:6.01:62,6,0 ./. 1/1:0,1:1:3.01:37,3,0 0/1:1,1:2:30.96:35,0,31 1/1:0,1:1:3.01:33,3,0 ./. ./. 1/1:0,1:1:3.01:41,3,0 0/1:1,2:3:29.55:74,0,30 ./. 1/1:0,2:2:6.02:70,6,0 1/1:0,2:2:6.02:76,6,0 ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 1/1:0,2:2:6.02:78,6,0 ./. ./. 1/1:0,1:1:3.01:40,3,0 0/0:1,0:1:3.01:0,3,40 ./. 1/1:0,1:1:3:26,3,0 ./. ./. 1/1:0,1:1:3.01:39,3,0 1/1:0,4:4:12.04:156,12,0 1/1:0,1:1:3.01:42,3,0 ./. 1/1:0,1:1:3.01:40,3,0 ./. 1/1:0,2:2:3.01:45,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. 1/1:0,1:1:2.99:24,3,0 ./. -chr1 901607 . C G 1775.67 . AC=57;AF=0.983;AN=58;BaseQRankSum=-0.817;DP=56;Dels=0.00;FS=0.000;HRun=6;HaplotypeScore=0.0000;InbreedingCoeff=-0.1683;MQ=56.62;MQ0=0;MQRankSum=-0.443;QD=32.28;ReadPosRankSum=-0.303;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:35,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:41,3,0 ./. ./. 1/1:0,1:1:3.01:41,3,0 0/1:2,2:4:54.83:55,0,69 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:80,6,0 1/1:0,2:2:6.02:80,6,0 1/1:0,2:2:6.02:72,6,0 1/1:0,3:3:9.03:119,9,0 ./. 1/1:0,1:1:3.01:37,3,0 1/1:0,3:3:9.03:125,9,0 1/1:0,2:2:3.01:45,3,0 ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 ./. ./. ./. 1/1:0,2:2:3.01:37,3,0 ./. 1/1:0,3:3:3.01:45,3,0 ./. ./. ./. 1/1:0,5:5:12.04:156,12,0 1/1:0,3:3:9.03:116,9,0 ./. ./. 1/1:0,2:2:6.02:81,6,0 1/1:0,2:2:6.02:75,6,0 ./. ./. 1/1:0,2:2:6.02:77,6,0 ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,4:4:9.03:126,9,0 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. 1/1:0,1:1:3.01:39,3,0 1/1:0,1:1:3.01:40,3,0 -chr1 901652 . A G 2979.53 . AC=72;AF=1.000;AN=72;DP=87;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0518;InbreedingCoeff=-0.1163;MQ=57.30;MQ0=0;QD=34.65;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,2:2:6.02:65,6,0 1/1:0,5:5:15.04:175,15,0 ./. 1/1:0,2:2:3.01:33,3,0 1/1:0,3:3:6.02:74,6,0 1/1:0,1:1:3.01:41,3,0 1/1:0,3:3:9.03:114,9,0 ./. 1/1:0,3:3:9.03:122,9,0 1/1:0,2:2:6.02:81,6,0 1/1:0,3:3:9.03:107,9,0 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:79,6,0 1/1:0,2:2:6:61,6,0 1/1:0,5:5:15.05:198,15,0 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:81,6,0 1/1:0,4:4:9.03:121,9,0 1/1:0,3:3:6.02:83,6,0 ./. ./. 1/1:0,1:1:3.01:35,3,0 1/1:0,2:2:6.02:77,6,0 1/1:0,4:4:12.04:155,12,0 1/1:0,2:2:6.02:80,6,0 ./. 1/1:0,1:1:3.01:41,3,0 ./. 1/1:0,3:3:6.01:73,6,0 ./. 1/1:0,1:1:3.01:38,3,0 ./. 1/1:0,4:4:12.04:154,12,0 1/1:0,2:2:6.02:73,6,0 1/1:0,1:1:3.01:40,3,0 1/1:0,1:1:3.01:37,3,0 1/1:0,3:3:9.03:114,9,0 1/1:0,3:3:9.03:108,9,0 ./. ./. 1/1:0,4:4:9.03:121,9,0 ./. ./. ./. ./. ./. 1/1:0,6:6:15.05:207,15,0 ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:34,3,0 ./. ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:39,3,0 -chr1 901806 . G C 1993.1 . AC=13;AF=0.1204;AN=108;BaseQRankSum=0.578;DP=624;Dels=0.00;FS=2.492;HRun=3;HaplotypeScore=0.2501;InbreedingCoeff=0.2481;MQ=58.77;MQ0=0;MQRankSum=1.452;QD=19.16;ReadPosRankSum=0.786;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|),UPSTREAM(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|),UPSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:4,0:4:12.04:0,12,149 0/0:3,0:3:6.02:0,6,69 0/0:7,0:7:21.07:0,21,278 0/0:12,0:12:30.10:0,30,390 0/0:16,0:16:42.13:0,42,531 0/0:19,0:19:54.17:0,54,697 0/1:5,3:8:96.18:96,0,166 0/0:22,0:22:66.20:0,66,843 0/0:24,0:24:69.22:0,69,894 0/0:8,0:8:21.06:0,21,255 0/0:11,0:11:33.11:0,33,434 0/0:17,0:17:51.16:0,51,643 0/0:17,0:17:48.12:0,48,604 0/0:19,0:19:54.16:0,54,669 0/0:11,0:11:30.09:0,30,373 0/0:21,0:21:54.16:0,54,671 0/0:21,0:21:60.19:0,60,782 0/0:23,0:23:60.18:0,60,773 0/0:14,0:14:39.13:0,39,521 0/1:12,7:19:99:163,0,393 0/0:20,0:20:54.18:0,54,727 0/0:20,0:20:54.17:0,54,712 0/0:15,0:15:45.14:0,45,592 0/0:14,0:14:42.13:0,42,541 0/0:14,0:14:42.13:0,42,539 1/1:0,16:16:48.15:618,48,0 0/1:8,6:14:99:160,0,204 0/0:21,0:21:57.18:0,57,743 0/0:14,0:14:39.12:0,39,504 0/0:20,0:20:57.18:0,57,719 0/0:22,0:22:63.19:0,63,817 0/0:13,0:13:36.11:0,36,448 1/1:0,14:14:39.13:533,39,0 0/1:4,6:10:99:162,0,125 0/0:15,0:15:42.12:0,42,541 0/1:6,10:16:99:314,0,189 0/0:24,0:24:69.21:0,69,893 ./. ./. 0/0:5,0:5:9.03:0,9,121 0/0:3,0:3:6.02:0,6,86 0/0:3,0:3:9.03:0,9,117 0/0:1,0:1:3.01:0,3,36 1/1:0,2:2:6.01:64,6,0 0/0:1,0:1:3.01:0,3,42 ./. 0/1:1,1:2:23.61:27,0,24 ./. 0/1:2,1:3:27.10:27,0,65 0/0:4,0:4:9.02:0,9,103 0/0:3,0:3:9.03:0,9,122 0/0:3,1:4:9:0,9,92 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.04:0,12,153 0/0:2,0:2:6.02:0,6,78 ./. 0/0:2,0:2:6.02:0,6,77 0/0:2,0:2:6.02:0,6,67 0/0:2,0:2:6.02:0,6,81 -chr1 901919 . A C 43.36 . AC=5;AF=0.0417;AN=120;BaseQRankSum=-7.616;DP=1450;Dels=0.00;FS=55.854;HRun=1;HaplotypeScore=0.9087;InbreedingCoeff=-0.0627;MQ=58.76;MQ0=0;MQRankSum=-1.305;QD=0.46;ReadPosRankSum=-4.128;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N3T|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N3T|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aCc|N3T|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,missense_variant|aAc/aCc|N/T|ENSG00000187583|PLEKHN1|ENST00000379409|1/15|possibly_damaging(0.471)|deleterious(0.01)|3/663|protein_coding|1,missense_variant|aAc/aCc|N/T|ENSG00000187583|PLEKHN1|ENST00000379407|1/15|benign(0.331)|deleterious(0.01)|3/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,missense_variant|aAc/aCc|N/T|ENSG00000187583|PLEKHN1|ENST00000379410|1/16|benign(0.444)|deleterious(0.01)|3/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,1:6:12.04:0,12,148 0/1:8,1:9:9.36:9,0,230 0/1:4,1:5:14.68:15,0,55 0/0:4,1:5:9.03:0,9,120 0/0:22,3:25:36.50:0,36,739 0/0:17,9:26:23.43:0,23,547 0/1:27,14:41:40.81:41,0,839 0/1:17,4:21:12.13:12,0,466 0/0:45,9:54:74.99:0,75,1476 0/0:32,10:42:47.91:0,48,1148 0/0:16,2:18:45.14:0,45,583 0/1:13,4:18:60.40:60,0,366 0/0:20,7:27:0.03:0,0,572 0/0:39,0:39:87.27:0,87,1141 0/0:57,0:58:99:0,123,1625 0/0:24,0:24:57.18:0,57,749 0/0:38,1:40:87.28:0,87,1166 0/0:54,0:54:99:0,126,1640 0/0:45,0:45:99:0,102,1294 0/0:34,1:35:81.26:0,81,1064 0/0:38,1:39:87.28:0,87,1141 0/0:40,0:40:99:0,108,1395 0/0:34,0:34:78.23:0,78,1005 0/0:50,1:51:99:0,114,1419 0/0:45,0:45:99:0,114,1466 0/0:37,1:38:90.27:0,90,1156 0/0:44,0:44:99:0,105,1382 0/0:28,0:28:63.20:0,63,842 0/0:40,0:40:84.22:0,84,1049 0/0:58,0:58:99:0,129,1761 0/0:39,0:39:99:0,102,1314 0/0:35,0:35:90.27:0,90,1135 0/0:43,1:44:99:0,102,1316 0/0:39,0:39:90.27:0,90,1162 0/0:28,0:28:72.21:0,72,899 0/0:38,0:38:84.24:0,84,1111 0/0:31,0:31:87.26:0,87,1086 0/0:53,1:54:99:0,117,1546 0/0:4,0:4:9.03:0,9,122 0/0:4,0:4:9.03:0,9,122 0/0:7,0:7:15.04:0,15,178 0/0:5,0:5:12.03:0,12,145 0/0:8,0:8:24.07:0,24,292 0/0:6,0:6:9:0,9,111 0/0:2,0:2:6.02:0,6,75 0/0:6,0:6:15.05:0,15,199 0/0:5,0:5:15.04:0,15,187 0/0:1,0:1:3.01:0,3,36 0/0:7,0:7:15.05:0,15,196 0/0:12,1:13:27.09:0,27,352 0/0:10,0:10:27.08:0,27,338 0/0:9,0:9:18.06:0,18,233 0/0:6,0:6:15.05:0,15,191 0/0:9,0:9:24.08:0,24,314 0/0:5,0:5:12.04:0,12,163 0/0:8,0:8:18.06:0,18,240 0/0:3,0:3:9.03:0,9,123 0/0:3,0:3:9:0,9,101 0/0:3,0:3:6.02:0,6,72 0/0:8,1:9:21.06:0,21,265 -chr1 902043 . G A 169.05 . AC=2;AF=0.0172;AN=116;BaseQRankSum=-1.369;DP=777;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0432;InbreedingCoeff=-0.0431;MQ=58.28;MQ0=0;MQRankSum=0.826;QD=5.45;ReadPosRankSum=-0.446;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|1),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|1),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|1),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:6,0:6:3:0,3,29 ./. 0/0:5,0:5:3.01:0,3,40 0/0:14,0:14:39.12:0,39,504 0/0:19,0:19:45.12:0,45,535 0/0:16,0:16:30.02:0,30,307 0/0:14,0:14:36.09:0,36,427 0/0:40,0:40:96.24:0,96,1154 0/0:35,0:35:75.20:0,75,901 0/0:21,0:21:48.10:0,48,558 0/0:14,0:14:30.02:0,30,325 0/0:19,0:19:33.06:0,33,384 0/1:11,2:13:8.48:8,0,313 0/0:30,0:30:69.20:0,69,870 0/0:15,0:15:36.11:0,36,465 0/0:18,0:18:39.12:0,39,502 0/0:20,0:20:51.15:0,51,654 0/0:15,0:15:39.11:0,39,483 0/0:18,0:19:39.08:0,39,473 0/0:21,0:21:51.15:0,51,656 0/0:32,0:32:75.24:0,75,982 0/0:17,0:17:42.11:0,42,509 0/0:16,2:19:3.37:0,3,500 0/0:19,0:19:48.12:0,48,573 0/0:11,0:11:27.08:0,27,341 0/1:9,8:18:99:216,0,240 0/0:9,0:9:24.08:0,24,312 0/0:15,0:15:45.12:0,45,550 0/0:18,0:18:36.10:0,36,446 0/0:16,0:18:36.12:0,36,467 0/0:15,0:15:33.11:0,33,442 0/0:14,0:15:30.10:0,30,404 0/0:17,0:17:42.14:0,42,567 0/0:14,0:14:33.10:0,33,423 0/0:17,0:17:39.10:0,39,467 0/0:21,0:21:45.10:0,45,559 0/0:29,0:29:75.21:0,75,942 0/0:3,0:3:9.03:0,9,113 0/0:7,0:8:12.03:0,12,151 0/0:10,0:10:21.06:0,21,260 0/0:4,0:4:9.03:0,9,125 0/0:6,0:6:15.05:0,15,199 0/0:2,0:2:3:0,3,27 0/0:5,0:5:15.04:0,15,178 0/0:3,0:3:9.03:0,9,107 0/0:11,0:11:24.08:0,24,314 0/0:4,0:4:9.03:0,9,111 0/0:4,0:5:9.02:0,9,101 0/0:8,0:8:21.07:0,21,274 0/0:4,0:6:9.03:0,9,118 0/0:8,0:8:18.04:0,18,221 0/0:5,0:5:12.03:0,12,137 0/0:6,0:6:15.05:0,15,191 0/0:4,0:4:9.03:0,9,117 0/0:7,0:7:21.05:0,21,246 0/0:3,0:3:9.03:0,9,116 0/0:5,0:5:9.01:0,9,99 0/0:1,0:1:3.01:0,3,37 0/0:3,0:3:9.03:0,9,122 -chr1 902069 . T C 177.69 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.199;DP=717;Dels=0.00;FS=3.490;HRun=4;HaplotypeScore=0.5354;InbreedingCoeff=-0.0340;MQ=58.23;MQ0=0;MQRankSum=0.502;QD=7.11;ReadPosRankSum=0.208;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|1),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|1),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|1),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,27 0/0:6,0:6:15.05:0,15,184 0/0:3,0:3:9.03:0,9,117 0/0:5,0:5:15.04:0,15,181 0/0:14,0:14:42.14:0,42,557 0/0:16,0:16:48.16:0,48,633 0/0:18,0:18:54.17:0,54,706 0/1:9,6:15:99:191,0,306 0/0:34,0:34:99:0,102,1341 0/0:31,0:31:90.29:0,90,1169 0/0:19,0:19:54.17:0,54,713 0/0:14,0:14:42.13:0,42,536 0/0:14,0:14:39.12:0,39,492 0/0:11,0:11:30.07:0,30,387 0/0:25,0:25:69.22:0,69,889 0/0:13,0:13:33.10:0,33,437 0/0:14,0:14:42.14:0,42,543 0/0:18,0:18:51.16:0,51,657 0/0:16,0:16:39.13:0,39,506 0/0:11,0:11:30.10:0,30,386 0/0:14,0:14:39.12:0,39,505 0/0:24,0:24:69.22:0,69,894 0/0:17,0:17:48.15:0,48,625 0/0:19,0:19:45.13:0,45,567 0/0:15,0:15:42.13:0,42,535 0/0:11,0:11:30.09:0,30,389 0/0:11,0:11:27.09:0,27,347 0/0:11,0:11:30.10:0,30,404 0/0:17,0:17:45.13:0,45,548 0/0:16,0:16:42.13:0,42,520 0/0:18,0:18:48.15:0,48,600 0/0:11,0:11:27.09:0,27,375 0/0:14,0:14:42.11:0,42,530 0/0:15,0:15:39.13:0,39,520 0/0:15,0:15:39.10:0,39,498 0/0:15,0:15:42.14:0,42,555 0/0:16,0:16:42.11:0,42,541 0/0:24,0:24:69.21:0,69,887 0/0:5,0:5:15.05:0,15,199 0/0:7,1:8:18.06:0,18,231 0/0:9,1:10:24.07:0,24,285 0/0:2,0:2:6.02:0,6,80 0/0:6,0:6:18.05:0,18,216 0/0:2,0:2:6.01:0,6,65 0/0:4,1:5:9.03:0,9,111 0/0:4,0:4:12.04:0,12,157 0/0:10,2:12:30.09:0,30,379 0/0:6,0:6:12.04:0,12,156 0/0:6,1:7:15.05:0,15,193 0/1:7,3:10:51.59:52,0,205 0/0:6,0:6:15.05:0,15,188 0/0:9,0:9:15.05:0,15,195 0/0:10,1:11:30.09:0,30,374 0/0:7,0:7:15.05:0,15,203 0/0:4,0:4:12.04:0,12,157 0/0:8,0:8:18.06:0,18,242 0/0:2,1:3:6.02:0,6,84 0/0:6,0:6:15.01:0,15,170 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.04:0,12,147 -chr1 902108 . C T 116.44 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.766;DP=558;Dels=0.00;FS=3.848;HRun=0;HaplotypeScore=0.5318;InbreedingCoeff=-0.0325;MQ=58.52;MQ0=0;MQRankSum=-0.417;QD=8.96;ReadPosRankSum=0.186;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A36|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A36|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A36|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,synonymous_variant|gcC/gcT|A|ENSG00000187583|PLEKHN1|ENST00000379409|2/15|||36/663|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000187583|PLEKHN1|ENST00000379407|2/15|||36/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,synonymous_variant|gcC/gcT|A|ENSG00000187583|PLEKHN1|ENST00000379410|2/16|||36/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3.01:0,3,39 0/0:2,0:2:3.01:0,3,39 0/0:3,0:3:9.03:0,9,116 0/0:3,0:4:9.01:0,9,92 0/0:10,0:10:27.07:0,27,348 0/0:8,0:8:24.08:0,24,318 0/0:6,0:6:15.04:0,15,184 0/0:10,0:10:30.10:0,30,393 0/0:10,0:10:27.09:0,27,352 0/0:5,0:5:15.04:0,15,183 0/0:6,0:6:18.06:0,18,232 0/0:6,0:6:18.06:0,18,223 0/0:5,0:5:12.04:0,12,145 0/0:10,0:10:27.09:0,27,362 0/0:23,0:23:54.14:0,54,650 0/0:8,0:8:12.04:0,12,165 0/0:11,0:11:30.10:0,30,388 0/0:17,0:17:48.14:0,48,605 0/0:10,0:10:27.09:0,27,343 0/0:11,0:11:33.11:0,33,432 0/0:12,0:12:33.10:0,33,431 0/0:19,0:19:48.15:0,48,640 0/0:12,0:12:30.10:0,30,403 0/0:16,0:16:33.09:0,33,413 0/0:15,0:15:33.10:0,33,414 0/0:10,0:10:24.06:0,24,293 0/0:9,0:9:24.06:0,24,294 0/1:6,7:13:99:164,0,133 0/0:17,0:17:30.07:0,30,357 0/0:12,0:12:21.04:0,21,245 0/0:16,0:16:45.14:0,45,575 0/0:8,0:8:18.05:0,18,231 0/0:16,0:16:42.14:0,42,554 0/0:18,0:18:42.14:0,42,550 0/0:10,0:10:24.07:0,24,303 0/0:11,0:11:33.08:0,33,387 0/0:14,0:14:39.12:0,39,514 0/0:26,0:26:63.19:0,63,814 0/0:4,0:4:9.03:0,9,125 0/0:7,0:7:18.05:0,18,226 0/0:7,0:7:12.04:0,12,148 0/0:4,0:4:12.03:0,12,138 0/0:5,0:5:12.04:0,12,149 0/0:3,0:3:6.02:0,6,81 0/0:3,0:3:6.02:0,6,74 0/0:5,0:5:15.04:0,15,175 0/0:14,0:14:36.11:0,36,442 0/0:3,0:3:6.02:0,6,81 0/0:6,0:6:15.04:0,15,166 0/0:13,0:13:27.08:0,27,334 0/0:10,0:10:18.06:0,18,222 0/0:9,0:9:21.07:0,21,279 0/0:7,0:7:21.06:0,21,248 0/0:6,0:7:12.04:0,12,169 0/0:2,0:2:6.01:0,6,70 0/0:10,0:10:24.07:0,24,298 0/0:6,0:6:15.04:0,15,189 0/0:7,0:7:15.05:0,15,194 0/0:2,0:2:6.02:0,6,83 0/0:3,0:3:9.02:0,9,96 -chr1 902128 . C T 375.73 . AC=3;AF=0.0254;AN=118;BaseQRankSum=-0.165;DP=545;Dels=0.00;FS=0.993;HRun=1;HaplotypeScore=0.3151;InbreedingCoeff=-0.0508;MQ=58.23;MQ0=0;MQRankSum=0.962;QD=11.39;ReadPosRankSum=-1.116;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A43V|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A43V|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A43V|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,missense_variant|gCt/gTt|A/V|ENSG00000187583|PLEKHN1|ENST00000379409|2/15|possibly_damaging(0.586)|deleterious(0.01)|43/663|protein_coding|1,missense_variant|gCt/gTt|A/V|ENSG00000187583|PLEKHN1|ENST00000379407|2/15|benign(0.209)|deleterious(0.01)|43/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,missense_variant|gCt/gTt|A/V|ENSG00000187583|PLEKHN1|ENST00000379410|2/16|benign(0.209)|deleterious(0.01)|43/611|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:4,0:4:12.04:0,12,150 0/0:3,0:3:3:0,3,26 0/0:4,0:4:12.03:0,12,147 0/0:8,0:8:18.06:0,18,231 0/0:7,0:7:15.05:0,15,201 0/0:6,0:6:15.03:0,15,171 0/0:5,0:5:12.04:0,12,153 0/0:13,0:13:27.08:0,27,346 0/0:8,0:8:15.05:0,15,191 0/0:5,0:5:6.02:0,6,79 0/0:3,0:4:9.03:0,9,122 0/0:4,0:4:6.01:0,6,66 0/0:14,0:14:36.10:0,36,458 0/0:18,0:18:51.16:0,51,650 0/0:8,0:8:18.05:0,18,228 0/0:9,0:9:27.09:0,27,349 0/0:15,0:15:42.13:0,42,533 0/0:9,0:9:24.07:0,24,303 0/0:11,0:11:30.10:0,30,396 0/0:11,0:11:27.09:0,27,364 0/0:15,0:15:39.13:0,39,514 0/0:11,0:11:24.08:0,24,318 0/0:15,0:15:30.08:0,30,368 0/0:17,0:17:45.14:0,45,578 0/0:8,0:8:21.06:0,21,267 0/1:5,2:7:55.52:56,0,163 0/0:15,0:15:36.12:0,36,475 0/0:17,0:17:42.14:0,42,559 0/0:13,0:13:30.09:0,30,384 0/0:21,0:21:57.17:0,57,742 0/0:6,0:6:18.06:0,18,231 0/0:14,0:14:39.13:0,39,507 0/0:18,0:18:39.10:0,39,495 0/1:6,4:10:96.13:96,0,164 0/0:7,0:7:21.06:0,21,259 0/1:4,12:16:99:303,0,118 0/0:28,0:28:66.20:0,66,851 0/0:3,0:3:6.02:0,6,83 0/0:6,0:6:18.05:0,18,219 0/0:7,0:7:18.06:0,18,228 0/0:3,0:3:9.02:0,9,98 0/0:3,0:3:9.02:0,9,113 0/0:3,0:3:6.02:0,6,70 0/0:2,0:2:3.01:0,3,38 0/0:5,0:5:15.03:0,15,165 0/0:12,0:12:27.08:0,27,330 0/0:3,0:3:9.03:0,9,116 0/0:6,0:6:12.04:0,12,149 0/0:15,0:15:33.10:0,33,423 0/0:8,0:8:24.07:0,24,295 0/0:9,0:9:21.06:0,21,263 0/0:10,0:10:27.08:0,27,342 0/0:11,0:11:27.08:0,27,332 0/0:3,0:3:9.02:0,9,105 0/0:11,0:11:27.07:0,27,342 0/0:6,0:6:15.02:0,15,162 0/0:6,0:6:18.06:0,18,231 0/0:2,0:2:6.01:0,6,65 0/0:6,0:6:18.06:0,18,225 -chr1 902288 . G A 297.6 . AC=8;AF=0.083;AN=96;BaseQRankSum=-1.235;DP=169;Dels=0.00;FS=6.677;HRun=0;HaplotypeScore=0.1735;InbreedingCoeff=0.2484;MQ=58.34;MQ0=0;MQRankSum=1.682;QD=12.94;ReadPosRankSum=-1.820;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000463212|),DOWNSTREAM(MODIFIER|||||KLHL17|retained_intron|CODING|ENST00000481067|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|2),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|2),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|2),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000466300||||-/154|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000463212|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000481067|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:6.02:0,6,78 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.02:0,6,71 ./. ./. ./. ./. 0/0:4,0:4:12.04:0,12,152 1/1:0,4:5:12.04:152,12,0 0/0:2,0:2:6.02:0,6,81 0/0:2,0:2:6.02:0,6,77 0/0:2,0:2:3.01:0,3,39 0/0:4,0:4:12.04:0,12,159 0/0:5,0:5:9.03:0,9,118 0/0:1,0:1:3.01:0,3,38 0/0:2,0:2:6.02:0,6,77 0/0:3,0:3:9.03:0,9,112 0/0:3,0:3:9.03:0,9,114 0/0:3,0:3:9.03:0,9,119 0/0:2,0:2:6.02:0,6,71 0/1:3,2:5:59.66:60,0,99 1/1:0,3:3:9.03:111,9,0 0/0:2,0:2:6.02:0,6,76 0/0:5,0:5:15.05:0,15,193 0/0:4,0:4:12.04:0,12,154 ./. 0/0:1,0:1:3.01:0,3,32 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,42 0/0:5,0:5:12.04:0,12,155 0/0:2,0:2:3.01:0,3,41 0/0:3,0:3:6.02:0,6,80 ./. 0/0:5,0:5:12.04:0,12,160 0/0:2,0:2:6.02:0,6,76 0/0:6,0:6:15.05:0,15,189 0/0:6,0:6:18.06:0,18,239 ./. 0/0:2,0:2:6.02:0,6,80 0/0:5,0:5:12.04:0,12,164 0/0:2,0:2:6.02:0,6,76 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:9.03:0,9,118 0/0:10,0:10:24.07:0,24,305 ./. 0/0:7,0:7:21.07:0,21,262 0/0:4,0:4:12.04:0,12,154 0/1:5,1:6:19.74:20,0,175 0/0:4,0:4:12.03:0,12,137 0/0:3,0:3:9.03:0,9,111 1/1:1,3:4:6.02:73,6,0 ./. 0/0:3,0:3:9.02:0,9,107 ./. 0/0:4,0:5:9.03:0,9,120 0/0:5,0:5:12.03:0,12,136 0/0:2,0:2:6.02:0,6,82 -chr1 905130 . ATG A 1155.32 . AC=23;AF=0.442;AN=52;BaseQRankSum=1.417;DP=60;FS=3.885;HRun=0;HaplotypeScore=17.3266;InbreedingCoeff=0.3250;MQ=54.35;MQ0=0;MQRankSum=-1.757;QD=30.40;ReadPosRankSum=1.061;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|2),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|2),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|2),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL 1/1:2,7:9:21.07:292,21,0 1/1:0,6:6:18.06:258,18,0 0/1:3,1:4:30.53:31,0,153 0/0:2,0:2:6.02:0,6,101 0/0:1,0:1:3.01:0,3,50 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,55 ./. ./. ./. 0/0:1,0:1:3.01:0,3,55 0/0:1,0:1:3.01:0,3,55 ./. ./. 0/0:1,0:1:3.01:0,3,55 1/1:0,1:1:3.01:43,3,0 ./. ./. 1/1:0,3:3:9.03:129,9,0 ./. 1/1:0,2:2:6.02:86,6,0 ./. 1/1:0,1:1:3.01:43,3,0 ./. ./. ./. 1/1:0,1:1:3.01:43,3,0 0/1:1,3:4:43:116,0,43 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,31 ./. 0/0:2,0:2:3.48:0,3,56 ./. 1/1:0,3:3:9.03:129,9,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:43,3,0 ./. 0/0:2,0:2:3.01:0,3,55 ./. ./. 0/0:1,0:1:3.01:0,3,55 0/0:2,0:2:6.02:0,6,110 ./. ./. ./. ./. 0/1:1,1:2:36.99:37,0,49 0/0:2,0:2:6.02:0,6,110 ./. 1/1:0,1:1:3.01:43,3,0 0/0:4,0:4:12.04:0,12,220 -chr1 905158 . TGC T 181.75 . AC=10;AF=0.200;AN=50;BaseQRankSum=-3.797;DP=55;FS=1.587;HRun=0;HaplotypeScore=23.4217;InbreedingCoeff=0.1863;MQ=54.38;MQ0=0;MQRankSum=0.194;QD=12.98;ReadPosRankSum=-2.056;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|2),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|2),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|2),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:7.14:0,7,30 0/0:7,0:7:14.35:0,14,65 0/0:4,0:4:11.08:0,11,50 0/1:2,0:2:6.65:31,0,7 ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:43,3,0 ./. ./. ./. 0/0:1,0:1:2.50:0,2,9 1/1:0,1:1:3.01:43,3,0 ./. ./. 0/0:3,0:3:8.03:0,8,37 ./. 0/1:2,1:3:0.41:62,0,0 ./. 0/0:2,0:2:5.94:0,6,42 ./. ./. ./. 0/0:1,0:1:2.99:0,3,24 0/1:1,1:2:6.36:37,0,6 ./. 0/0:1,0:1:2.88:0,3,15 ./. ./. ./. 0/0:2,0:2:5.55:0,6,26 0/0:1,0:1:2.68:0,3,11 1/1:0,1:1:3.01:43,3,0 0/0:2,0:2:5.27:0,5,21 ./. ./. ./. ./. 0/0:1,0:1:2.74:0,3,12 ./. ./. ./. 0/0:2,0:2:5.92:0,6,38 0/0:1,0:1:3.01:0,3,58 0/0:2,0:2:2.13:0,2,10 ./. ./. ./. ./. 0/0:2,0:2:5.17:0,5,20 0/0:2,0:2:5.37:0,5,24 ./. 0/0:2,0:2:5.77:0,6,30 0/1:4,0:4:23.24:23,0,24 -chr1 905165 . A G 1906.87 . AC=48;AF=0.960;AN=50;BaseQRankSum=0.088;DP=59;Dels=0.00;FS=5.156;HRun=0;HaplotypeScore=0.3866;InbreedingCoeff=0.0421;MQ=56.05;MQ0=0;MQRankSum=1.086;QD=32.88;ReadPosRankSum=-1.380;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|2),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|2),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|2),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,4:4:12.04:144,12,0 1/1:0,7:7:21.06:246,21,0 1/1:0,6:6:18.06:230,18,0 1/1:0,3:3:9.03:119,9,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 1/1:0,1:1:3.01:33,3,0 ./. ./. 1/1:0,4:4:12.04:155,12,0 ./. 1/1:0,2:2:6.02:83,6,0 ./. 1/1:0,2:2:3.01:45,3,0 ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:73,6,0 ./. 1/1:0,1:1:3.01:40,3,0 ./. ./. ./. 1/1:0,2:2:3.01:45,3,0 1/1:0,2:2:3.01:45,3,0 1/1:0,1:1:3.01:36,3,0 1/1:0,3:3:6.02:83,6,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. 1/1:0,2:2:3.01:45,3,0 0/0:1,0:1:3.01:0,3,40 1/1:0,2:2:6.02:78,6,0 ./. ./. ./. ./. 1/1:0,2:2:6.02:82,6,0 1/1:0,2:2:6.02:84,6,0 ./. 1/1:0,2:2:3.01:45,3,0 1/1:0,4:4:6.02:90,6,0 -chr1 905894 . C T 1520.95 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-2.494;DP=3276;Dels=0.00;FS=2.372;HRun=0;HaplotypeScore=1.4299;InbreedingCoeff=-0.0172;MQ=58.58;MQ0=0;MQRankSum=0.861;QD=13.46;ReadPosRankSum=-0.683;EFF=DOWNSTREAM(MODIFIER||||412|KLHL17|protein_coding|CODING|ENST00000455747|),DOWNSTREAM(MODIFIER||||642|KLHL17|protein_coding|CODING|ENST00000338591|),DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|3),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|3),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|3),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|),UPSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1,downstream_gene_variant|||ENSG00000187961|KLHL17|ENST00000338591||||-/642|protein_coding|1 GT:AD:DP:GQ:PL 0/0:11,0:11:30.10:0,30,386 0/0:13,0:13:36.11:0,36,445 0/0:13,0:13:39.12:0,39,500 0/0:5,0:5:15.05:0,15,196 0/0:37,0:37:99:0,111,1491 0/0:28,0:28:81.27:0,81,1091 0/0:57,0:57:99:0,166,2214 0/0:35,0:35:99:0,102,1338 0/0:67,0:67:99:0,202,2663 0/0:61,0:61:99:0,181,2363 0/0:30,0:30:87.29:0,87,1166 0/0:26,0:26:75.24:0,75,994 0/0:38,0:38:99:0,111,1436 0/0:52,0:52:99:0,141,1851 0/0:68,0:69:99:0,184,2385 0/0:46,0:46:99:0,117,1553 0/0:72,0:74:99:0,178,2326 0/0:69,0:70:99:0,172,2214 0/0:68,1:69:99:0,151,2407 0/0:55,0:55:99:0,141,1868 0/1:27,26:53:99:689,0,844 0/0:67,0:67:99:0,163,2178 0/0:49,0:49:99:0,123,1629 0/0:55,0:55:99:0,147,1941 0/0:73,0:73:99:0,184,2404 0/0:57,0:57:99:0,144,1928 0/0:45,0:46:99:0,111,1470 0/0:47,0:47:99:0,123,1614 0/0:77,0:77:99:0,199,2522 0/0:49,0:49:99:0,117,1554 0/1:28,32:60:99:897,0,898 0/0:41,0:41:99:0,117,1532 0/0:62,1:63:99:0,122,2059 0/0:58,0:58:99:0,156,2056 0/0:64,0:64:99:0,172,2270 0/0:54,0:54:99:0,138,1793 0/0:76,0:76:99:0,214,2785 0/0:74,0:74:99:0,202,2634 0/0:48,0:48:99:0,129,1672 0/0:86,0:87:99:0,235,3009 0/0:66,0:66:99:0,181,2297 0/0:56,0:56:99:0,162,2091 0/0:59,0:59:99:0,153,2019 0/0:39,0:39:99:0,111,1447 0/0:58,0:58:99:0,153,1975 0/0:60,0:60:99:0,172,2222 0/0:102,0:102:99:0,289,3665 0/0:39,0:39:99:0,105,1316 0/0:52,0:52:99:0,147,1935 0/0:104,0:104:99:0,295,3746 0/0:90,0:90:99:0,250,3209 0/0:74,0:74:99:0,211,2677 0/0:69,0:69:99:0,190,2432 0/0:57,0:57:99:0,163,2134 0/0:63,0:63:99:0,184,2345 0/0:55,0:55:99:0,147,1901 0/0:41,0:41:99:0,114,1494 0/0:51,0:51:99:0,144,1879 0/0:40,0:40:99:0,108,1442 0/0:45,0:45:99:0,132,1643 -chr1 906272 . A C 2509.21 . AC=19;AF=0.1583;AN=120;BaseQRankSum=3.923;DP=937;Dels=0.00;FS=33.565;HRun=4;HaplotypeScore=0.7062;InbreedingCoeff=0.0234;MQ=58.16;MQ0=0;MQRankSum=0.166;QD=10.72;ReadPosRankSum=0.823;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),EXON(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|1),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A166|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A166|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A206|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,synonymous_variant|gcA/gcC|A|ENSG00000187583|PLEKHN1|ENST00000379409|5/15|||206/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|1/3||||retained_intron|1,synonymous_variant|gcA/gcC|A|ENSG00000187583|PLEKHN1|ENST00000379407|6/15|||166/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|gcA/gcC|A|ENSG00000187583|PLEKHN1|ENST00000379410|6/16|||166/611|protein_coding|1 GT:AD:DP:GQ:PL 0/1:2,2:4:27.42:29,0,27 0/0:3,1:4:6.01:0,6,61 0/1:3,1:4:19.67:31,0,20 1/1:3,1:4:3.01:32,3,0 0/1:3,3:6:64.76:99,0,65 0/0:18,0:18:48.15:0,48,615 0/0:31,1:32:75.15:0,75,862 0/0:13,2:16:33.11:0,33,435 0/0:24,2:26:60.15:0,60,729 0/0:28,1:29:69.17:0,69,826 0/0:16,1:17:45.10:0,45,520 0/0:16,1:17:36.08:0,36,427 0/0:17,1:18:42.11:0,42,516 0/0:15,0:15:39.09:0,39,459 0/0:10,0:10:18.02:0,18,199 0/0:13,1:14:27.07:0,27,332 0/0:12,1:13:6.42:0,6,366 0/0:24,0:24:57.10:0,57,672 0/0:26,2:28:60.13:0,60,714 0/0:16,1:17:36.08:0,36,447 0/0:22,2:25:48.11:0,48,576 0/0:26,1:27:54.11:0,54,651 0/1:11,9:20:99:258,0,215 0/1:14,5:19:0.52:1,0,284 0/0:19,0:19:36.10:0,36,442 0/0:16,3:19:39.09:0,39,455 0/1:10,9:19:99:243,0,218 0/1:7,3:10:9.65:10,0,140 0/0:20,0:20:36.12:0,36,483 0/1:15,14:29:99:434,0,368 0/0:28,3:31:60.15:0,60,732 0/0:16,0:17:36.08:0,36,416 0/0:18,0:18:42.11:0,42,494 0/0:17,1:19:33.06:0,33,404 0/1:10,7:17:99:235,0,192 0/0:22,1:23:45.13:0,45,560 0/1:13,13:27:99:298,0,253 0/0:26,2:28:57.15:0,57,667 0/0:6,2:9:15.04:0,15,168 0/1:13,1:16:0.64:1,0,233 0/0:13,0:13:30.09:0,30,369 0/0:2,0:2:3:0,3,29 0/0:9,1:10:15.01:0,15,138 0/0:10,1:11:24.05:0,24,274 0/1:5,4:10:98.98:99,0,118 0/0:10,0:10:24.04:0,24,259 0/0:18,1:19:48.11:0,48,530 0/1:2,3:5:49.22:106,0,49 0/0:10,1:11:24.06:0,24,273 0/1:8,11:19:99:334,0,105 0/0:22,2:24:39.09:0,39,454 0/0:10,0:10:27.03:0,27,291 1/1:0,13:13:30.10:400,30,0 0/1:8,4:12:91.87:92,0,165 0/0:5,0:7:9.02:0,9,106 0/0:7,1:8:15.02:0,15,170 0/0:7,1:8:15.05:0,15,192 0/0:7,0:7:12.01:0,12,117 0/0:7,1:8:15.04:0,15,177 0/0:2,0:2:6.02:0,6,70 -chr1 906302 . C T 240.96 . AC=1;AF=0.0085;AN=118;BaseQRankSum=-1.006;DP=838;Dels=0.00;FS=7.521;HRun=0;HaplotypeScore=0.4687;InbreedingCoeff=-0.0191;MQ=58.08;MQ0=0;MQRankSum=-0.315;QD=8.03;ReadPosRankSum=-2.447;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),EXON(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|1),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A176|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A176|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A216|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000187583|PLEKHN1|ENST00000379409|5/15|||216/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|1/3||||retained_intron|1,synonymous_variant|gcC/gcT|A|ENSG00000187583|PLEKHN1|ENST00000379407|6/15|||176/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|gcC/gcT|A|ENSG00000187583|PLEKHN1|ENST00000379410|6/16|||176/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:9.02:0,9,102 0/0:3,0:3:9.03:0,9,117 0/0:6,0:6:18.06:0,18,229 0/0:11,0:11:30.09:0,30,354 0/0:9,0:9:27.09:0,27,358 0/0:22,0:22:66.20:0,66,846 0/1:18,12:30:99:289,0,631 0/0:24,0:24:66.19:0,66,835 0/0:32,0:32:93.30:0,93,1210 0/0:31,0:31:93.30:0,93,1202 0/0:14,0:14:42.14:0,42,546 0/0:17,0:17:51.16:0,51,666 0/0:21,0:21:60.16:0,60,743 0/0:19,0:19:45.14:0,45,567 0/0:13,0:13:33.10:0,33,415 0/0:16,0:16:39.13:0,39,523 0/0:10,0:10:27.08:0,27,350 0/0:19,0:19:48.15:0,48,620 0/0:20,0:20:45.14:0,45,601 0/0:15,0:15:39.12:0,39,525 0/0:20,0:20:51.16:0,51,664 0/0:21,0:21:54.18:0,54,722 0/0:16,0:16:39.12:0,39,506 0/0:18,0:18:48.15:0,48,612 0/0:20,0:20:48.15:0,48,620 0/0:17,0:17:36.12:0,36,489 0/0:17,0:17:42.14:0,42,558 0/0:13,0:13:33.08:0,33,410 0/0:16,0:16:39.13:0,39,522 0/0:25,0:25:72.21:0,72,919 0/0:29,0:29:69.22:0,69,922 0/0:11,0:11:27.09:0,27,351 0/0:16,0:16:39.12:0,39,502 0/0:20,0:20:42.14:0,42,557 0/0:17,0:17:45.12:0,45,553 0/0:18,0:18:51.16:0,51,650 0/0:17,0:18:45.13:0,45,557 0/0:26,0:26:54.18:0,54,738 0/0:10,0:10:24.07:0,24,299 0/0:13,0:14:33.10:0,33,417 0/0:12,0:12:36.11:0,36,456 0/0:3,0:3:9.03:0,9,122 0/0:9,0:9:24.07:0,24,306 0/0:5,0:5:12.04:0,12,148 0/0:7,0:7:15.05:0,15,191 0/0:5,0:5:15.04:0,15,178 0/0:7,0:7:21.07:0,21,281 ./. 0/0:5,0:5:15.05:0,15,202 0/0:14,0:14:36.10:0,36,439 0/0:17,0:17:42.13:0,42,538 0/0:7,0:7:18.05:0,18,229 0/0:10,0:10:24.07:0,24,313 0/0:10,0:10:27.08:0,27,347 0/0:6,0:6:15.05:0,15,196 0/0:5,0:5:12.04:0,12,156 0/0:5,0:5:15.04:0,15,182 0/0:2,0:3:6.02:0,6,81 0/0:8,0:8:18.06:0,18,241 0/0:1,0:1:3.01:0,3,41 -chr1 906850 . C T 840.9 . AC=1;AF=0.0085;AN=118;BaseQRankSum=0.291;DP=1812;Dels=0.00;FS=2.912;HRun=0;HaplotypeScore=1.3291;InbreedingCoeff=-0.0167;MQ=58.39;MQ0=0;MQRankSum=0.375;QD=15.02;ReadPosRankSum=0.230;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),EXON(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|3),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|8),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|8),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|7),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|3/3||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:6,0:6:15.05:0,15,191 0/0:2,0:2:6.02:0,6,79 0/0:5,0:5:12.04:0,12,151 0/0:3,0:3:9.03:0,9,116 0/0:3,0:3:6.02:0,6,82 0/0:3,0:3:9.03:0,9,108 0/0:2,0:2:6.02:0,6,82 0/0:12,0:12:36.12:0,36,490 0/0:13,0:13:39.09:0,39,467 0/0:7,0:7:21.07:0,21,277 0/0:6,0:6:18.04:0,18,206 0/0:10,0:11:30.09:0,30,384 0/0:57,0:57:99:0,153,1979 0/0:53,0:53:99:0,153,2032 0/0:28,0:28:84.25:0,84,1089 0/0:30,0:30:78.25:0,78,1036 0/0:66,0:66:99:0,175,2312 0/0:47,0:47:99:0,117,1588 0/0:51,0:51:99:0,138,1790 0/0:51,0:51:99:0,144,1895 0/0:54,0:54:99:0,156,2011 0/0:52,0:52:99:0,144,1927 0/0:31,0:32:93.28:0,93,1196 0/0:45,0:45:99:0,120,1578 0/0:42,0:42:99:0,108,1431 0/0:42,0:42:99:0,108,1422 0/0:44,0:44:99:0,117,1558 0/0:53,0:53:99:0,150,1994 0/0:44,0:44:99:0,114,1493 0/0:62,0:63:99:0,169,2191 0/0:40,0:40:99:0,108,1433 0/0:43,0:43:99:0,117,1503 0/1:29,27:56:99:888,0,879 0/0:45,0:45:99:0,117,1524 0/0:50,0:50:99:0,132,1708 0/0:55,0:55:99:0,150,1968 0/0:63,0:63:99:0,181,2352 0/0:21,0:21:60.18:0,60,746 0/0:46,0:46:99:0,123,1567 0/0:35,0:36:93.30:0,93,1227 0/0:23,0:23:57.18:0,57,754 0/0:22,0:22:63.21:0,63,848 0/0:17,0:17:42.14:0,42,558 0/0:16,0:16:42.13:0,42,551 0/0:27,0:27:63.15:0,63,779 0/0:47,0:48:99:0,132,1673 0/0:17,0:17:45.13:0,45,595 0/0:26,0:26:66.20:0,66,863 0/0:34,0:34:84.26:0,84,1071 0/0:28,0:28:75.20:0,75,899 0/0:17,0:18:51.16:0,51,671 0/0:23,0:23:63.17:0,63,796 0/0:25,0:25:72.23:0,72,935 0/0:25,0:25:63.20:0,63,821 0/0:13,0:13:36.12:0,36,483 0/0:12,0:12:30.09:0,30,381 0/0:28,0:28:75.24:0,75,984 0/0:14,0:14:36.10:0,36,442 0/0:13,0:13:39.12:0,39,502 -chr1 906872 . C T 490.99 . AC=1;AF=0.0085;AN=118;BaseQRankSum=0.837;DP=1326;Dels=0.00;FS=11.727;HRun=3;HaplotypeScore=0.8532;InbreedingCoeff=-0.0185;MQ=58.72;MQ0=0;MQRankSum=0.435;QD=14.88;ReadPosRankSum=0.427;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),EXON(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|3),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|8),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|8),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|7),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|3/3||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:5,0:5:15.05:0,15,198 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.04:0,12,158 0/0:3,0:3:9.03:0,9,119 0/0:2,0:2:6.02:0,6,79 0/0:3,0:3:9.03:0,9,124 0/0:2,0:2:6.02:0,6,82 0/0:10,0:10:30.10:0,30,411 0/0:11,0:11:33.10:0,33,409 0/0:5,0:5:15.05:0,15,202 0/0:4,0:4:12.04:0,12,161 0/0:11,0:11:33.11:0,33,430 0/0:39,0:39:99:0,108,1381 0/0:36,0:36:99:0,102,1324 0/0:22,0:22:66.21:0,66,842 0/0:27,0:27:72.23:0,72,952 0/0:42,0:42:99:0,126,1632 0/0:34,0:35:96.30:0,96,1242 0/0:33,0:33:96.30:0,96,1250 0/0:38,0:38:99:0,108,1408 0/0:40,0:40:99:0,114,1477 0/0:40,0:40:99:0,105,1404 0/0:24,0:24:69.22:0,69,900 0/0:33,0:34:87.28:0,87,1138 0/0:26,0:26:78.25:0,78,1027 0/0:30,0:30:84.27:0,84,1112 0/0:34,0:34:93.29:0,93,1205 0/1:16,17:33:99:539,0,540 0/0:39,0:39:99:0,108,1365 0/0:47,0:47:99:0,129,1681 0/0:35,0:35:99:0,99,1265 0/0:30,0:30:81.25:0,81,1030 0/0:35,0:35:99:0,105,1395 0/0:31,0:31:90.27:0,90,1148 0/0:33,0:33:93.28:0,93,1206 0/0:39,0:39:99:0,105,1350 0/0:46,0:46:99:0,132,1717 0/0:15,0:15:42.13:0,42,529 0/0:33,0:34:87.26:0,87,1085 0/0:20,0:20:54.15:0,54,680 0/0:18,0:18:45.13:0,45,588 0/0:16,0:16:45.14:0,45,594 0/0:10,0:10:27.08:0,27,338 0/0:14,0:14:39.12:0,39,497 0/0:24,0:24:63.18:0,63,774 0/0:41,0:41:99:0,108,1391 0/0:9,0:9:24.08:0,24,317 0/0:15,0:15:36.11:0,36,460 0/0:24,0:26:66.20:0,66,834 0/0:21,0:21:60.17:0,60,725 0/0:14,0:14:33.09:0,33,423 0/0:19,0:19:51.15:0,51,663 0/0:18,0:18:45.14:0,45,576 0/0:20,0:21:57.16:0,57,723 0/0:10,0:10:30.10:0,30,402 0/0:9,0:9:27.08:0,27,346 0/0:23,0:23:63.19:0,63,812 0/0:9,0:9:21.04:0,21,252 0/0:11,0:11:30.09:0,30,381 -chr1 906974 . G A 150.57 . AC=2;AF=0.0185;AN=108;BaseQRankSum=0.388;DP=247;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1707;InbreedingCoeff=-0.0985;MQ=58.20;MQ0=0;MQRankSum=0.405;QD=12.55;ReadPosRankSum=0.062;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|8),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|8),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|7),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.01:0,6,69 ./. 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,40 0/0:3,0:3:9.03:0,9,122 0/0:4,0:4:12.04:0,12,163 ./. 0/0:1,0:1:3.01:0,3,38 ./. 0/0:14,0:14:42.14:0,42,555 0/0:3,0:3:9.03:0,9,121 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,80 0/0:6,0:6:18.06:0,18,231 0/0:8,0:8:18.05:0,18,233 0/0:14,0:14:42.13:0,42,557 0/1:2,3:5:69.41:107,0,69 0/0:9,0:9:27.09:0,27,358 0/0:3,0:3:9.03:0,9,125 0/0:7,0:7:15.05:0,15,199 0/0:3,0:3:9.03:0,9,120 0/0:9,0:9:18.06:0,18,244 0/0:11,0:11:30.10:0,30,394 0/0:2,0:2:6.02:0,6,84 0/0:12,0:12:36.12:0,36,482 0/0:4,0:4:9.03:0,9,121 0/0:7,0:7:21.07:0,21,267 0/0:4,0:4:9.03:0,9,108 0/0:12,0:12:36.12:0,36,483 0/1:2,4:7:69.41:106,0,69 0/0:8,0:8:21.07:0,21,274 0/0:2,0:2:6.02:0,6,79 0/0:7,0:7:21.06:0,21,270 0/0:13,0:13:39.13:0,39,515 0/0:3,0:3:9.03:0,9,112 0/0:4,0:4:12.04:0,12,163 0/0:1,0:1:3.01:0,3,42 0/0:5,0:5:9.03:0,9,123 0/0:1,0:1:3.01:0,3,42 0/0:3,0:3:9.03:0,9,114 0/0:3,0:4:9.03:0,9,110 ./. 0/0:5,0:5:15.04:0,15,189 0/0:1,0:1:3.01:0,3,32 0/0:2,0:2:6.02:0,6,76 0/0:5,0:5:12.03:0,12,150 0/0:7,0:7:18.06:0,18,224 0/0:3,0:3:9.03:0,9,119 0/0:4,0:4:12.04:0,12,158 ./. ./. 0/0:2,0:2:3.01:0,3,38 0/0:1,0:1:3.01:0,3,40 0/0:3,0:3:9.03:0,9,115 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,33 -chr1 907023 . G A 49.9 . AC=4;AF=0.048;AN=84;BaseQRankSum=0.466;DP=145;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1426;InbreedingCoeff=0.2013;MQ=59.04;MQ0=0;MQRankSum=0.872;QD=16.63;ReadPosRankSum=-0.015;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|8),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|8),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|7),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. 0/0:1,0:1:3.01:0,3,34 ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:6.02:0,6,82 0/0:3,0:3:9.03:0,9,122 ./. ./. 0/0:8,0:8:21.07:0,21,282 0/0:3,0:3:9.01:0,9,103 ./. 0/0:2,0:2:6.02:0,6,77 0/0:2,0:2:6.02:0,6,82 0/0:7,0:8:15.05:0,15,194 0/0:7,0:7:21.06:0,21,250 1/1:0,2:2:6.02:80,6,0 0/0:5,0:5:12.04:0,12,162 0/0:2,0:2:3.01:0,3,35 0/0:6,0:6:12.04:0,12,151 0/0:6,0:6:18.03:0,18,215 0/0:6,0:6:18.06:0,18,240 0/0:7,0:7:18.05:0,18,224 ./. 0/0:3,0:3:6.02:0,6,84 0/0:2,0:2:6.02:0,6,80 0/0:4,0:4:12.04:0,12,162 0/0:2,0:2:6.02:0,6,78 0/0:4,0:4:12.01:0,12,135 1/1:0,1:1:3.01:39,3,0 0/0:5,0:5:12.04:0,12,155 0/0:2,0:2:6.02:0,6,80 0/0:10,0:10:30.10:0,30,386 0/0:9,0:9:27.08:0,27,345 0/0:3,0:3:9.03:0,9,123 0/0:2,0:2:6.02:0,6,78 ./. 0/0:2,0:2:6.02:0,6,76 0/0:2,0:2:6.02:0,6,72 0/0:2,0:2:6.02:0,6,76 0/0:3,0:3:6.02:0,6,81 ./. ./. 0/0:1,0:1:3.01:0,3,32 0/0:2,0:2:6.02:0,6,80 ./. 0/0:2,0:2:6.01:0,6,62 0/0:2,0:2:6.02:0,6,72 0/0:1,0:1:3.01:0,3,42 ./. 0/0:2,0:2:6.02:0,6,80 0/0:1,0:1:3.01:0,3,40 ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,38 ./. -chr1 907170 . AG A 1280.62 . AC=36;AF=0.3462;AN=104;BaseQRankSum=3.258;DP=132;FS=0.000;HRun=3;HaplotypeScore=8.3225;InbreedingCoeff=0.2957;MQ=57.69;MQ0=0;MQRankSum=0.182;QD=20.99;ReadPosRankSum=0.423;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|8),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|8),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|7),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,43 0/0:3,0:3:9.03:0,9,130 ./. 0/1:1,1:2:31.19:31,0,37 ./. 0/0:3,0:3:9.03:0,9,130 1/1:1,4:5:12.04:149,12,0 0/0:2,0:2:6.02:0,6,86 1/1:0,2:2:6.02:74,6,0 0/1:3,2:5:59.38:59,0,115 0/0:1,0:1:3.01:0,3,43 1/1:1,0:1:3.01:37,3,0 1/1:0,2:2:3.01:37,3,0 1/1:0,1:1:3.01:37,3,0 1/1:0,1:1:3.01:37,3,0 0/0:3,0:3:9.03:0,9,129 0/1:2,2:4:62.39:62,0,74 0/0:3,0:3:9.03:0,9,120 0/0:2,0:2:6.02:0,6,86 0/0:3,0:3:9.03:0,9,130 1/1:0,4:4:12.04:149,12,0 0/0:1,0:1:3.01:0,3,43 ./. 0/0:1,0:1:3.01:0,3,43 ./. 0/0:1,0:1:3.01:0,3,43 0/0:2,0:2:3.01:0,3,43 0/0:4,0:4:12.04:0,12,173 0/0:2,0:2:6.02:0,6,86 ./. 1/1:0,3:3:9.03:112,9,0 0/0:2,0:2:6.02:0,6,86 ./. 0/0:2,0:2:3.01:0,3,43 1/1:0,1:1:3.01:37,3,0 0/0:1,0:1:3.01:0,3,43 0/0:3,0:2:9.03:0,9,129 1/1:1,1:2:6.02:74,6,0 0/0:1,0:1:3.01:0,3,43 0/0:3,0:3:9.03:0,9,130 0/1:2,1:3:28.18:28,0,77 ./. 0/0:4,0:4:9.03:0,9,129 0/0:2,0:2:3.01:0,3,43 1/1:0,2:2:6.02:74,6,0 0/0:4,0:4:12.04:0,12,173 0/1:2,4:6:57.76:131,0,58 0/1:2,0:2:30.98:31,0,37 0/0:2,0:2:6.02:0,6,86 0/0:1,0:1:3.01:0,3,43 1/1:0,3:3:9.03:112,9,0 0/0:4,0:4:12.04:0,12,166 0/1:2,1:3:28.18:28,0,77 0/0:4,0:4:12.04:0,12,173 0/0:2,0:2:6.02:0,6,86 0/0:1,0:1:3.01:0,3,43 ./. 0/1:2,1:3:28.18:28,0,77 1/1:0,3:3:6.02:74,6,0 1/1:0,3:3:9.03:112,9,0 -chr1 907609 . T C 2023.79 . AC=4;AF=0.0333;AN=120;BaseQRankSum=-2.518;DP=2587;Dels=0.00;FS=0.956;HRun=0;HaplotypeScore=2.5448;InbreedingCoeff=-0.0366;MQ=48.44;MQ0=0;MQRankSum=4.469;QD=10.76;ReadPosRankSum=2.738;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|9),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|9),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|8),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:15.03:0,15,177 0/0:6,0:6:18.06:0,18,228 0/0:6,0:6:12.04:0,12,160 0/0:3,0:3:9.03:0,9,105 0/0:9,0:9:24.08:0,24,325 0/0:14,0:15:27.08:0,27,346 0/0:26,0:26:69.22:0,69,915 0/0:9,0:9:18.06:0,18,245 0/0:34,0:34:90.30:0,90,1214 0/0:34,0:34:78.26:0,78,1047 0/0:10,0:10:30.10:0,30,408 0/0:10,0:10:24.07:0,24,313 0/0:31,0:31:87.28:0,87,1156 0/0:44,0:44:69.21:0,69,863 0/0:41,0:42:78.24:0,78,973 0/0:32,0:32:72.20:0,72,904 0/0:38,0:39:84.24:0,84,1060 0/0:33,0:35:87.20:0,87,1057 0/0:39,0:40:87.27:0,87,1098 0/0:53,0:55:99:0,114,1427 0/0:36,0:37:84.23:0,84,1029 0/0:48,0:48:99:0,117,1464 0/0:29,0:30:63.18:0,63,771 0/0:49,0:50:99:0,102,1271 0/0:38,0:38:87.27:0,87,1084 0/0:29,1:31:54.16:0,54,664 0/1:21,19:41:99:385,0,562 0/0:29,0:29:57.17:0,57,709 0/0:42,1:44:84.26:0,84,1056 0/0:35,0:36:78.23:0,78,956 0/0:58,0:60:99:0,120,1500 0/0:36,0:38:75.18:0,75,896 0/0:39,0:40:78.22:0,78,989 0/0:55,1:57:99:0,114,1429 0/1:20,21:42:99:549,0,402 0/0:27,0:28:54.15:0,54,696 0/1:25,19:44:99:512,0,650 0/0:48,0:50:99:0,105,1331 0/0:48,0:49:96.28:0,96,1193 0/0:79,0:82:99:0,150,1808 0/0:59,0:64:99:0,123,1488 0/0:55,0:59:96.20:0,96,1093 0/0:38,0:41:75.20:0,75,901 0/0:45,1:47:81.18:0,81,949 0/0:57,0:59:99:0,102,1230 0/0:46,1:48:87.25:0,87,1066 0/0:99,0:106:99:0,199,2372 0/0:36,0:37:81.23:0,81,978 0/0:55,0:58:99:0,105,1274 0/0:83,0:90:99:0,138,1611 0/0:95,0:97:99:0,165,2014 0/0:70,0:72:99:0,138,1662 0/0:88,0:91:99:0,153,1914 0/1:28,30:61:99:670,0,420 0/0:68,0:70:99:0,117,1428 0/0:45,0:48:96.28:0,96,1205 0/0:28,0:30:57.15:0,57,668 0/0:56,1:60:96.27:0,96,1187 0/0:33,0:37:63.19:0,63,788 0/0:49,0:49:99:0,111,1337 -chr1 907622 . G C 3088.17 . AC=7;AF=0.0583;AN=120;BaseQRankSum=-1.813;DP=2382;Dels=0.00;FS=1.696;HRun=0;HaplotypeScore=13.8552;InbreedingCoeff=0.2112;MQ=46.67;MQ0=0;MQRankSum=5.413;QD=12.21;ReadPosRankSum=2.166;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|9),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|9),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|8),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:8,0:9:15.05:0,15,185 0/0:2,0:2:6.02:0,6,78 0/0:4,0:4:6.02:0,6,79 0/0:3,0:3:9.03:0,9,117 0/0:8,0:8:15.05:0,15,198 0/0:13,0:14:21.07:0,21,279 0/0:22,0:22:30.09:0,30,378 0/0:8,0:8:15.05:0,15,202 0/0:31,0:31:63.20:0,63,837 0/0:28,0:28:57.16:0,57,714 0/0:8,0:8:15.05:0,15,198 0/0:18,0:18:21.04:0,21,250 0/0:28,0:28:63.20:0,63,823 0/0:46,0:46:69.15:0,69,787 0/0:44,0:44:81.19:0,81,939 0/0:30,0:30:60.15:0,60,702 0/0:34,0:34:63.19:0,63,774 0/0:38,0:38:87.24:0,87,1053 0/0:37,0:37:63.18:0,63,778 0/0:53,0:53:99:0,111,1266 0/1:16,24:40:99:470,0,239 0/0:45,0:46:96.27:0,96,1144 0/0:27,0:28:54.13:0,54,629 0/0:41,0:41:69.17:0,69,801 0/0:37,0:37:84.18:0,84,971 0/0:31,0:31:48.08:0,48,547 1/1:1,40:41:81.22:966,81,0 0/0:25,0:25:42.07:0,42,464 0/0:45,0:45:69.17:0,69,822 0/0:25,0:25:42.11:0,42,496 0/0:51,0:51:96.27:0,96,1160 0/0:34,0:34:60.14:0,60,705 0/0:39,0:39:69.17:0,69,830 0/0:54,0:54:99:0,99,1155 0/1:20,23:43:99:476,0,338 0/0:29,0:29:45.09:0,45,523 0/1:27,18:45:99:384,0,556 0/0:53,0:53:99:0,99,1143 0/0:38,0:39:60.15:0,60,690 0/0:80,0:80:99:0,123,1397 0/0:59,0:59:93.21:0,93,1077 0/0:52,0:52:69.11:0,69,717 0/0:37,1:39:54.13:0,54,631 0/0:42,0:42:60.09:0,60,626 0/0:49,0:49:69.11:0,69,722 0/0:49,0:49:66.16:0,66,778 0/0:73,0:75:99:0,105,1149 0/1:13,18:31:72.99:462,0,73 0/0:50,0:50:87.17:0,87,973 0/0:93,0:94:99:0,123,1354 0/0:93,0:93:99:0,147,1642 0/0:73,0:74:99:0,120,1324 0/0:85,1:86:99:0,114,1273 0/1:28,22:52:99:461,0,362 0/0:60,0:60:90.16:0,90,973 0/0:37,1:38:60.15:0,60,700 0/0:29,0:29:45.08:0,45,483 0/0:49,0:50:78.13:0,78,869 0/0:29,0:30:42.10:0,42,491 0/0:35,0:35:72.20:0,72,861 -chr1 907631 . A C 2295.85 . AC=35;AF=0.2917;AN=120;BaseQRankSum=-20.997;DP=2266;Dels=0.00;FS=665.053;HRun=7;HaplotypeScore=7.6604;InbreedingCoeff=-0.4342;MQ=46.08;MQ0=0;MQRankSum=-14.611;QD=1.46;ReadPosRankSum=13.032;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|9),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|9),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|8),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,4:7:6.01:0,6,61 0/0:2,0:2:6.02:0,6,79 0/0:2,2:4:6.02:0,6,74 0/0:2,0:2:3.01:0,3,41 0/0:3,3:6:6.02:0,6,70 0/0:4,9:13:9.03:0,9,120 0/0:10,11:21:18.05:0,18,226 0/0:4,6:10:12.03:0,12,140 0/0:13,12:25:36.09:0,36,455 0/1:11,17:28:49.58:50,0,333 0/1:4,5:9:14.64:15,0,112 0/0:5,12:17:15.04:0,15,177 0/0:9,6:15:24.05:0,24,285 0/1:24,24:50:99:135,0,621 0/1:24,19:43:85.41:85,0,650 0/0:14,16:30:22.28:0,22,432 0/1:19,14:33:3.98:4,0,518 0/0:29,14:44:28.84:0,29,836 0/0:20,19:39:30.34:0,30,569 0/1:30,21:51:98.80:99,0,802 0/0:19,17:37:15.96:0,16,392 0/0:28,14:42:22.09:0,22,803 0/1:16,11:27:15.94:16,0,433 0/1:23,15:38:17.29:17,0,542 0/0:27,12:39:53:0,53,833 0/1:12,19:33:99:167,0,272 0/0:28,8:38:35.46:0,35,650 0/1:14,12:26:39.65:40,0,401 0/0:27,19:46:8.79:0,9,635 0/1:17,11:28:55.25:55,0,502 0/0:33,20:53:16.03:0,16,906 0/0:24,14:38:0.39:0,0,554 0/1:23,20:43:69.66:70,0,693 0/0:24,24:48:69.19:0,69,808 0/0:27,15:42:41.47:0,41,714 0/1:15,12:28:47.71:48,0,305 0/0:25,19:44:35.52:0,36,712 0/1:30,23:53:25.21:25,0,880 0/1:11,17:30:40.01:40,0,231 0/1:26,44:70:99:109,0,687 0/1:22,31:54:76.92:77,0,397 0/1:14,37:52:99:118,0,293 0/1:17,18:37:18.02:18,0,377 0/1:14,26:42:53.45:53,0,303 0/1:14,30:45:62.41:62,0,302 0/1:13,31:44:30.97:31,0,350 0/1:23,50:73:99:113,0,389 0/1:14,16:30:27.23:27,0,176 0/1:15,24:40:84.83:85,0,395 0/1:29,59:88:99:161,0,668 0/1:30,57:87:99:245,0,612 0/1:27,41:70:65.76:66,0,638 0/1:24,51:77:96.52:97,0,538 0/1:28,20:49:54.44:54,0,382 0/1:19,33:55:69.29:69,0,341 0/1:15,17:32:3.61:4,0,222 0/1:9,19:29:31.03:31,0,242 0/1:16,24:42:99:126,0,261 0/1:12,17:29:99:116,0,259 0/0:19,12:31:22.38:0,22,455 -chr1 907758 . A G 191.93 . AC=13;AF=0.1140;AN=114;BaseQRankSum=-12.237;DP=1481;Dels=0.01;FS=153.003;HRun=5;HaplotypeScore=5.2587;InbreedingCoeff=-0.1585;MQ=51.66;MQ0=0;MQRankSum=-11.759;QD=0.46;ReadPosRankSum=1.329;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E319G|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E331G|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E371G|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,missense_variant|gAg/gGg|E/G|ENSG00000187583|PLEKHN1|ENST00000379409|9/15|benign(0.005)|tolerated(0.28)|371/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,missense_variant|gAg/gGg|E/G|ENSG00000187583|PLEKHN1|ENST00000379407|10/15|benign(0.001)|tolerated(0.21)|331/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,missense_variant|gAg/gGg|E/G|ENSG00000187583|PLEKHN1|ENST00000379410|10/16|benign(0.003)|tolerated(0.26)|319/611|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:6.02:0,6,67 0/0:1,1:2:3.01:0,3,41 ./. 0/0:1,2:4:3.01:0,3,37 0/0:2,3:5:3.01:0,3,41 0/0:6,3:10:15.05:0,15,203 0/0:4,2:6:9.03:0,9,120 0/0:16,8:24:48.14:0,48,612 0/0:10,4:14:18.04:0,18,220 0/1:3,4:7:9.65:10,0,106 ./. 0/1:8,2:11:9.36:9,0,244 0/1:30,13:43:52.07:52,0,652 0/1:34,12:46:42.60:43,0,717 0/0:15,8:23:2.48:0,2,343 0/0:26,1:30:60.19:0,60,770 0/1:30,9:39:28.28:28,0,778 0/1:22,11:33:19.97:20,0,483 0/0:24,12:37:4.75:0,5,577 0/0:16,12:28:2.67:0,3,380 0/1:39,16:55:19.40:19,0,859 0/0:19,5:25:36.11:0,36,465 0/1:23,11:34:52.31:52,0,538 0/0:39,6:45:61.55:0,62,1063 0/0:21,11:32:51.15:0,51,653 0/0:31,10:41:51.12:0,51,624 0/0:28,12:40:32.49:0,32,713 0/0:24,11:35:48.13:0,48,584 0/1:21,13:36:31.91:32,0,455 0/0:34,12:47:69.20:0,69,854 0/0:20,10:31:42.13:0,42,546 0/0:26,15:41:35.43:0,35,668 0/1:28,14:42:10.90:11,0,634 0/0:29,4:33:42.14:0,42,567 0/0:19,3:22:39.12:0,39,492 0/0:30,11:41:35.75:0,36,788 0/0:33,10:43:72.22:0,72,903 0/0:14,5:19:15.05:0,15,221 0/0:19,12:31:0.73:0,1,453 0/0:19,5:24:42.10:0,42,517 0/0:12,4:16:27.06:0,27,352 0/1:10,7:17:44.04:44,0,202 0/0:16,4:20:36.11:0,36,451 0/0:16,8:25:36.11:0,36,453 0/0:8,4:12:15.04:0,15,174 0/0:19,9:28:36.11:0,36,443 0/0:9,2:12:18.03:0,18,210 0/1:14,5:20:0.33:0,0,343 0/1:20,12:32:22.04:22,0,319 0/0:19,8:27:23.45:0,23,531 0/0:27,4:32:48.13:0,48,567 0/0:24,6:30:33.09:0,33,424 0/0:12,4:16:24.07:0,24,305 0/0:17,4:21:2.67:0,3,368 0/0:13,4:17:7.40:0,7,322 0/0:14,1:15:21.03:0,21,259 0/0:15,4:19:33.10:0,33,411 0/0:11,3:14:21.06:0,21,261 0/0:11,2:13:30.08:0,30,367 -chr1 907774 . G A 268.81 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.645;DP=1416;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.8695;InbreedingCoeff=-0.0177;MQ=51.53;MQ0=0;MQRankSum=0.725;QD=7.47;ReadPosRankSum=-2.464;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L324|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L336|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L376|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,synonymous_variant|ctG/ctA|L|ENSG00000187583|PLEKHN1|ENST00000379409|9/15|||376/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,synonymous_variant|ctG/ctA|L|ENSG00000187583|PLEKHN1|ENST00000379407|10/15|||336/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|ctG/ctA|L|ENSG00000187583|PLEKHN1|ENST00000379410|10/16|||324/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,70 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.02:0,6,74 0/0:3,0:3:6.02:0,6,74 0/0:6,0:6:18.05:0,18,215 0/0:6,0:6:15.04:0,15,182 0/0:7,0:7:18.05:0,18,205 0/0:4,0:4:12.04:0,12,157 0/0:14,0:14:42.13:0,42,512 0/0:13,0:13:39.12:0,39,490 0/0:5,0:5:15.05:0,15,190 0/0:3,0:3:9.02:0,9,100 0/0:7,0:7:21.05:0,21,237 0/0:40,0:40:99:0,99,1241 0/0:45,0:45:99:0,114,1366 0/0:24,0:24:63.16:0,63,755 0/0:29,0:29:63.19:0,63,813 0/0:31,0:31:75.20:0,75,907 0/0:36,0:37:87.26:0,87,1078 0/0:39,0:40:96.25:0,96,1147 0/1:18,18:36:99:316,0,484 0/0:56,0:56:99:0,132,1600 0/0:25,0:25:57.17:0,57,725 0/0:35,0:35:84.24:0,84,1016 0/0:44,0:44:99:0,108,1322 0/0:30,0:30:78.23:0,78,963 0/0:46,0:46:99:0,111,1369 0/0:38,0:38:87.27:0,87,1109 0/0:35,0:35:81.24:0,81,1006 0/0:37,0:37:87.26:0,87,1079 0/0:48,0:48:99:0,123,1434 0/0:32,0:32:72.21:0,72,892 0/0:36,0:37:96.29:0,96,1166 0/0:35,0:35:87.26:0,87,1064 0/0:31,0:31:60.18:0,60,745 0/0:23,0:23:57.18:0,57,738 0/0:35,0:35:90.27:0,90,1111 0/0:39,0:39:93.25:0,93,1150 0/0:20,0:20:48.15:0,48,597 0/0:31,0:31:81.25:0,81,1006 0/0:23,0:23:60.16:0,60,752 0/0:14,0:14:36.11:0,36,460 0/0:15,0:15:42.13:0,42,507 0/0:17,0:17:36.11:0,36,461 0/0:19,0:19:54.16:0,54,643 0/0:10,0:10:18.05:0,18,224 0/0:29,0:29:66.19:0,66,800 0/0:14,0:14:33.10:0,33,408 0/0:20,0:20:48.11:0,48,563 0/0:31,0:31:84.22:0,84,967 0/0:24,0:24:51.15:0,51,630 0/0:31,0:31:78.23:0,78,946 0/0:28,0:28:57.17:0,57,716 0/0:13,0:13:27.08:0,27,345 0/0:20,0:20:51.16:0,51,648 0/0:17,0:17:45.13:0,45,552 0/0:13,0:13:27.06:0,27,326 0/0:19,0:19:39.12:0,39,518 0/0:13,0:13:36.11:0,36,440 0/0:13,0:13:30.09:0,30,378 -chr1 907816 . A G 331.68 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.634;DP=1030;Dels=0.00;FS=2.656;HRun=0;HaplotypeScore=0.8456;InbreedingCoeff=-0.0346;MQ=55.40;MQ0=0;MQRankSum=0.355;QD=10.05;ReadPosRankSum=3.222;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|10),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|10),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|9),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,30 0/0:5,0:5:15.04:0,15,184 0/0:2,0:2:3.01:0,3,34 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.04:0,12,157 0/0:5,0:5:15.05:0,15,206 0/0:9,0:9:27.08:0,27,348 0/0:11,0:11:33.11:0,33,441 0/0:4,0:4:12.04:0,12,165 0/0:2,0:2:6.02:0,6,71 0/0:5,0:5:15.05:0,15,202 0/0:28,0:28:72.23:0,72,945 0/0:35,0:35:81.26:0,81,1070 0/0:22,0:22:57.17:0,57,727 0/0:29,0:29:69.21:0,69,891 0/0:26,0:26:63.20:0,63,816 0/0:27,0:27:69.21:0,69,884 0/0:30,0:30:72.23:0,72,923 0/1:11,12:23:99:378,0,324 0/0:38,1:39:65.87:0,66,1212 0/0:24,0:24:60.18:0,60,783 0/0:27,0:28:78.23:0,78,967 0/0:33,0:33:72.21:0,72,925 0/0:22,0:22:57.16:0,57,730 0/0:29,0:29:72.22:0,72,936 0/0:22,0:22:57.18:0,57,750 0/0:23,0:23:60.19:0,60,771 0/0:27,0:27:72.23:0,72,929 0/0:39,0:39:99:0,102,1250 0/0:26,0:26:63.19:0,63,801 0/0:22,1:23:35.78:0,36,793 0/0:22,0:22:57.18:0,57,743 0/0:26,0:26:60.18:0,60,773 0/0:22,0:22:51.16:0,51,671 0/0:26,0:26:69.20:0,69,870 0/0:32,0:32:75.24:0,75,997 0/0:8,0:8:21.06:0,21,274 0/0:21,0:21:60.19:0,60,759 0/0:17,0:17:45.14:0,45,572 0/0:12,0:12:24.08:0,24,323 0/0:10,0:10:30.09:0,30,373 0/0:15,0:15:36.11:0,36,447 0/0:12,0:12:30.09:0,30,374 0/0:8,0:8:18.05:0,18,216 0/0:18,0:18:48.15:0,48,618 0/1:8,2:10:11.49:11,0,284 0/0:16,0:16:39.12:0,39,474 0/0:19,0:19:51.16:0,51,635 0/0:14,0:14:33.10:0,33,415 0/0:21,0:21:54.15:0,54,669 0/0:15,0:15:33.10:0,33,427 0/0:6,0:6:18.06:0,18,239 0/0:14,0:14:39.12:0,39,501 0/0:8,0:8:21.07:0,21,281 0/0:9,0:9:21.07:0,21,269 0/0:17,0:17:36.12:0,36,484 0/0:12,0:12:30.09:0,30,383 0/0:14,0:14:33.10:0,33,414 -chr1 907920 . C G 216.19 . AC=4;AF=0.0377;AN=106;BaseQRankSum=0.780;DP=253;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=0.2690;InbreedingCoeff=0.1203;MQ=58.25;MQ0=0;MQRankSum=-0.123;QD=16.63;ReadPosRankSum=-0.212;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|10),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|10),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|9),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,29 ./. 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.01:0,6,67 ./. 0/0:2,0:2:6.02:0,6,81 0/0:6,0:6:18.06:0,18,231 0/0:1,0:1:3.01:0,3,41 0/0:1,2:3:3.01:0,3,41 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:6,0:6:18.06:0,18,245 0/0:10,0:10:27.08:0,27,339 0/0:9,0:9:24.07:0,24,318 0/0:6,0:6:18.06:0,18,243 0/0:6,0:6:18.06:0,18,233 0/0:8,0:8:18.06:0,18,235 0/0:9,0:9:27.09:0,27,358 0/0:6,0:6:18.06:0,18,243 0/0:9,0:9:21.06:0,21,275 0/0:5,0:5:15.04:0,15,186 0/0:6,0:6:18.06:0,18,241 0/0:9,0:9:27.08:0,27,349 0/0:6,0:6:18.06:0,18,243 1/1:0,6:6:15.05:208,15,0 0/0:2,0:2:6.02:0,6,76 0/0:9,0:9:24.08:0,24,326 0/0:9,0:9:27.09:0,27,370 0/0:10,1:11:30.10:0,30,389 0/0:7,1:8:21.07:0,21,284 0/0:3,0:3:9.03:0,9,120 0/0:5,0:7:15.05:0,15,193 0/1:1,1:2:24.57:35,0,25 0/0:5,0:5:15.05:0,15,190 0/1:3,2:5:62.74:63,0,63 0/0:7,0:7:21.07:0,21,282 0/0:1,0:1:3.01:0,3,37 0/0:3,0:3:9.03:0,9,117 0/0:5,0:5:15.05:0,15,198 ./. 0/0:4,0:4:12.04:0,12,159 0/0:1,0:1:3.01:0,3,42 0/0:3,0:3:6.02:0,6,79 0/0:5,0:5:12.01:0,12,141 0/0:3,0:3:9.03:0,9,121 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,42 0/0:7,0:7:21.04:0,21,261 0/0:5,0:5:15.05:0,15,198 0/0:3,0:3:9.03:0,9,113 ./. ./. 0/0:6,0:6:15.03:0,15,182 0/0:3,0:3:9.03:0,9,121 0/0:4,0:4:12.04:0,12,158 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:9.03:0,9,116 -chr1 907991 . CA C 106.79 . AC=5;AF=0.054;AN=92;BaseQRankSum=4.179;DP=101;FS=1.708;HRun=7;HaplotypeScore=8.2099;InbreedingCoeff=0.0500;MQ=56.72;MQ0=0;MQRankSum=-1.342;QD=11.87;ReadPosRankSum=1.095;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|10),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|10),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|9),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3.01:0,3,38 0/0:2,0:2:6.02:0,6,75 0/0:3,0:3:9.03:0,9,110 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. 0/0:2,0:2:3.01:0,3,38 0/0:3,0:3:9.03:0,9,113 0/0:2,0:2:3.01:0,3,38 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,38 0/0:5,0:5:9.03:0,9,108 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,38 0/0:4,0:4:9.02:0,9,101 0/0:3,0:3:9.03:0,9,106 0/0:2,0:2:3.01:0,3,38 0/0:2,0:2:6.02:0,6,76 0/0:2,0:2:6.02:0,6,76 0/0:5,0:5:15.05:0,15,189 0/0:1,0:1:3.01:0,3,38 0/0:3,0:3:9.03:0,9,113 ./. 1/1:0,3:3:9.02:90,9,0 ./. 0/0:1,0:1:3.01:0,3,38 0/0:3,0:3:9.03:0,9,113 0/0:6,0:6:15.05:0,15,184 0/0:1,0:1:3.01:0,3,38 0/0:7,0:7:18.06:0,18,227 0/0:2,0:2:6.02:0,6,76 1/1:0,1:1:3.01:30,3,0 0/0:2,0:2:3.01:0,3,38 0/1:2,3:5:25.72:78,0,26 0/0:4,0:4:9.03:0,9,113 ./. 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,38 0/0:2,0:2:6.02:0,6,76 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 ./. 0/0:2,0:2:6.02:0,6,76 0/0:1,0:1:3.01:0,3,38 ./. 0/0:2,0:2:6.02:0,6,75 ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 0/0:2,0:2:6.02:0,6,76 -chr1 907994 . A C 162.44 . AC=5;AF=0.054;AN=92;BaseQRankSum=3.562;DP=99;Dels=0.00;FS=3.801;HRun=0;HaplotypeScore=0.0865;InbreedingCoeff=0.0684;MQ=56.41;MQ0=0;MQRankSum=-2.224;QD=16.24;ReadPosRankSum=1.331;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|10),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|10),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|9),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,80 0/0:2,0:2:6.02:0,6,77 0/0:3,0:3:9.03:0,9,121 0/0:1,0:1:3.01:0,3,36 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:9.03:0,9,123 0/0:2,0:2:6.02:0,6,77 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:9.03:0,9,122 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.04:0,12,158 0/0:3,0:3:9.03:0,9,115 0/0:2,0:2:6.02:0,6,80 0/0:2,0:2:6.02:0,6,83 0/0:2,0:2:6.02:0,6,84 0/0:5,0:5:12.04:0,12,161 0/0:1,0:1:3.01:0,3,42 0/0:3,0:3:9.03:0,9,117 ./. 1/1:0,3:3:9.03:109,9,0 ./. 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:6.02:0,6,85 0/0:6,0:6:18.06:0,18,238 0/0:2,0:2:6.02:0,6,80 0/0:7,0:7:21.07:0,21,271 0/0:2,0:2:6.02:0,6,82 1/1:0,1:1:3.01:42,3,0 0/0:2,0:2:6.02:0,6,80 0/1:3,3:6:58.78:94,0,59 0/0:3,0:3:9.03:0,9,125 ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,31 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:2.99:0,3,23 ./. 0/0:2,0:2:6.02:0,6,81 ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,82 -chr1 907998 . A T 165.43 . AC=5;AF=0.053;AN=94;BaseQRankSum=2.279;DP=96;Dels=0.00;FS=1.648;HRun=2;HaplotypeScore=0.0847;InbreedingCoeff=0.0537;MQ=56.29;MQ0=0;MQRankSum=-1.944;QD=18.38;ReadPosRankSum=1.172;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|10),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|10),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|9),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.01:0,6,57 0/0:3,0:3:9.03:0,9,117 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:4,0:4:12.04:0,12,159 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3:0,3,29 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,38 0/0:4,0:4:9.03:0,9,118 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,37 0/0:3,0:3:9.03:0,9,118 0/0:3,0:3:9.03:0,9,109 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,84 0/0:2,0:2:6.02:0,6,83 0/0:5,0:5:15.03:0,15,185 0/0:1,0:1:3.01:0,3,42 0/0:3,0:3:9.03:0,9,115 0/0:2,0:2:6.02:0,6,72 1/1:0,3:3:9.03:109,9,0 ./. 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:6.02:0,6,85 0/0:6,0:6:15.05:0,15,195 0/0:2,0:2:6.02:0,6,78 0/0:6,0:6:18.06:0,18,239 0/0:3,0:3:9.03:0,9,116 1/1:0,1:1:3.01:42,3,0 0/0:1,0:1:3.01:0,3,41 0/1:2,3:5:29.19:97,0,29 0/0:3,0:3:9.03:0,9,123 ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,31 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:2,0:2:6.02:0,6,68 0/0:1,0:1:3.01:0,3,30 ./. 0/0:2,0:2:6.02:0,6,73 ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,79 -chr1 908170 . C G 938.77 . AC=9;AF=0.0763;AN=118;BaseQRankSum=-2.147;DP=536;Dels=0.00;FS=1.531;HRun=2;HaplotypeScore=0.5568;InbreedingCoeff=0.1081;MQ=53.86;MQ0=0;MQRankSum=0.079;QD=11.31;ReadPosRankSum=0.858;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|10),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|10),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|9),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12.04:0,12,143 0/0:2,0:2:6.02:0,6,79 0/0:4,0:4:12.04:0,12,159 0/0:2,0:2:6.02:0,6,75 0/0:3,0:3:9.03:0,9,123 0/0:2,0:2:6.02:0,6,82 0/0:2,0:2:6.02:0,6,76 ./. 0/0:4,0:4:12.04:0,12,157 0/0:6,0:6:15.04:0,15,186 0/0:3,0:3:9.03:0,9,120 0/0:2,0:2:6.02:0,6,78 0/0:3,0:3:9.03:0,9,121 0/0:13,0:13:36.11:0,36,443 0/0:21,0:21:54.16:0,54,672 0/0:8,0:8:24.07:0,24,292 0/0:16,0:16:48.15:0,48,586 0/0:6,0:6:15.03:0,15,164 0/0:10,0:10:27.06:0,27,304 0/0:11,0:11:30.09:0,30,380 0/1:8,3:11:87.05:87,0,204 0/0:20,0:20:54.17:0,54,684 0/0:6,0:6:18.06:0,18,230 0/0:8,0:8:21.07:0,21,265 0/0:10,0:10:27.08:0,27,337 0/0:6,0:6:18.06:0,18,220 1/1:0,12:12:30.09:355,30,0 0/0:7,0:7:18.06:0,18,229 0/0:12,0:12:33.07:0,33,388 0/0:6,0:6:18.06:0,18,225 0/0:14,0:14:39.12:0,39,481 0/0:12,0:12:36.10:0,36,426 0/0:15,0:15:36.11:0,36,459 0/1:5,11:16:99:323,0,102 0/1:4,3:7:91.50:91,0,124 0/0:5,0:5:15.05:0,15,179 0/1:5,6:11:99:156,0,160 0/0:9,0:9:24.07:0,24,298 0/0:11,0:11:33.10:0,33,396 0/0:15,0:15:42.12:0,42,491 0/1:9,1:10:3.51:4,0,280 0/0:8,0:8:24.07:0,24,286 0/0:7,0:7:21.07:0,21,271 0/0:8,0:8:24.07:0,24,283 0/0:5,0:5:12.04:0,12,162 0/0:15,0:16:42.12:0,42,504 0/0:13,0:13:39.11:0,39,447 0/1:4,1:5:26.54:27,0,110 0/0:8,1:9:21.06:0,21,260 0/0:21,0:21:57.18:0,57,700 0/0:21,0:21:63.19:0,63,755 0/0:9,0:9:27.08:0,27,338 0/0:12,0:12:33.08:0,33,387 0/1:9,2:11:37.02:37,0,304 0/0:9,0:9:18.06:0,18,223 0/0:6,0:6:15.05:0,15,190 0/0:6,0:6:18.05:0,18,216 0/0:9,0:9:27.08:0,27,326 0/0:7,1:8:15.05:0,15,188 0/0:6,0:6:12.04:0,12,155 -chr1 908228 . A G 406.65 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.194;DP=1035;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5043;InbreedingCoeff=-0.0201;MQ=55.14;MQ0=0;MQRankSum=1.782;QD=12.32;ReadPosRankSum=-0.055;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|10),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|10),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|9),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:6.02:0,6,69 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:12.04:0,12,151 0/0:1,0:1:3.01:0,3,41 0/0:7,0:7:21.07:0,21,271 0/0:3,0:3:9.03:0,9,122 0/0:9,1:10:21.07:0,21,273 0/0:2,0:2:6.02:0,6,74 0/0:14,0:14:42.14:0,42,553 0/0:12,0:12:36.12:0,36,469 0/0:6,0:6:18.06:0,18,232 0/0:4,0:4:12.04:0,12,155 0/0:6,0:6:18.06:0,18,233 0/0:22,1:23:60.16:0,60,735 0/0:31,0:32:75.21:0,75,950 0/0:18,0:19:39.12:0,39,514 0/0:33,0:33:72.23:0,72,932 0/0:13,0:13:30.08:0,30,371 0/0:15,0:15:39.12:0,39,494 0/0:23,0:23:60.14:0,60,736 0/0:20,0:20:42.14:0,42,571 0/0:26,0:26:66.20:0,66,855 0/0:17,0:17:39.13:0,39,520 0/0:21,0:21:54.14:0,54,658 0/0:26,0:28:69.20:0,69,852 0/0:19,0:19:39.11:0,39,507 0/0:16,0:16:39.11:0,39,462 0/0:18,0:18:45.13:0,45,543 0/0:26,0:26:60.18:0,60,757 0/0:16,0:16:39.11:0,39,492 0/0:31,0:31:72.22:0,72,944 0/0:16,0:16:36.12:0,36,489 0/0:20,0:20:54.13:0,54,670 0/0:26,0:26:69.21:0,69,863 0/0:21,0:21:39.12:0,39,497 0/0:13,0:13:33.11:0,33,444 0/0:22,0:23:54.15:0,54,692 0/0:32,0:33:81.25:0,81,1034 0/0:12,0:12:30.09:0,30,363 0/0:29,0:31:69.18:0,69,850 0/0:13,0:13:33.11:0,33,430 0/0:16,0:16:33.10:0,33,411 0/0:19,0:20:54.17:0,54,690 0/0:15,0:15:39.12:0,39,483 0/0:13,0:13:36.07:0,36,424 0/0:34,0:34:87.24:0,87,1078 0/0:26,0:26:60.18:0,60,744 0/0:13,0:13:36.11:0,36,447 0/0:13,0:13:21.06:0,21,259 0/1:15,18:33:99:454,0,416 0/0:39,0:40:99:0,105,1244 0/0:20,0:21:51.12:0,51,633 0/0:20,0:21:48.14:0,48,587 0/0:16,0:16:42.13:0,42,531 0/0:16,0:16:48.14:0,48,575 0/0:12,0:12:30.07:0,30,366 0/0:10,0:10:27.08:0,27,341 0/0:17,0:17:45.14:0,45,556 0/0:12,0:13:27.08:0,27,329 0/0:9,0:9:18.03:0,18,208 -chr1 908275 . G A 810.31 . AC=3;AF=0.0250;AN=120;BaseQRankSum=0.050;DP=1417;Dels=0.00;FS=4.591;HRun=0;HaplotypeScore=0.6695;InbreedingCoeff=-0.0308;MQ=55.19;MQ0=0;MQRankSum=1.728;QD=10.39;ReadPosRankSum=0.854;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G346D|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G358D|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gAc|G398D|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,missense_variant|gGc/gAc|G/D|ENSG00000187583|PLEKHN1|ENST00000379409|10/15|benign(0.006)|tolerated(1)|398/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,missense_variant|gGc/gAc|G/D|ENSG00000187583|PLEKHN1|ENST00000379407|11/15|benign(0.006)|tolerated(1)|358/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,missense_variant|gGc/gAc|G/D|ENSG00000187583|PLEKHN1|ENST00000379410|11/16|benign(0.002)|tolerated(1)|346/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,116 0/0:3,0:3:6.02:0,6,78 0/0:6,0:6:18.06:0,18,239 0/0:3,0:3:6.02:0,6,80 0/0:14,0:14:39.12:0,39,512 0/0:9,0:9:27.09:0,27,359 0/0:13,0:13:39.13:0,39,529 0/0:4,0:4:12.04:0,12,142 0/0:26,0:26:69.21:0,69,892 0/0:19,0:19:54.17:0,54,720 0/0:13,0:13:39.12:0,39,500 0/0:12,0:12:33.11:0,33,432 0/0:15,0:15:39.12:0,39,503 0/0:23,0:23:57.18:0,57,731 0/0:30,0:31:81.25:0,81,1054 0/0:24,0:24:54.17:0,54,721 0/0:39,0:39:87.28:0,87,1146 0/0:23,0:23:51.17:0,51,694 0/0:18,0:18:42.13:0,42,550 0/0:22,0:23:51.16:0,51,677 0/0:17,0:17:45.15:0,45,594 0/0:31,0:31:72.23:0,72,918 0/0:17,0:17:39.13:0,39,525 0/0:27,0:27:69.21:0,69,873 0/0:29,0:29:63.18:0,63,806 0/0:21,0:21:42.14:0,42,568 0/1:12,9:21:99:255,0,367 0/0:16,0:16:39.09:0,39,461 0/0:27,0:27:69.21:0,69,899 0/0:23,0:23:60.19:0,60,776 0/0:37,0:37:87.27:0,87,1135 0/0:25,0:26:54.17:0,54,713 0/0:25,0:26:66.19:0,66,803 0/0:30,0:30:78.25:0,78,1022 0/1:12,9:21:99:238,0,338 0/0:25,0:25:57.17:0,57,746 0/1:21,15:36:99:397,0,632 0/0:41,0:41:87.27:0,87,1146 0/0:17,0:17:36.11:0,36,472 0/0:47,0:47:99:0,114,1441 0/0:30,0:30:81.23:0,81,995 0/0:28,0:28:57.16:0,57,727 0/0:29,0:29:78.24:0,78,974 0/0:29,0:29:72.23:0,72,938 0/0:23,0:23:63.20:0,63,810 0/0:36,0:36:90.28:0,90,1150 0/0:36,0:36:90.28:0,90,1144 0/0:24,0:24:66.20:0,66,817 0/0:22,0:22:45.14:0,45,581 0/0:49,0:49:99:0,117,1428 0/0:48,0:48:99:0,129,1551 0/0:31,0:31:63.20:0,63,835 0/0:30,0:30:78.23:0,78,953 0/0:21,0:21:54.17:0,54,708 0/0:25,0:25:54.17:0,54,673 0/0:21,0:21:57.18:0,57,738 0/0:18,0:18:39.12:0,39,507 0/0:25,0:25:63.19:0,63,796 0/0:17,0:17:39.12:0,39,491 0/0:18,0:18:39.12:0,39,503 -chr1 908325 . A C 267.79 . AC=14;AF=0.1167;AN=120;BaseQRankSum=-17.215;DP=1827;Dels=0.00;FS=693.401;HRun=2;HaplotypeScore=3.2868;InbreedingCoeff=-0.1506;MQ=55.13;MQ0=0;MQRankSum=-1.642;QD=0.79;ReadPosRankSum=0.894;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T363P|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T375P|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acc/Ccc|T415P|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,missense_variant|Acc/Ccc|T/P|ENSG00000187583|PLEKHN1|ENST00000379409|10/15|probably_damaging(0.998)|tolerated(0.08)|415/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,missense_variant|Acc/Ccc|T/P|ENSG00000187583|PLEKHN1|ENST00000379407|11/15|probably_damaging(0.998)|tolerated(0.09)|375/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,missense_variant|Acc/Ccc|T/P|ENSG00000187583|PLEKHN1|ENST00000379410|11/16|probably_damaging(0.995)|tolerated(0.11)|363/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,2:6:6.02:0,6,80 0/0:3,0:3:9.03:0,9,110 0/1:6,1:7:14.44:14,0,177 0/0:2,0:2:6.02:0,6,81 0/0:14,2:16:11.68:0,12,517 0/0:5,0:5:15.05:0,15,199 0/0:18,1:19:14.17:0,14,628 0/0:4,1:5:12.04:0,12,154 0/1:11,4:15:57.27:57,0,330 0/0:19,1:20:34.49:0,34,690 0/0:9,1:10:27.09:0,27,350 0/0:9,1:10:27.09:0,27,356 0/0:8,2:10:21.06:0,21,264 0/0:18,8:26:44.91:0,45,522 0/1:23,12:35:6.65:7,0,591 0/1:13,9:22:60.52:61,0,259 0/1:24,13:37:35.24:35,0,581 0/1:17,13:30:23.45:23,0,374 0/0:22,8:30:60.17:0,60,755 0/0:12,10:22:2.48:0,2,313 0/1:9,6:15:3.53:4,0,260 0/0:18,12:30:11.70:0,12,477 0/1:16,6:22:17.97:18,0,448 0/0:21,8:29:17.70:0,18,554 0/1:13,10:23:32.15:32,0,312 0/0:13,4:17:0.91:0,1,310 0/1:14,7:21:18.92:19,0,371 0/1:6,6:12:48.84:49,0,113 0/0:17,8:25:27.94:0,28,364 0/1:19,7:26:2.04:2,0,561 0/1:24,11:36:78.73:79,0,507 0/0:15,10:25:38.91:0,39,485 0/0:21,7:28:51.14:0,51,630 0/0:18,12:30:42.12:0,42,503 0/0:10,8:18:0.40:0,0,267 0/0:22,2:24:46.35:0,46,517 0/1:27,11:38:26.91:27,0,604 0/0:22,12:34:49.90:0,50,549 0/0:29,6:36:41.57:0,42,803 0/0:64,19:83:92.07:0,92,1856 0/0:51,9:60:99:0,137,1750 0/0:32,7:39:78.23:0,78,965 0/0:29,12:41:14.19:0,14,822 0/0:35,8:44:45.94:0,46,1130 0/0:39,4:43:52.90:0,53,996 0/0:37,10:47:16.64:0,17,1149 0/0:60,18:78:99:0,145,1813 0/0:34,5:39:90.24:0,90,1089 0/0:42,5:47:79.62:0,80,1303 0/0:50,11:61:99:0,102,1189 0/0:50,16:66:56.04:0,56,1242 0/0:43,3:46:99:0,99,1176 0/0:38,7:46:62.31:0,62,1125 0/0:40,7:47:73.73:0,74,1209 0/0:35,8:43:72.20:0,72,866 0/0:30,8:38:78.22:0,78,961 0/0:20,5:25:51.15:0,51,632 0/0:35,13:48:0.81:0,1,951 0/0:25,3:29:44.53:0,45,796 0/0:28,8:36:12.16:0,12,805 -chr1 908414 . C T 3063.53 . AC=7;AF=0.0583;AN=120;BaseQRankSum=-1.682;DP=2413;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.8594;InbreedingCoeff=-0.0636;MQ=57.64;MQ0=0;MQRankSum=2.858;QD=12.66;ReadPosRankSum=0.752;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|11),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|11),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|10),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:18.05:0,18,219 0/0:3,0:3:9.03:0,9,113 0/0:7,0:7:21.07:0,21,272 0/0:6,0:6:18.06:0,18,232 0/0:15,0:15:42.14:0,42,575 0/0:7,0:7:21.07:0,21,279 0/0:24,0:24:66.21:0,66,858 0/0:10,0:10:30.10:0,30,405 0/0:32,0:32:96.30:0,96,1266 0/0:25,0:25:75.23:0,75,981 0/0:12,0:12:36.09:0,36,452 0/0:18,0:18:54.15:0,54,691 0/0:19,0:19:57.18:0,57,733 0/0:21,0:21:45.15:0,45,624 0/0:30,0:30:78.25:0,78,1025 0/0:11,0:11:33.08:0,33,396 0/0:14,0:14:39.13:0,39,516 0/0:18,0:18:54.18:0,54,712 0/0:19,0:19:48.12:0,48,596 0/0:15,0:15:36.11:0,36,475 0/1:12,6:18:99:182,0,311 0/0:31,0:31:78.25:0,78,1035 0/0:23,0:23:57.18:0,57,763 0/0:21,0:21:45.14:0,45,600 0/0:13,0:13:36.10:0,36,451 0/0:8,0:8:21.07:0,21,269 0/1:8,7:15:99:194,0,270 0/0:8,0:8:21.07:0,21,272 0/0:12,0:13:33.10:0,33,428 0/0:14,0:14:42.13:0,42,543 0/0:21,0:21:45.15:0,45,603 0/0:13,0:13:33.11:0,33,445 0/0:18,0:18:48.15:0,48,634 0/1:11,7:18:99:210,0,304 0/1:9,6:15:99:188,0,245 0/0:24,0:24:60.17:0,60,791 0/1:14,9:23:99:236,0,453 0/0:19,0:19:57.17:0,57,715 0/0:66,0:66:99:0,156,2062 0/0:129,0:130:99:0,334,4296 0/0:102,0:102:99:0,244,3110 0/0:75,0:75:99:0,184,2394 0/0:63,0:64:99:0,165,2099 0/0:53,0:53:99:0,123,1630 0/0:65,0:65:99:0,165,2135 0/0:86,0:86:99:0,205,2662 0/0:121,0:121:99:0,301,3826 0/1:28,38:66:99:996,0,754 0/0:89,0:89:99:0,220,2909 0/0:106,0:107:99:0,253,3298 0/0:108,1:110:99:0,241,3556 0/0:74,0:75:99:0,181,2341 0/0:77,0:77:99:0,205,2650 0/1:39,48:87:99:1182,0,1040 0/0:75,0:75:99:0,178,2351 0/0:65,0:65:99:0,153,2026 0/0:50,0:50:99:0,117,1477 0/0:77,0:77:99:0,187,2423 0/0:67,0:67:99:0,157,2067 0/0:76,0:76:99:0,159,2127 -chr1 908823 . G A 12829.44 . AC=23;AF=0.1917;AN=120;BaseQRankSum=-0.746;DP=2383;Dels=0.00;FS=3.440;HRun=0;HaplotypeScore=1.6658;InbreedingCoeff=-0.0220;MQ=59.01;MQ0=0;MQRankSum=0.792;QD=15.61;ReadPosRankSum=1.037;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|11),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|12),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|11),UPSTREAM(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,upstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:28,0:28:75.21:0,75,895 0/0:18,0:18:45.14:0,45,562 0/1:10,10:20:99:288,0,254 0/1:13,8:21:99:250,0,331 0/0:79,0:79:99:0,229,3047 0/0:60,0:60:99:0,178,2350 0/1:62,47:110:99:1500,0,2147 0/0:53,0:53:99:0,153,1992 0/0:113,0:113:99:0,340,4501 0/0:133,0:133:99:0,388,5022 0/1:43,25:68:99:808,0,1442 0/0:72,0:72:99:0,208,2629 0/1:33,43:76:99:1457,0,1098 0/1:12,13:25:99:407,0,409 0/1:13,15:28:99:481,0,418 0/0:13,0:13:39.13:0,39,520 0/0:25,0:25:72.24:0,72,968 0/1:17,17:34:99:564,0,528 0/1:13,8:21:99:262,0,392 0/1:16,9:25:99:213,0,581 0/0:20,0:20:54.17:0,54,703 0/0:39,0:39:99:0,108,1457 0/0:24,0:24:66.21:0,66,870 0/0:14,0:14:39.12:0,39,513 0/0:29,0:29:84.27:0,84,1122 0/1:14,10:25:99:256,0,413 0/0:30,0:30:87.28:0,87,1135 0/1:9,6:15:99:192,0,316 0/0:22,0:22:66.21:0,66,858 0/0:21,0:22:60.19:0,60,786 0/0:40,0:40:99:0,105,1386 0/0:20,0:20:51.17:0,51,675 0/1:15,12:27:99:361,0,458 0/0:27,0:27:78.25:0,78,1027 0/1:18,21:39:99:583,0,555 0/1:15,13:28:99:357,0,395 0/0:34,0:34:93.28:0,93,1216 1/1:0,29:29:81.26:1089,81,0 0/0:40,0:40:99:0,99,1323 0/0:63,1:64:99:0,159,2087 0/1:16,17:33:99:526,0,380 0/0:39,0:39:99:0,102,1357 0/0:36,0:36:93.27:0,93,1202 0/0:28,0:28:60.20:0,60,840 0/0:25,0:25:66.20:0,66,883 0/0:31,0:31:75.24:0,75,980 0/1:24,32:56:99:975,0,557 0/0:16,0:16:42.13:0,42,558 0/0:40,0:40:99:0,111,1440 0/1:37,25:62:99:678,0,1032 0/1:29,26:55:99:808,0,852 0/0:42,0:42:99:0,111,1448 0/0:52,0:52:99:0,120,1606 0/0:46,0:47:99:0,123,1602 0/0:39,0:39:93.28:0,93,1217 0/0:31,0:31:75.25:0,75,1026 0/0:36,0:36:90.26:0,90,1177 0/0:41,0:41:99:0,102,1358 0/0:39,0:39:99:0,102,1360 1/1:0,24:24:57.19:777,57,0 -chr1 909053 . G A 230.8 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.716;DP=1523;Dels=0.00;FS=1.669;HRun=1;HaplotypeScore=1.0522;InbreedingCoeff=-0.0166;MQ=59.32;MQ0=0;MQRankSum=-0.371;QD=14.43;ReadPosRankSum=0.854;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|1),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|12),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|13),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|12);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:10,0:10:21.05:0,21,243 0/0:15,0:16:39.11:0,39,475 0/0:25,0:25:72.20:0,72,890 0/0:12,0:12:27.08:0,27,341 0/0:43,0:43:99:0,129,1713 0/0:33,0:33:90.29:0,90,1183 0/0:75,1:76:99:0,217,2819 0/0:44,0:44:99:0,126,1679 0/0:101,0:101:99:0,295,3894 0/0:105,0:105:99:0,304,3905 0/0:43,0:43:99:0,126,1686 0/0:39,0:39:99:0,117,1535 0/0:59,0:60:99:0,175,2277 0/0:37,0:37:99:0,102,1354 0/0:30,0:30:84.23:0,84,1054 0/0:31,0:31:81.24:0,81,1069 0/0:28,0:28:66.21:0,66,868 0/0:36,0:36:99:0,102,1307 0/0:28,0:29:75.24:0,75,975 0/0:38,0:38:99:0,108,1436 0/0:29,0:29:87.28:0,87,1139 0/0:33,0:33:96.31:0,96,1263 0/0:24,0:25:66.22:0,66,891 0/0:22,0:22:60.19:0,60,777 0/0:23,0:23:69.21:0,69,895 0/0:28,0:29:81.24:0,81,1027 0/0:24,0:24:69.21:0,69,872 0/0:13,0:13:36.12:0,36,479 0/0:36,0:36:93.29:0,93,1220 0/0:32,0:32:93.28:0,93,1189 0/0:31,0:31:81.24:0,81,1054 0/0:23,0:23:66.21:0,66,873 0/0:33,0:33:93.31:0,93,1253 0/0:42,0:42:99:0,117,1477 0/0:25,0:25:66.21:0,66,863 0/0:38,0:38:99:0,102,1328 0/0:32,0:32:84.27:0,84,1107 0/0:33,0:33:96.28:0,96,1221 0/0:6,0:6:15.03:0,15,179 0/0:14,0:14:42.10:0,42,517 0/0:7,0:8:18.06:0,18,236 0/0:8,0:8:21.07:0,21,288 0/0:4,0:4:12.04:0,12,149 0/0:8,0:8:12.04:0,12,174 0/0:3,0:3:6.02:0,6,76 0/0:4,0:4:12.04:0,12,139 0/0:14,0:14:39.10:0,39,495 0/0:3,0:3:9.03:0,9,106 0/0:9,0:9:21.04:0,21,274 0/0:13,0:13:36.11:0,36,466 0/1:6,10:16:99:278,0,187 0/0:6,0:6:15.05:0,15,211 0/0:11,0:11:27.09:0,27,354 0/0:6,0:6:15.03:0,15,188 0/0:3,0:3:9.03:0,9,122 0/0:5,0:5:12.04:0,12,158 0/0:5,0:5:15.05:0,15,209 0/0:7,0:8:18.06:0,18,231 0/0:4,0:4:12.04:0,12,153 0/0:5,0:5:12.04:0,12,167 -chr1 909073 . C T 14861.74 . AC=51;AF=0.4250;AN=120;BaseQRankSum=-2.886;DP=1297;Dels=0.00;FS=1.649;HRun=1;HaplotypeScore=0.9560;InbreedingCoeff=-0.2187;MQ=59.41;MQ0=0;MQRankSum=-0.581;QD=17.08;ReadPosRankSum=-1.066;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|1),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|12),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|13),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|12);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/1:5,2:7:19.74:20,0,155 0/1:8,6:14:99:186,0,227 0/1:10,10:20:99:327,0,337 0/1:7,6:14:99:179,0,222 1/1:0,35:35:99:1353,102,0 1/1:0,34:34:96.26:1224,96,0 0/0:62,0:62:99:0,184,2448 0/1:16,18:34:99:619,0,539 0/0:88,0:88:99:0,262,3471 0/1:53,39:92:99:1189,0,1771 0/1:13,29:42:99:1019,0,391 0/0:34,0:34:99:0,102,1375 0/1:24,24:48:99:776,0,772 0/1:20,10:30:99:266,0,618 0/1:11,18:29:99:608,0,304 0/1:13,11:24:99:293,0,439 0/1:14,8:22:99:180,0,426 0/1:18,14:32:99:353,0,604 0/1:7,16:23:99:484,0,230 0/0:28,0:28:81.26:0,81,1076 0/0:20,0:20:60.19:0,60,784 0/1:9,14:23:99:401,0,302 0/1:12,6:18:99:173,0,396 0/1:10,6:16:99:178,0,355 0/1:12,5:17:99:146,0,417 0/1:10,11:21:99:373,0,326 0/0:21,0:21:60.19:0,60,778 0/1:6,5:11:99:166,0,202 0/1:14,19:33:99:574,0,427 0/1:13,12:25:99:355,0,439 0/1:17,9:27:99:232,0,491 0/1:10,8:18:99:250,0,335 0/1:14,14:28:99:436,0,440 0/0:36,0:36:99:0,102,1303 0/0:25,0:25:69.22:0,69,909 0/1:11,21:32:99:727,0,268 0/0:32,0:32:81.24:0,81,1034 0/0:25,0:25:75.23:0,75,953 1/1:0,6:6:18.06:225,18,0 0/1:5,5:11:99:139,0,154 0/0:8,0:8:21.06:0,21,274 0/1:3,7:10:94.36:211,0,94 0/1:3,2:5:21.42:21,0,89 1/1:0,9:10:18.05:218,18,0 0/1:2,2:4:60.11:64,0,60 1/1:0,4:4:9.02:99,9,0 0/1:7,5:12:99:117,0,244 1/1:0,2:2:6.02:76,6,0 0/0:8,0:8:18.06:0,18,250 0/0:12,0:12:30.10:0,30,404 0/0:14,0:14:36.12:0,36,470 0/1:2,3:5:32.73:102,0,33 0/1:4,4:9:96.50:140,0,97 0/1:5,1:6:22.75:23,0,142 0/0:4,0:4:9.03:0,9,125 1/1:0,3:3:9.03:116,9,0 1/1:0,5:5:15.02:172,15,0 0/1:7,2:9:53.55:54,0,209 0/0:4,0:4:12.04:0,12,158 0/0:6,0:6:15.05:0,15,191 -chr1 909221 . T C 1120.5 . AC=5;AF=0.0417;AN=120;BaseQRankSum=-0.121;DP=1389;Dels=0.00;FS=9.505;HRun=0;HaplotypeScore=0.7261;InbreedingCoeff=-0.0453;MQ=58.91;MQ0=0;MQRankSum=0.284;QD=11.55;ReadPosRankSum=3.442;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S446|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S46|176|PLEKHN1|protein_coding|CODING|ENST00000491024|),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S481|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S533|663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,synonymous_variant|agT/agC|S|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|||46/176|protein_coding|1,synonymous_variant|agT/agC|S|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|||533/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,synonymous_variant|agT/agC|S|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|||446/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|agT/agC|S|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|||481/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:20,0:20:54.14:0,54,623 0/0:17,1:18:48.15:0,48,603 0/0:13,0:13:30.09:0,30,374 0/0:12,0:12:36.11:0,36,455 0/0:26,0:26:75.24:0,75,983 0/0:37,1:38:99:0,108,1397 0/0:53,0:53:99:0,150,1966 0/0:31,0:31:90.28:0,90,1161 0/0:81,0:81:99:0,241,3145 0/0:85,0:85:99:0,253,3233 0/0:29,0:29:87.28:0,87,1151 0/0:34,0:34:99:0,99,1284 0/0:40,0:40:99:0,108,1373 0/0:19,0:19:36.11:0,36,473 0/0:20,0:20:54.17:0,54,692 0/0:15,0:15:36.12:0,36,471 0/0:17,0:17:42.11:0,42,529 0/0:21,0:21:54.15:0,54,684 0/0:23,0:23:60.19:0,60,786 0/1:11,10:21:99:276,0,316 0/0:16,0:16:36.12:0,36,471 0/0:21,0:21:57.18:0,57,757 0/0:12,0:13:33.11:0,33,450 0/0:23,0:23:54.17:0,54,713 0/0:15,0:15:42.11:0,42,535 0/0:38,1:39:90.29:0,90,1208 0/0:26,0:26:69.22:0,69,898 0/0:15,0:15:45.12:0,45,544 0/0:30,0:30:72.23:0,72,949 0/0:33,0:33:78.25:0,78,1032 0/0:38,0:39:96.30:0,96,1264 0/0:22,0:22:45.14:0,45,582 0/0:35,0:36:78.22:0,78,1009 0/0:24,0:25:57.18:0,57,747 0/0:21,0:21:51.15:0,51,667 0/0:15,0:15:39.11:0,39,485 0/1:17,9:27:99:189,0,443 0/0:33,0:33:84.26:0,84,1098 0/0:6,0:6:15.04:0,15,177 0/0:29,0:29:69.22:0,69,901 0/0:18,0:18:48.15:0,48,602 0/0:16,0:16:36.10:0,36,458 0/1:6,9:15:99:243,0,195 0/0:20,1:21:9.40:0,9,561 0/0:11,0:11:33.10:0,33,425 0/0:12,0:12:27.08:0,27,351 0/0:18,1:19:39.13:0,39,511 0/0:11,0:11:24.07:0,24,307 0/1:4,7:11:45.81:212,0,46 0/0:25,0:25:60.18:0,60,761 0/0:17,0:18:45.14:0,45,588 0/1:11,12:23:99:305,0,232 0/0:15,0:15:30.10:0,30,395 0/0:11,0:11:27.08:0,27,350 0/0:11,0:12:30.09:0,30,376 0/0:8,0:8:15.05:0,15,205 0/0:7,0:7:18.06:0,18,249 0/0:16,0:16:39.12:0,39,498 0/0:12,0:12:33.10:0,33,408 0/0:8,0:8:21.07:0,21,269 -chr1 909222 . G A 252.5 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.084;DP=1392;Dels=0.00;FS=1.211;HRun=0;HaplotypeScore=0.7091;InbreedingCoeff=-0.0090;MQ=58.92;MQ0=0;MQRankSum=0.700;QD=9.71;ReadPosRankSum=0.715;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A447T|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A47T|176|PLEKHN1|protein_coding|CODING|ENST00000491024|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A482T|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A534T|663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,missense_variant|Gcc/Acc|A/T|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|benign(0.273)|tolerated(0.13)|47/176|protein_coding|1,missense_variant|Gcc/Acc|A/T|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|benign(0.273)|tolerated(0.47)|534/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,missense_variant|Gcc/Acc|A/T|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|benign(0.273)|tolerated(0.34)|447/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,missense_variant|Gcc/Acc|A/T|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|benign(0.273)|tolerated(0.48)|482/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:18,0:18:48.13:0,48,566 0/0:18,0:18:48.15:0,48,599 0/0:10,0:10:30.07:0,30,369 0/0:12,0:12:36.12:0,36,471 0/0:25,0:25:72.24:0,72,968 0/0:38,0:38:99:0,108,1409 0/0:52,0:52:99:0,147,1927 0/0:29,0:29:84.28:0,84,1123 0/0:82,0:82:99:0,247,3265 0/0:84,0:84:99:0,247,3182 0/0:29,0:29:87.28:0,87,1152 0/0:36,0:36:99:0,105,1366 0/0:38,0:38:99:0,111,1439 0/0:19,0:19:42.13:0,42,552 0/0:20,0:20:54.17:0,54,688 0/0:14,0:15:36.12:0,36,487 0/0:17,0:17:45.10:0,45,553 0/0:20,1:21:51.16:0,51,657 0/0:23,0:23:60.19:0,60,783 0/0:21,0:21:54.17:0,54,712 0/0:16,0:16:36.12:0,36,480 0/0:21,0:21:54.18:0,54,736 0/0:13,0:13:33.11:0,33,454 0/0:22,0:22:54.18:0,54,723 0/0:16,0:16:39.13:0,39,526 0/0:41,0:41:93.30:0,93,1268 0/0:26,0:26:69.22:0,69,911 0/0:16,0:16:45.13:0,45,568 0/0:30,0:30:66.21:0,66,878 0/0:32,0:32:78.25:0,78,1042 0/0:41,0:41:96.31:0,96,1265 0/0:22,0:22:48.15:0,48,633 0/0:36,0:36:81.25:0,81,1068 0/1:13,13:26:99:300,0,362 0/0:21,0:21:51.16:0,51,685 0/0:16,0:16:45.13:0,45,550 0/0:27,0:27:63.20:0,63,821 0/0:33,0:33:87.28:0,87,1154 0/0:7,0:7:18.05:0,18,213 0/0:30,0:30:75.23:0,75,972 0/0:18,0:18:48.14:0,48,592 0/0:16,0:16:39.10:0,39,502 0/0:15,0:15:36.12:0,36,473 0/0:21,0:21:54.14:0,54,687 0/0:11,0:11:33.11:0,33,428 0/0:12,0:13:27.09:0,27,358 0/0:19,0:19:42.11:0,42,534 0/0:11,0:11:24.08:0,24,314 0/0:10,0:10:24.08:0,24,316 0/0:24,0:24:57.18:0,57,732 0/0:18,0:18:45.14:0,45,603 0/0:23,0:23:51.16:0,51,675 0/0:17,0:17:36.11:0,36,464 0/0:12,0:12:27.09:0,27,349 0/0:12,0:12:30.09:0,30,379 0/0:9,0:9:18.06:0,18,241 0/0:7,0:7:18.06:0,18,252 0/0:16,0:16:42.12:0,42,528 0/0:13,0:13:33.09:0,33,419 0/0:8,0:8:21.07:0,21,272 -chr1 909238 . G C 30583.03 . AC=81;AF=0.6750;AN=120;BaseQRankSum=0.003;DP=1510;Dels=0.00;FS=15.547;HRun=1;HaplotypeScore=2.2700;InbreedingCoeff=-0.0333;MQ=58.99;MQ0=0;MQRankSum=-0.442;QD=22.47;ReadPosRankSum=2.247;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cCt|R452P|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cCt|R487P|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cCt|R52P|176|PLEKHN1|protein_coding|CODING|ENST00000491024|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cCt|R539P|663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,missense_variant|cGt/cCt|R/P|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|benign(0)|tolerated(0.17)|52/176|protein_coding|1,missense_variant|cGt/cCt|R/P|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|benign(0)|tolerated(0.25)|539/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,missense_variant|cGt/cCt|R/P|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|benign(0)|tolerated(0.23)|452/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,missense_variant|cGt/cCt|R/P|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|benign(0)|tolerated(0.23)|487/611|protein_coding|1 GT:AD:DP:GQ:PL 0/1:9,8:17:99:169,0,240 0/1:8,6:14:99:149,0,265 1/1:0,15:15:42.13:524,42,0 1/1:0,11:11:33.11:423,33,0 1/1:0,25:25:75.25:1009,75,0 1/1:0,33:33:99:1299,99,0 0/1:35,32:67:99:1020,0,1073 0/1:17,14:31:99:453,0,529 0/1:44,42:86:99:1374,0,1439 0/1:45,35:80:99:1126,0,1478 1/1:0,28:28:84.26:1093,84,0 0/0:41,0:41:99:0,120,1573 1/1:0,36:36:99:1376,105,0 1/1:0,21:21:45.15:605,45,0 1/1:0,26:26:72.23:941,72,0 0/1:7,10:17:99:276,0,230 0/1:9,9:18:99:245,0,270 1/1:0,23:23:51.14:666,51,0 1/1:0,26:26:57.19:771,57,0 0/1:12,12:24:99:346,0,315 0/1:10,9:19:99:236,0,263 0/1:16,9:25:99:246,0,470 0/1:10,8:18:99:169,0,278 0/1:9,16:25:99:491,0,235 0/1:11,6:17:99:188,0,292 1/1:0,44:44:99:1345,99,0 1/1:0,28:28:63.20:837,63,0 1/1:0,16:16:42.13:548,42,0 0/1:12,22:34:99:648,0,309 0/1:11,19:30:99:530,0,364 0/1:16,21:37:99:575,0,441 1/1:0,26:26:60.19:796,60,0 1/1:0,33:33:81.26:1063,81,0 0/1:14,15:29:99:367,0,412 1/1:0,21:21:51.15:655,51,0 1/1:0,15:15:39.13:519,39,0 0/1:8,21:30:99:571,0,149 1/1:0,33:33:78.26:1059,78,0 1/1:0,8:8:21.06:248,21,0 0/0:36,0:36:81.21:0,81,1035 1/1:0,22:22:54.17:694,54,0 0/1:12,7:19:99:230,0,276 0/1:9,6:15:99:181,0,206 1/1:1,19:20:11.85:593,12,0 1/1:0,13:13:36.12:486,36,0 0/1:11,3:14:77.07:77,0,245 1/1:0,23:23:48.16:648,48,0 0/1:5,5:10:99:140,0,119 0/0:19,0:19:42.14:0,42,566 0/1:17,12:29:99:314,0,456 0/1:12,9:21:99:237,0,344 0/1:10,12:22:99:235,0,314 1/1:1,19:20:5.14:520,5,0 0/1:3,10:13:83.49:233,0,83 0/0:14,0:14:36.11:0,36,475 1/1:0,12:12:24.08:316,24,0 1/1:0,10:10:24.08:330,24,0 0/0:20,0:20:45.14:0,45,595 0/0:19,0:19:33.11:0,33,442 1/1:0,12:12:30.10:389,30,0 -chr1 909242 . A G 1739.34 . AC=6;AF=0.0500;AN=120;BaseQRankSum=1.162;DP=1524;Dels=0.00;FS=7.264;HRun=2;HaplotypeScore=2.2302;InbreedingCoeff=-0.0532;MQ=58.97;MQ0=0;MQRankSum=0.469;QD=11.75;ReadPosRankSum=2.640;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G453|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G488|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G53|176|PLEKHN1|protein_coding|CODING|ENST00000491024|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G540|663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,synonymous_variant|ggA/ggG|G|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|||53/176|protein_coding|1,synonymous_variant|ggA/ggG|G|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|||540/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,synonymous_variant|ggA/ggG|G|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|||453/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|ggA/ggG|G|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|||488/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:16,0:16:39.12:0,39,476 0/0:13,0:13:36.11:0,36,453 0/0:15,0:15:39.12:0,39,490 0/0:11,0:11:33.10:0,33,411 0/0:25,0:25:72.23:0,72,947 0/0:33,0:33:96.31:0,96,1243 0/0:62,1:65:99:0,181,2245 0/0:32,0:33:87.27:0,87,1113 0/0:85,0:85:99:0,247,3125 0/0:85,0:85:99:0,250,3126 0/0:29,0:29:87.24:0,87,1086 0/0:42,1:43:99:0,117,1514 0/0:32,0:32:93.27:0,93,1173 0/0:18,0:20:36.11:0,36,468 0/0:24,1:27:66.18:0,66,810 0/0:19,0:19:39.10:0,39,499 0/0:14,0:16:39.09:0,39,483 0/0:20,0:22:45.13:0,45,586 0/0:24,1:25:57.18:0,57,752 0/0:23,0:23:57.18:0,57,729 0/0:21,0:21:45.11:0,45,550 0/0:25,0:25:63.19:0,63,819 0/0:18,0:18:39.11:0,39,494 0/0:26,0:26:60.15:0,60,751 0/0:19,0:20:48.14:0,48,611 0/0:43,0:43:93.27:0,93,1213 0/1:15,12:27:99:284,0,320 0/0:15,0:15:39.12:0,39,495 0/0:31,0:32:78.24:0,78,1022 0/0:29,0:29:72.20:0,72,905 0/0:34,0:35:69.19:0,69,860 0/0:26,0:26:57.14:0,57,705 0/0:31,0:32:72.18:0,72,897 0/0:32,0:32:72.21:0,72,917 0/1:10,13:23:99:308,0,256 0/0:15,0:17:33.08:0,33,417 0/1:10,23:33:99:604,0,211 0/0:34,0:34:75.21:0,75,962 0/0:8,0:8:21.06:0,21,244 0/0:34,0:37:75.20:0,75,923 0/0:21,0:22:54.09:0,54,621 0/0:18,0:19:45.13:0,45,573 0/0:14,0:14:30.08:0,30,363 0/0:19,0:20:45.13:0,45,579 0/0:14,0:14:39.11:0,39,499 0/0:12,0:12:24.07:0,24,304 0/0:24,0:25:45.11:0,45,542 0/0:7,0:8:18.06:0,18,230 0/0:19,0:19:39.09:0,39,492 0/1:16,11:29:99:243,0,353 0/0:22,0:22:54.16:0,54,688 0/0:23,3:26:51.14:0,51,622 0/1:14,7:21:99:196,0,342 0/1:4,8:15:99:220,0,124 0/0:12,0:12:27.08:0,27,355 0/0:12,0:12:18.06:0,18,235 0/0:9,0:9:21.06:0,21,278 0/0:20,0:20:45.13:0,45,576 0/0:19,0:20:33.10:0,33,431 0/0:12,0:13:27.08:0,27,354 -chr1 909309 . T C 7707.57 . AC=26;AF=0.2167;AN=120;BaseQRankSum=5.567;DP=1519;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.7523;InbreedingCoeff=-0.0786;MQ=58.79;MQ0=0;MQRankSum=1.234;QD=13.69;ReadPosRankSum=1.249;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S476P|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S511P|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S563P|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S76P|176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,missense_variant|Tcc/Ccc|S/P|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|benign(0.013)|tolerated(0.25)|76/176|protein_coding|1,missense_variant|Tcc/Ccc|S/P|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|benign(0.013)|tolerated(0.3)|563/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,missense_variant|Tcc/Ccc|S/P|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|benign(0)|tolerated(0.3)|476/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,missense_variant|Tcc/Ccc|S/P|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|benign(0.02)|tolerated(0.29)|511/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:18.05:0,18,220 0/0:19,0:19:51.08:0,51,566 0/1:7,11:18:99:310,0,217 0/1:8,1:9:14.54:15,0,206 0/0:34,0:34:99:0,102,1245 0/0:31,0:31:90.21:0,90,1070 0/1:26,23:49:99:736,0,734 0/0:38,0:38:99:0,99,1263 0/0:81,0:82:99:0,229,2865 0/0:67,1:68:99:0,189,2322 0/1:16,14:30:99:455,0,471 0/0:21,0:21:60.14:0,60,699 0/1:26,18:44:99:495,0,766 0/1:6,12:18:99:357,0,147 0/1:17,10:27:99:223,0,464 0/0:22,0:23:54.14:0,54,683 0/1:7,8:15:99:207,0,164 0/1:12,5:17:99:162,0,275 0/1:19,4:23:23.19:23,0,592 0/1:12,10:22:99:244,0,345 0/0:24,0:24:60.19:0,60,777 0/0:29,0:29:69.20:0,69,908 0/0:20,1:21:42.12:0,42,534 0/0:30,0:30:72.23:0,72,942 0/0:20,0:20:51.13:0,51,636 0/1:22,15:37:99:401,0,558 0/1:10,11:21:99:303,0,254 0/1:6,6:12:99:164,0,172 0/0:31,0:31:69.18:0,69,851 0/0:30,1:31:72.23:0,72,934 0/0:36,2:38:90.26:0,90,1140 0/0:26,0:26:54.12:0,54,691 0/1:17,12:29:99:249,0,462 0/0:25,0:25:57.16:0,57,743 0/1:11,10:21:99:175,0,264 0/0:17,2:20:2.15:0,2,460 0/0:30,0:30:60.18:0,60,776 1/1:0,39:39:96.31:1292,96,0 0/0:13,0:13:24.05:0,24,302 0/0:39,1:40:96.28:0,96,1235 0/1:14,10:24:99:227,0,419 0/1:15,2:17:0.90:1,0,341 0/0:18,0:18:42.10:0,42,505 0/0:17,1:18:39.10:0,39,454 0/1:9,8:17:99:205,0,212 0/0:17,0:17:36.10:0,36,459 0/1:13,13:26:99:402,0,355 0/1:3,7:10:84.13:180,0,84 0/0:28,0:28:51.16:0,51,705 0/0:22,0:22:42.12:0,42,539 0/1:7,9:16:99:222,0,206 0/0:20,1:21:45.14:0,45,597 0/0:23,1:24:45.13:0,45,569 0/0:22,0:22:54.14:0,54,686 0/0:16,0:16:30.09:0,30,381 0/0:12,0:12:33.10:0,33,425 0/0:13,0:13:33.09:0,33,417 0/0:22,0:22:48.14:0,48,581 0/0:22,0:22:48.15:0,48,628 1/1:0,22:22:48.16:659,48,0 -chr1 909320 . C T 232.62 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.426;DP=1387;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.8928;InbreedingCoeff=-0.0090;MQ=58.83;MQ0=0;MQRankSum=0.287;QD=10.57;ReadPosRankSum=2.476;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P479|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P514|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P566|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P79|176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,synonymous_variant|ccC/ccT|P|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|||79/176|protein_coding|1,synonymous_variant|ccC/ccT|P|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|||566/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,synonymous_variant|ccC/ccT|P|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|||479/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|ccC/ccT|P|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|||514/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:18.04:0,18,206 0/0:13,0:13:39.12:0,39,484 0/0:15,0:15:45.12:0,45,563 0/0:5,0:5:15.03:0,15,167 0/0:28,0:28:84.27:0,84,1117 0/0:32,0:32:96.27:0,96,1235 0/0:39,0:39:99:0,111,1474 0/0:35,0:35:99:0,102,1361 0/0:80,0:81:99:0,235,3120 0/0:66,0:66:99:0,199,2612 0/0:23,0:23:63.20:0,63,836 0/0:19,0:19:57.18:0,57,723 0/0:39,0:40:99:0,117,1518 0/0:13,0:13:30.10:0,30,417 0/0:29,0:29:72.23:0,72,967 0/0:18,0:19:45.15:0,45,619 0/0:14,0:14:36.11:0,36,464 0/0:13,0:13:33.10:0,33,435 0/0:16,0:16:42.12:0,42,549 0/0:20,0:21:57.18:0,57,726 0/1:11,11:22:99:280,0,323 0/0:31,0:31:66.22:0,66,902 0/0:19,0:19:48.15:0,48,643 0/0:26,0:26:63.20:0,63,834 0/0:19,0:19:51.17:0,51,686 0/0:30,0:30:75.24:0,75,999 0/0:24,0:24:57.17:0,57,739 0/0:15,0:15:39.12:0,39,493 0/0:30,0:31:66.21:0,66,887 0/0:31,0:31:75.24:0,75,990 0/0:32,0:32:84.27:0,84,1090 0/0:22,0:22:51.17:0,51,681 0/0:25,0:25:54.17:0,54,725 0/0:22,0:22:54.17:0,54,705 0/0:21,0:21:48.15:0,48,620 0/0:19,0:19:39.13:0,39,542 0/0:25,0:25:63.20:0,63,842 0/0:39,0:39:99:0,99,1332 0/0:14,0:14:27.08:0,27,340 0/0:33,0:33:75.23:0,75,963 0/0:19,0:19:48.15:0,48,621 0/0:17,0:17:39.12:0,39,491 0/0:17,0:17:48.14:0,48,610 0/0:15,0:15:36.09:0,36,435 0/0:16,0:16:36.09:0,36,455 0/0:18,0:18:42.13:0,42,552 0/0:25,0:25:60.19:0,60,791 0/0:8,0:8:18.06:0,18,240 0/0:27,0:27:54.17:0,54,745 0/0:18,1:19:45.15:0,45,596 0/0:15,0:15:42.13:0,42,533 0/0:18,0:18:42.14:0,42,559 0/0:21,0:21:42.13:0,42,556 0/0:22,0:22:51.15:0,51,645 0/0:17,0:17:33.11:0,33,450 0/0:11,0:11:30.09:0,30,384 0/0:14,0:14:36.11:0,36,467 0/0:18,0:19:45.11:0,45,551 0/0:20,0:20:45.15:0,45,610 0/0:22,0:22:42.14:0,42,599 -chr1 909326 . C T 373.87 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.393;DP=1276;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.8069;InbreedingCoeff=-0.0180;MQ=58.80;MQ0=0;MQRankSum=0.099;QD=8.90;ReadPosRankSum=1.847;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G481|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G516|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G568|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G81|176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,synonymous_variant|ggC/ggT|G|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|||81/176|protein_coding|1,synonymous_variant|ggC/ggT|G|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|||568/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,synonymous_variant|ggC/ggT|G|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|||481/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|ggC/ggT|G|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|||516/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:15.04:0,15,178 0/0:9,0:9:27.07:0,27,329 0/0:13,0:13:39.12:0,39,495 0/0:5,0:5:12.02:0,12,128 0/0:19,0:19:57.19:0,57,757 0/0:29,0:29:87.27:0,87,1142 0/0:38,0:38:99:0,108,1390 0/0:31,0:31:90.29:0,90,1192 0/0:75,0:75:99:0,223,2912 0/0:60,0:60:99:0,178,2319 0/0:25,0:25:75.24:0,75,994 0/0:19,0:19:54.16:0,54,670 0/0:34,0:35:99:0,99,1274 0/0:14,0:14:30.10:0,30,408 0/0:24,0:24:63.19:0,63,819 0/0:20,0:20:51.16:0,51,676 0/0:14,0:14:36.12:0,36,477 0/0:10,0:10:27.09:0,27,352 0/0:16,0:16:39.13:0,39,517 0/0:20,0:20:57.17:0,57,708 0/1:11,12:23:99:293,0,306 0/0:31,0:31:69.22:0,69,917 0/0:17,0:17:42.13:0,42,556 0/0:23,0:23:54.16:0,54,734 0/0:16,0:16:42.14:0,42,561 0/0:25,0:25:60.19:0,60,806 0/0:23,0:23:57.17:0,57,732 0/0:14,1:15:36.11:0,36,462 0/0:28,0:28:72.23:0,72,936 0/0:32,0:32:75.24:0,75,1006 0/0:30,0:30:75.23:0,75,970 0/0:21,0:22:54.17:0,54,706 0/0:19,0:19:48.15:0,48,622 0/1:12,7:19:99:147,0,362 0/0:20,0:20:57.17:0,57,727 0/0:18,0:19:39.13:0,39,546 0/0:23,1:24:33.51:0,34,733 0/0:39,0:39:99:0,99,1282 0/0:13,0:13:30.08:0,30,365 0/0:29,0:29:60.19:0,60,774 0/0:18,0:18:45.14:0,45,572 0/0:17,0:17:39.10:0,39,476 0/0:17,0:18:48.15:0,48,620 0/0:14,0:14:33.11:0,33,439 0/0:12,0:12:24.08:0,24,313 0/0:17,0:17:36.11:0,36,456 0/0:20,0:20:48.15:0,48,642 0/0:9,0:9:21.07:0,21,289 0/0:24,0:24:51.16:0,51,686 0/0:17,0:17:42.13:0,42,549 0/0:15,0:15:39.09:0,39,494 0/0:16,0:16:36.11:0,36,474 0/0:18,0:18:42.13:0,42,554 0/0:20,0:20:48.14:0,48,601 0/0:15,0:15:27.09:0,27,376 0/0:10,0:10:27.06:0,27,320 0/0:12,0:12:27.08:0,27,346 0/0:17,0:17:36.10:0,36,454 0/0:17,0:17:36.12:0,36,494 0/0:20,0:20:39.12:0,39,537 -chr1 909363 . A C 203.29 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.679;DP=1010;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.5429;InbreedingCoeff=-0.0117;MQ=59.04;MQ0=0;MQRankSum=0.409;QD=11.29;ReadPosRankSum=2.880;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R494|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R529|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R581|663|PLEKHN1|protein_coding|CODING|ENST00000379409|),SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R94|176|PLEKHN1|protein_coding|CODING|ENST00000491024|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,synonymous_variant|Aga/Cga|R|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|||94/176|protein_coding|1,synonymous_variant|Aga/Cga|R|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|||581/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,synonymous_variant|Aga/Cga|R|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|||494/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|Aga/Cga|R|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|||529/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:21.06:0,21,258 0/0:12,0:12:21.05:0,21,241 0/0:10,0:10:30.10:0,30,397 0/0:4,0:4:12.03:0,12,138 0/0:21,0:21:63.21:0,63,856 0/0:25,0:25:75.25:0,75,1004 0/0:37,0:37:99:0,108,1415 0/0:22,0:22:63.20:0,63,825 0/0:55,1:56:99:0,153,2012 0/0:58,0:58:99:0,169,2184 0/0:30,0:30:87.28:0,87,1141 0/0:23,0:23:69.19:0,69,875 0/0:34,0:34:99:0,102,1310 0/0:7,0:7:15.04:0,15,187 0/0:23,0:23:51.14:0,51,674 0/0:18,0:18:42.14:0,42,572 0/0:12,0:12:33.10:0,33,440 0/0:8,0:8:21.07:0,21,276 0/0:12,0:12:24.04:0,24,297 0/0:16,0:16:48.15:0,48,623 0/0:15,0:15:39.11:0,39,485 0/0:25,0:25:60.17:0,60,778 0/0:9,0:9:24.08:0,24,314 0/0:18,0:18:42.13:0,42,560 0/0:12,0:12:33.11:0,33,431 0/0:18,0:18:42.14:0,42,563 0/1:10,8:18:99:251,0,267 0/0:11,0:11:33.11:0,33,442 0/0:17,0:17:45.14:0,45,575 0/0:22,0:22:60.18:0,60,769 0/0:21,0:22:63.19:0,63,798 0/0:19,0:19:48.16:0,48,640 0/0:16,0:16:42.13:0,42,542 0/0:15,0:15:45.15:0,45,604 0/0:14,0:14:36.11:0,36,465 0/0:11,0:11:24.08:0,24,326 0/0:17,0:17:42.14:0,42,569 0/0:36,0:36:96.31:0,96,1279 0/0:8,0:8:21.06:0,21,247 0/0:25,0:26:72.21:0,72,911 0/0:18,1:19:42.14:0,42,573 0/0:18,0:18:36.11:0,36,472 0/0:17,0:17:42.14:0,42,565 0/0:7,0:7:21.04:0,21,250 0/0:8,0:8:15.05:0,15,195 0/0:13,0:13:36.09:0,36,452 0/0:13,0:13:30.10:0,30,395 0/0:4,0:4:12.04:0,12,156 0/0:13,0:13:30.10:0,30,417 0/0:10,0:10:24.08:0,24,315 0/0:12,0:12:33.10:0,33,421 0/0:9,0:9:18.06:0,18,233 0/0:15,0:15:39.12:0,39,508 0/0:11,0:11:27.08:0,27,321 0/0:8,0:8:24.08:0,24,310 0/0:3,0:3:9.02:0,9,106 0/0:11,0:11:27.09:0,27,350 0/0:12,0:12:30.09:0,30,382 0/0:8,0:8:21.04:0,21,255 0/0:15,0:15:24.08:0,24,348 -chr1 909419 . C T 1837.1 . AC=16;AF=0.1333;AN=120;BaseQRankSum=-3.072;DP=694;Dels=0.00;FS=2.424;HRun=0;HaplotypeScore=0.2284;InbreedingCoeff=-0.0370;MQ=58.46;MQ0=0;MQRankSum=0.397;QD=12.17;ReadPosRankSum=1.761;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D112|176|PLEKHN1|protein_coding|CODING|ENST00000491024|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D512|576|PLEKHN1|protein_coding|CODING|ENST00000379407|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D547|611|PLEKHN1|protein_coding|CODING|ENST00000379410|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D599|663|PLEKHN1|protein_coding|CODING|ENST00000379409|);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,synonymous_variant|gaC/gaT|D|ENSG00000187583|PLEKHN1|ENST00000491024|2/5|||112/176|protein_coding|1,synonymous_variant|gaC/gaT|D|ENSG00000187583|PLEKHN1|ENST00000379409|13/15|||599/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,synonymous_variant|gaC/gaT|D|ENSG00000187583|PLEKHN1|ENST00000379407|13/15|||512/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,synonymous_variant|gaC/gaT|D|ENSG00000187583|PLEKHN1|ENST00000379410|14/16|||547/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:6.02:0,6,77 0/0:6,0:6:15.04:0,15,179 0/0:11,0:11:30.09:0,30,373 0/0:5,0:5:15.04:0,15,180 0/0:17,0:17:48.15:0,48,636 0/0:25,0:25:69.16:0,69,852 0/1:14,20:34:99:626,0,415 0/0:20,0:20:57.18:0,57,745 0/0:39,0:39:99:0,108,1428 0/0:37,0:38:99:0,108,1405 0/0:18,0:18:54.18:0,54,723 0/0:9,0:9:27.09:0,27,359 0/0:23,0:23:69.22:0,69,903 0/0:4,0:4:12.04:0,12,149 0/0:21,0:21:57.16:0,57,724 0/0:8,0:8:21.07:0,21,285 0/1:8,1:9:16.73:17,0,220 0/0:4,0:4:12.04:0,12,148 0/0:13,0:13:27.08:0,27,353 0/1:3,5:8:94.67:170,0,95 0/0:11,0:11:30.10:0,30,390 0/0:15,0:15:42.14:0,42,548 0/1:2,3:5:61.79:71,0,62 0/1:3,1:4:21.40:21,0,94 0/1:6,5:11:99:158,0,156 0/0:9,0:9:21.07:0,21,270 0/0:6,0:6:15.05:0,15,198 0/0:5,0:5:15.05:0,15,183 0/1:5,4:9:99:120,0,157 0/0:15,0:15:45.13:0,45,553 0/0:12,0:12:36.10:0,36,430 0/0:13,0:13:33.11:0,33,441 0/0:11,0:12:27.09:0,27,349 0/0:9,0:9:18.06:0,18,245 0/0:5,0:5:15.04:0,15,179 0/0:6,0:6:12.04:0,12,158 0/1:4,7:11:99:160,0,129 0/0:22,0:22:57.15:0,57,732 0/0:7,0:7:21.05:0,21,241 0/0:21,0:21:57.18:0,57,725 0/0:17,0:17:45.13:0,45,572 0/1:9,4:13:99:118,0,260 0/1:7,7:14:99:216,0,203 0/0:6,0:6:18.04:0,18,204 0/0:9,0:9:18.05:0,18,214 0/0:6,0:6:15.05:0,15,203 0/0:8,0:9:18.06:0,18,220 0/1:2,3:5:67.77:71,0,68 1/1:0,3:3:9.03:118,9,0 0/0:10,0:11:24.08:0,24,312 0/1:9,4:13:99:123,0,217 0/1:6,1:7:17.20:17,0,176 0/0:8,0:8:21.06:0,21,268 0/0:8,0:8:18.06:0,18,231 0/0:9,0:9:15.05:0,15,188 0/0:4,0:4:12.04:0,12,155 0/0:7,0:7:18.06:0,18,239 0/0:10,0:10:24.07:0,24,307 0/1:4,1:5:17.59:18,0,96 0/0:5,0:5:15.05:0,15,189 -chr1 909523 . G A 539.82 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.755;DP=1030;Dels=0.00;FS=12.426;HRun=1;HaplotypeScore=0.5627;InbreedingCoeff=-0.0151;MQ=58.16;MQ0=0;MQRankSum=0.665;QD=10.80;ReadPosRankSum=0.177;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|2),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|13),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|14),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|13);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:10,0:10:27.08:0,27,338 0/0:10,0:10:24.04:0,24,274 0/0:7,0:7:21.07:0,21,265 0/0:7,0:7:21.06:0,21,261 0/0:17,0:17:48.13:0,48,623 0/0:26,0:26:75.25:0,75,999 0/0:30,0:30:87.29:0,87,1187 0/0:25,0:25:75.25:0,75,1016 0/0:51,0:51:99:0,147,1991 0/0:66,0:66:99:0,187,2475 0/0:32,0:32:93.31:0,93,1248 0/0:18,0:18:54.17:0,54,707 0/0:27,0:27:81.24:0,81,1041 0/0:4,0:4:12.04:0,12,155 0/0:9,0:9:27.09:0,27,348 0/0:11,0:11:30.08:0,30,379 0/0:11,0:11:33.11:0,33,431 0/0:12,0:12:36.12:0,36,463 0/0:17,0:17:48.15:0,48,610 0/0:6,0:6:15.05:0,15,203 0/0:11,0:11:30.09:0,30,395 0/0:8,0:8:18.06:0,18,225 0/0:14,0:14:36.11:0,36,463 0/0:8,0:8:18.06:0,18,237 0/0:12,0:12:36.12:0,36,475 0/0:13,0:13:33.10:0,33,430 0/0:8,0:8:24.08:0,24,322 0/0:10,0:10:27.08:0,27,339 0/0:17,0:17:48.13:0,48,607 0/0:7,0:7:21.07:0,21,268 0/0:20,0:20:51.16:0,51,654 0/0:5,0:5:15.04:0,15,183 0/1:12,1:13:0.03:0,0,388 0/0:5,0:5:15.05:0,15,192 0/0:8,0:8:24.08:0,24,314 0/0:5,0:5:15.05:0,15,195 0/0:17,0:17:51.16:0,51,655 0/0:21,0:21:57.18:0,57,751 0/0:16,0:16:45.14:0,45,573 0/0:26,0:26:75.21:0,75,938 0/0:14,0:14:42.13:0,42,537 0/0:6,0:6:18.06:0,18,226 0/0:26,0:26:78.25:0,78,1018 0/0:19,0:19:54.15:0,54,682 0/0:22,0:22:63.20:0,63,794 0/0:23,0:23:66.21:0,66,854 0/0:35,0:35:90.29:0,90,1167 0/0:13,0:13:36.11:0,36,449 0/0:15,0:15:45.14:0,45,563 0/1:17,20:37:99:587,0,564 0/0:37,0:37:99:0,105,1238 0/0:25,0:25:69.21:0,69,864 0/0:25,0:25:69.20:0,69,884 0/0:12,0:12:36.11:0,36,461 0/0:17,0:17:48.14:0,48,603 0/0:11,0:11:30.09:0,30,373 0/0:6,0:6:18.05:0,18,216 0/0:18,0:18:51.16:0,51,654 0/0:12,0:12:33.10:0,33,424 0/0:17,0:17:51.15:0,51,652 -chr1 909554 . CA C 2082.11 . AC=48;AF=0.4000;AN=120;BaseQRankSum=7.755;DP=1646;FS=15.954;HRun=1;HaplotypeScore=179.7893;InbreedingCoeff=-0.1499;MQ=58.00;MQ0=0;MQRankSum=2.728;QD=1.74;ReadPosRankSum=-12.687;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|2),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|13),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|14),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|13);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/1:8,0:8:6.82:22,0,7 0/1:15,0:15:27.97:49,0,28 0/1:9,1:10:0.18:85,0,0 0/1:15,0:15:18.57:19,0,31 0/1:38,0:38:3.62:13,0,4 0/0:35,0:35:10.38:0,10,581 0/0:53,0:53:10.83:0,11,1144 1/1:47,0:47:8.99:196,9,0 1/1:87,0:87:33.41:295,33,0 1/1:78,0:78:12.31:296,12,0 0/1:35,0:35:5.62:90,0,6 0/1:33,0:33:15.93:48,0,16 0/1:40,0:40:12.71:66,0,13 0/0:6,0:6:2.21:0,2,6 0/1:14,0:14:1.63:2,0,5 0/0:11,0:11:5.49:0,5,25 0/0:13,0:13:2.90:0,3,45 0/1:13,0:13:0.81:25,0,1 0/1:18,0:18:34.17:47,0,34 1/1:12,0:12:4.67:43,5,0 0/1:16,0:16:10.49:10,0,313 0/0:12,0:12:4.02:0,4,17 0/1:16,0:16:25.37:38,0,25 0/0:11,0:11:12.93:0,13,41 0/1:14,0:14:19.42:21,0,19 0/0:17,0:17:11.04:0,11,44 0/0:11,0:11:4.26:0,4,23 0/0:15,0:15:6.63:0,7,253 0/0:24,0:24:8.78:0,9,61 1/1:20,0:20:1.39:69,1,0 0/1:18,0:19:30.80:36,0,31 1/1:7,1:8:1.94:57,2,0 0/1:13,2:15:25.57:70,0,26 0/0:11,0:11:3.19:0,3,11 0/1:11,1:12:7.24:42,0,7 1/1:11,0:11:1.35:7,1,0 0/1:22,0:22:4.68:66,0,5 0/1:27,0:27:6.70:7,0,58 0/0:23,0:23:3.56:0,4,42 0/1:53,0:53:52.97:53,0,76 0/1:30,0:30:16.62:17,0,24 0/1:24,0:24:0.31:19,0,0 0/1:40,1:41:12.32:12,0,62 0/1:32,0:32:7.98:8,0,28 0/0:29,0:28:11.82:0,12,577 0/0:27,0:27:41.62:0,42,654 0/1:57,0:56:32.95:123,0,33 0/1:24,2:26:2.77:97,0,3 0/0:30,0:30:13.42:0,13,67 0/0:70,2:73:9.56:0,10,1516 0/1:76,0:76:48.32:79,0,48 0/1:54,1:55:33.14:33,0,65 0/1:44,1:45:66.13:66,0,73 0/0:26,0:26:7.45:0,7,31 0/1:33,1:34:21.91:40,0,22 0/1:15,0:15:1.72:2,0,17 0/1:14,0:13:1.52:2,0,14 0/1:29,1:30:26.50:36,0,27 0/1:20,0:20:16.28:16,0,24 0/0:24,0:24:22.73:0,23,90 -chr1 909555 . A G 55343.84 . AC=113;AF=0.9417;AN=120;BaseQRankSum=2.487;DP=1646;Dels=0.01;FS=6.244;HRun=6;HaplotypeScore=1.1341;InbreedingCoeff=-0.0625;MQ=58.00;MQ0=0;MQRankSum=0.381;QD=33.62;ReadPosRankSum=-0.430;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|2),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|13),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|14),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|13);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,7:8:18.06:233,18,0 1/1:0,15:15:45.14:555,45,0 1/1:0,9:9:27.08:333,27,0 1/1:0,15:15:42.11:515,42,0 1/1:0,38:38:99:1520,114,0 0/1:13,22:35:99:706,0,415 0/1:28,25:53:99:792,0,814 1/1:0,47:47:99:1839,138,0 1/1:0,87:87:99:3491,262,0 1/1:0,78:78:99:2952,226,0 1/1:0,35:35:99:1349,102,0 1/1:0,33:33:99:1283,99,0 1/1:0,40:40:99:1587,120,0 1/1:0,6:6:15.05:198,15,0 1/1:0,14:14:42.14:556,42,0 1/1:0,11:11:33.10:424,33,0 1/1:0,13:13:36.10:464,36,0 1/1:0,13:13:39.12:497,39,0 1/1:0,18:18:51.15:632,51,0 1/1:0,12:12:33.11:440,33,0 0/1:8,8:16:99:243,0,201 1/1:0,12:12:33.10:414,33,0 1/1:0,16:16:45.12:544,45,0 1/1:0,11:11:30.09:381,30,0 1/1:0,14:14:42.13:529,42,0 1/1:0,17:17:42.13:547,42,0 1/1:0,11:11:33.10:416,33,0 0/1:5,10:15:99:288,0,140 1/1:0,24:24:69.18:861,69,0 1/1:0,20:20:60.18:778,60,0 1/1:0,19:19:54.16:686,54,0 1/1:0,7:7:21.05:257,21,0 1/1:0,13:13:36.11:464,36,0 1/1:0,11:11:33.11:436,33,0 1/1:0,11:11:33.09:422,33,0 1/1:0,11:11:33.11:436,33,0 1/1:0,22:22:63.20:807,63,0 1/1:1,26:27:39.67:930,40,0 1/1:0,23:23:66.21:846,66,0 1/1:0,53:53:99:1953,153,0 1/1:0,30:30:84.27:1075,84,0 1/1:0,24:24:69.22:891,69,0 1/1:1,39:40:99:1421,111,0 1/1:0,32:32:93.28:1165,93,0 0/1:13,16:29:99:475,0,374 0/1:13,14:27:99:428,0,402 1/1:0,57:57:99:2042,163,0 1/1:0,24:24:69.22:888,69,0 1/1:0,30:30:84.25:1070,84,0 0/1:36,35:71:99:1100,0,1016 1/1:0,76:76:99:2763,220,0 1/1:0,53:54:99:1997,156,0 1/1:0,44:44:99:1538,120,0 1/1:0,26:26:75.24:961,75,0 1/1:0,33:33:96.30:1234,96,0 1/1:0,15:15:42.13:544,42,0 1/1:0,14:14:42.13:530,42,0 1/1:0,29:29:81.25:1043,81,0 1/1:0,20:20:57.17:715,57,0 1/1:0,24:24:69.21:863,69,0 -chr1 909768 . A G 183199.18 . AC=120;AF=1.0000;AN=120;BaseQRankSum=0.728;DP=5372;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=2.6976;InbreedingCoeff=-0.0000;MQ=58.76;MQ0=0;MQRankSum=2.388;QD=34.10;ReadPosRankSum=1.847;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|3),INTRON(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|14),INTRON(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|15),INTRON(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|14);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000379410||||-/611|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,31:31:84.24:1010,84,0 1/1:0,41:41:99:1322,108,0 1/1:0,33:33:90.26:1143,90,0 1/1:0,33:33:87.26:1088,87,0 1/1:0,76:77:99:2843,217,0 1/1:0,89:89:99:3473,262,0 1/1:0,139:139:99:5432,409,0 1/1:1,81:82:99:3136,235,0 1/1:0,164:164:99:6528,491,0 1/1:1,172:173:99:6698,478,0 1/1:0,94:94:99:3717,283,0 1/1:0,101:101:99:3850,295,0 1/1:0,120:121:99:4473,340,0 1/1:0,70:70:99:2354,178,0 1/1:1,87:88:99:3160,238,0 1/1:0,52:52:99:1611,120,0 1/1:0,84:85:99:2850,214,0 1/1:0,88:88:99:2961,226,0 1/1:0,80:80:99:2481,187,0 1/1:0,86:87:99:2830,211,0 1/1:0,79:79:99:2625,199,0 1/1:0,91:91:99:3090,232,0 1/1:0,84:84:99:2764,211,0 1/1:0,67:67:99:2031,150,0 1/1:0,72:72:99:2443,187,0 1/1:0,79:79:99:2460,184,0 1/1:0,101:101:99:3395,253,0 1/1:0,53:53:99:1790,135,0 1/1:0,85:85:99:2942,217,0 1/1:0,63:63:99:2091,162,0 1/1:0,85:85:99:2918,223,0 1/1:0,73:73:99:2338,172,0 1/1:0,78:78:99:2492,184,0 1/1:0,82:82:99:2670,202,0 1/1:0,58:59:99:1921,144,0 1/1:0,68:70:99:2364,175,0 1/1:0,91:92:99:3065,232,0 1/1:0,101:101:99:3579,268,0 1/1:0,74:74:99:2502,193,0 1/1:0,187:187:99:5891,445,0 1/1:1,93:95:99:2895,229,0 1/1:0,81:81:99:2678,205,0 1/1:0,83:84:99:2734,214,0 1/1:0,64:64:99:2273,172,0 1/1:0,74:74:99:2435,187,0 1/1:0,101:101:99:3423,262,0 1/1:0,156:157:99:5059,391,0 1/1:0,60:60:99:1869,144,0 1/1:0,101:101:99:3240,247,0 1/1:0,146:146:99:5052,391,0 1/1:0,150:150:99:4972,385,0 1/1:1,132:134:99:4523,346,0 1/1:0,114:114:99:3850,301,0 1/1:0,96:96:99:3122,241,0 1/1:0,100:100:99:3442,262,0 1/1:1,81:83:99:2726,208,0 1/1:0,66:66:99:2242,172,0 1/1:0,90:90:99:2839,217,0 1/1:0,72:72:99:2501,190,0 1/1:0,97:97:99:2991,223,0 -chr1 909960 . C T 318.47 . AC=1;AF=0.0085;AN=118;BaseQRankSum=-0.416;DP=1592;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.2673;InbreedingCoeff=-0.0090;MQ=58.66;MQ0=0;MQRankSum=-0.101;QD=11.80;ReadPosRankSum=1.233;EFF=DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),UTR_3_PRIME(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|4),UTR_3_PRIME(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|15),UTR_3_PRIME(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|16),UTR_3_PRIME(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|15);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,3_prime_UTR_variant|||ENSG00000187583|PLEKHN1|ENST00000491024|4/5|||-/176|protein_coding|1,3_prime_UTR_variant|||ENSG00000187583|PLEKHN1|ENST00000379409|15/15|||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187583|PLEKHN1|ENST00000379407|15/15|||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187583|PLEKHN1|ENST00000379410|16/16|||-/611|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:7,1:8:18.06:0,18,231 0/0:8,0:8:24.06:0,24,298 0/0:6,0:6:15.05:0,15,190 0/0:16,0:16:45.15:0,45,598 0/0:13,0:13:36.12:0,36,470 0/0:25,0:25:72.20:0,72,935 0/0:23,0:23:66.21:0,66,871 0/0:30,0:30:84.26:0,84,1124 0/0:37,0:37:99:0,105,1382 0/0:14,0:14:42.13:0,42,558 0/0:17,0:17:51.14:0,51,647 0/0:22,0:22:60.18:0,60,759 0/0:28,0:28:78.23:0,78,999 0/0:40,0:40:99:0,105,1351 0/0:14,0:14:36.11:0,36,456 0/0:21,0:21:54.17:0,54,706 0/0:38,0:38:90.29:0,90,1220 0/0:31,0:31:84.26:0,84,1076 0/0:21,0:21:48.15:0,48,635 0/0:24,0:24:63.20:0,63,817 0/0:28,0:28:72.23:0,72,947 0/0:30,0:30:66.19:0,66,830 0/0:26,0:26:69.22:0,69,919 0/0:29,0:29:75.22:0,75,978 0/0:33,0:33:84.26:0,84,1089 0/0:22,0:22:57.19:0,57,767 0/0:16,0:16:36.10:0,36,466 0/0:38,1:39:63.73:0,64,1249 0/0:18,0:18:48.14:0,48,603 0/0:35,0:35:84.26:0,84,1103 0/0:31,1:32:56.80:0,57,1045 0/0:27,0:27:72.23:0,72,938 0/0:31,0:31:84.25:0,84,1080 0/0:19,0:19:45.14:0,45,588 0/0:28,0:28:75.24:0,75,999 0/0:39,0:39:99:0,102,1364 0/0:42,0:42:99:0,108,1394 0/0:15,0:15:39.13:0,39,540 0/0:40,0:40:99:0,102,1296 0/0:35,0:35:90.26:0,90,1141 0/0:37,0:38:96.30:0,96,1263 0/0:27,0:27:66.20:0,66,850 0/0:22,0:22:57.18:0,57,731 0/0:24,0:24:63.20:0,63,839 0/0:38,0:38:99:0,102,1269 0/0:47,0:47:99:0,132,1699 0/0:20,0:20:42.12:0,42,547 0/0:34,0:34:81.22:0,81,1017 0/0:44,0:44:99:0,108,1368 0/0:35,0:36:87.28:0,87,1140 0/0:38,0:38:99:0,102,1271 0/0:30,0:31:87.23:0,87,1076 0/0:30,0:30:66.19:0,66,841 0/0:27,0:27:72.21:0,72,914 0/0:25,0:25:60.17:0,60,770 0/0:22,0:22:57.18:0,57,750 0/1:14,13:27:99:366,0,243 0/0:26,0:27:69.22:0,69,886 0/0:15,0:15:39.13:0,39,513 -chr1 910394 . C T 398.09 . AC=13;AF=0.361;AN=36;BaseQRankSum=1.775;DP=46;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0554;InbreedingCoeff=0.3755;MQ=58.99;MQ0=0;MQRankSum=0.823;QD=23.42;ReadPosRankSum=0.051;EFF=DOWNSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|4),UTR_3_PRIME(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|15),UTR_3_PRIME(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|16);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187583|PLEKHN1|ENST00000379410|16/16|||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,41 0/0:8,0:8:24.06:0,24,272 0/1:3,4:7:97.47:136,0,97 1/1:1,3:4:9.03:119,9,0 0/0:1,0:1:3.01:0,3,41 ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:38,3,0 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,116 1/1:0,2:2:6.02:82,6,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,72 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 0/0:5,0:5:12.04:0,12,154 ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,40 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. -chr1 910438 . A G 1374.53 . AC=42;AF=1.000;AN=42;DP=42;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=-0.1458;MQ=57.77;MQ0=0;QD=33.53;EFF=DOWNSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|4),UTR_3_PRIME(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|15),UTR_3_PRIME(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|16);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187583|PLEKHN1|ENST00000379410|16/16|||-/611|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3.01:39,3,0 1/1:0,3:3:9.03:115,9,0 1/1:0,6:6:18.06:231,18,0 1/1:0,5:5:15.04:174,15,0 1/1:0,3:3:9.03:119,9,0 ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. 1/1:0,2:2:6.02:81,6,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:34,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. 1/1:0,1:1:3.01:40,3,0 1/1:0,3:3:6.02:85,6,0 1/1:0,1:1:3.01:40,3,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. 1/1:0,1:1:3.01:38,3,0 1/1:0,1:1:3.01:33,3,0 ./. ./. 1/1:0,1:1:2.99:23,3,0 1/1:0,3:3:6.02:73,6,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. 1/1:0,1:1:3.01:41,3,0 ./. 1/1:0,2:2:6:63,6,0 ./. ./. ./. ./. -chr1 910473 . G A 299.74 . AC=11;AF=0.250;AN=44;BaseQRankSum=-1.316;DP=64;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;InbreedingCoeff=0.1771;MQ=59.28;MQ0=0;MQRankSum=0.212;QD=12.49;ReadPosRankSum=-0.144;EFF=DOWNSTREAM(MODIFIER||||663|PLEKHN1|protein_coding|CODING|ENST00000379409|),DOWNSTREAM(MODIFIER||||676|C1orf170|protein_coding|CODING|ENST00000341290|),DOWNSTREAM(MODIFIER||||696|C1orf170|protein_coding|CODING|ENST00000433179|),DOWNSTREAM(MODIFIER|||||C1orf170|retained_intron|CODING|ENST00000479361|),DOWNSTREAM(MODIFIER|||||PLEKHN1|retained_intron|CODING|ENST00000480267|),INTRON(MODIFIER||||176|PLEKHN1|protein_coding|CODING|ENST00000491024|4),UTR_3_PRIME(MODIFIER||||576|PLEKHN1|protein_coding|CODING|ENST00000379407|15),UTR_3_PRIME(MODIFIER||||611|PLEKHN1|protein_coding|CODING|ENST00000379410|16);CSQ=downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000341290||||-/676|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000433179||||-/696|protein_coding|1,intron_variant|||ENSG00000187583|PLEKHN1|ENST00000491024||||-/176|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379409||||-/663|protein_coding|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000480267|||||retained_intron|1,downstream_gene_variant|||ENSG00000187583|PLEKHN1|ENST00000379407||||-/576|protein_coding|1,downstream_gene_variant|||ENSG00000187642|C1orf170|ENST00000479361|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000187583|PLEKHN1|ENST00000379410|16/16|||-/611|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:21.07:0,21,275 0/0:6,0:6:18.03:0,18,200 0/1:7,3:10:88.54:89,0,243 0/1:3,4:7:97.47:135,0,97 0/0:2,0:2:6.02:0,6,80 ./. 1/1:0,1:1:3.01:41,3,0 0/1:1,1:2:20.66:21,0,35 0/0:7,0:7:21.07:0,21,287 0/0:2,0:2:6.02:0,6,81 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,31 ./. 0/0:1,0:1:3.01:0,3,37 ./. ./. 0/0:2,0:2:6.02:0,6,73 0/0:2,0:2:6.02:0,6,82 1/1:0,2:2:3.01:45,3,0 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 1/1:0,1:1:2.98:22,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,73 ./. ./. ./. 0/0:3,0:3:9.03:0,9,113 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. -chr1 934099 . G C 525.65 . AC=24;AF=1.000;AN=24;DP=17;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=-0.1752;MQ=57.23;MQ0=0;QD=30.92;EFF=DOWNSTREAM(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|),DOWNSTREAM(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|),DOWNSTREAM(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|),DOWNSTREAM(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|),INTERGENIC(MODIFIER|||||||||);CSQ=downstream_gene_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000428771||||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000481869|||||retained_intron|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:76,6,0 ./. ./. 1/1:0,1:1:3.01:34,3,0 ./. 1/1:0,2:2:6.02:75,6,0 1/1:0,1:1:3.01:31,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:40,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3:28,3,0 1/1:0,3:3:6.02:78,6,0 1/1:0,2:2:3.01:45,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 934106 . A G 492.03 . AC=22;AF=1.000;AN=22;DP=17;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=-0.1738;MQ=57.23;MQ0=0;QD=30.75;EFF=DOWNSTREAM(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|),DOWNSTREAM(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|),DOWNSTREAM(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|),DOWNSTREAM(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|),INTERGENIC(MODIFIER|||||||||);CSQ=downstream_gene_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000428771||||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000481869|||||retained_intron|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:79,6,0 ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. 1/1:0,2:2:6.02:75,6,0 1/1:0,1:1:3.01:34,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:37,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,3:3:6.01:69,6,0 1/1:0,2:2:3.01:45,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:37,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 934130 . G C 64.94 . AC=4;AF=0.222;AN=18;BaseQRankSum=-0.306;DP=15;Dels=0.00;FS=2.515;HRun=0;HaplotypeScore=0.2219;MQ=56.85;MQ0=0;MQRankSum=-0.551;QD=12.99;ReadPosRankSum=2.388;EFF=DOWNSTREAM(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|),DOWNSTREAM(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|),DOWNSTREAM(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|),DOWNSTREAM(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|),INTERGENIC(MODIFIER|||||||||);CSQ=downstream_gene_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000428771||||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000481869|||||retained_intron|1,downstream_gene_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. 0/0:2,0:2:6.02:0,6,76 ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,75 0/0:2,0:2:6.01:0,6,69 ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,37 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,34 1/1:0,3:3:6.01:72,6,0 1/1:0,2:2:3.01:45,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3:0,3,29 ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 934797 . T G 52.82 . AC=6;AF=0.067;AN=90;BaseQRankSum=-1.481;DP=224;Dels=0.00;FS=43.747;HRun=4;HaplotypeScore=0.0853;InbreedingCoeff=-0.0492;MQ=49.44;MQ0=0;MQRankSum=-1.914;QD=1.51;ReadPosRankSum=0.524;EFF=EXON(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D103A|221|HES4|protein_coding|CODING|ENST00000304952|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D129A|247|HES4|protein_coding|CODING|ENST00000428771|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gCc|D71A|189|HES4|protein_coding|CODING|ENST00000484667|);CSQ=missense_variant|gAc/gCc|D/A|ENSG00000188290|HES4|ENST00000484667|3/3|probably_damaging(0.994)|deleterious(0)|71/189|protein_coding|1,missense_variant|gAc/gCc|D/A|ENSG00000188290|HES4|ENST00000428771|3/3|benign(0.358)|deleterious(0)|129/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188290|HES4|ENST00000481869|2/2||||retained_intron|1,missense_variant|gAc/gCc|D/A|ENSG00000188290|HES4|ENST00000304952|4/4|probably_damaging(0.979)|deleterious(0)|103/221|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,77 0/0:3,1:4:9.03:0,9,106 ./. 0/0:2,1:3:6:0,6,58 0/0:1,0:1:3.01:0,3,41 ./. 0/1:3,2:5:9.65:10,0,107 0/0:1,1:2:3.01:0,3,41 0/0:6,3:9:18.04:0,18,222 0/0:8,2:10:24.08:0,24,312 ./. 0/0:1,0:1:3.01:0,3,38 0/0:2,1:3:5.99:0,6,54 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,39 ./. 0/0:1,1:2:1.56:0,2,4 ./. ./. ./. ./. 0/0:1,1:2:3.01:0,3,39 0/0:1,1:2:3.01:0,3,32 0/0:1,0:1:3.01:0,3,36 0/0:3,0:3:9.02:0,9,103 ./. 0/0:1,1:2:3.01:0,3,37 ./. 0/0:2,0:2:3.01:0,3,40 0/0:3,0:3:9.03:0,9,115 0/0:1,1:2:3.01:0,3,41 0/0:2,0:2:6.02:0,6,75 0/0:4,0:4:12.03:0,12,138 0/0:1,0:1:3.01:0,3,37 0/0:3,2:5:3:0,3,29 0/0:2,2:4:3.01:0,3,35 0/0:3,4:7:9.03:0,9,111 0/0:1,0:1:3.01:0,3,33 0/0:3,2:5:9.03:0,9,104 0/1:2,4:6:24.41:24,0,51 0/0:7,3:11:15.04:0,15,174 1/1:0,4:4:3.01:33,3,0 0/0:5,2:7:12.03:0,12,135 0/0:3,0:3:9.03:0,9,112 0/0:1,0:1:3.01:0,3,37 0/0:11,5:16:27.08:0,27,312 0/0:4,6:10:6.02:0,6,76 0/1:5,6:11:21.40:21,0,88 0/0:10,6:16:9.01:0,9,91 0/0:4,3:7:6.01:0,6,63 0/0:3,5:8:6.02:0,6,86 0/0:4,1:5:9.02:0,9,101 0/0:2,5:7:3.01:0,3,33 0/1:4,5:9:54.83:55,0,68 ./. 0/0:5,3:8:15.03:0,15,166 -chr1 934888 . C A 233.29 . AC=2;AF=0.0172;AN=116;BaseQRankSum=-1.550;DP=738;Dels=0.00;FS=2.017;HRun=0;HaplotypeScore=1.1956;InbreedingCoeff=-0.0253;MQ=56.42;MQ0=0;MQRankSum=-0.145;QD=7.07;ReadPosRankSum=-0.918;EFF=INTRON(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|2),INTRON(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|3),INTRON(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|2),INTRON(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|1);CSQ=intron_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,intron_variant|||ENSG00000188290|HES4|ENST00000428771||||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,intron_variant&nc_transcript_variant|||ENSG00000188290|HES4|ENST00000481869|||||retained_intron|1,intron_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:4,0:4:9.03:0,9,116 ./. 0/0:2,0:2:6.02:0,6,81 0/0:5,0:5:6.02:0,6,82 0/0:6,0:6:18.06:0,18,244 0/0:9,0:9:24.08:0,24,312 0/0:7,0:7:15.05:0,15,189 0/0:11,0:11:27.07:0,27,340 0/0:16,0:16:45.15:0,45,598 0/0:7,0:7:15.03:0,15,168 0/0:7,0:7:21.07:0,21,265 0/0:9,0:9:27.09:0,27,357 0/0:6,0:6:15.05:0,15,200 0/0:10,0:10:27.09:0,27,355 0/0:6,0:6:12.04:0,12,166 0/0:10,0:10:24.08:0,24,319 0/0:8,0:8:24.07:0,24,298 0/0:12,0:12:30.09:0,30,377 0/0:8,0:8:21.07:0,21,279 0/0:12,0:12:33.07:0,33,416 0/0:9,0:9:24.08:0,24,316 0/0:14,0:14:36.11:0,36,454 0/0:16,0:16:42.13:0,42,541 0/0:10,0:11:27.06:0,27,323 0/0:11,0:11:30.09:0,30,381 0/0:13,0:13:27.09:0,27,367 0/0:7,0:7:21.05:0,21,264 0/1:13,1:14:6.12:6,0,401 0/0:8,0:8:18.06:0,18,240 0/0:14,0:14:33.09:0,33,417 0/0:12,0:12:27.09:0,27,371 0/0:8,0:8:18.05:0,18,224 0/0:18,0:18:45.14:0,45,585 0/0:18,0:18:45.14:0,45,579 0/0:13,0:13:36.11:0,36,451 0/0:16,0:16:42.12:0,42,528 0/0:8,0:8:24.08:0,24,316 0/0:18,0:18:45.14:0,45,569 0/1:6,12:19:38.92:280,0,39 0/0:23,0:23:57.17:0,57,718 0/0:10,0:10:24.07:0,24,298 0/0:10,0:10:30.09:0,30,374 0/0:13,0:13:36.11:0,36,459 0/0:16,0:16:45.14:0,45,578 0/0:18,0:18:45.12:0,45,555 0/0:26,1:27:54.16:0,54,666 0/0:10,0:10:27.08:0,27,336 0/0:6,0:6:12.04:0,12,146 0/0:38,0:38:81.24:0,81,992 0/0:35,0:35:66.19:0,66,818 0/0:27,0:27:63.19:0,63,772 0/0:20,0:20:45.13:0,45,539 0/0:18,0:18:39.12:0,39,508 0/0:16,0:16:42.11:0,42,506 0/0:15,0:15:33.09:0,33,404 0/0:2,0:2:6.02:0,6,77 0/0:16,0:16:39.08:0,39,445 0/0:7,0:7:15.04:0,15,188 0/0:8,0:8:21.06:0,21,267 -chr1 934990 . A G 108.0 . AC=12;AF=0.1017;AN=118;BaseQRankSum=-13.261;DP=1923;Dels=0.00;FS=97.152;HRun=3;HaplotypeScore=3.2884;InbreedingCoeff=-0.1051;MQ=46.21;MQ0=0;MQRankSum=-9.305;QD=0.35;ReadPosRankSum=0.938;EFF=EXON(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S38P|189|HES4|protein_coding|CODING|ENST00000484667|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S70P|221|HES4|protein_coding|CODING|ENST00000304952|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tcc/Ccc|S96P|247|HES4|protein_coding|CODING|ENST00000428771|);CSQ=missense_variant|Tcc/Ccc|S/P|ENSG00000188290|HES4|ENST00000484667|2/3|probably_damaging(0.979)|deleterious(0)|38/189|protein_coding|1,missense_variant|Tcc/Ccc|S/P|ENSG00000188290|HES4|ENST00000428771|2/3|benign(0.444)|deleterious(0.02)|96/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188290|HES4|ENST00000481869|1/2||||retained_intron|1,missense_variant|Tcc/Ccc|S/P|ENSG00000188290|HES4|ENST00000304952|3/4|possibly_damaging(0.534)|deleterious(0.01)|70/221|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,6:9:9.03:0,9,108 0/0:3,3:6:3.01:0,3,34 ./. 0/1:6,9:15:30.22:30,0,200 0/0:6,7:14:12.03:0,12,151 0/1:3,13:16:31:47,0,31 0/1:5,13:18:46.24:46,0,63 0/1:5,7:12:48.98:49,0,106 0/0:17,20:38:36.12:0,36,469 0/1:18,22:41:0.25:0,0,456 0/1:4,12:16:22.63:23,0,35 0/1:4,5:10:6.65:7,0,131 0/0:6,15:21:12.04:0,12,162 0/0:15,4:20:21.04:0,21,238 0/0:33,10:43:54.13:0,54,651 0/0:13,4:18:15.02:0,15,163 0/0:25,10:35:23.97:0,24,285 0/0:22,6:28:33.09:0,33,383 0/0:12,5:17:0.37:0,0,230 0/0:18,7:25:24.07:0,24,306 0/1:11,11:22:3.64:4,0,188 0/0:20,2:22:39.08:0,39,461 0/0:17,1:18:36.09:0,36,424 0/0:20,3:24:51.13:0,51,617 0/0:24,10:34:28.20:0,28,633 0/0:20,4:25:42.11:0,42,511 0/0:19,5:24:45.14:0,45,562 0/0:13,4:17:27.08:0,27,335 0/0:23,6:30:39.11:0,39,502 0/0:15,2:18:12.04:0,12,155 0/0:22,8:30:16.42:0,16,436 0/0:18,7:25:30.07:0,30,365 0/1:17,11:28:0.29:0,0,433 0/0:27,7:35:51.14:0,51,613 0/0:21,4:26:29.45:0,29,578 0/0:15,4:19:36.11:0,36,439 0/0:23,6:30:51.15:0,51,631 0/0:23,6:29:36.10:0,36,445 0/0:26,8:35:13.52:0,14,408 0/0:32,23:55:17.87:0,18,698 0/0:42,13:57:27.80:0,28,767 0/1:35,16:51:2.92:3,0,537 0/1:33,11:44:3.82:4,0,490 0/0:31,9:43:66.09:0,66,712 0/0:25,12:38:39.07:0,39,419 0/0:38,9:48:32.72:0,33,673 0/0:63,29:94:65.84:0,66,1124 0/0:16,9:25:21.05:0,21,240 0/0:31,8:40:48.08:0,48,525 0/0:64,23:87:99:0,126,1442 0/0:50,18:69:73.53:0,74,1026 0/0:39,10:50:69.17:0,69,789 0/0:37,13:52:63.13:0,63,723 0/0:52,8:60:52.47:0,52,793 0/0:25,8:33:45.13:0,45,527 0/1:24,8:33:20.02:20,0,340 0/0:12,4:16:24.06:0,24,267 0/0:42,10:54:11.98:0,12,718 0/0:30,6:36:63.14:0,63,701 0/0:26,8:34:14.69:0,15,468 -chr1 935046 . G A 2684.85 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-3.713;DP=2876;Dels=0.00;FS=0.372;HRun=0;HaplotypeScore=3.4737;InbreedingCoeff=-0.0181;MQ=51.17;MQ0=0;MQRankSum=0.144;QD=11.88;ReadPosRankSum=0.789;EFF=EXON(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|1),INTRON(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|1),INTRON(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|2),INTRON(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|1);CSQ=intron_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,intron_variant|||ENSG00000188290|HES4|ENST00000428771||||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188290|HES4|ENST00000481869|1/2||||retained_intron|1,intron_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.01:0,9,94 0/0:14,0:15:42.10:0,42,515 0/0:11,0:11:30.07:0,30,349 0/0:8,0:8:18.06:0,18,227 0/0:14,0:14:39.13:0,39,520 0/0:21,0:21:54.18:0,54,708 0/0:30,0:30:90.28:0,90,1181 0/0:12,0:12:30.10:0,30,401 0/0:44,0:44:99:0,120,1584 0/0:41,0:41:99:0,108,1440 0/0:15,0:15:45.14:0,45,591 0/0:23,0:23:63.18:0,63,773 0/0:23,0:23:66.17:0,66,831 0/0:18,0:18:42.12:0,42,519 0/0:44,0:45:99:0,99,1212 0/0:28,0:28:51.15:0,51,644 0/0:36,0:36:93.26:0,93,1155 0/0:22,0:22:54.15:0,54,653 0/0:28,0:28:48.15:0,48,627 0/0:23,0:23:60.17:0,60,734 0/0:30,0:30:81.21:0,81,982 0/0:40,0:40:81.23:0,81,1054 0/0:29,0:29:66.21:0,66,865 0/0:35,0:35:75.21:0,75,932 0/0:42,0:42:99:0,114,1425 0/0:34,0:34:81.24:0,81,1025 0/0:22,0:22:63.18:0,63,767 0/0:21,0:21:48.15:0,48,610 0/0:31,0:31:75.20:0,75,910 0/0:21,0:21:48.15:0,48,613 0/0:45,0:45:96.29:0,96,1226 0/0:24,0:24:54.16:0,54,682 0/0:39,0:39:93.28:0,93,1160 0/0:51,0:51:99:0,120,1522 0/0:33,0:33:69.20:0,69,874 0/0:23,0:24:57.17:0,57,729 0/0:38,0:38:93.26:0,93,1145 0/0:31,0:31:63.18:0,63,805 0/0:72,0:72:99:0,153,1867 0/0:117,0:117:99:0,274,3422 0/0:104,0:104:99:0,229,2728 0/0:89,0:90:99:0,205,2503 0/0:69,0:69:99:0,126,1578 0/0:73,0:74:99:0,168,2062 0/0:60,0:60:99:0,135,1665 0/0:64,0:64:99:0,144,1729 0/0:145,1:146:99:0,343,4044 0/0:37,0:37:78.22:0,78,935 0/0:72,1:73:99:0,135,1968 0/1:53,84:140:99:2059,0,1176 0/0:121,0:121:99:0,289,3514 0/0:74,0:74:99:0,175,2108 0/1:55,30:86:99:691,0,1357 0/0:89,0:89:99:0,202,2413 0/0:69,0:69:99:0,168,2068 0/0:62,0:62:99:0,144,1775 0/0:43,0:43:93.28:0,93,1160 0/0:89,0:90:99:0,211,2537 0/0:76,0:76:99:0,171,2042 0/0:70,0:70:99:0,141,1766 -chr1 935222 . C A 15396.75 . AC=74;AF=0.6167;AN=120;BaseQRankSum=-9.471;DP=941;Dels=0.00;FS=3.802;HRun=0;HaplotypeScore=1.0918;InbreedingCoeff=-0.0313;MQ=53.20;MQ0=0;MQRankSum=2.504;QD=20.02;ReadPosRankSum=1.296;EFF=EXON(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|1),INTRON(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|1),INTRON(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agG/agT|R44S|247|HES4|protein_coding|CODING|ENST00000428771|);CSQ=intron_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,missense_variant|agG/agT|R/S|ENSG00000188290|HES4|ENST00000428771|1/3|benign(0)|tolerated(0.95)|44/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188290|HES4|ENST00000481869|1/2||||retained_intron|1,intron_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,1:2:3.01:40,3,0 1/1:0,1:1:3.01:33,3,0 0/1:1,2:3:30.11:31,0,30 0/0:1,0:1:3.01:0,3,33 0/1:3,6:9:92.14:203,0,92 1/1:0,9:10:27.05:303,27,0 0/1:7,14:21:99:361,0,214 0/1:2,1:3:30.98:31,0,63 0/1:12,14:27:99:451,0,354 0/1:7,12:19:99:356,0,214 1/1:0,8:8:24.07:278,24,0 1/1:1,10:11:4.45:356,4,0 1/1:0,9:9:24.07:288,24,0 0/0:3,0:3:9.03:0,9,115 1/1:0,6:6:18.06:235,18,0 1/1:1,6:7:18.06:222,18,0 0/1:7,5:12:99:149,0,236 1/1:1,14:15:42.10:487,42,0 0/1:7,6:13:99:176,0,149 0/0:12,0:12:36.11:0,36,459 0/1:4,1:5:29.55:30,0,70 1/1:0,5:5:15.04:174,15,0 0/1:3,3:6:83.17:83,0,101 0/1:4,7:11:99:169,0,124 0/1:9,3:12:81.79:82,0,216 0/1:2,7:9:51.50:226,0,51 0/1:7,2:9:12.37:12,0,223 0/1:2,5:7:62.44:104,0,62 0/1:5,6:11:99:172,0,143 1/1:0,11:11:33.10:399,33,0 1/1:0,11:11:30.09:369,30,0 1/1:0,10:10:18.03:207,18,0 0/1:7,8:15:99:182,0,122 0/0:12,0:12:33.10:0,33,423 0/1:1,6:7:23.18:158,0,23 0/1:4,4:8:89.65:111,0,90 0/1:14,6:20:92.84:93,0,418 1/1:0,11:11:30.07:355,30,0 1/1:1,23:24:34.58:662,35,0 1/1:2,32:35:93.26:1111,93,0 0/0:22,0:22:60.16:0,60,718 0/0:23,0:23:69.21:0,69,843 0/1:10,11:21:99:222,0,306 1/1:3,17:20:48.12:571,48,0 0/1:15,10:25:99:274,0,347 1/1:0,19:19:48.08:522,48,0 0/1:21,30:51:99:704,0,574 0/0:13,0:13:39.11:0,39,467 0/1:14,17:31:99:396,0,288 0/0:49,0:49:99:0,129,1543 0/0:37,0:37:99:0,102,1210 1/1:2,22:24:51.15:599,51,0 0/1:12,10:22:99:248,0,348 1/1:3,24:27:60.17:706,60,0 1/1:0,20:20:54.12:600,54,0 1/1:0,23:23:57.12:660,57,0 0/1:7,8:15:99:174,0,201 0/1:18,9:27:99:196,0,495 0/1:12,12:24:99:308,0,295 1/1:1,16:17:48.09:516,48,0 -chr1 935459 . A G 44.02 . AC=4;AF=0.67;AN=6;BaseQRankSum=-0.736;DP=4;Dels=0.00;FS=4.771;HRun=2;HaplotypeScore=0.0000;MQ=47.12;MQ0=0;MQRankSum=0.736;QD=22.01;ReadPosRankSum=0.736;EFF=EXON(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|1),UPSTREAM(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|),UTR_5_PRIME(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|1),UTR_5_PRIME(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|1);CSQ=upstream_gene_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,5_prime_UTR_variant|||ENSG00000188290|HES4|ENST00000428771|1/3|||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188290|HES4|ENST00000481869|1/2||||retained_intron|1,5_prime_UTR_variant|||ENSG00000188290|HES4|ENST00000304952|1/4|||-/221|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 ./. ./. ./. ./. 0/0:1,1:2:3.01:0,3,33 ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. ./. ./. ./. -chr1 935492 . G T 38.54 . AC=4;AF=0.50;AN=8;BaseQRankSum=1.026;DP=5;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=0.2167;MQ=49.96;MQ0=0;MQRankSum=1.026;QD=19.27;ReadPosRankSum=-1.026;EFF=START_GAINED(LOW||||247|HES4|protein_coding|CODING|ENST00000428771|1),UPSTREAM(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|),UPSTREAM(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|),UPSTREAM(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|);CSQ=upstream_gene_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,5_prime_UTR_variant|||ENSG00000188290|HES4|ENST00000428771|1/3|||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000481869|||||retained_intron|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,32 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 935715 . C T 119.53 . AC=6;AF=0.75;AN=8;BaseQRankSum=0.731;DP=6;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=60.00;MQ0=0;MQRankSum=0.731;QD=29.88;ReadPosRankSum=0.731;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|),UPSTREAM(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|),UPSTREAM(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|),UPSTREAM(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|);CSQ=upstream_gene_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000428771||||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000481869|||||retained_intron|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. 1/1:0,2:2:6.02:78,6,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 935833 . C G 205.67 . AC=10;AF=1.00;AN=10;DP=7;Dels=0.00;FS=0.000;HRun=4;HaplotypeScore=0.0000;MQ=56.62;MQ0=0;QD=29.38;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||189|HES4|protein_coding|CODING|ENST00000484667|),UPSTREAM(MODIFIER||||221|HES4|protein_coding|CODING|ENST00000304952|),UPSTREAM(MODIFIER||||247|HES4|protein_coding|CODING|ENST00000428771|),UPSTREAM(MODIFIER|||||HES4|retained_intron|CODING|ENST00000481869|);CSQ=upstream_gene_variant|||ENSG00000188290|HES4|ENST00000484667||||-/189|protein_coding|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000428771||||-/247|protein_coding|1,upstream_gene_variant|||ENSG00000272512|RP11-54O7.17|ENST00000606034|||||lincRNA|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000481869|||||retained_intron|1,upstream_gene_variant|||ENSG00000188290|HES4|ENST00000304952||||-/221|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:6.02:75,6,0 ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:45,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. -chr1 948421 . A AAAC 726.92 . AC=22;AF=1.000;AN=22;DP=20;FS=0.000;HRun=0;HaplotypeScore=4.9337;InbreedingCoeff=-0.1734;MQ=46.54;MQ0=0;QD=45.43;EFF=EXON(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|1),UPSTREAM(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.10|processed_pseudogene|NON_CODING|ENST00000423619|);CSQ=upstream_gene_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000231702|RP11-54O7.10|ENST00000423619|||||processed_pseudogene|1,non_coding_exon_variant&nc_transcript_variant&feature_elongation|||ENSG00000224969|RP11-54O7.11|ENST00000458555|1/2||||antisense|1 GT:AD:DP:GQ:PL 1/1:0,2:2:6.02:100,6,0 1/1:0,1:1:3.01:31,3,0 1/1:0,1:1:3.01:37,3,0 1/1:1,4:5:12.04:197,12,0 ./. ./. ./. 1/1:0,1:1:3.01:62,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:62,3,0 1/1:1,0:1:3.01:62,3,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:62,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:62,3,0 ./. ./. 1/1:0,1:1:3.01:62,3,0 ./. ./. ./. ./. ./. -chr1 948692 . G A 6273.5 . AC=98;AF=0.8909;AN=110;BaseQRankSum=0.890;DP=195;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1286;InbreedingCoeff=0.1904;MQ=57.72;MQ0=0;MQRankSum=0.244;QD=33.91;ReadPosRankSum=-0.202;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=upstream_gene_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 1/1:0,1:2:3.01:33,3,0 ./. 1/1:0,4:4:9.02:102,9,0 1/1:0,3:3:6.02:74,6,0 1/1:0,6:6:15.05:198,15,0 1/1:0,4:4:12.04:148,12,0 1/1:0,10:10:30.10:396,30,0 1/1:0,5:5:15.05:191,15,0 1/1:0,10:10:27.09:349,27,0 1/1:0,12:12:33.10:423,33,0 1/1:0,4:4:12.04:152,12,0 1/1:0,7:7:21.07:280,21,0 1/1:0,6:6:18.06:231,18,0 1/1:0,2:2:6.02:75,6,0 1/1:0,3:3:9.03:122,9,0 1/1:0,2:2:6.02:78,6,0 1/1:0,1:1:3.01:42,3,0 1/1:0,2:2:6.02:79,6,0 1/1:0,5:5:12.04:157,12,0 1/1:0,1:1:3.01:33,3,0 0/0:2,0:3:6.02:0,6,72 1/1:0,2:2:3.01:42,3,0 1/1:0,1:1:3.01:35,3,0 1/1:0,2:2:6.02:83,6,0 1/1:0,2:2:6:60,6,0 1/1:0,5:6:15.05:199,15,0 1/1:1,2:3:6.02:81,6,0 1/1:0,1:1:3.01:31,3,0 1/1:0,2:2:6.02:82,6,0 1/1:0,5:5:12.04:154,12,0 1/1:0,8:8:24.06:286,24,0 ./. 1/1:0,1:1:3.01:40,3,0 0/1:3,1:4:30.29:30,0,70 0/0:2,0:2:6.02:0,6,83 1/1:0,5:5:15.05:193,15,0 1/1:0,1:1:3.01:33,3,0 1/1:0,9:9:27.09:357,27,0 1/1:0,3:3:6.02:83,6,0 1/1:0,1:1:3.01:42,3,0 0/1:1,1:2:17.68:18,0,33 1/1:0,2:2:6.02:81,6,0 1/1:0,2:2:6.02:80,6,0 ./. 1/1:0,1:1:3.01:42,3,0 1/1:0,2:2:6.02:78,6,0 1/1:0,6:6:18.05:218,18,0 0/0:2,0:2:3.01:0,3,39 1/1:0,1:1:3.01:40,3,0 0/1:2,3:5:57.15:104,0,57 1/1:0,3:3:9.03:125,9,0 1/1:0,3:3:9.03:117,9,0 0/0:2,0:2:6.02:0,6,74 1/1:0,5:5:12.03:143,12,0 1/1:0,1:1:3.01:40,3,0 ./. 0/1:1,1:2:18.68:36,0,19 1/1:0,3:3:6.02:83,6,0 ./. 1/1:0,2:2:6.02:73,6,0 -chr1 948844 . C CT 12812.2 . AC=110;AF=0.9167;AN=120;BaseQRankSum=12.848;DP=1613;FS=0.638;HRun=2;HaplotypeScore=267.6122;InbreedingCoeff=0.3293;MQ=57.07;MQ0=0;MQRankSum=-0.300;QD=8.17;ReadPosRankSum=0.729;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_5_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1);CSQ=5_prime_UTR_variant&feature_elongation|||ENSG00000187608|ISG15|ENST00000379389|1/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 1/1:10,0:10:22.32:99,22,0 0/1:9,0:9:33.56:34,0,121 1/1:7,1:8:12.91:55,13,0 1/1:5,0:5:13.71:65,14,0 1/1:23,0:23:43.46:165,43,0 1/1:38,0:38:72.06:282,72,0 1/1:53,1:54:77.98:372,78,0 1/1:29,0:29:56.97:235,57,0 1/1:66,0:66:99:511,127,0 1/1:61,0:60:99:484,121,0 1/1:38,0:38:76.72:280,77,0 1/1:28,1:29:56.89:238,57,0 1/1:46,1:49:99:366,101,0 1/1:32,0:32:66.38:284,66,0 1/1:39,0:39:83.93:327,84,0 1/1:24,0:24:58.17:249,58,0 1/1:25,0:25:29.61:257,30,0 1/1:26,0:26:42.50:226,42,0 0/1:34,0:34:50.48:50,0,547 1/1:24,0:24:54.79:203,55,0 0/1:27,0:27:54.44:54,0,420 1/1:45,0:45:99:409,100,0 1/1:29,0:29:70.65:327,71,0 1/1:20,0:20:41.59:172,42,0 1/1:31,0:31:61.37:213,61,0 1/1:22,0:22:48.69:188,49,0 0/1:22,0:22:65.02:65,0,208 1/1:21,0:21:50.62:228,51,0 1/1:26,0:26:57.30:224,57,0 1/1:30,0:30:73.76:337,74,0 1/1:36,0:36:75.64:331,76,0 1/1:17,0:17:43.64:210,44,0 1/1:28,0:28:68.64:327,69,0 0/0:31,0:31:9.67:0,10,772 0/1:27,0:27:24.79:25,0,377 1/1:27,0:27:53.27:201,53,0 1/1:28,0:28:62.12:261,62,0 1/1:41,0:41:87.01:358,87,0 1/1:13,0:13:24.35:115,24,0 1/1:33,0:33:73.72:333,74,0 1/1:23,0:23:47.43:237,47,0 1/1:21,0:21:48.36:217,48,0 1/1:15,0:15:26.95:108,27,0 1/1:24,0:24:45.99:199,46,0 1/1:17,0:17:36.70:155,37,0 1/1:19,0:19:35.39:137,35,0 1/1:35,0:35:76.16:319,76,0 0/0:13,0:13:0.72:0,1,230 1/1:24,0:25:47.01:183,47,0 1/1:47,1:49:87.24:498,87,0 1/1:37,1:40:85.46:423,85,0 1/1:26,0:26:56.08:268,56,0 1/1:21,0:21:44.35:167,44,0 1/1:20,0:20:44.41:201,44,0 1/1:18,0:18:28.20:103,28,0 1/1:13,0:13:28.80:120,29,0 0/1:13,0:13:0.14:0,0,326 1/1:17,0:18:29.98:146,30,0 1/1:11,0:11:19.62:90,20,0 1/1:15,0:15:25.36:85,25,0 -chr1 948846 . T A 156.11 . AC=8;AF=0.0667;AN=120;BaseQRankSum=-3.754;DP=1643;Dels=0.00;FS=73.746;HRun=1;HaplotypeScore=23.6593;InbreedingCoeff=-0.0805;MQ=57.11;MQ0=0;MQRankSum=1.518;QD=0.75;ReadPosRankSum=-12.345;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_5_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1);CSQ=5_prime_UTR_variant|||ENSG00000187608|ISG15|ENST00000379389|1/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 0/0:10,0:10:27.06:0,27,302 0/0:9,0:9:27.07:0,27,326 0/0:8,0:8:15.05:0,15,195 0/0:5,0:5:15.05:0,15,184 0/1:23,3:26:57.48:57,0,691 0/1:35,3:38:14.78:15,0,1175 0/0:52,3:55:26.78:0,27,1751 0/0:29,1:30:37.02:0,37,961 0/0:65,2:67:92.11:0,92,2160 0/0:60,1:61:99:0,118,2026 0/0:38,1:39:61.09:0,61,1256 0/0:27,2:29:0.02:0,0,901 0/0:46,3:49:99:0,108,1686 0/0:32,2:34:22.38:0,22,1097 0/0:37,2:39:65.95:0,66,1243 0/0:24,0:24:63.18:0,63,784 0/0:25,0:25:69.17:0,69,850 0/0:25,1:26:69.66:0,70,856 0/0:34,1:35:61.52:0,62,1215 0/0:24,1:25:39.98:0,40,898 0/0:26,1:27:68.02:0,68,837 0/0:44,1:45:99:0,114,1486 0/0:28,2:30:45.16:0,45,954 0/1:20,3:23:41.89:42,0,656 0/0:30,1:31:43:0,43,987 0/0:22,0:22:66.18:0,66,841 0/0:21,1:22:19.38:0,19,668 0/0:20,1:21:22.36:0,22,649 0/0:25,2:27:33.67:0,34,766 0/1:27,3:30:27.58:28,0,814 0/0:36,2:38:61.48:0,61,1168 0/0:16,1:17:46.68:0,47,558 0/0:28,0:28:78.21:0,78,965 0/0:31,0:31:90.27:0,90,1147 0/0:26,1:27:65.02:0,65,832 0/1:23,5:28:75.04:75,0,687 0/0:27,0:28:69.22:0,69,905 0/0:41,1:42:85.12:0,85,1455 0/0:12,0:13:30.08:0,30,349 0/0:32,1:33:46.46:0,46,996 0/1:22,3:25:44.95:45,0,557 0/0:21,2:23:25.39:0,25,715 0/0:14,1:15:36.11:0,36,465 0/0:24,0:24:63.20:0,63,808 0/0:17,0:17:36.11:0,36,463 0/0:18,1:19:45.15:0,45,594 0/0:33,2:35:49.01:0,49,1000 0/0:13,0:13:36.11:0,36,454 0/0:23,3:26:25.41:0,25,766 0/0:47,3:50:77.21:0,77,1320 0/0:36,5:41:59.89:0,60,1002 0/0:25,1:26:60.17:0,60,737 0/0:20,2:23:22.38:0,22,646 0/1:18,2:20:14.52:15,0,545 0/0:17,1:18:2.68:0,3,404 0/0:13,1:14:3.87:0,4,450 0/0:13,0:13:36.11:0,36,454 0/1:15,3:18:4.91:5,0,387 0/0:11,0:11:24.05:0,24,297 0/0:15,0:15:33.11:0,33,454 -chr1 948846 . T TA 63344.05 . AC=112;AF=0.9333;AN=120;BaseQRankSum=7.480;DP=1716;FS=0.000;HRun=1;HaplotypeScore=206.0209;InbreedingCoeff=-0.0721;MQ=56.50;MQ0=0;MQRankSum=0.146;QD=36.91;ReadPosRankSum=-0.823;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_5_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1);CSQ=5_prime_UTR_variant&feature_elongation|||ENSG00000187608|ISG15|ENST00000379389|1/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 1/1:0,10:10:27.09:388,27,0 0/1:4,5:9:99:198,0,129 1/1:4,5:9:15.05:225,15,0 1/1:1,5:6:15.05:221,15,0 1/1:8,21:29:75.25:1090,75,0 1/1:13,30:43:99:1697,117,0 1/1:11,47:59:99:2300,157,0 1/1:5,26:31:78.26:1163,78,0 1/1:15,55:70:99:2566,175,0 1/1:12,53:64:99:2577,175,0 1/1:6,32:38:99:1519,102,0 1/1:5,24:29:81.27:1192,81,0 1/1:13,43:56:99:2245,151,0 1/1:4,30:34:99:1447,99,0 1/1:4,37:41:99:1650,111,0 1/1:3,21:24:69.23:1011,69,0 1/1:3,23:26:72.24:1062,72,0 1/1:6,23:29:84.24:1221,84,0 0/1:22,15:37:99:690,0,587 1/1:1,24:25:75.25:1111,75,0 0/1:16,11:27:99:377,0,467 1/1:2,42:44:99:1845,123,0 1/1:3,28:31:87.29:1292,87,0 1/1:4,19:23:66.21:934,66,0 1/1:4,30:34:93.31:1365,93,0 1/1:2,22:24:69.23:1020,69,0 0/1:9,13:22:99:525,0,213 1/1:2,20:22:66.22:978,66,0 1/1:3,24:27:75.25:1110,75,0 1/1:7,25:32:93.31:1391,93,0 1/1:5,34:39:99:1515,102,0 1/1:4,15:19:51.17:759,51,0 1/1:2,27:29:84.28:1256,84,0 0/1:27,8:35:99:308,0,800 0/1:15,13:28:99:483,0,392 1/1:8,22:30:81.26:1181,81,0 1/1:2,27:29:75.25:1125,75,0 1/1:4,39:43:99:1798,123,0 1/1:5,11:16:36.12:539,36,0 1/1:2,32:34:93.31:1383,93,0 1/1:4,21:25:63.21:915,63,0 1/1:2,21:23:66.22:978,66,0 1/1:2,14:16:42.14:630,42,0 1/1:3,22:25:69.22:1014,69,0 1/1:0,17:17:45.15:675,45,0 1/1:4,16:20:48.16:720,48,0 1/1:3,33:36:96.32:1411,96,0 0/1:9,6:15:99:189,0,237 1/1:6,22:29:72.24:1057,72,0 1/1:8,43:52:99:1899,132,0 1/1:9,32:41:99:1558,105,0 1/1:1,25:26:69.23:1020,69,0 1/1:3,20:23:60.20:889,60,0 1/1:2,18:20:57.19:840,57,0 1/1:3,15:18:39.13:584,39,0 1/1:2,12:14:42.14:616,42,0 0/1:10,3:13:53.74:54,0,354 1/1:4,14:18:45.11:644,45,0 1/1:0,10:11:24.08:360,24,0 1/1:1,15:16:36.12:540,36,0 -chr1 948869 . C T 230.26 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.821;DP=2138;Dels=0.00;FS=1.991;HRun=0;HaplotypeScore=1.4232;InbreedingCoeff=-0.0088;MQ=56.52;MQ0=0;MQRankSum=2.379;QD=11.51;ReadPosRankSum=-0.420;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_5_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1);CSQ=5_prime_UTR_variant|||ENSG00000187608|ISG15|ENST00000379389|1/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 0/0:9,0:9:18.06:0,18,221 0/0:11,0:11:24.07:0,24,292 0/0:12,0:12:33.09:0,33,404 0/0:6,1:7:15.04:0,15,178 0/0:35,0:35:96.29:0,96,1248 0/0:57,0:57:99:0,166,2098 0/0:75,0:75:99:0,223,2935 0/0:28,0:28:84.27:0,84,1112 0/0:76,0:76:99:0,223,2917 0/0:64,1:65:99:0,164,2425 0/0:40,0:40:99:0,120,1546 0/0:41,0:41:99:0,117,1483 0/0:59,0:59:99:0,169,2097 0/0:43,0:43:99:0,111,1456 0/0:60,0:60:99:0,147,1903 0/0:30,0:30:72.23:0,72,955 0/0:28,0:28:75.22:0,75,926 0/0:43,0:43:99:0,111,1418 0/0:50,0:50:99:0,132,1716 0/0:31,0:31:90.29:0,90,1194 0/0:35,0:35:84.27:0,84,1085 0/0:50,0:51:99:0,129,1633 0/0:46,0:46:99:0,120,1522 0/0:25,0:25:72.23:0,72,934 0/0:45,0:45:99:0,108,1439 0/0:39,0:39:99:0,108,1424 0/0:34,0:34:78.25:0,78,1035 0/0:30,0:30:69.16:0,69,875 0/0:38,0:38:99:0,102,1318 0/0:33,0:33:90.25:0,90,1122 0/0:49,0:49:99:0,126,1653 0/0:27,0:27:72.23:0,72,938 0/0:35,0:35:90.28:0,90,1174 0/0:48,0:48:99:0,120,1555 0/0:42,0:42:99:0,99,1340 0/0:38,0:38:99:0,99,1281 0/0:43,0:43:96.31:0,96,1288 0/0:59,0:59:99:0,160,2117 0/0:23,0:23:60.18:0,60,749 0/0:33,0:33:90.28:0,90,1158 0/0:34,0:34:90.28:0,90,1162 0/0:30,0:30:81.24:0,81,1014 0/0:24,0:24:69.21:0,69,889 0/0:26,0:26:69.22:0,69,910 0/0:23,0:23:60.19:0,60,755 0/0:26,0:26:75.23:0,75,969 0/0:47,0:47:99:0,117,1473 0/1:9,11:20:99:278,0,248 0/0:36,0:36:99:0,102,1313 0/0:49,0:49:99:0,111,1364 0/0:45,1:46:77.91:0,78,1354 0/0:31,0:31:84.25:0,84,1042 0/0:25,0:25:66.16:0,66,803 0/0:30,0:30:72.20:0,72,906 0/0:21,0:21:54.17:0,54,711 0/0:18,0:18:51.16:0,51,666 0/0:19,0:19:48.15:0,48,616 0/0:23,0:24:60.19:0,60,769 0/0:16,0:16:36.12:0,36,471 0/0:20,0:20:45.14:0,45,608 -chr1 948870 . C G 69163.2 . AC=112;AF=0.9333;AN=120;BaseQRankSum=0.502;DP=2189;Dels=0.00;FS=1.037;HRun=1;HaplotypeScore=1.4157;InbreedingCoeff=-0.0719;MQ=56.60;MQ0=0;MQRankSum=-0.899;QD=31.60;ReadPosRankSum=-1.945;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_5_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1);CSQ=5_prime_UTR_variant|||ENSG00000187608|ISG15|ENST00000379389|1/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 1/1:0,9:9:18.06:232,18,0 0/1:6,4:11:99:131,0,111 1/1:0,13:13:39.10:474,39,0 1/1:0,7:7:15.05:179,15,0 1/1:0,37:37:99:1328,102,0 1/1:0,60:60:99:2240,175,0 1/1:0,76:76:99:2975,226,0 1/1:0,28:28:84.27:1110,84,0 1/1:0,76:76:99:2894,220,0 1/1:0,67:67:99:2560,199,0 1/1:0,43:43:99:1677,129,0 1/1:0,40:40:99:1439,111,0 1/1:0,58:58:99:2114,166,0 1/1:1,43:44:99:1451,111,0 1/1:0,61:61:99:1860,141,0 1/1:0,30:30:72.23:957,72,0 1/1:0,30:30:81.21:970,81,0 1/1:0,43:43:99:1419,108,0 0/1:22,30:52:99:956,0,574 1/1:0,31:31:90.29:1203,90,0 0/1:14,21:35:99:505,0,381 1/1:0,56:56:99:1839,144,0 1/1:0,48:48:99:1630,126,0 1/1:0,25:25:69.22:916,69,0 1/1:0,47:47:99:1452,108,0 1/1:0,39:39:99:1384,105,0 0/1:17,18:35:99:511,0,418 1/1:1,29:30:69.21:889,69,0 1/1:0,37:37:99:1305,99,0 1/1:0,36:36:99:1264,99,0 1/1:1,48:50:99:1699,129,0 1/1:0,29:29:75.22:969,75,0 1/1:0,36:36:90.27:1170,90,0 0/1:32,15:48:99:322,0,939 0/1:18,25:43:99:642,0,540 1/1:0,40:40:99:1406,108,0 1/1:0,44:44:99:1332,99,0 1/1:0,60:60:99:2135,162,0 1/1:0,23:23:60.17:739,60,0 1/1:0,35:35:96.29:1228,96,0 0/1:17,18:35:99:557,0,467 1/1:0,31:31:84.26:1064,84,0 1/1:0,24:24:66.21:868,66,0 1/1:0,26:26:69.21:894,69,0 1/1:0,24:24:63.19:788,63,0 1/1:0,28:28:81.24:1027,81,0 1/1:1,48:49:99:1509,120,0 1/1:0,21:21:54.15:668,54,0 1/1:0,36:36:99:1319,102,0 1/1:0,50:50:99:1383,108,0 1/1:0,46:46:99:1408,111,0 1/1:0,31:31:81.19:965,81,0 1/1:0,26:26:72.21:887,72,0 1/1:0,30:30:78.22:959,78,0 1/1:0,21:21:54.17:714,54,0 1/1:0,18:18:51.16:664,51,0 0/1:15,5:20:73.76:74,0,467 1/1:0,24:24:60.18:761,60,0 1/1:0,17:17:42.13:536,42,0 1/1:0,20:20:45.14:612,45,0 -chr1 948921 . T C 105377.26 . AC=112;AF=0.9333;AN=120;BaseQRankSum=0.554;DP=3568;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.5426;InbreedingCoeff=-0.0712;MQ=57.76;MQ0=0;MQRankSum=-1.329;QD=29.53;ReadPosRankSum=-3.423;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_5_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1);CSQ=5_prime_UTR_variant|||ENSG00000187608|ISG15|ENST00000379389|1/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 1/1:0,13:13:30.03:335,30,0 0/1:2,10:12:15.91:206,0,16 1/1:0,17:17:45.14:553,45,0 1/1:0,8:8:24.07:273,24,0 1/1:0,58:58:99:2066,157,0 1/1:1,49:50:99:1585,126,0 1/1:0,101:101:99:3562,277,0 1/1:0,52:52:99:1965,153,0 1/1:0,102:102:99:3793,292,0 1/1:0,104:104:99:3569,274,0 1/1:0,68:68:99:2381,187,0 1/1:0,58:58:99:2092,163,0 1/1:0,71:71:99:2613,208,0 1/1:0,75:75:99:2517,193,0 1/1:0,86:87:99:2718,211,0 1/1:0,50:50:99:1585,117,0 1/1:0,63:63:99:1961,150,0 1/1:0,66:66:99:2012,156,0 0/1:28,54:82:99:1360,0,683 1/1:0,63:63:99:2007,150,0 0/1:29,33:62:99:843,0,742 1/1:0,113:113:99:3423,256,0 1/1:0,71:71:99:2334,175,0 1/1:0,60:60:99:1950,150,0 1/1:0,78:78:99:2306,177,0 1/1:0,75:76:99:2225,172,0 0/1:37,34:71:99:822,0,987 1/1:0,52:52:99:1543,117,0 1/1:0,71:71:99:2027,150,0 1/1:0,55:55:99:1879,144,0 1/1:0,82:82:99:2690,205,0 1/1:0,48:48:99:1452,111,0 1/1:0,73:73:99:2219,168,0 0/1:43,26:69:99:674,0,1184 0/1:40,28:69:99:767,0,1171 1/1:0,88:88:99:2558,193,0 1/1:0,79:79:99:2465,190,0 1/1:0,105:105:99:3194,241,0 1/1:0,41:41:96.30:1249,96,0 1/1:0,57:57:99:1737,135,0 0/1:22,29:51:99:703,0,653 1/1:0,48:48:99:1429,114,0 1/1:0,37:37:99:1270,99,0 1/1:0,47:47:99:1581,123,0 1/1:0,27:27:72.20:887,72,0 1/1:0,40:40:99:1326,102,0 1/1:0,89:89:99:2900,226,0 1/1:0,30:30:66.19:835,66,0 1/1:0,60:60:99:1948,156,0 1/1:0,67:67:99:2144,171,0 1/1:1,76:77:99:2288,181,0 1/1:0,43:43:99:1260,99,0 1/1:0,48:48:99:1281,99,0 1/1:0,53:53:99:1654,129,0 1/1:0,40:40:90.27:1158,90,0 1/1:0,36:36:87.24:1092,87,0 0/1:28,10:38:99:272,0,709 1/1:0,49:49:99:1601,120,0 1/1:0,28:29:75.23:954,75,0 1/1:0,39:39:99:1285,99,0 -chr1 949053 . C G 1016.17 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.017;DP=2444;Dels=0.00;FS=9.350;HRun=2;HaplotypeScore=1.7725;InbreedingCoeff=0.6430;MQ=57.83;MQ0=0;MQRankSum=-0.809;QD=17.22;ReadPosRankSum=0.511;EFF=INTRON(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=intron_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 0/0:8,0:8:24.04:0,24,273 0/0:10,0:10:27.08:0,27,328 0/0:11,0:12:27.07:0,27,312 0/0:5,0:5:12.04:0,12,141 0/0:35,0:36:99:0,102,1282 0/0:33,0:34:93.28:0,93,1169 0/0:64,0:64:99:0,184,2355 0/0:29,0:30:87.28:0,87,1124 0/0:70,0:70:99:0,208,2635 0/0:71,0:71:99:0,208,2648 0/0:34,0:34:99:0,99,1227 0/0:34,0:34:99:0,99,1230 0/0:33,1:35:93.27:0,93,1150 0/0:41,0:42:99:0,102,1345 0/0:38,0:39:99:0,99,1253 0/0:23,0:23:57.17:0,57,735 0/0:38,0:38:96.29:0,96,1203 0/0:32,0:32:81.27:0,81,1095 0/0:38,0:38:99:0,102,1296 0/0:44,0:47:99:0,117,1453 0/0:36,0:37:84.23:0,84,1053 0/0:58,0:58:99:0,153,1969 0/0:36,0:36:90.29:0,90,1214 0/0:40,0:40:93.29:0,93,1215 0/0:44,0:44:99:0,105,1422 0/0:40,0:43:99:0,105,1353 0/0:34,0:34:75.24:0,75,989 0/0:30,0:31:81.25:0,81,1062 0/0:32,0:32:87.26:0,87,1121 0/0:28,0:28:75.23:0,75,961 0/0:52,0:52:99:0,138,1776 0/0:36,1:38:96.29:0,96,1234 0/0:34,0:34:75.24:0,75,987 0/0:33,1:35:90.26:0,90,1152 0/0:45,0:45:99:0,123,1550 0/0:42,0:42:99:0,105,1361 0/0:41,0:41:96.27:0,96,1192 0/0:52,0:52:99:0,126,1638 0/0:38,0:38:93.28:0,93,1199 0/0:46,0:46:99:0,105,1369 0/0:45,0:45:99:0,111,1361 0/0:34,1:35:90.27:0,90,1128 0/0:39,0:39:99:0,114,1425 0/0:33,0:33:84.26:0,84,1109 0/1:21,14:35:99:387,0,456 0/0:45,0:45:99:0,120,1588 0/0:85,1:88:99:0,196,2473 1/1:0,24:24:57.17:716,57,0 0/0:54,1:56:99:0,126,1636 0/0:69,1:70:99:0,162,2044 0/0:74,1:75:99:0,181,2311 0/0:36,0:38:87.25:0,87,1087 0/0:49,0:49:99:0,111,1426 0/0:53,0:53:99:0,135,1680 0/0:53,0:53:99:0,126,1630 0/0:33,0:33:90.27:0,90,1144 0/0:43,0:43:99:0,102,1343 0/0:44,0:44:99:0,102,1321 0/0:38,0:38:90.28:0,90,1147 0/0:40,0:40:99:0,99,1275 -chr1 949123 . G A 102.54 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.767;DP=1126;Dels=0.00;FS=2.226;HRun=0;HaplotypeScore=0.7464;InbreedingCoeff=-0.0173;MQ=58.11;MQ0=0;MQRankSum=0.187;QD=6.03;ReadPosRankSum=-1.626;EFF=INTRON(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=intron_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 0/0:6,0:6:18.05:0,18,222 0/0:7,0:7:21.07:0,21,265 0/1:7,3:10:43.20:43,0,227 0/1:3,4:7:93.66:125,0,94 0/0:16,0:16:48.15:0,48,616 0/0:27,0:27:78.23:0,78,996 0/0:33,0:33:99:0,99,1271 0/0:12,0:12:36.12:0,36,482 0/0:39,0:39:99:0,114,1539 0/0:37,0:37:99:0,108,1431 0/0:15,0:15:42.14:0,42,551 0/0:23,0:24:69.20:0,69,871 0/0:20,0:21:57.13:0,57,707 0/0:18,0:18:51.16:0,51,665 0/0:22,0:22:60.20:0,60,796 0/0:11,0:11:33.10:0,33,427 0/0:17,0:17:51.16:0,51,672 0/0:9,0:9:27.08:0,27,346 0/0:18,0:18:51.17:0,51,675 0/0:16,0:16:48.16:0,48,628 0/0:21,0:21:60.20:0,60,814 0/0:25,0:26:75.24:0,75,989 0/0:11,0:11:33.11:0,33,430 0/0:7,0:8:21.07:0,21,271 0/0:13,0:13:36.11:0,36,475 0/0:9,0:9:27.09:0,27,352 0/0:12,0:12:36.11:0,36,472 0/0:10,0:10:30.07:0,30,366 0/0:11,0:11:30.10:0,30,402 0/0:13,0:13:39.12:0,39,509 0/0:19,0:19:57.16:0,57,719 0/0:13,0:13:39.13:0,39,504 0/0:10,0:10:30.10:0,30,394 0/0:8,0:8:24.08:0,24,316 0/0:13,0:13:39.13:0,39,515 0/0:15,0:15:42.14:0,42,560 0/0:17,0:17:51.17:0,51,675 0/0:23,0:23:66.20:0,66,849 0/0:19,0:19:54.17:0,54,704 0/0:32,0:32:87.24:0,87,1093 0/0:39,0:39:99:0,108,1422 0/0:15,0:15:45.13:0,45,553 0/0:17,0:17:48.16:0,48,657 0/0:11,1:12:33.11:0,33,430 0/0:18,0:18:51.16:0,51,652 0/0:22,0:22:66.21:0,66,859 0/0:45,0:45:99:0,129,1702 0/0:13,0:13:39.11:0,39,476 0/0:23,0:23:66.21:0,66,842 0/0:24,0:24:69.21:0,69,884 0/0:44,0:44:99:0,126,1612 0/0:17,0:18:45.11:0,45,536 0/0:27,0:27:63.20:0,63,832 0/0:29,0:29:78.25:0,78,1031 0/0:18,0:18:54.16:0,54,689 0/0:19,0:20:51.16:0,51,675 0/0:14,0:14:39.13:0,39,525 0/0:28,0:28:81.27:0,81,1089 0/0:18,0:18:48.15:0,48,624 0/0:14,0:14:39.12:0,39,511 -chr1 949235 . G A 32604.9 . AC=112;AF=0.9333;AN=120;BaseQRankSum=-0.988;DP=993;Dels=0.00;FS=7.691;HRun=0;HaplotypeScore=0.4657;InbreedingCoeff=-0.0787;MQ=58.29;MQ0=0;MQRankSum=-1.787;QD=32.83;ReadPosRankSum=-1.094;EFF=INTRON(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=intron_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 1/1:0,6:6:18.06:232,18,0 0/1:1,7:8:14.50:241,0,15 1/1:0,3:3:9.03:118,9,0 1/1:0,3:3:9.03:119,9,0 1/1:0,10:10:30.10:392,30,0 1/1:0,12:12:36.12:476,36,0 1/1:0,9:9:27.09:353,27,0 1/1:0,10:10:30.09:388,30,0 1/1:0,19:20:57.19:770,57,0 1/1:0,32:33:96.30:1233,96,0 1/1:0,14:14:39.13:514,39,0 1/1:1,8:9:24.08:305,24,0 1/1:0,8:8:21.07:270,21,0 1/1:0,9:9:21.07:268,21,0 1/1:0,9:9:27.08:331,27,0 1/1:0,8:8:24.07:299,24,0 1/1:0,4:4:12.02:141,12,0 1/1:0,16:16:45.14:586,45,0 0/1:4,4:8:99:131,0,136 1/1:0,7:7:21.07:279,21,0 0/1:7,8:15:99:213,0,167 1/1:0,8:8:21.07:266,21,0 1/1:0,9:9:27.07:344,27,0 1/1:0,1:1:3.01:39,3,0 1/1:0,10:10:24.08:329,24,0 1/1:0,13:13:39.13:521,39,0 0/1:1,3:4:24.94:102,0,25 1/1:0,4:4:12.04:155,12,0 1/1:0,5:5:15.05:187,15,0 1/1:0,8:8:24.08:320,24,0 1/1:0,12:12:30.10:403,30,0 1/1:0,11:11:33.11:448,33,0 1/1:0,12:12:33.10:426,33,0 0/1:3,3:6:92.38:94,0,92 0/1:2,7:9:36.87:212,0,37 1/1:0,10:10:27.07:319,27,0 1/1:0,8:8:24.08:312,24,0 1/1:0,8:8:21.07:284,21,0 1/1:0,21:21:57.18:759,57,0 1/1:0,52:53:99:1743,141,0 0/1:21,22:43:99:689,0,590 1/1:1,20:22:54.16:680,54,0 1/1:0,32:32:87.27:1118,87,0 1/1:1,26:27:78.24:999,78,0 1/1:0,27:27:78.23:983,78,0 1/1:0,28:28:78.23:982,78,0 1/1:0,52:52:99:1692,135,0 1/1:0,11:11:30.09:383,30,0 1/1:0,24:24:63.17:774,63,0 1/1:0,38:38:96.31:1254,96,0 1/1:0,40:41:93.28:1174,93,0 1/1:0,28:28:81.24:1019,81,0 1/1:0,23:23:69.20:870,69,0 1/1:1,31:33:87.27:1104,87,0 1/1:0,24:25:60.16:780,60,0 1/1:0,28:28:75.21:920,75,0 0/1:12,10:22:99:314,0,372 1/1:0,19:20:51.17:683,51,0 1/1:0,11:11:30.10:393,30,0 1/1:0,25:25:69.20:873,69,0 -chr1 949302 . G A 113.2 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.449;DP=1914;Dels=0.00;FS=2.069;HRun=0;HaplotypeScore=1.3393;InbreedingCoeff=-0.0087;MQ=58.25;MQ0=0;MQRankSum=1.862;QD=8.71;ReadPosRankSum=1.655;EFF=INTRON(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|1),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=intron_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 0/0:13,0:13:33.09:0,33,397 0/0:9,0:9:27.07:0,27,317 0/0:10,0:10:30.08:0,30,379 0/0:6,0:6:18.06:0,18,229 0/0:22,0:22:63.20:0,63,837 0/0:18,0:18:51.15:0,51,648 0/0:18,0:18:51.16:0,51,667 0/0:10,0:10:30.09:0,30,376 0/0:41,0:41:99:0,117,1514 0/0:40,0:40:99:0,105,1359 0/0:19,0:19:54.17:0,54,717 0/0:20,0:21:54.18:0,54,711 0/0:25,0:25:75.23:0,75,963 0/0:14,0:15:42.13:0,42,547 0/0:10,0:10:24.07:0,24,299 0/0:11,0:11:24.06:0,24,307 0/0:12,0:12:33.10:0,33,432 0/0:20,0:20:57.13:0,57,708 0/0:19,0:19:48.16:0,48,665 0/0:27,0:27:81.26:0,81,1075 0/0:16,0:16:45.15:0,45,594 0/0:31,0:31:84.24:0,84,1070 0/0:13,0:13:39.13:0,39,508 0/0:12,0:12:36.12:0,36,468 0/0:25,0:25:72.22:0,72,913 0/1:7,6:13:99:161,0,171 0/0:15,0:15:42.13:0,42,557 0/0:12,0:12:33.11:0,33,443 0/0:25,0:25:66.21:0,66,854 0/0:18,0:18:51.16:0,51,673 0/0:20,0:20:54.18:0,54,715 0/0:15,0:15:33.11:0,33,439 0/0:12,0:13:30.09:0,30,381 0/0:13,0:13:30.10:0,30,383 0/0:11,0:11:30.10:0,30,391 0/0:20,0:20:60.19:0,60,762 0/0:18,0:18:45.14:0,45,584 0/0:27,0:27:75.22:0,75,962 0/0:62,0:63:99:0,132,1730 0/0:85,0:85:99:0,202,2563 0/0:76,0:76:99:0,187,2338 0/0:48,0:48:99:0,114,1468 0/0:40,0:40:99:0,105,1336 0/0:42,0:42:99:0,105,1367 0/0:46,0:46:99:0,102,1371 0/0:56,0:56:99:0,144,1854 0/0:105,0:105:99:0,259,3323 0/0:35,0:36:87.27:0,87,1095 0/0:46,0:46:96.27:0,96,1217 0/0:78,0:78:99:0,181,2338 0/0:78,0:78:99:0,187,2363 0/0:67,0:67:99:0,159,2050 0/0:64,0:64:99:0,162,2103 0/0:70,0:70:99:0,156,2039 0/0:38,0:41:93.26:0,93,1189 0/0:41,0:41:99:0,105,1324 0/0:47,0:47:99:0,108,1398 0/0:35,0:35:81.26:0,81,1067 0/0:20,0:20:48.13:0,48,585 0/0:46,0:46:99:0,111,1444 -chr1 949422 . G A 479.41 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.293;DP=3045;Dels=0.00;FS=6.680;HRun=1;HaplotypeScore=1.7335;InbreedingCoeff=-0.0084;MQ=58.77;MQ0=0;MQRankSum=-1.068;QD=12.29;ReadPosRankSum=-1.019;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S21N|165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=missense_variant|aGc/aAc|S/N|ENSG00000187608|ISG15|ENST00000379389|2/2|benign(0)|tolerated(0.74)|21/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 0/0:18,0:18:42.13:0,42,522 0/0:17,0:17:48.15:0,48,613 0/0:18,0:18:51.16:0,51,643 0/0:18,0:18:48.15:0,48,601 0/0:34,0:34:96.31:0,96,1262 0/0:36,0:36:99:0,105,1374 0/0:42,0:42:99:0,126,1630 0/0:25,0:25:66.21:0,66,858 0/0:72,0:72:99:0,214,2790 0/0:76,0:76:99:0,211,2719 0/0:40,0:40:99:0,108,1419 0/0:32,0:32:87.28:0,87,1136 0/0:39,0:39:99:0,108,1366 0/0:43,0:43:99:0,99,1325 0/0:43,0:43:99:0,105,1395 0/0:41,0:41:93.27:0,93,1244 0/0:51,0:51:99:0,111,1504 0/0:51,0:51:99:0,129,1664 0/0:48,1:49:80.38:0,80,1506 0/0:66,0:68:99:0,156,1989 0/0:57,0:57:99:0,129,1761 0/0:68,1:69:99:0,178,2341 0/0:41,0:41:99:0,102,1317 0/0:35,0:35:84.27:0,84,1103 0/0:42,0:42:99:0,99,1311 0/0:36,0:37:84.27:0,84,1104 0/0:45,0:45:99:0,111,1463 0/0:37,0:37:87.28:0,87,1157 0/0:54,0:54:99:0,144,1833 0/0:57,0:57:99:0,138,1830 0/0:62,0:62:99:0,147,1926 0/0:42,0:42:99:0,102,1330 0/0:57,0:57:99:0,138,1829 0/0:39,0:39:87.28:0,87,1156 0/0:42,0:42:99:0,105,1371 0/0:46,0:46:99:0,111,1447 0/0:65,0:65:99:0,153,2000 0/0:62,0:62:99:0,166,2209 0/0:65,0:66:99:0,150,1964 0/0:65,1:67:99:0,165,2115 0/0:88,0:88:99:0,220,2886 0/0:49,0:49:99:0,132,1702 0/0:51,0:51:99:0,123,1627 0/0:54,0:54:99:0,123,1630 0/0:52,0:53:99:0,126,1659 0/0:56,0:56:99:0,141,1814 0/0:96,0:96:99:0,250,3202 0/1:18,20:39:99:527,0,505 0/0:56,0:56:99:0,129,1682 0/0:90,0:90:99:0,220,2793 0/0:99,0:99:99:0,235,3109 0/0:66,0:66:99:0,174,2207 0/0:66,0:68:99:0,168,2148 0/0:58,1:60:99:0,144,1922 0/0:52,0:52:99:0,138,1819 0/0:46,0:46:99:0,114,1460 0/0:38,0:38:90.29:0,90,1209 0/0:64,0:64:99:0,129,1732 0/0:40,0:40:90.29:0,90,1182 0/0:45,0:45:99:0,120,1581 -chr1 949608 . G A 34851.76 . AC=42;AF=0.3500;AN=120;BaseQRankSum=0.005;DP=2776;Dels=0.00;FS=11.466;HRun=1;HaplotypeScore=1.6893;InbreedingCoeff=-0.0991;MQ=58.46;MQ0=0;MQRankSum=1.157;QD=19.90;ReadPosRankSum=1.625;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S83N|165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=missense_variant|aGc/aAc|S/N|ENSG00000187608|ISG15|ENST00000379389|2/2|benign(0.002)|tolerated(0.25)|83/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 0/0:7,0:7:21.06:0,21,256 0/0:14,0:14:42.13:0,42,531 0/1:6,4:10:99:129,0,172 0/1:4,4:8:99:128,0,135 0/1:13,12:25:99:405,0,414 0/0:42,0:42:99:0,123,1622 0/1:26,25:51:99:857,0,846 0/1:12,8:20:99:255,0,425 0/1:44,30:74:99:978,0,1470 0/1:38,30:68:99:948,0,1301 0/0:26,0:26:78.22:0,78,1017 0/1:21,15:36:99:471,0,660 0/0:40,0:41:99:0,120,1589 0/0:21,0:21:54.18:0,54,717 0/0:52,0:52:99:0,132,1722 0/0:27,0:27:69.22:0,69,910 0/1:17,14:31:99:427,0,511 0/0:42,0:42:99:0,114,1502 0/1:31,10:41:99:175,0,994 1/1:1,32:33:55.66:1184,56,0 0/0:28,0:28:69.22:0,69,916 0/0:56,0:56:99:0,147,1969 0/1:16,16:32:99:559,0,386 0/1:11,16:27:99:532,0,343 0/1:10,16:26:99:442,0,290 0/1:14,10:24:99:330,0,428 0/0:32,0:32:84.24:0,84,1108 0/1:15,20:35:99:611,0,411 0/1:22,14:36:99:381,0,725 0/0:30,0:30:72.24:0,72,976 0/1:20,24:44:99:746,0,580 0/0:22,0:22:63.20:0,63,815 0/1:25,27:52:99:794,0,656 0/0:33,0:33:81.26:0,81,1090 0/0:37,0:38:90.27:0,90,1194 0/1:11,15:26:99:485,0,371 0/1:20,25:45:99:807,0,586 1/1:0,53:53:99:1898,144,0 0/0:55,0:56:99:0,150,1959 0/0:100,0:100:99:0,277,3592 0/1:35,39:74:99:1180,0,1034 1/1:0,65:65:99:2365,181,0 0/1:16,29:45:99:997,0,467 0/1:25,26:51:99:764,0,758 0/0:47,0:49:99:0,126,1683 0/0:59,0:59:99:0,178,2309 0/1:50,56:107:99:1685,0,1346 0/1:23,21:44:99:668,0,672 0/1:37,32:69:99:815,0,1051 1/1:2,102:105:99:3443,198,0 1/1:1,123:125:99:4552,326,0 0/1:33,23:56:99:658,0,919 0/1:34,32:67:99:985,0,979 0/0:81,2:83:99:0,165,2863 0/0:65,0:65:99:0,190,2468 0/0:52,0:52:99:0,147,1970 0/0:50,0:50:99:0,138,1780 0/1:22,24:47:99:696,0,692 0/1:23,20:43:99:570,0,719 1/1:1,54:55:99:1933,115,0 -chr1 949654 . A G 103598.95 . AC=108;AF=0.9000;AN=120;BaseQRankSum=3.046;DP=3818;Dels=0.00;FS=9.083;HRun=0;HaplotypeScore=2.1911;InbreedingCoeff=0.0821;MQ=58.12;MQ0=0;MQRankSum=-0.993;QD=27.83;ReadPosRankSum=-2.811;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V98|165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=synonymous_variant|gtA/gtG|V|ENSG00000187608|ISG15|ENST00000379389|2/2|||98/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 1/1:0,6:6:18.05:205,18,0 0/1:8,1:9:12.38:12,0,187 1/1:0,12:12:36.11:458,36,0 1/1:0,9:9:18.04:212,18,0 1/1:0,25:25:72.23:936,72,0 1/1:0,31:31:93.30:1205,93,0 1/1:0,44:44:99:1644,126,0 1/1:0,26:26:72.23:952,72,0 1/1:0,64:64:99:2295,175,0 1/1:0,56:57:99:2108,162,0 1/1:0,23:23:66.21:862,66,0 1/1:0,18:18:45.13:584,45,0 1/1:0,43:43:99:1472,117,0 1/1:0,24:24:66.16:796,66,0 1/1:0,54:54:99:1644,129,0 1/1:0,23:23:54.16:705,54,0 1/1:0,26:26:66.18:826,66,0 1/1:0,36:36:84.26:1093,84,0 0/1:9,30:39:99:805,0,208 1/1:0,42:42:90.21:1127,90,0 0/1:18,12:30:99:294,0,501 1/1:0,55:55:99:1562,123,0 1/1:0,35:35:81.19:1011,81,0 1/1:0,26:26:57.17:725,57,0 1/1:0,34:34:93.30:1202,93,0 1/1:0,25:25:60.19:781,60,0 0/1:16,23:39:99:605,0,420 1/1:0,31:31:81.24:1032,81,0 1/1:0,33:33:84.26:1080,84,0 1/1:0,34:35:78.25:1039,78,0 1/1:0,43:43:99:1297,99,0 1/1:0,30:30:75.23:971,75,0 1/1:0,40:40:99:1302,102,0 0/1:23,14:38:99:324,0,617 0/1:14,19:33:99:568,0,286 1/1:0,33:33:75.24:1001,75,0 1/1:0,44:44:99:1365,105,0 1/1:0,53:53:99:1908,144,0 1/1:0,91:91:99:2809,226,0 1/1:0,161:161:99:4986,397,0 0/1:60,48:109:99:1216,0,1628 1/1:0,116:116:99:3742,295,0 1/1:0,108:108:99:3399,265,0 1/1:0,79:80:99:2506,202,0 1/1:0,93:93:99:2779,214,0 1/1:0,92:92:99:2870,226,0 1/1:0,192:192:99:5695,451,0 0/0:96,0:96:99:0,208,2537 1/1:0,118:118:99:3351,262,0 0/1:95,81:176:99:2102,0,2673 1/1:0,184:184:99:5442,439,0 1/1:0,108:108:99:3292,265,0 0/1:71,66:137:99:1831,0,1694 1/1:1,126:127:99:3709,267,0 1/1:0,100:101:99:3218,256,0 1/1:0,100:100:99:3075,241,0 0/1:34,30:64:99:825,0,981 1/1:0,113:113:99:3436,271,0 1/1:0,77:78:99:2285,178,0 1/1:0,105:105:99:3026,247,0 -chr1 949655 . C T 133.5 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-2.364;DP=3843;Dels=0.00;FS=4.847;HRun=0;HaplotypeScore=2.2366;InbreedingCoeff=-0.0167;MQ=58.08;MQ0=0;MQRankSum=1.217;QD=2.97;ReadPosRankSum=-1.553;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R99W|165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=missense_variant|Cgg/Tgg|R/W|ENSG00000187608|ISG15|ENST00000379389|2/2|benign(0.007)|tolerated(0.2)|99/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 0/1:5,1:6:13.50:13,0,164 0/0:9,0:9:27.06:0,27,300 0/0:12,0:12:36.10:0,36,449 0/0:9,0:9:18.05:0,18,219 0/0:25,0:26:72.22:0,72,925 0/0:32,0:32:96.31:0,96,1241 0/0:42,0:42:99:0,120,1544 0/0:26,0:26:72.23:0,72,933 0/0:61,1:63:99:0,137,2145 0/0:58,0:58:99:0,162,2093 0/0:23,0:23:66.21:0,66,845 0/0:18,0:18:48.15:0,48,625 0/0:42,0:42:99:0,117,1478 0/0:24,0:24:66.20:0,66,842 0/0:54,1:55:99:0,104,1583 0/0:23,0:23:54.17:0,54,715 0/0:26,0:26:66.20:0,66,855 0/0:36,0:36:84.26:0,84,1111 0/1:31,8:39:99:180,0,956 0/0:42,0:42:96.30:0,96,1252 0/0:30,0:30:78.23:0,78,1006 0/0:54,0:54:99:0,123,1604 0/0:34,0:34:81.26:0,81,1064 0/0:26,0:26:60.19:0,60,784 0/0:35,0:35:96.30:0,96,1251 0/0:26,0:26:63.20:0,63,828 0/0:39,0:39:93.30:0,93,1252 0/0:31,0:31:84.27:0,84,1097 0/0:34,0:34:81.26:0,81,1081 0/0:34,0:34:84.27:0,84,1124 0/0:42,0:42:96.30:0,96,1294 0/0:32,0:32:75.24:0,75,994 0/0:40,0:40:99:0,102,1336 0/0:38,0:38:90.28:0,90,1185 0/0:33,0:33:78.22:0,78,998 0/0:33,0:33:72.24:0,72,978 0/0:45,0:45:99:0,108,1420 0/0:52,1:53:99:0,110,1845 0/0:92,0:92:99:0,217,2805 0/0:160,1:162:99:0,356,5027 0/0:110,0:110:99:0,277,3539 0/0:115,0:115:99:0,295,3869 0/0:109,0:109:99:0,274,3569 0/0:80,2:82:99:0,119,2409 0/0:94,0:94:99:0,220,2884 0/0:93,0:94:99:0,220,2894 0/0:192,0:194:99:0,454,5856 0/0:93,0:95:99:0,211,2709 0/0:119,0:119:99:0,268,3454 0/0:175,0:176:99:0,466,5985 0/0:185,0:185:99:0,436,5585 0/0:107,0:107:99:0,271,3442 0/0:138,0:139:99:0,343,4382 0/0:130,0:130:99:0,301,3884 0/0:100,2:102:99:0,215,3219 0/0:101,2:103:99:0,199,3137 0/0:65,0:65:99:0,181,2297 0/0:113,0:113:99:0,274,3555 0/0:80,0:80:99:0,184,2439 0/0:105,1:107:99:0,219,3120 -chr1 949831 . C T 3120.79 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.506;DP=2204;Dels=0.00;FS=25.676;HRun=0;HaplotypeScore=2.0744;InbreedingCoeff=-0.0327;MQ=57.33;MQ0=0;MQRankSum=-0.396;QD=12.43;ReadPosRankSum=2.936;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G157|165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=synonymous_variant|ggC/ggT|G|ENSG00000187608|ISG15|ENST00000379389|2/2|||157/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 0/0:12,0:12:36.08:0,36,411 0/0:19,0:19:48.12:0,48,564 0/0:10,0:10:24.06:0,24,282 0/0:17,0:18:45.14:0,45,553 0/0:23,0:23:69.18:0,69,882 0/0:25,0:25:72.23:0,72,935 0/0:46,0:46:99:0,132,1707 0/0:25,0:25:69.19:0,69,851 0/0:59,0:59:99:0,169,2234 0/0:53,0:53:99:0,153,1997 0/0:37,0:37:99:0,99,1288 0/0:36,0:36:99:0,105,1343 0/0:34,0:35:99:0,102,1307 0/0:8,0:8:24.07:0,24,301 0/0:5,0:5:12.04:0,12,158 0/0:3,0:3:9.03:0,9,111 0/0:14,0:14:39.12:0,39,514 0/0:9,0:9:21.07:0,21,278 0/0:12,0:12:33.11:0,33,434 0/0:4,0:4:9.03:0,9,124 0/0:7,0:7:21.07:0,21,286 0/0:9,0:9:24.08:0,24,323 0/0:7,0:7:18.06:0,18,249 0/0:9,0:9:24.07:0,24,293 0/0:8,0:8:21.07:0,21,265 0/0:11,0:11:33.11:0,33,438 0/0:13,0:13:39.12:0,39,503 0/0:7,0:7:21.07:0,21,279 0/0:3,0:3:6.02:0,6,81 0/0:12,0:12:36.11:0,36,446 0/0:7,0:7:21.06:0,21,261 0/0:13,0:13:30.10:0,30,408 0/0:3,0:3:6.02:0,6,74 0/0:5,0:5:15.05:0,15,200 0/0:7,0:7:21.07:0,21,273 0/0:10,0:10:27.09:0,27,373 0/0:11,0:11:30.08:0,30,370 0/0:8,0:8:24.08:0,24,321 0/0:49,0:49:99:0,126,1596 0/0:99,0:101:99:0,253,3265 0/0:100,0:101:99:0,247,3153 0/0:73,1:74:99:0,196,2518 0/0:62,0:62:99:0,159,2027 0/0:50,0:50:99:0,132,1702 0/1:35,26:63:99:739,0,1000 0/0:75,0:75:99:0,184,2367 0/0:94,0:94:99:0,244,3091 0/0:50,0:50:99:0,138,1740 0/0:76,0:77:99:0,184,2381 0/1:52,49:102:99:1399,0,1486 0/0:78,0:79:99:0,208,2674 0/0:75,0:75:99:0,199,2563 0/1:43,41:86:99:1062,0,1240 0/0:73,0:74:99:0,184,2373 0/0:59,1:60:99:0,111,1903 0/0:73,0:75:99:0,187,2412 0/0:41,0:41:99:0,108,1433 0/0:79,0:80:99:0,217,2788 0/0:69,0:69:99:0,175,2269 0/0:63,0:63:99:0,156,2004 -chr1 949832 . G A 1258.11 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.608;DP=2177;Dels=0.00;FS=0.646;HRun=0;HaplotypeScore=2.0191;InbreedingCoeff=-0.0169;MQ=57.31;MQ0=0;MQRankSum=2.168;QD=12.21;ReadPosRankSum=-0.092;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G158S|165|ISG15|protein_coding|CODING|ENST00000379389|),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=missense_variant|Ggc/Agc|G/S|ENSG00000187608|ISG15|ENST00000379389|2/2|benign(0.009)|tolerated(0.54)|158/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 0/0:12,0:12:36.11:0,36,444 0/0:18,0:18:51.15:0,51,619 0/0:10,1:11:30.10:0,30,385 0/0:17,1:18:5.83:0,6,489 0/0:23,0:23:66.21:0,66,870 0/0:24,0:24:69.22:0,69,910 0/0:44,0:44:99:0,129,1680 0/0:28,0:28:81.25:0,81,1037 0/0:61,0:61:99:0,172,2281 0/0:53,0:53:99:0,150,1963 0/0:38,0:38:99:0,102,1344 0/0:34,0:34:99:0,99,1280 0/0:34,0:34:96.31:0,96,1251 0/0:8,0:8:24.08:0,24,308 0/0:5,0:5:12.04:0,12,159 0/0:3,0:3:9.03:0,9,113 0/0:14,0:14:39.13:0,39,526 0/0:9,0:9:24.08:0,24,320 0/0:11,0:11:30.10:0,30,401 0/0:4,0:4:9.03:0,9,124 0/0:7,0:7:21.07:0,21,284 0/0:9,0:9:24.08:0,24,325 0/0:7,0:7:18.06:0,18,250 0/0:9,0:9:27.08:0,27,339 0/0:8,0:8:21.07:0,21,281 0/0:10,0:10:30.10:0,30,398 0/0:13,0:13:39.12:0,39,503 0/0:7,0:7:21.07:0,21,274 0/0:3,0:3:6.02:0,6,81 0/0:11,0:11:33.10:0,33,415 0/0:7,0:7:21.05:0,21,259 0/0:13,0:13:30.10:0,30,402 0/0:3,0:3:6.02:0,6,76 0/0:5,0:5:15.05:0,15,203 0/0:7,0:7:21.05:0,21,259 0/0:10,0:10:27.09:0,27,373 0/0:11,0:11:30.10:0,30,383 0/0:8,0:8:24.08:0,24,319 0/0:49,0:49:99:0,123,1592 0/0:99,0:99:99:0,250,3220 0/0:99,0:99:99:0,259,3291 0/0:73,0:74:99:0,199,2533 0/0:62,0:62:99:0,156,2008 0/0:50,0:50:99:0,132,1695 0/0:65,0:65:99:0,168,2148 0/0:69,1:70:99:0,126,2150 0/0:93,0:93:99:0,244,3125 0/0:49,0:50:99:0,141,1820 0/0:76,0:76:99:0,181,2345 0/1:55,48:103:99:1306,0,1658 0/0:79,1:80:99:0,173,2623 0/0:70,0:72:99:0,184,2379 0/0:80,0:81:99:0,211,2690 0/0:71,0:71:99:0,166,2174 0/0:59,0:59:99:0,147,1921 0/0:72,0:72:99:0,190,2452 0/0:44,0:44:99:0,114,1481 0/0:76,0:77:99:0,205,2630 0/0:69,0:69:99:0,172,2266 0/0:61,0:62:99:0,150,1989 -chr1 949884 . A C 542.9 . AC=1;AF=0.0086;AN=116;BaseQRankSum=0.716;DP=1463;Dels=0.00;FS=4.086;HRun=0;HaplotypeScore=1.0630;InbreedingCoeff=-0.0204;MQ=58.08;MQ0=0;MQRankSum=-0.256;QD=14.67;ReadPosRankSum=3.251;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_3_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|2);CSQ=3_prime_UTR_variant|||ENSG00000187608|ISG15|ENST00000379389|2/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 0/0:9,0:9:24.07:0,24,303 0/0:24,0:24:66.19:0,66,815 0/0:12,0:12:33.10:0,33,414 0/0:11,0:11:33.07:0,33,375 0/0:30,0:30:87.28:0,87,1140 0/0:41,0:41:99:0,111,1465 0/0:63,0:63:99:0,187,2459 0/0:30,0:30:84.27:0,84,1124 0/0:74,0:74:99:0,217,2867 0/0:76,0:76:99:0,223,2985 0/0:31,0:31:93.29:0,93,1208 0/0:36,0:36:99:0,108,1446 0/0:42,0:42:99:0,123,1607 0/0:5,0:5:15.05:0,15,193 0/0:3,0:3:9.03:0,9,109 ./. 0/0:6,0:6:18.06:0,18,252 0/0:6,0:6:15.05:0,15,204 0/0:4,0:4:12.04:0,12,166 0/0:4,0:4:9.03:0,9,123 0/0:3,0:3:9.03:0,9,120 0/0:5,0:5:15.04:0,15,182 0/0:3,0:3:9.03:0,9,126 0/0:8,0:8:21.07:0,21,290 0/0:7,0:7:21.06:0,21,274 0/0:7,0:7:21.07:0,21,275 0/0:8,0:8:24.08:0,24,323 0/0:5,0:5:15.05:0,15,195 0/0:3,0:3:9.03:0,9,113 0/0:3,0:3:9.03:0,9,120 0/0:6,0:6:18.06:0,18,239 0/0:7,0:7:21.07:0,21,285 0/0:4,0:4:12.04:0,12,159 0/0:4,0:4:9.03:0,9,123 0/0:2,0:2:6.02:0,6,80 ./. 0/0:8,0:8:24.08:0,24,318 0/0:5,0:5:15.05:0,15,201 0/0:21,0:21:57.18:0,57,751 0/0:56,0:56:99:0,153,2029 0/0:60,0:60:99:0,159,2040 0/0:34,0:34:96.30:0,96,1236 0/0:29,0:29:84.25:0,84,1096 0/0:34,0:34:84.27:0,84,1125 0/1:17,19:37:99:590,0,447 0/0:40,0:40:99:0,105,1364 0/0:59,0:59:99:0,159,2063 0/0:27,1:28:72.23:0,72,956 0/0:42,0:42:99:0,108,1379 0/0:52,0:52:99:0,144,1805 0/0:47,0:47:99:0,126,1662 0/0:44,0:44:99:0,120,1552 0/0:54,0:54:99:0,150,1930 0/0:42,0:43:99:0,108,1390 0/0:31,0:31:84.27:0,84,1111 0/0:38,0:39:99:0,102,1299 0/0:22,0:22:60.18:0,60,760 0/0:38,0:38:99:0,99,1317 0/0:29,0:29:75.23:0,75,1014 0/0:29,0:29:72.23:0,72,940 -chr1 949889 . G A 1254.48 . AC=2;AF=0.0172;AN=116;BaseQRankSum=-1.111;DP=1383;Dels=0.00;FS=3.846;HRun=2;HaplotypeScore=1.0736;InbreedingCoeff=-0.0309;MQ=58.18;MQ0=0;MQRankSum=-0.749;QD=12.93;ReadPosRankSum=2.198;EFF=UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|),UTR_3_PRIME(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|2);CSQ=3_prime_UTR_variant|||ENSG00000187608|ISG15|ENST00000379389|2/2|||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 0/0:8,0:8:21.07:0,21,277 0/0:22,0:22:63.20:0,63,819 0/0:11,0:11:33.10:0,33,417 0/0:11,0:11:33.10:0,33,409 0/0:28,0:28:84.27:0,84,1120 0/0:42,0:42:99:0,123,1644 0/0:63,0:63:99:0,187,2495 0/0:30,1:31:90.28:0,90,1195 0/0:74,0:74:99:0,217,2907 0/0:74,0:74:99:0,217,2934 0/0:32,0:32:93.30:0,93,1214 0/0:39,0:39:99:0,117,1551 0/0:42,0:42:99:0,120,1603 0/0:4,0:4:12.03:0,12,147 0/0:3,0:3:9.02:0,9,108 ./. 0/0:6,0:6:18.06:0,18,249 0/0:6,0:6:15.04:0,15,192 0/0:4,0:4:12.04:0,12,163 0/0:4,0:4:9.03:0,9,124 0/0:3,0:3:9.03:0,9,115 0/0:5,0:5:15.05:0,15,188 0/0:3,0:3:9.03:0,9,121 0/0:9,0:9:24.06:0,24,311 0/0:8,0:8:21.05:0,21,262 0/0:6,0:6:15.05:0,15,202 0/0:7,0:7:21.07:0,21,277 0/0:4,0:4:12.04:0,12,161 0/0:3,0:3:9.03:0,9,121 0/0:4,0:4:12.04:0,12,160 0/0:6,0:6:18.06:0,18,237 0/0:8,0:8:24.06:0,24,307 0/0:4,0:4:12.04:0,12,158 0/0:3,0:3:6.02:0,6,87 0/0:2,0:2:6.02:0,6,79 ./. 0/0:6,0:7:18.06:0,18,235 0/0:4,0:4:12.04:0,12,162 0/0:20,0:20:54.18:0,54,716 0/0:46,0:47:99:0,129,1708 0/0:54,0:54:99:0,138,1817 0/0:33,0:33:87.27:0,87,1135 0/0:27,0:27:81.25:0,81,1050 0/0:30,0:30:75.24:0,75,1002 0/0:34,1:35:93.29:0,93,1204 0/0:34,0:35:93.30:0,93,1231 0/0:55,0:55:99:0,156,2026 0/0:25,0:25:66.20:0,66,866 0/0:39,0:39:96.30:0,96,1249 0/1:22,24:46:99:741,0,676 0/0:43,0:44:99:0,117,1540 0/0:41,0:41:99:0,108,1428 0/1:30,21:51:99:579,0,1000 0/0:42,0:42:99:0,105,1351 0/0:24,0:24:63.20:0,63,838 0/0:31,0:31:87.27:0,87,1105 0/0:19,0:19:54.16:0,54,667 0/0:37,0:37:99:0,99,1317 0/0:27,1:28:75.25:0,75,1012 0/0:30,0:30:75.24:0,75,978 -chr1 949925 . C T 25659.52 . AC=103;AF=0.8879;AN=116;BaseQRankSum=0.388;DP=769;Dels=0.00;FS=1.403;HRun=0;HaplotypeScore=0.4309;InbreedingCoeff=0.1833;MQ=58.18;MQ0=0;MQRankSum=0.782;QD=33.54;ReadPosRankSum=-1.626;EFF=DOWNSTREAM(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=downstream_gene_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 0/1:1,9:10:19.31:136,0,19 0/1:6,6:12:99:116,0,192 1/1:0,7:7:15.05:179,15,0 1/1:0,8:8:21.05:248,21,0 1/1:0,14:14:42.13:543,42,0 1/1:0,20:20:60.19:784,60,0 1/1:0,40:40:99:1552,117,0 1/1:0,22:22:63.19:809,63,0 1/1:0,42:42:99:1575,120,0 1/1:0,39:39:99:1518,114,0 1/1:0,16:16:48.15:612,48,0 1/1:0,27:27:78.26:1040,78,0 1/1:0,21:21:63.19:802,63,0 1/1:0,2:2:6.02:71,6,0 1/1:0,3:3:9:98,9,0 ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:76,6,0 0/0:1,0:1:3.01:0,3,40 1/1:0,2:2:6.02:72,6,0 1/1:0,1:1:3.01:41,3,0 1/1:0,3:3:9.03:118,9,0 1/1:0,2:2:6.02:83,6,0 1/1:0,5:5:12.04:160,12,0 1/1:0,7:7:18.06:236,18,0 1/1:0,5:5:12.03:148,12,0 0/0:1,0:1:3.01:0,3,37 1/1:0,3:3:9.03:114,9,0 1/1:0,3:3:9.03:126,9,0 1/1:0,3:3:9.03:119,9,0 1/1:0,5:5:9.03:119,9,0 1/1:0,4:4:12.04:152,12,0 1/1:0,3:3:9.03:119,9,0 0/0:2,0:2:6.02:0,6,79 0/1:1,2:3:32.73:70,0,33 ./. 1/1:0,3:3:9.03:119,9,0 1/1:0,3:3:9.03:124,9,0 1/1:0,10:10:27.06:341,27,0 1/1:0,17:17:48.16:639,48,0 0/1:8,18:26:99:530,0,189 1/1:0,19:19:51.13:640,51,0 1/1:0,19:19:54.17:714,54,0 1/1:0,11:12:33.11:441,33,0 1/1:0,21:21:60.19:759,60,0 1/1:0,19:19:54.17:691,54,0 1/1:0,30:30:84.28:1122,84,0 1/1:0,13:13:36.11:455,36,0 1/1:0,16:16:45.14:569,45,0 0/1:18,22:40:99:664,0,548 1/1:0,24:24:69.22:888,69,0 1/1:0,25:25:72.23:944,72,0 0/1:9,19:28:99:647,0,234 1/1:0,26:26:72.20:873,72,0 1/1:0,11:11:27.09:359,27,0 1/1:0,16:16:48.12:581,48,0 0/1:5,6:11:99:199,0,156 1/1:0,20:20:60.19:778,60,0 1/1:0,11:11:27.09:352,27,0 1/1:0,10:10:27.09:352,27,0 -chr1 950113 . GAAGT G 1437.6 . AC=33;AF=0.532;AN=62;BaseQRankSum=4.162;DP=62;FS=0.000;HRun=0;HaplotypeScore=9.8036;InbreedingCoeff=0.1341;MQ=49.27;MQ0=0;MQRankSum=-5.026;QD=34.23;ReadPosRankSum=-1.205;EFF=DOWNSTREAM(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=downstream_gene_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:9.03:0,9,243 0/1:1,2:3:70.29:105,0,70 0/1:2,2:4:99:102,0,150 0/0:2,0:2:3.01:0,3,81 1/1:0,2:2:6.02:114,6,0 0/1:3,1:4:44.95:45,0,231 0/1:1,1:2:50.97:51,0,75 0/1:3,2:5:99:102,0,150 1/1:0,3:3:9.03:171,9,0 ./. 0/1:1,2:3:72.04:105,0,72 1/1:0,2:2:6.02:114,6,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3:25,3,0 0/0:1,0:1:3.01:0,3,81 0/0:1,0:1:3.01:0,3,81 ./. ./. ./. ./. ./. 0/1:1,1:2:50.97:51,0,75 ./. ./. 1/1:0,1:1:3.01:57,3,0 ./. 1/1:0,1:1:3.01:57,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,81 ./. ./. 0/0:2,0:2:6.02:0,6,162 1/1:0,1:1:3.01:56,3,0 1/1:0,2:2:6.02:114,6,0 0/0:3,0:3:9.03:0,9,243 0/0:1,0:1:3.01:0,3,81 1/1:0,1:1:3.01:57,3,0 0/0:1,0:1:3.01:0,3,81 1/1:0,1:1:3.01:57,3,0 ./. ./. 0/0:2,0:2:6.02:0,6,162 ./. ./. ./. 1/1:0,1:1:3.01:57,3,0 1/1:0,1:1:3.01:57,3,0 ./. 1/1:0,2:2:6.02:92,6,0 ./. 0/0:2,0:2:6.02:0,6,162 ./. ./. ./. -chr1 950243 . A C 341.55 . AC=21;AF=0.553;AN=38;BaseQRankSum=1.286;DP=25;Dels=0.00;FS=2.282;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=0.2744;MQ=57.17;MQ0=0;MQRankSum=1.615;QD=24.40;ReadPosRankSum=0.099;EFF=DOWNSTREAM(MODIFIER||||165|ISG15|protein_coding|CODING|ENST00000379389|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||RP11-54O7.11|antisense|NON_CODING|ENST00000458555|);CSQ=downstream_gene_variant|||ENSG00000187608|ISG15|ENST00000379389||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000224969|RP11-54O7.11|ENST00000458555|||||antisense|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3.01:0,3,39 0/0:2,0:2:6.02:0,6,80 0/0:1,0:1:3.01:0,3,32 0/1:1,1:2:34.63:35,0,35 1/1:0,1:1:3.01:40,3,0 ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:2.99:24,3,0 1/1:0,1:1:3.01:41,3,0 1/1:1,1:2:3.01:41,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:42,3,0 1/1:0,1:1:3.01:42,3,0 1/1:0,1:1:3.01:40,3,0 ./. ./. ./. 0/0:1,0:1:2.99:0,3,23 ./. ./. ./. 1/1:0,2:2:3.01:45,3,0 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. ./. -chr1 955016 . A G 41.68 . AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.0000;MQ=47.12;MQ0=0;QD=20.84;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. -chr1 955213 . T C 205.28 . AC=12;AF=1.000;AN=12;DP=7;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.0000;MQ=49.17;MQ0=0;QD=29.33;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:6.02:77,6,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:30,3,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3:29,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. -chr1 955597 . G T 397.16 . AC=19;AF=0.339;AN=56;BaseQRankSum=-2.859;DP=48;Dels=0.00;FS=4.867;HRun=0;HaplotypeScore=0.0297;InbreedingCoeff=0.3749;MQ=53.41;MQ0=0;MQRankSum=0.000;QD=22.06;ReadPosRankSum=2.226;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P15|2045|AGRN|protein_coding|CODING|ENST00000379370|);CSQ=synonymous_variant|ccG/ccT|P|ENSG00000188157|AGRN|ENST00000379370|1/36|||15/2045|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. 0/0:2,0:2:6.01:0,6,69 ./. ./. ./. 1/1:0,2:2:6.02:77,6,0 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. 0/0:2,0:2:6.02:0,6,83 ./. ./. ./. ./. 1/1:0,2:2:3.01:45,3,0 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:2,0:2:6.01:0,6,68 ./. 0/0:2,0:2:6.02:0,6,81 ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:2,0:2:6.02:0,6,77 0/0:4,0:4:12.04:0,12,160 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:36,3,0 1/1:0,2:2:6.02:72,6,0 ./. 0/0:2,0:2:6.02:0,6,73 1/1:0,1:1:3.01:38,3,0 ./. 0/1:3,1:4:21.40:21,0,99 1/1:0,2:2:6.02:76,6,0 1/1:0,2:2:6.02:73,6,0 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,73 1/1:0,1:1:3.01:41,3,0 ./. -chr1 956061 . A AG 112.73 . AC=10;AF=0.556;AN=18;BaseQRankSum=0.851;DP=13;FS=0.000;HRun=7;HaplotypeScore=6.0534;MQ=48.24;MQ0=0;MQRankSum=-1.268;QD=22.55;ReadPosRankSum=0.103;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|1);CSQ=intron_variant&feature_elongation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:36,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3:0,3,29 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3:0,3,29 ./. 1/1:0,1:1:3.01:36,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:36,3,0 ./. ./. ./. 1/1:0,1:1:3.01:36,3,0 0/0:3,0:3:6.01:0,6,58 ./. ./. 0/0:1,0:1:3:0,3,29 ./. ./. ./. 1/1:0,1:1:3.01:36,3,0 ./. -chr1 956077 . C T 53.71 . AC=5;AF=0.250;AN=20;BaseQRankSum=1.109;DP=15;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=0.1223;MQ=51.77;MQ0=0;MQRankSum=0.370;QD=13.43;ReadPosRankSum=0.925;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,38 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. 0/1:1,1:2:25.53:27,0,26 ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 0/0:3,0:3:6.01:0,6,62 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. -chr1 957120 . G C 112.86 . AC=7;AF=0.250;AN=28;BaseQRankSum=-0.158;DP=18;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=0.0000;InbreedingCoeff=0.1430;MQ=57.39;MQ0=0;MQRankSum=-0.791;QD=18.81;ReadPosRankSum=0.791;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 0/1:1,2:3:32.20:71,0,32 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:32,3,0 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,38 ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. ./. ./. -chr1 957474 . C G 88.48 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.393;DP=913;Dels=0.00;FS=13.654;HRun=0;HaplotypeScore=0.3942;InbreedingCoeff=-0.0138;MQ=58.75;MQ0=0;MQRankSum=0.079;QD=4.02;ReadPosRankSum=2.320;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:18.05:0,18,223 0/0:6,0:6:18.05:0,18,212 0/0:12,0:12:36.12:0,36,485 0/0:6,0:6:15.04:0,15,186 0/0:9,0:9:27.09:0,27,371 0/0:4,0:4:12.04:0,12,157 0/0:9,0:10:27.09:0,27,362 0/0:2,0:2:6.02:0,6,82 0/0:13,0:13:36.12:0,36,493 0/0:17,0:17:51.17:0,51,688 0/0:7,0:7:21.06:0,21,275 0/0:6,0:6:18.06:0,18,242 0/0:11,0:11:33.11:0,33,448 0/0:8,0:8:21.07:0,21,271 0/0:4,0:4:12.04:0,12,160 0/0:7,0:7:21.07:0,21,267 0/0:10,0:10:30.07:0,30,368 0/0:8,0:8:21.07:0,21,283 0/0:10,0:10:27.09:0,27,364 0/0:4,0:4:12.04:0,12,154 0/0:7,0:7:18.06:0,18,235 0/0:12,0:12:36.12:0,36,461 0/0:10,0:10:27.08:0,27,344 0/0:10,0:11:24.08:0,24,318 0/0:7,0:7:21.07:0,21,274 0/0:12,0:12:36.12:0,36,483 0/0:10,0:10:27.09:0,27,355 0/0:7,0:7:21.07:0,21,276 0/0:11,0:11:30.09:0,30,394 0/0:5,0:5:12.04:0,12,159 0/0:16,1:17:45.14:0,45,578 0/0:10,0:10:30.08:0,30,389 0/0:6,0:6:15.05:0,15,202 0/0:12,0:12:36.12:0,36,474 0/0:10,0:10:24.07:0,24,318 0/0:11,0:11:30.10:0,30,402 0/0:10,0:10:30.10:0,30,407 0/0:21,0:21:60.19:0,60,797 0/0:16,0:16:42.14:0,42,566 0/0:39,1:40:99:0,102,1337 0/0:37,0:37:96.31:0,96,1280 0/0:22,0:22:60.19:0,60,782 0/0:19,0:19:48.16:0,48,634 0/0:15,0:15:39.12:0,39,496 0/1:15,7:22:99:136,0,483 0/0:26,0:26:63.20:0,63,834 0/0:47,0:47:99:0,117,1552 0/0:20,0:20:45.15:0,45,603 0/0:32,0:32:81.26:0,81,1077 0/0:36,0:36:84.24:0,84,1067 0/0:29,0:29:87.27:0,87,1119 0/0:21,0:21:54.17:0,54,708 0/0:24,1:25:57.18:0,57,764 0/0:30,0:30:75.23:0,75,984 0/0:24,0:24:69.20:0,69,876 0/0:21,0:21:54.17:0,54,708 0/0:20,0:20:48.15:0,48,620 0/0:10,0:10:24.07:0,24,307 0/0:28,0:28:75.24:0,75,983 0/0:24,0:24:63.21:0,63,846 -chr1 957568 . A G 559.04 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.476;DP=2810;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.8451;InbreedingCoeff=-0.0085;MQ=58.63;MQ0=0;MQRankSum=0.035;QD=11.41;ReadPosRankSum=2.360;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL 0/0:12,0:12:33.09:0,33,400 0/0:9,0:9:27.09:0,27,353 0/0:9,0:9:21.07:0,21,276 0/0:11,0:11:33.11:0,33,430 0/0:28,0:28:81.27:0,81,1091 0/0:26,0:26:75.21:0,75,968 0/0:32,0:32:96.31:0,96,1277 0/0:29,0:29:87.28:0,87,1159 0/0:58,0:58:99:0,175,2346 0/0:55,0:55:99:0,166,2166 0/0:20,0:20:60.19:0,60,795 0/0:18,0:18:54.18:0,54,719 0/0:34,0:34:99:0,102,1362 0/0:48,0:48:99:0,138,1814 0/0:34,0:34:84.26:0,84,1091 0/0:24,0:25:60.19:0,60,781 0/0:35,0:35:84.26:0,84,1089 0/0:35,0:35:90.28:0,90,1198 0/0:45,0:45:99:0,117,1576 0/0:52,0:52:99:0,129,1737 0/0:47,0:47:99:0,120,1613 0/0:55,0:55:99:0,153,2012 0/0:36,0:37:99:0,99,1341 0/0:37,0:37:99:0,105,1390 0/0:41,0:41:99:0,108,1417 0/0:44,0:44:99:0,132,1724 0/0:31,1:32:55.04:0,55,1120 0/0:45,0:45:99:0,117,1529 0/0:42,0:42:99:0,117,1549 0/0:48,0:49:99:0,129,1704 0/0:50,0:50:99:0,135,1805 0/0:41,0:41:99:0,105,1420 0/0:36,0:36:99:0,99,1295 0/0:50,0:50:99:0,117,1576 0/0:42,0:42:99:0,108,1446 0/0:45,0:45:99:0,123,1648 0/0:44,0:44:99:0,126,1677 0/0:67,0:67:99:0,178,2323 0/0:62,0:62:99:0,156,2053 0/0:84,0:85:99:0,205,2675 0/0:79,0:79:99:0,199,2607 0/0:76,0:76:99:0,175,2277 0/0:49,0:49:99:0,135,1765 0/0:64,1:65:99:0,162,2082 0/0:47,0:47:99:0,114,1501 0/0:59,0:59:99:0,141,1888 0/0:98,0:98:99:0,256,3303 0/1:24,23:49:99:607,0,591 0/0:59,1:60:99:0,150,1946 0/0:71,0:73:99:0,199,2523 0/0:93,0:93:99:0,223,2887 0/0:68,0:68:99:0,159,2060 0/0:62,0:64:99:0,162,2071 0/0:57,0:57:99:0,147,1906 0/0:54,0:54:99:0,132,1733 0/0:69,0:69:99:0,163,2177 0/0:35,0:35:87.23:0,87,1089 0/0:50,0:50:99:0,117,1575 0/0:51,0:51:99:0,123,1602 0/0:48,0:48:99:0,123,1605 -chr1 957640 . C T 832.22 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.040;DP=3915;Dels=0.00;FS=3.301;HRun=0;HaplotypeScore=2.0922;InbreedingCoeff=-0.0143;MQ=58.81;MQ0=0;MQRankSum=0.961;QD=12.06;ReadPosRankSum=1.475;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D87|2045|AGRN|protein_coding|CODING|ENST00000379370|);CSQ=synonymous_variant|gaC/gaT|D|ENSG00000188157|AGRN|ENST00000379370|2/36|||87/2045|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:18.06:0,18,230 0/0:10,0:10:30.09:0,30,367 0/0:8,0:9:24.08:0,24,314 0/1:10,1:11:2.16:2,0,332 0/0:23,1:24:27.99:0,28,838 0/0:19,0:19:54.17:0,54,718 0/0:33,0:33:99:0,99,1319 0/0:18,1:19:12.94:0,13,632 0/0:53,0:53:99:0,160,2128 0/0:58,0:58:99:0,172,2249 0/0:19,0:19:57.19:0,57,778 0/0:22,0:22:66.22:0,66,891 0/0:19,0:19:54.18:0,54,729 0/0:81,0:81:99:0,184,2411 0/0:83,0:83:99:0,187,2462 0/0:64,0:64:99:0,147,1956 0/0:60,0:60:99:0,144,1879 0/0:66,0:67:99:0,175,2286 0/0:92,0:92:99:0,226,2947 0/0:93,0:93:99:0,220,2944 0/0:64,0:64:99:0,153,2042 0/0:89,0:90:99:0,211,2759 0/0:86,0:86:99:0,199,2623 0/0:95,0:95:99:0,220,2912 0/0:72,0:72:99:0,184,2389 0/0:70,0:70:99:0,187,2442 0/0:68,0:69:99:0,166,2197 0/0:65,0:65:99:0,157,2073 0/0:83,0:85:99:0,202,2667 0/0:88,0:88:99:0,214,2810 0/0:92,0:92:99:0,229,2959 0/0:77,0:77:99:0,193,2555 0/0:56,0:56:99:0,144,1862 0/0:86,0:86:99:0,202,2641 0/0:75,0:75:99:0,175,2308 0/0:75,0:75:99:0,187,2423 0/0:77,0:77:99:0,187,2429 0/0:133,0:133:99:0,328,4328 0/0:68,0:68:99:0,159,2108 0/0:106,0:106:99:0,238,3171 0/0:83,0:83:99:0,214,2748 0/0:75,0:75:99:0,175,2337 0/0:48,0:48:99:0,123,1631 0/0:69,0:70:99:0,163,2132 0/0:41,0:42:99:0,111,1421 0/0:72,0:72:99:0,166,2201 0/0:114,0:114:99:0,292,3725 0/1:24,34:58:99:880,0,666 0/0:92,0:92:99:0,226,2942 0/0:106,0:107:99:0,238,3111 0/0:101,0:102:99:0,238,3091 0/0:68,0:69:99:0,165,2120 0/0:80,0:80:99:0,181,2360 0/0:69,0:71:99:0,159,2082 0/0:67,0:67:99:0,159,2049 0/0:56,0:56:99:0,138,1771 0/0:50,0:50:99:0,117,1529 0/0:62,0:62:99:0,153,2036 0/0:68,0:68:99:0,166,2118 0/0:57,0:57:99:0,141,1820 -chr1 957667 . C T 1421.68 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-3.679;DP=4208;Dels=0.00;FS=3.179;HRun=3;HaplotypeScore=2.6513;InbreedingCoeff=-0.0085;MQ=58.87;MQ0=0;MQRankSum=-0.384;QD=13.94;ReadPosRankSum=1.504;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G96|2045|AGRN|protein_coding|CODING|ENST00000379370|);CSQ=synonymous_variant|ggC/ggT|G|ENSG00000188157|AGRN|ENST00000379370|2/36|||96/2045|protein_coding|1 GT:AD:DP:GQ:PL 0/0:10,0:10:27.08:0,27,342 0/0:9,0:9:24.07:0,24,295 0/0:12,0:12:36.12:0,36,468 0/0:13,0:13:36.11:0,36,458 0/0:29,0:29:81.26:0,81,1071 0/0:24,0:24:72.23:0,72,944 0/0:38,0:38:99:0,108,1422 0/0:22,0:22:63.21:0,63,846 0/0:65,0:65:99:0,193,2534 0/0:75,0:75:99:0,211,2800 0/0:26,0:26:78.25:0,78,1030 0/0:25,0:25:75.25:0,75,999 0/0:26,0:26:75.24:0,75,983 0/0:87,0:87:99:0,220,2873 0/0:98,0:98:99:0,238,3144 0/0:77,0:77:99:0,178,2341 0/0:71,1:73:99:0,172,2278 0/0:82,0:82:99:0,208,2715 0/0:100,0:100:99:0,235,3073 0/1:46,56:102:99:1469,0,1279 0/0:69,0:69:99:0,172,2282 0/0:101,0:101:99:0,256,3332 0/0:92,0:92:99:0,223,2925 0/0:104,0:104:99:0,238,3174 0/0:81,0:81:99:0,202,2628 0/0:76,0:76:99:0,202,2666 0/0:100,0:100:99:0,244,3195 0/0:67,0:68:99:0,163,2154 0/0:99,0:99:99:0,253,3316 0/0:98,0:98:99:0,238,3151 0/0:100,0:100:99:0,244,3190 0/0:92,0:92:99:0,217,2870 0/0:78,0:78:99:0,202,2660 0/0:91,0:91:99:0,217,2849 0/0:79,0:79:99:0,190,2534 0/0:91,0:91:99:0,232,3044 0/0:83,0:83:99:0,211,2748 0/0:156,0:156:99:0,379,5023 0/0:64,0:64:99:0,156,1993 0/0:110,0:110:99:0,262,3420 0/0:65,1:67:99:0,159,2038 0/0:69,0:69:99:0,163,2128 0/0:49,0:49:99:0,126,1611 0/0:66,0:66:99:0,159,2102 0/0:51,0:51:99:0,126,1659 0/0:70,0:70:99:0,166,2185 0/0:108,0:109:99:0,268,3356 0/0:54,0:54:99:0,123,1602 0/0:95,0:95:99:0,223,2902 0/0:109,0:110:99:0,274,3572 0/0:94,0:94:99:0,220,2861 0/0:56,0:56:99:0,144,1849 0/0:73,0:74:99:0,175,2263 0/0:64,0:65:99:0,162,2061 0/0:68,0:68:99:0,153,2031 0/0:54,0:54:99:0,138,1779 0/0:50,0:50:99:0,114,1478 0/0:65,0:65:99:0,141,1866 0/0:67,0:67:99:0,160,2117 0/0:50,0:50:99:0,117,1575 -chr1 957898 . G T 11511.79 . AC=35;AF=0.2917;AN=120;BaseQRankSum=-2.213;DP=1017;Dels=0.00;FS=12.996;HRun=0;HaplotypeScore=0.9917;InbreedingCoeff=-0.0796;MQ=55.78;MQ0=0;MQRankSum=2.025;QD=19.92;ReadPosRankSum=0.609;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,111 0/0:5,0:5:15.05:0,15,197 0/1:4,3:7:96.05:96,0,137 0/1:2,5:7:59.52:103,0,60 0/1:4,5:9:99:168,0,131 0/0:7,0:7:21.05:0,21,256 0/1:4,7:11:99:249,0,131 0/1:3,5:8:97.70:174,0,98 0/1:4,7:11:99:250,0,129 0/1:9,10:19:99:344,0,299 0/0:6,1:7:18:0,18,204 0/0:1,0:1:3.01:0,3,40 0/0:10,1:11:30.10:0,30,396 0/1:9,16:25:99:445,0,267 0/0:35,0:35:96.30:0,96,1238 0/0:26,0:26:75.20:0,75,917 0/1:10,21:31:99:583,0,287 0/0:28,0:28:72.22:0,72,917 0/1:19,5:24:83.30:83,0,615 1/1:0,45:45:99:1567,123,0 0/0:40,0:40:99:0,99,1308 0/0:29,0:29:84.26:0,84,1087 0/1:13,24:37:99:713,0,354 0/1:17,19:36:99:610,0,470 0/0:27,0:27:75.23:0,75,962 0/1:12,22:34:99:655,0,369 0/0:24,0:24:69.21:0,69,848 0/1:16,20:36:99:581,0,448 0/0:33,0:33:78.24:0,78,1005 0/0:26,0:26:72.19:0,72,899 0/1:14,24:38:99:686,0,403 0/0:26,0:26:69.22:0,69,925 0/1:18,19:37:99:579,0,460 1/1:0,43:43:99:1490,120,0 0/0:31,0:31:90.28:0,90,1161 0/1:13,17:30:99:454,0,371 0/1:17,25:42:99:842,0,475 0/0:44,0:44:99:0,126,1586 0/0:5,0:5:15.04:0,15,173 0/0:5,0:5:15.05:0,15,186 0/0:4,0:4:12.04:0,12,166 1/1:0,5:5:15.04:185,15,0 0/1:5,3:8:92.95:93,0,162 0/1:4,1:5:21.40:21,0,102 0/0:3,0:3:9.03:0,9,115 0/0:2,0:2:6.02:0,6,81 0/1:2,3:5:58.74:93,0,59 1/1:0,2:2:6.02:79,6,0 0/0:1,0:1:3.01:0,3,38 0/1:1,3:4:26.54:100,0,27 1/1:0,7:7:15.05:191,15,0 0/0:3,0:3:9.03:0,9,107 0/0:5,0:5:15.02:0,15,183 0/1:3,1:4:28.61:29,0,104 0/0:3,0:3:6.02:0,6,74 0/0:3,0:3:6.02:0,6,70 0/0:1,0:1:3.01:0,3,35 0/1:4,1:5:18.39:18,0,123 0/1:2,1:3:30.98:31,0,70 0/0:1,0:1:3.01:0,3,42 -chr1 957967 . T TTGTAGTCTGACCTGTGGTCTGAC 98446.19 . AC=111;AF=0.9737;AN=114;BaseQRankSum=-1.879;DP=448;FS=0.000;HRun=0;HaplotypeScore=117.9611;InbreedingCoeff=-0.0725;MQ=36.18;MQ0=0;MQRankSum=-4.523;QD=220.24;ReadPosRankSum=-0.243;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant&feature_elongation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL 1/1:6,0:6:12.04:796,12,0 1/1:8,0:8:24.04:1368,24,0 1/1:8,0:8:21.07:1278,21,0 1/1:8,0:8:18.06:1617,18,0 1/1:5,0:5:15.05:793,15,0 1/1:5,0:5:9.03:657,9,0 1/1:8,0:8:24.08:1688,24,0 1/1:5,0:5:12.04:1227,12,0 1/1:7,0:7:21.07:1246,21,0 1/1:12,0:12:33.11:2231,33,0 1/1:7,0:7:18.06:1499,18,0 1/1:6,0:6:18.06:1420,18,0 1/1:5,0:5:12.04:1036,12,0 1/1:8,1:9:21.07:1996,21,0 1/1:12,1:13:33.11:2834,33,0 1/1:11,1:12:36.12:3302,36,0 1/1:9,1:10:27.09:2308,27,0 1/1:9,6:15:45.15:4402,45,0 1/1:8,2:10:24.08:2109,24,0 1/1:15,5:20:57.19:5125,57,0 0/1:13,0:13:99:1280,0,1125 1/1:3,4:8:24.08:2624,24,0 1/1:13,2:15:42.14:2805,42,0 1/1:6,1:7:15.05:1239,15,0 1/1:7,1:8:24.08:2061,24,0 1/1:11,2:14:42.13:3332,42,0 1/1:11,1:12:33.11:3149,33,0 1/1:7,4:11:27.09:2855,27,0 1/1:10,0:10:24.08:1903,24,0 1/1:16,1:17:45.15:4191,45,0 1/1:19,3:23:57.19:4251,57,0 1/1:3,1:4:9.03:686,9,0 1/1:7,1:8:24.08:1425,24,0 1/1:14,4:19:57.19:4226,57,0 1/1:6,4:10:30.10:2581,30,0 1/1:14,0:14:39.13:3192,39,0 1/1:11,8:19:54.18:4938,54,0 1/1:11,3:15:42.14:3643,42,0 1/1:3,0:3:6.02:330,6,0 1/1:1,0:1:3.01:95,3,0 1/1:1,0:1:3.01:134,3,0 1/1:2,0:2:6.02:535,6,0 1/1:1,0:1:3.01:104,3,0 1/1:1,0:1:3.01:326,3,0 ./. 1/1:2,0:2:6.02:656,6,0 1/1:4,0:4:12.04:969,12,0 1/1:1,0:1:3.01:71,3,0 ./. 0/1:3,1:4:99:883,0,178 1/1:3,1:5:15.05:1326,15,0 1/1:3,1:4:12.04:1059,12,0 0/1:2,0:2:99:322,0,184 1/1:1,0:1:3.01:287,3,0 1/1:1,1:2:3.01:328,3,0 1/1:1,0:1:3.01:208,3,0 1/1:1,1:2:3.01:328,3,0 1/1:2,0:2:6.02:513,6,0 1/1:2,0:2:6.02:656,6,0 ./. -chr1 957971 . G A 6538.45 . AC=64;AF=0.5614;AN=114;BaseQRankSum=3.096;DP=423;Dels=0.00;FS=0.554;HRun=0;HaplotypeScore=1.4918;InbreedingCoeff=-0.6704;MQ=34.45;MQ0=0;MQRankSum=-1.012;QD=15.60;ReadPosRankSum=0.359;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL 0/1:1,5:6:21.40:90,0,21 0/1:2,6:8:42.81:168,0,43 0/1:3,4:7:85.82:115,0,86 0/1:2,6:8:45.81:146,0,46 0/1:3,3:6:90.04:90,0,95 0/1:2,2:4:24.41:24,0,53 0/1:3,6:9:79.10:181,0,79 1/1:1,4:5:12.03:134,12,0 0/1:3,4:7:79.24:128,0,79 0/1:7,5:12:99:131,0,193 0/1:1,5:6:15.38:149,0,15 0/1:2,4:6:48.82:116,0,49 0/1:3,1:4:21.40:21,0,88 0/1:1,6:7:12.38:180,0,12 0/1:7,5:12:99:134,0,166 0/1:4,8:12:97.63:233,0,98 0/1:1,6:9:18.39:123,0,18 0/1:10,5:15:99:122,0,289 0/1:5,5:10:80.60:143,0,81 0/1:10,9:19:99:244,0,282 0/1:8,4:12:99:101,0,238 0/1:6,2:8:42.80:43,0,177 0/1:3,11:14:58.18:333,0,58 0/1:1,4:5:18.39:119,0,18 0/1:5,3:8:77.15:77,0,143 0/1:6,8:14:99:227,0,158 0/1:4,6:11:99:171,0,104 0/1:8,2:10:36.78:37,0,240 0/1:1,7:8:9.37:217,0,9 0/1:5,9:14:99:259,0,125 0/1:13,9:22:99:251,0,304 0/1:1,2:3:24.41:59,0,24 0/1:1,7:8:9.36:227,0,9 0/1:8,11:19:99:312,0,204 0/1:6,4:10:99:110,0,162 0/1:5,8:13:99:240,0,120 0/1:11,7:18:99:193,0,222 0/1:7,8:15:99:225,0,158 1/1:0,2:2:6.02:67,6,0 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:33,3,0 1/1:0,2:2:6.02:67,6,0 1/1:0,1:1:3.01:39,3,0 0/0:1,0:1:3:0,3,29 ./. 0/1:1,1:2:27.42:27,0,27 0/1:2,2:4:48.08:55,0,48 1/1:0,1:1:3.01:40,3,0 ./. 0/1:2,2:4:54.83:55,0,58 0/1:4,1:5:18.40:18,0,113 0/1:2,2:4:45.10:45,0,55 0/1:1,1:2:27.42:27,0,27 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 0/0:2,0:2:6.02:0,6,73 1/1:0,2:2:6.02:67,6,0 0/1:1,1:2:27.42:27,0,27 ./. -chr1 957975 . C T 5244.2 . AC=61;AF=0.5446;AN=112;BaseQRankSum=3.205;DP=388;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.4483;InbreedingCoeff=-0.7134;MQ=33.55;MQ0=0;MQRankSum=-2.362;QD=13.66;ReadPosRankSum=-15.499;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL 0/1:1,5:6:21.40:92,0,21 0/1:2,3:5:51.83:80,0,52 0/1:4,4:8:99:120,0,123 0/1:3,6:9:86.45:113,0,86 0/1:3,2:5:51.82:52,0,101 0/1:3,1:4:21.40:21,0,84 0/1:3,5:8:82.11:143,0,82 1/1:1,4:5:12.03:134,12,0 0/1:3,2:5:59.62:60,0,85 0/1:7,3:10:70.22:70,0,212 0/1:1,5:6:15.38:149,0,15 0/1:2,4:6:45.98:116,0,46 0/1:3,1:4:21.40:21,0,88 0/1:1,6:7:12.38:180,0,12 0/1:7,5:12:99:134,0,163 0/1:4,7:11:99:205,0,101 0/1:3,5:8:42.97:146,0,43 0/1:10,4:14:91.62:92,0,292 0/1:5,5:10:81.38:143,0,81 0/1:10,6:16:99:152,0,283 0/1:8,4:12:97.63:98,0,263 0/1:6,2:8:42.80:43,0,177 0/1:4,6:10:73.23:174,0,73 0/1:1,4:5:18.39:119,0,18 0/1:5,2:7:46.73:47,0,146 0/1:6,6:12:99:165,0,163 0/1:5,6:11:99:171,0,104 0/1:8,2:10:36.79:37,0,231 0/1:1,6:7:12.37:181,0,12 0/1:5,9:14:99:259,0,121 0/1:13,5:18:99:121,0,320 0/1:1,1:2:27.42:27,0,27 0/1:1,5:6:15.38:153,0,15 0/1:9,8:17:99:219,0,218 0/1:6,3:9:73.23:73,0,173 0/1:5,7:12:99:188,0,131 0/1:11,6:17:99:149,0,312 0/1:7,7:14:99:192,0,193 0/1:1,2:3:29.55:58,0,30 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:33,3,0 1/1:0,2:2:6.02:67,6,0 1/1:0,1:1:3.01:39,3,0 0/0:1,0:1:3.01:0,3,31 ./. 0/1:1,1:2:27.42:27,0,27 0/1:2,1:3:24.58:27,0,25 1/1:0,1:1:3.01:38,3,0 ./. 0/1:2,2:4:54.83:55,0,56 0/1:4,1:5:18.40:18,0,110 0/1:2,2:4:50.05:55,0,50 0/1:1,1:2:17.68:27,0,18 ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 0/0:2,0:2:6.02:0,6,73 1/1:0,2:2:6.02:67,6,0 0/1:1,1:2:27.42:27,0,27 ./. -chr1 957976 . A G 4910.47 . AC=60;AF=0.5455;AN=110;BaseQRankSum=4.309;DP=381;Dels=0.00;FS=1.187;HRun=0;HaplotypeScore=1.4201;InbreedingCoeff=-0.7088;MQ=32.86;MQ0=0;MQRankSum=-2.293;QD=13.03;ReadPosRankSum=-15.805;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL 0/1:1,5:6:21.40:93,0,21 0/1:2,3:5:51.83:82,0,52 0/1:4,3:7:82.78:83,0,126 0/1:3,6:9:83.45:143,0,83 0/1:3,2:5:51.82:52,0,101 0/1:3,1:4:21.40:21,0,85 0/1:4,5:9:99:140,0,118 1/1:1,4:5:12.03:134,12,0 0/1:3,1:4:21.40:21,0,88 0/1:7,3:10:70.22:70,0,212 0/1:1,5:6:15.38:149,0,15 0/1:2,4:6:48.82:116,0,49 0/1:3,1:4:21.40:21,0,88 0/1:1,6:7:12.38:180,0,12 0/1:7,5:12:99:104,0,165 0/1:4,7:11:99:205,0,101 0/1:3,5:8:45.81:144,0,46 0/1:10,4:14:91.62:92,0,290 0/1:5,5:10:98.46:140,0,98 0/1:9,5:16:99:125,0,265 0/1:8,4:12:99:101,0,228 0/1:6,2:8:42.80:43,0,176 0/1:4,6:10:99:171,0,101 0/1:1,4:5:18.39:119,0,18 0/1:5,1:6:15.38:15,0,149 0/1:6,6:12:99:164,0,159 0/1:5,6:11:99:171,0,104 0/1:8,2:10:36.79:37,0,236 0/1:1,5:6:15.38:149,0,15 0/1:5,9:14:99:228,0,125 0/1:13,4:17:88.61:89,0,322 0/1:1,1:2:27.42:27,0,27 0/1:1,4:5:18.39:119,0,18 0/1:9,8:17:99:219,0,208 0/1:6,3:9:73.23:73,0,171 0/1:5,6:11:99:156,0,134 0/1:11,6:17:99:149,0,298 0/1:7,7:14:99:192,0,190 0/1:1,2:3:29.55:58,0,30 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:33,3,0 1/1:0,2:2:6.02:67,6,0 1/1:0,1:1:3.01:38,3,0 0/0:1,0:1:3.01:0,3,33 ./. 0/1:1,1:2:27.42:27,0,27 0/1:2,1:3:27.42:27,0,27 ./. ./. 0/1:2,2:4:47.09:55,0,47 0/1:4,1:5:18.41:18,0,107 0/1:2,2:4:52.95:55,0,53 1/1:1,1:2:3.01:33,3,0 ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 0/0:2,0:2:6.02:0,6,75 1/1:0,2:2:6.02:67,6,0 0/1:1,1:2:27.42:27,0,27 ./. -chr1 958204 . C A 854.8 . AC=2;AF=0.025;AN=80;BaseQRankSum=1.546;DP=704;Dels=0.00;FS=3.962;HRun=1;HaplotypeScore=0.3471;InbreedingCoeff=-0.0900;MQ=57.09;MQ0=0;MQRankSum=0.211;QD=16.13;ReadPosRankSum=1.802;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:6.01:0,6,64 0/0:2,0:2:6.02:0,6,69 0/0:2,0:2:6.02:0,6,73 0/0:3,0:3:9.03:0,9,104 ./. 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:9.03:0,9,115 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,81 ./. 0/0:2,0:2:6.02:0,6,67 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:2,0:2:3.01:0,3,45 0/0:2,0:2:6.01:0,6,69 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 ./. 0/0:25,0:25:72.23:0,72,959 0/0:53,0:53:99:0,150,1948 0/0:31,0:31:87.27:0,87,1119 0/0:21,0:21:63.20:0,63,835 0/0:34,0:34:99:0,99,1306 0/1:10,11:21:99:335,0,301 0/0:35,0:35:99:0,105,1367 0/0:42,0:42:99:0,123,1641 0/0:48,0:48:99:0,132,1716 0/0:16,0:16:45.14:0,45,570 0/0:24,0:24:72.23:0,72,938 0/0:40,0:40:99:0,114,1523 0/0:61,0:61:99:0,178,2313 0/1:15,17:32:99:580,0,448 0/0:27,0:27:81.26:0,81,1060 0/0:32,0:32:96.29:0,96,1216 0/0:24,0:24:66.21:0,66,876 0/0:23,0:23:69.22:0,69,913 0/0:22,0:22:60.19:0,60,794 0/0:14,0:14:42.14:0,42,568 0/0:23,0:23:66.22:0,66,894 0/0:24,0:24:69.22:0,69,925 -chr1 958236 . T C 367.45 . AC=1;AF=0.013;AN=76;BaseQRankSum=-0.984;DP=1202;Dels=0.00;FS=6.974;HRun=2;HaplotypeScore=0.8541;InbreedingCoeff=-0.0759;MQ=56.81;MQ0=0;MQRankSum=0.871;QD=11.85;ReadPosRankSum=-0.134;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:6.02:0,6,74 0/0:3,0:3:9.03:0,9,115 0/0:3,0:3:9.02:0,9,102 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.02:0,6,78 ./. 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,82 ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:2.99:0,3,23 ./. ./. ./. 0/0:1,0:1:3:0,3,29 0/0:1,0:1:3.01:0,3,38 ./. ./. 0/0:2,0:2:3.01:0,3,45 0/0:1,0:1:3.01:0,3,37 ./. ./. ./. ./. ./. ./. ./. 0/0:39,0:39:99:0,108,1384 0/0:70,1:71:99:0,193,2494 0/0:55,1:56:99:0,153,1933 0/0:46,1:48:99:0,126,1599 0/0:57,0:57:99:0,159,2001 0/0:38,0:38:99:0,105,1367 0/0:45,0:45:99:0,120,1539 0/0:64,0:64:99:0,175,2228 0/0:79,1:80:99:0,171,2533 0/1:15,16:31:99:412,0,488 0/0:52,2:54:99:0,135,1744 0/0:83,1:84:99:0,223,2863 0/0:94,2:96:99:0,256,3240 0/0:53,0:53:99:0,141,1761 0/0:55,0:56:99:0,141,1761 0/0:55,1:56:99:0,132,1677 0/0:45,0:45:99:0,120,1510 0/0:34,0:34:93.29:0,93,1200 0/0:28,0:28:69.20:0,69,853 0/0:44,0:44:99:0,117,1511 0/0:50,0:50:99:0,144,1826 0/0:47,1:48:99:0,129,1692 -chr1 958248 . A G 14600.85 . AC=22;AF=0.297;AN=74;BaseQRankSum=6.262;DP=1397;Dels=0.00;FS=8.143;HRun=2;HaplotypeScore=1.8858;InbreedingCoeff=0.1339;MQ=57.01;MQ0=0;MQRankSum=0.270;QD=19.06;ReadPosRankSum=0.054;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,32 0/1:2,2:4:62.67:66,0,63 0/0:3,0:3:6.02:0,6,73 0/0:2,0:2:6.02:0,6,81 ./. ./. 1/1:0,1:1:3.01:41,3,0 0/1:2,1:3:30.98:31,0,73 1/1:0,1:1:3.01:39,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. 0/0:1,0:1:3:0,3,28 ./. ./. ./. 0/0:2,0:2:3.01:0,3,42 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. 0/0:49,0:50:99:0,123,1512 0/0:82,0:84:99:0,217,2704 0/0:64,1:65:99:0,165,2028 1/1:0,58:59:99:1784,144,0 0/1:31,33:64:99:954,0,788 0/1:22,29:51:99:860,0,508 0/0:48,1:49:99:0,117,1429 0/0:59,2:62:99:0,162,2019 0/1:52,44:96:99:1165,0,1359 1/1:1,38:39:99:1312,102,0 0/1:33,31:64:99:843,0,761 0/1:38,59:99:99:1667,0,1062 1/1:0,103:103:99:3322,262,0 0/1:31,31:62:99:884,0,607 0/0:69,2:71:99:0,178,2177 0/0:61,1:64:99:0,132,1685 0/0:43,2:46:99:0,114,1408 0/0:40,1:41:99:0,105,1282 0/0:30,0:31:66.21:0,66,837 0/1:23,30:53:99:866,0,627 0/1:39,26:65:99:725,0,1146 0/0:51,2:53:81.62:0,82,1556 -chr1 970215 . G C 1422.62 . AC=29;AF=0.483;AN=60;BaseQRankSum=-0.953;DP=94;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0644;InbreedingCoeff=0.4677;MQ=55.42;MQ0=0;MQRankSum=2.956;QD=30.27;ReadPosRankSum=1.616;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. 0/0:2,0:2:6.02:0,6,80 ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 0/1:1,1:2:30.11:30,0,34 ./. ./. 1/1:0,3:3:9.03:112,9,0 ./. 1/1:0,1:1:3.01:35,3,0 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,37 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,37 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. 1/1:0,3:3:9.02:100,9,0 1/1:0,7:7:21.07:274,21,0 0/0:3,0:3:9.03:0,9,112 0/0:5,0:5:15.05:0,15,179 0/0:5,0:5:15.05:0,15,201 0/0:3,0:3:9.03:0,9,112 1/1:0,4:4:12.04:149,12,0 1/1:0,2:2:3.01:39,3,0 0/1:1,4:5:26.18:145,0,26 ./. 0/0:4,0:4:12.04:0,12,141 0/0:12,0:12:36.11:0,36,436 0/0:4,0:4:9.03:0,9,117 1/1:0,5:5:15.05:185,15,0 0/1:1,2:3:29.55:67,0,30 1/1:0,5:5:15.04:178,15,0 1/1:0,3:3:9.03:118,9,0 1/1:0,1:1:3.01:33,3,0 ./. 0/0:1,0:1:3.01:0,3,36 0/0:2,0:2:6.02:0,6,76 0/0:1,0:1:3.01:0,3,33 -chr1 970549 . TGG T 8449.83 . AC=65;AF=0.5603;AN=116;BaseQRankSum=-6.256;DP=1747;FS=120.761;HRun=13;HaplotypeScore=284.3804;InbreedingCoeff=-0.5216;MQ=44.59;MQ0=0;MQRankSum=0.141;QD=5.09;ReadPosRankSum=4.437;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|1);CSQ=intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000469403|1/3||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. ./. 0/0:7,0:7:5.29:0,5,23 0/1:6,0:6:0:0,0,0 1/1:6,0:6:5.04:34,5,0 0/0:12,0:12:5.52:0,6,25 0/0:7,0:7:1.85:0,2,23 1/1:2,1:3:3:28,3,0 1/1:16,0:18:19.69:113,20,0 0/1:21,1:22:47.12:73,0,47 0/1:8,0:8:8.70:22,0,9 0/1:6,0:6:22.42:22,0,37 0/1:10,1:12:7.32:24,0,7 1/1:34,6:45:7.45:319,7,0 0/1:41,3:48:9.05:402,0,9 0/1:23,2:28:13.69:190,0,14 0/1:45,3:56:99:326,0,120 0/1:29,2:32:52.07:152,0,52 0/1:47,3:54:99:332,0,152 1/1:32,2:42:30:389,30,0 0/1:44,0:50:21.79:22,0,106 0/1:38,2:42:99:118,0,140 0/1:34,3:39:61.23:251,0,61 0/1:38,7:49:9.73:347,0,10 0/1:34,3:39:99:171,0,145 0/1:29,4:35:8.40:266,0,8 0/1:30,0:37:99:155,0,108 0/1:34,1:39:99:256,0,115 0/0:53,0:58:32.12:0,32,508 0/1:35,0:38:76.33:76,0,164 0/1:42,3:47:9.22:349,0,9 0/1:30,2:34:60.74:61,0,117 0/1:27,3:35:3.80:212,0,4 0/1:36,3:43:99:103,0,223 0/1:23,2:26:20.05:161,0,20 1/1:45,1:49:7.80:397,8,0 0/1:45,1:49:42.04:269,0,42 0/1:58,0:60:47.48:47,0,454 0/1:16,2:19:22.17:93,0,22 0/1:29,1:32:41.69:100,0,42 0/1:27,2:32:74.48:74,0,209 0/1:19,2:26:87.63:160,0,88 1/1:15,2:18:8.41:118,8,0 0/1:22,2:25:45.36:144,0,45 0/1:25,1:27:54.62:120,0,55 0/1:19,0:22:0.33:91,0,0 0/1:39,0:45:99:175,0,114 1/1:17,3:22:5.80:172,6,0 0/1:18,2:21:18.16:103,0,18 0/1:36,2:43:49.50:231,0,50 1/1:29,2:35:40.24:261,40,0 0/1:25,0:28:15.45:195,0,15 1/1:29,1:32:0.75:154,1,0 0/1:17,0:19:42.50:42,0,60 0/1:17,1:18:30.92:31,0,70 1/1:9,0:12:8.02:97,8,0 0/1:16,1:17:57.01:57,0,64 0/1:18,1:22:26.13:185,0,26 0/1:20,3:26:72.24:132,0,72 0/1:16,2:18:26.58:27,0,162 -chr1 970559 . GGGGT G 251.0 . AC=12;AF=0.1017;AN=118;BaseQRankSum=-0.439;DP=2064;FS=2.290;HRun=0;HaplotypeScore=346.6420;InbreedingCoeff=-0.1291;MQ=46.51;MQ0=0;MQRankSum=-12.374;QD=0.60;ReadPosRankSum=6.900;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|1);CSQ=intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000469403|1/3||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:6.01:0,6,61 0/0:9,0:9:9.28:0,9,83 0/0:5,0:5:3.01:0,3,34 0/1:8,0:8:3.49:3,0,63 0/0:13,0:13:8.81:0,9,76 0/0:11,0:11:5.47:0,5,129 0/0:6,0:6:11.39:0,11,105 0/1:25,0:25:1.83:2,0,267 0/0:31,0:31:36.40:0,36,371 0/0:12,0:12:12.78:0,13,170 0/0:9,0:9:13.99:0,14,145 0/0:14,0:14:15.55:0,16,152 0/0:55,0:55:52:0,52,521 0/0:57,0:57:25.45:0,25,507 0/0:30,0:30:27.34:0,27,198 0/1:57,1:58:79.94:80,0,414 0/0:43,0:43:68.69:0,69,510 0/0:70,0:70:21.84:0,22,663 0/1:51,0:51:8.98:9,0,245 0/0:55,0:55:27.02:0,27,364 0/0:47,0:47:27.80:0,28,451 0/0:50,0:50:38.10:0,38,439 0/1:52,2:53:66.13:66,0,270 0/0:46,0:46:29.08:0,29,495 0/0:35,0:35:12.44:0,12,360 0/0:42,0:42:9.46:0,9,357 0/0:42,1:43:13.95:0,14,385 0/0:66,0:66:68.48:0,68,813 0/0:44,0:44:70.57:0,71,613 0/0:56,0:55:22.88:0,23,425 0/0:40,0:40:49.19:0,49,455 0/0:43,0:43:13.60:0,14,271 0/0:52,0:52:38.83:0,39,785 0/0:29,0:29:12.65:0,13,311 0/0:61,0:61:37.14:0,37,418 0/1:56,1:57:66.20:66,0,385 0/0:72,0:72:60.30:0,60,1082 0/0:24,0:24:27.98:0,28,196 0/0:41,0:41:54.59:0,55,433 0/0:37,0:37:27.70:0,28,516 0/1:34,0:34:70.06:70,0,208 0/0:22,0:22:8.61:0,9,123 0/0:26,1:27:6.03:0,6,324 0/0:32,0:32:9.56:0,10,321 0/1:27,0:27:20.78:21,0,134 0/0:50,0:50:3.71:0,4,298 0/1:24,0:24:10.20:10,0,110 0/0:25,0:25:37.34:0,37,303 0/0:49,0:49:12.18:0,12,557 0/0:40,0:40:19.64:0,20,285 0/0:33,0:33:10.49:0,10,322 0/1:39,1:40:16.97:17,0,253 0/0:22,0:22:13.49:0,13,151 0/0:18,0:18:14.43:0,14,99 0/1:15,0:15:29.30:29,0,116 0/0:21,0:21:23.23:0,23,321 0/1:26,1:27:31.21:31,0,184 0/0:27,0:27:24.73:0,25,276 0/0:25,0:24:39.80:0,40,425 -chr1 970560 . GGGT G 6238.85 . AC=51;AF=0.4322;AN=118;BaseQRankSum=10.237;DP=2102;FS=59.155;HRun=0;HaplotypeScore=328.0111;InbreedingCoeff=-0.7958;MQ=46.78;MQ0=0;MQRankSum=-6.210;QD=3.10;ReadPosRankSum=17.494;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|1);CSQ=intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000469403|1/3||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 0/0:4,0:4:8.94:0,9,78 0/0:9,0:9:5.84:0,6,67 0/0:4,1:5:3.01:0,3,34 0/1:6,2:8:36.31:36,0,44 0/0:13,0:13:5.22:0,5,61 0/1:11,1:12:23.62:24,0,139 0/0:7,0:7:5.03:0,5,71 0/1:25,1:26:88.38:88,0,260 0/1:30,1:31:33.84:34,0,265 0/1:12,0:12:26.70:27,0,125 0/0:9,0:9:7.32:0,7,116 0/0:13,1:14:3.64:0,4,98 0/1:52,2:54:99:148,0,339 0/1:53,2:56:99:135,0,272 0/1:28,2:30:42.48:106,0,42 0/1:59,1:60:99:266,0,163 0/1:43,0:43:29.10:29,0,230 0/1:65,6:71:99:361,0,450 0/1:48,3:51:99:262,0,107 0/1:54,1:55:69.16:69,0,199 0/1:45,1:46:71.80:72,0,230 0/1:49,3:52:99:155,0,316 0/1:48,5:52:83.26:368,0,83 0/1:43,4:47:99:187,0,292 0/1:37,2:39:99:146,0,289 0/1:43,1:44:68.61:69,0,269 0/1:40,3:43:99:249,0,188 0/1:65,1:66:60.03:60,0,438 0/1:44,0:44:15.74:16,0,279 0/1:52,6:57:99:295,0,299 0/1:38,2:40:54.78:55,0,193 0/1:44,2:46:99:170,0,201 0/1:51,2:53:57.55:58,0,550 0/1:26,4:30:99:142,0,226 0/1:57,4:61:99:220,0,235 0/1:54,4:58:99:257,0,212 0/1:70,3:73:88.08:88,0,753 0/1:25,0:25:20.03:20,0,100 0/1:43,0:43:43.06:43,0,242 0/1:39,0:39:5.68:6,0,368 0/1:32,2:34:99:220,0,118 0/1:23,1:24:65.19:65,0,80 0/1:27,1:28:10.96:11,0,195 0/1:28,2:30:99:170,0,155 0/1:27,1:28:90.15:145,0,90 0/1:51,1:52:99:119,0,190 0/1:21,3:24:34.38:172,0,34 0/1:24,1:25:26.55:27,0,163 0/1:48,1:49:99:162,0,344 0/1:40,2:42:99:190,0,209 0/1:35,1:36:87.13:87,0,297 0/1:39,1:40:99:134,0,117 0/1:23,0:23:36.14:36,0,145 0/1:18,0:18:13.84:14,0,26 0/1:14,1:15:73.42:90,0,73 0/1:20,1:21:37.33:37,0,186 0/1:28,1:29:96.70:186,0,97 0/1:27,1:28:99:115,0,130 0/0:24,0:24:10.17:0,10,246 -chr1 970561 . GGT G 13756.94 . AC=57;AF=0.4831;AN=118;BaseQRankSum=18.075;DP=2129;FS=78.149;HRun=0;HaplotypeScore=306.3538;InbreedingCoeff=-0.8937;MQ=47.00;MQ0=0;MQRankSum=-8.327;QD=6.50;ReadPosRankSum=23.377;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|1);CSQ=intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000469403|1/3||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 0/0:5,0:5:11.94:0,12,108 0/1:8,1:9:2.67:3,0,89 0/0:5,0:5:3.01:0,3,33 0/1:6,2:8:22.49:48,0,22 0/1:11,2:13:3.50:4,0,82 0/1:13,0:13:18.54:19,0,159 0/1:6,1:7:20.27:20,0,64 0/1:23,2:25:99:106,0,260 0/1:31,2:33:99:100,0,372 0/1:10,2:12:48.11:48,0,110 0/1:9,1:10:15.54:16,0,122 0/1:12,1:13:36.63:37,0,64 0/1:43,11:54:99:387,0,291 0/1:45,14:59:99:539,0,270 0/1:24,7:31:1.47:321,0,1 0/1:46,13:59:65.89:494,0,66 0/1:36,9:45:99:341,0,179 0/1:56,16:72:99:600,0,374 0/1:39,15:54:99:409,0,102 0/1:56,1:57:99:135,0,148 0/1:40,6:46:99:242,0,135 0/1:43,9:52:99:325,0,263 0/1:44,9:52:30.79:550,0,31 0/1:40,7:47:99:333,0,214 0/1:32,7:39:99:341,0,234 0/1:38,8:46:99:199,0,227 0/1:29,14:43:86.72:532,0,87 0/1:64,3:67:99:252,0,223 0/1:38,7:45:99:223,0,186 0/1:48,13:60:99:591,0,328 0/1:35,4:39:99:231,0,131 0/1:38,9:47:99:383,0,197 0/1:51,3:54:99:184,0,422 0/1:23,7:30:99:247,0,189 0/1:39,21:60:99:640,0,156 0/1:49,10:59:99:490,0,212 0/1:70,4:74:99:197,0,534 0/1:21,4:25:49.79:187,0,50 0/1:35,8:43:99:209,0,169 0/1:36,2:38:99:129,0,281 0/1:28,6:34:99:299,0,106 0/1:22,2:24:67.85:127,0,68 0/1:23,5:28:99:158,0,113 0/1:26,5:31:99:224,0,132 0/1:21,7:28:73.21:178,0,73 0/1:44,10:54:99:309,0,149 0/1:20,4:24:12.88:251,0,13 0/1:22,3:25:99:113,0,135 0/1:42,7:49:99:256,0,254 0/1:34,8:42:99:294,0,154 0/1:26,10:36:99:232,0,276 0/1:31,9:40:50.07:291,0,50 0/1:22,2:24:26.02:26,0,146 0/1:15,3:18:2.14:100,0,2 0/1:11,4:15:57.16:135,0,57 0/1:17,4:21:99:152,0,132 0/1:24,6:30:84.43:278,0,84 0/1:25,2:27:99:153,0,123 0/1:24,1:25:72.81:73,0,129 -chr1 970562 . GT G 11726.17 . AC=56;AF=0.4746;AN=118;BaseQRankSum=20.100;DP=2148;FS=44.156;HRun=1;HaplotypeScore=301.2279;InbreedingCoeff=-0.8639;MQ=47.47;MQ0=0;MQRankSum=-8.868;QD=5.54;ReadPosRankSum=21.869;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|1);CSQ=intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000469403|1/3||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 0/0:4,1:5:11.94:0,12,107 0/1:6,4:10:24.73:25,0,122 0/0:5,2:7:9.03:0,9,104 0/1:9,1:10:15.27:15,0,126 0/1:8,3:11:28.50:29,0,81 0/1:11,2:13:61.12:61,0,155 0/0:8,0:8:0.55:0,1,99 0/1:22,5:27:34.27:34,0,327 0/1:26,8:34:71.23:71,0,445 0/1:9,3:12:77.47:77,0,105 0/0:9,2:11:0.23:0,0,148 0/1:10,2:12:45.61:46,0,61 0/1:50,4:54:99:196,0,314 0/1:48,9:57:99:261,0,257 0/1:23,7:30:5.58:298,0,6 0/1:50,10:60:99:467,0,124 0/1:33,13:46:99:425,0,166 0/1:64,9:73:99:421,0,358 0/1:53,3:56:99:192,0,181 0/1:38,20:58:99:317,0,157 0/1:33,15:48:76.20:265,0,76 0/1:37,15:52:99:230,0,293 0/1:43,11:54:83.50:385,0,84 0/1:35,12:47:99:340,0,184 0/1:33,7:40:99:263,0,270 0/1:39,8:47:99:178,0,243 0/1:33,7:40:51.45:365,0,51 0/1:45,22:67:86.92:554,0,87 0/1:33,13:46:99:390,0,136 0/1:56,7:62:99:427,0,336 0/1:28,10:38:99:367,0,144 0/1:41,8:49:99:275,0,201 0/1:41,16:57:99:287,0,375 0/1:24,6:30:99:191,0,221 0/1:52,10:62:99:389,0,240 0/1:50,8:58:99:314,0,226 0/1:55,20:75:99:366,0,452 0/1:19,6:25:27.89:162,0,28 0/1:30,12:42:99:287,0,150 0/1:30,6:36:99:186,0,218 0/1:27,5:32:94.69:252,0,95 0/1:21,3:24:70.64:71,0,75 0/1:26,3:29:70.95:71,0,101 0/1:28,2:31:99:119,0,99 0/1:24,4:28:70.87:155,0,71 0/1:46,9:55:99:289,0,176 0/1:23,1:24:45.31:142,0,45 0/1:21,5:27:84.10:84,0,203 0/1:47,3:50:99:112,0,302 0/1:41,0:41:99:153,0,164 0/1:30,5:35:99:125,0,258 0/1:31,9:40:54.40:247,0,54 0/1:20,3:23:23.49:23,0,131 1/1:13,5:18:11.49:151,11,0 0/1:14,1:15:49.27:96,0,49 0/1:17,4:21:99:166,0,116 0/1:29,1:30:73.16:129,0,73 0/1:24,3:27:99:108,0,126 0/1:22,4:26:74.08:74,0,109 -chr1 970573 . T G 1645.49 . AC=31;AF=0.2583;AN=120;BaseQRankSum=-22.121;DP=2678;Dels=0.00;FS=172.614;HRun=4;HaplotypeScore=23.1118;InbreedingCoeff=-0.3662;MQ=49.95;MQ0=0;MQRankSum=-11.517;QD=1.06;ReadPosRankSum=19.788;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|2),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|1/3||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:6,1:7:15.03:0,15,173 0/0:10,1:11:30.08:0,30,350 0/0:9,6:15:4.40:0,4,311 0/0:7,2:9:18.05:0,18,214 0/0:10,4:14:5.40:0,5,324 0/0:15,4:19:39.12:0,39,493 0/0:27,6:33:62.58:0,63,1033 0/0:19,3:24:51.16:0,51,662 0/0:41,5:46:99:0,117,1489 0/0:52,12:64:99:0,141,1802 0/0:13,4:17:36.09:0,36,450 0/0:10,5:16:30.10:0,30,396 0/1:11,7:18:61.29:61,0,335 0/0:35,26:62:9.17:0,9,841 0/1:37,31:68:25.38:25,0,808 0/1:15,19:35:48.62:49,0,348 0/1:41,27:68:39.89:40,0,849 0/1:30,20:52:81.58:82,0,640 0/1:41,37:79:99:129,0,717 0/0:46,19:66:58.84:0,59,844 0/0:40,32:73:0.82:0,1,818 0/1:30,28:58:99:140,0,675 0/1:31,31:62:72.70:73,0,746 0/1:33,31:65:30.31:30,0,650 0/1:25,28:54:22.78:23,0,532 0/1:23,21:44:42.49:42,0,537 0/0:35,18:56:39.60:0,40,790 0/1:22,25:47:99:111,0,479 0/1:31,44:75:99:238,0,727 0/1:28,27:55:60.95:61,0,668 0/0:50,27:78:14.81:0,15,1186 0/1:24,21:45:55.23:55,0,602 0/1:36,26:63:14.96:15,0,965 0/1:42,24:66:53.50:53,0,969 0/1:27,14:43:70.13:70,0,597 0/0:44,36:83:33.21:0,33,1095 0/1:37,29:67:20.54:21,0,703 0/1:44,45:90:99:145,0,1062 0/1:12,14:26:24.30:24,0,239 0/1:33,23:56:17.54:18,0,661 0/1:27,15:42:35.28:35,0,652 0/1:16,19:36:76.12:76,0,331 0/0:21,7:28:45.10:0,45,515 0/0:24,12:36:42.09:0,42,473 0/0:25,12:37:31.46:0,31,553 0/1:19,10:30:24.14:24,0,369 0/0:43,23:67:9.04:0,9,819 0/1:17,13:30:63.40:63,0,320 0/0:28,9:38:28.44:0,28,550 0/0:50,12:63:57.85:0,58,1075 0/0:30,14:44:63.17:0,63,737 0/1:26,17:43:43.51:44,0,518 0/1:26,21:47:21.69:22,0,549 0/0:21,7:28:16.46:0,16,462 0/1:10,13:23:74.55:75,0,198 0/0:16,5:21:36.07:0,36,403 0/0:20,10:30:17.53:0,18,507 0/0:24,15:39:28.18:0,28,543 0/1:23,10:33:19.78:20,0,527 0/1:15,12:29:15.31:15,0,250 -chr1 970765 . C T 1353.46 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.165;DP=4536;Dels=0.00;FS=22.500;HRun=0;HaplotypeScore=2.7925;InbreedingCoeff=-0.0084;MQ=57.72;MQ0=0;MQRankSum=1.115;QD=12.65;ReadPosRankSum=3.005;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|3),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|2),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:19,0:19:51.14:0,51,626 0/0:17,0:17:45.12:0,45,547 0/0:26,0:26:75.24:0,75,961 0/0:16,0:16:36.10:0,36,443 0/0:35,0:35:99:0,99,1310 0/0:33,0:33:99:0,99,1318 0/0:62,0:62:99:0,181,2389 0/0:46,0:46:99:0,135,1772 0/0:102,0:102:99:0,304,4063 0/0:90,0:90:99:0,271,3578 0/0:45,0:45:99:0,129,1659 0/0:32,0:32:96.31:0,96,1264 0/0:38,0:38:99:0,111,1413 0/0:64,0:64:99:0,178,2315 0/0:73,0:73:99:0,187,2437 0/0:44,0:44:99:0,129,1699 0/0:76,0:76:99:0,199,2561 0/0:75,0:76:99:0,205,2669 0/0:68,2:71:99:0,190,2441 0/0:47,0:47:99:0,135,1730 0/0:59,0:59:99:0,150,1909 0/0:59,0:59:99:0,175,2241 0/0:69,0:69:99:0,184,2370 0/0:51,0:51:99:0,147,1913 0/0:54,0:54:99:0,141,1743 0/0:56,1:57:99:0,153,2027 0/0:66,0:67:99:0,190,2460 0/0:39,0:39:99:0,111,1402 0/0:81,0:81:99:0,217,2773 0/0:43,1:44:99:0,123,1614 0/0:84,0:84:99:0,238,3080 0/0:52,0:53:99:0,138,1794 0/0:64,0:64:99:0,181,2302 0/0:69,0:69:99:0,184,2311 0/0:48,0:48:99:0,135,1760 0/0:60,0:60:99:0,163,2131 0/0:58,0:58:99:0,160,2083 0/0:112,0:112:99:0,307,3993 0/0:83,0:83:99:0,211,2704 0/0:150,0:150:99:0,349,4546 0/0:116,0:116:99:0,286,3678 0/1:53,54:107:99:1401,0,1216 0/0:82,0:82:99:0,205,2647 0/0:90,1:91:99:0,217,2891 0/0:72,0:74:99:0,178,2259 0/0:92,0:93:99:0,226,2909 0/0:194,0:197:99:0,448,5651 0/0:60,0:61:99:0,141,1844 0/0:159,0:159:99:0,331,4428 0/0:138,0:140:99:0,331,4199 0/0:154,0:154:99:0,388,4987 0/0:94,0:96:99:0,241,3058 0/0:114,0:114:99:0,250,3218 0/0:115,1:119:99:0,268,3479 0/0:84,0:84:99:0,205,2678 0/0:72,0:72:99:0,159,2064 0/0:93,1:94:99:0,208,2712 0/0:117,1:118:99:0,256,3377 0/0:82,0:82:99:0,196,2592 0/0:108,0:108:99:0,229,3081 -chr1 970836 . G A 214.73 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.962;DP=2105;Dels=0.00;FS=7.794;HRun=0;HaplotypeScore=1.1718;InbreedingCoeff=-0.0084;MQ=57.64;MQ0=0;MQRankSum=0.008;QD=10.74;ReadPosRankSum=1.304;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|3),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|2),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:14,0:14:33.10:0,33,410 0/0:18,0:18:48.13:0,48,589 0/0:15,0:15:42.14:0,42,550 0/0:15,0:15:42.13:0,42,539 0/0:21,0:21:63.20:0,63,838 0/0:21,0:21:60.17:0,60,762 0/0:40,0:40:99:0,117,1552 0/0:23,0:23:69.22:0,69,910 0/0:49,0:49:99:0,144,1936 0/0:65,0:65:99:0,196,2611 0/0:41,0:41:99:0,123,1619 0/0:12,0:12:36.12:0,36,477 0/0:24,0:24:72.23:0,72,955 0/0:20,0:20:57.15:0,57,723 0/0:36,0:36:99:0,102,1348 0/0:15,0:15:42.12:0,42,520 0/0:27,0:28:66.21:0,66,884 0/0:18,0:18:54.17:0,54,680 0/0:27,0:27:75.23:0,75,969 0/0:19,0:20:51.15:0,51,641 0/0:32,0:32:87.28:0,87,1114 0/0:32,0:32:90.28:0,90,1131 0/0:22,0:22:63.17:0,63,834 0/0:19,0:19:54.17:0,54,688 0/0:21,0:21:57.15:0,57,716 0/0:11,0:12:33.10:0,33,430 0/1:9,10:20:99:262,0,296 0/0:13,0:13:36.11:0,36,463 0/0:35,0:35:99:0,102,1330 0/0:15,0:15:42.13:0,42,539 0/0:32,0:32:81.23:0,81,1031 0/0:26,0:26:78.21:0,78,987 0/0:27,0:27:78.25:0,78,1027 0/0:32,0:32:87.28:0,87,1127 0/0:18,0:18:45.14:0,45,579 0/0:33,0:33:93.30:0,93,1219 0/0:15,0:15:39.09:0,39,483 0/0:34,0:34:93.30:0,93,1217 0/0:51,0:51:99:0,135,1751 0/0:69,0:70:99:0,187,2386 0/0:55,0:55:99:0,150,1951 0/0:44,0:44:99:0,120,1520 0/0:42,0:42:99:0,108,1402 0/0:32,0:32:81.25:0,81,1045 0/0:28,0:28:78.25:0,78,1022 0/0:58,0:59:99:0,157,2065 0/0:112,0:113:99:0,298,3755 0/0:22,0:22:60.16:0,60,740 0/0:74,0:74:99:0,193,2488 0/0:66,0:67:99:0,172,2213 0/0:73,0:73:99:0,196,2493 0/0:56,0:56:99:0,150,1895 0/0:49,0:49:99:0,123,1499 0/0:58,0:58:99:0,138,1786 0/0:41,0:41:99:0,102,1378 0/0:34,0:34:93.29:0,93,1193 0/0:36,0:36:96.30:0,96,1219 0/0:43,0:44:99:0,114,1477 0/0:47,0:47:99:0,117,1586 0/0:50,0:50:99:0,135,1757 -chr1 970915 . C T 377.1 . AC=2;AF=0.0167;AN=120;BaseQRankSum=2.244;DP=644;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.3824;InbreedingCoeff=-0.0289;MQ=57.36;MQ0=0;MQRankSum=0.823;QD=9.20;ReadPosRankSum=1.968;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|3),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|2),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.04:0,12,147 0/0:6,0:6:18.05:0,18,215 0/0:9,0:9:27.07:0,27,318 0/0:3,0:3:9.03:0,9,106 0/0:6,0:6:18.06:0,18,241 0/0:7,0:7:21.06:0,21,264 0/0:11,0:11:33.10:0,33,426 0/0:10,0:10:27.07:0,27,343 0/0:25,0:25:75.24:0,75,984 0/0:21,0:21:60.19:0,60,790 0/0:12,0:12:36.12:0,36,469 0/0:9,0:9:24.08:0,24,306 0/0:9,0:9:27.09:0,27,349 0/0:4,0:4:12.04:0,12,153 0/0:5,0:5:12.04:0,12,157 0/0:3,0:3:6.02:0,6,82 0/0:10,0:10:30.09:0,30,376 0/0:8,0:8:24.07:0,24,297 0/0:7,0:7:21.05:0,21,261 0/0:12,0:12:36.11:0,36,459 0/0:6,0:6:18.05:0,18,218 0/0:8,0:8:24.06:0,24,286 0/0:3,0:3:9.03:0,9,122 0/0:4,0:4:12.04:0,12,168 0/0:6,0:6:18.06:0,18,240 0/0:5,0:5:12.04:0,12,151 0/0:8,0:8:21.07:0,21,287 0/0:7,0:7:18.06:0,18,222 0/0:7,0:7:21.07:0,21,279 0/0:8,0:8:24.07:0,24,298 0/0:11,0:12:30.10:0,30,385 0/0:6,0:6:18.06:0,18,226 0/0:6,0:6:18.06:0,18,233 0/0:7,0:7:18.05:0,18,206 0/0:9,0:9:24.08:0,24,306 0/0:4,0:4:12.04:0,12,166 0/0:2,0:2:6.02:0,6,77 0/0:13,0:13:39.12:0,39,477 0/0:9,0:9:27.09:0,27,371 0/0:22,0:22:63.15:0,63,779 0/0:15,0:15:39.12:0,39,511 0/0:11,0:11:33.10:0,33,417 0/0:16,0:16:48.13:0,48,571 0/0:13,0:13:39.12:0,39,493 0/0:17,0:17:48.15:0,48,619 0/0:14,0:14:39.12:0,39,509 0/0:25,0:25:72.21:0,72,876 0/0:4,0:4:9.03:0,9,123 0/0:17,1:18:10.36:0,10,547 0/1:10,7:17:99:230,0,311 0/0:19,0:19:51.15:0,51,649 0/0:20,0:20:54.17:0,54,694 0/1:17,7:24:99:212,0,492 0/0:22,0:22:60.19:0,60,778 0/0:7,0:7:21.06:0,21,251 0/0:11,0:11:33.08:0,33,381 0/0:14,0:14:36.12:0,36,472 0/0:17,0:17:48.15:0,48,628 0/0:13,0:13:39.13:0,39,527 0/0:14,0:14:39.13:0,39,529 -chr1 971224 . A G 877.98 . AC=35;AF=0.921;AN=38;BaseQRankSum=0.367;DP=38;Dels=0.00;FS=6.105;HRun=6;HaplotypeScore=0.1297;InbreedingCoeff=0.0071;MQ=58.78;MQ0=0;MQRankSum=0.367;QD=27.44;ReadPosRankSum=0.768;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|3),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|2),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,3:3:9.03:109,9,0 1/1:1,2:3:6.02:75,6,0 1/1:0,4:4:12.03:136,12,0 1/1:0,2:2:3.01:40,3,0 ./. 1/1:0,1:1:3.01:41,3,0 ./. 1/1:0,1:1:3.01:41,3,0 ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. 1/1:0,2:2:3.01:45,3,0 1/1:0,1:1:3.01:36,3,0 ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:30,3,0 ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 0/1:1,1:2:22.63:30,0,23 ./. ./. ./. 1/1:0,2:2:6.02:75,6,0 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 1/1:0,2:2:3.01:45,3,0 ./. 0/0:2,0:2:6.02:0,6,78 ./. 1/1:0,2:2:3.01:45,3,0 ./. -chr1 975702 . A G 736.88 . AC=30;AF=0.833;AN=36;BaseQRankSum=1.380;DP=25;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.0438;InbreedingCoeff=0.2327;MQ=57.17;MQ0=0;MQRankSum=0.794;QD=33.49;ReadPosRankSum=-0.544;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|3),INTRON(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|2),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|1);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,39 1/1:0,3:3:9.02:106,9,0 ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:82,6,0 ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. ./. ./. 1/1:0,4:4:9.03:125,9,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:37,3,0 1/1:0,1:1:3.01:37,3,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,32 ./. 1/1:0,1:1:3.01:41,3,0 ./. 1/1:0,2:2:6.02:81,6,0 ./. ./. ./. 1/1:0,1:1:3.01:31,3,0 ./. 1/1:0,1:1:3.01:39,3,0 ./. 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 -chr1 976428 . C A 86.19 . AC=8;AF=1.00;AN=8;DP=10;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5990;MQ=29.00;MQ0=0;QD=21.55;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|4),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|2),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3:28,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3:28,3,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. -chr1 976514 . C A 153.87 . AC=10;AF=0.833;AN=12;BaseQRankSum=0.742;DP=14;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=40.36;MQ0=0;MQRankSum=-0.742;QD=25.65;ReadPosRankSum=-0.742;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|4),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|2),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. 1/1:0,1:1:3.01:32,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3:25,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:30,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3:0,3,26 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 ./. 1/1:0,2:2:6.02:75,6,0 ./. ./. ./. ./. ./. ./. ./. ./. -chr1 977203 . G C 14246.35 . AC=102;AF=0.8947;AN=114;BaseQRankSum=0.075;DP=497;Dels=0.00;FS=12.091;HRun=1;HaplotypeScore=0.3092;InbreedingCoeff=0.1183;MQ=53.27;MQ0=0;MQRankSum=-0.225;QD=29.99;ReadPosRankSum=0.784;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|6),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 0/1:1,1:2:27.42:27,0,27 ./. ./. 1/1:0,10:10:21.07:275,21,0 1/1:0,4:4:12.04:146,12,0 1/1:0,3:3:9.03:119,9,0 1/1:0,4:4:12.04:149,12,0 1/1:0,12:12:33.11:439,33,0 1/1:0,11:11:30.08:374,30,0 1/1:0,11:11:30.09:385,30,0 0/1:6,1:7:21.26:21,0,176 1/1:0,8:8:21.06:251,21,0 1/1:0,2:2:6.02:79,6,0 1/1:0,1:1:3.01:30,3,0 1/1:0,1:1:3.01:40,3,0 1/1:0,1:1:3.01:37,3,0 1/1:0,1:1:3.01:39,3,0 1/1:0,6:6:18.05:221,18,0 1/1:0,3:4:6.02:64,6,0 0/1:2,2:4:65.07:65,0,68 1/1:0,5:5:15.04:173,15,0 1/1:0,6:6:15.04:184,15,0 1/1:0,4:4:12.01:127,12,0 1/1:0,3:3:6.02:87,6,0 1/1:0,2:2:6.02:70,6,0 1/1:0,1:1:3.01:39,3,0 1/1:0,1:1:3.01:42,3,0 0/1:1,3:4:24.94:95,0,25 1/1:0,3:4:6.02:77,6,0 1/1:0,3:3:9.03:113,9,0 1/1:0,3:3:9.03:117,9,0 1/1:0,5:5:15.05:185,15,0 1/1:0,9:9:27.08:330,27,0 1/1:0,4:4:9.03:111,9,0 1/1:0,3:3:9:99,9,0 1/1:0,3:3:6.02:80,6,0 0/0:9,0:9:24.08:0,24,320 1/1:0,11:11:30.08:365,30,0 1/1:1,13:14:36.10:435,36,0 0/1:13,9:22:99:260,0,269 0/1:10,5:15:99:149,0,321 1/1:0,12:12:30.09:379,30,0 1/1:0,12:12:33.08:404,33,0 1/1:0,10:10:30.09:358,30,0 1/1:1,11:12:33.10:413,33,0 1/1:0,31:31:87.24:1027,87,0 1/1:0,4:4:12.04:141,12,0 1/1:0,7:7:21.06:250,21,0 1/1:0,39:40:99:1310,105,0 1/1:0,30:30:87.24:1044,87,0 1/1:0,31:31:78.20:935,78,0 1/1:0,24:24:72.22:903,72,0 1/1:0,6:6:15.04:177,15,0 1/1:0,13:13:36.11:452,36,0 1/1:0,2:2:6.02:76,6,0 0/1:4,2:6:54.46:54,0,122 0/1:7,6:13:99:195,0,198 1/1:0,8:8:18.06:230,18,0 0/0:12,0:12:33.10:0,33,406 -chr1 977220 . C T 77.62 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.664;DP=734;Dels=0.00;FS=6.335;HRun=1;HaplotypeScore=0.5865;InbreedingCoeff=-0.0433;MQ=54.41;MQ0=0;MQRankSum=-0.052;QD=3.53;ReadPosRankSum=0.239;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|6),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:1,1:2:3.01:0,3,31 0/0:6,0:6:18.05:0,18,217 0/0:3,0:3:6.02:0,6,79 0/0:1,0:1:3.01:0,3,41 0/0:14,1:15:42.13:0,42,526 0/0:7,0:8:21.07:0,21,275 0/0:13,0:13:39.13:0,39,516 0/0:6,0:6:18.06:0,18,232 0/0:30,0:30:87.27:0,87,1132 0/0:26,0:26:75.23:0,75,944 0/0:17,0:17:48.14:0,48,614 0/0:12,0:12:36.12:0,36,471 0/0:12,0:12:36.11:0,36,449 0/0:2,0:2:6.01:0,6,64 0/0:4,0:4:12.03:0,12,145 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,30 0/0:6,0:6:15.05:0,15,180 0/0:5,0:5:12.04:0,12,157 0/0:5,0:5:15.03:0,15,187 0/0:6,0:7:18.06:0,18,226 0/0:7,0:7:18.05:0,18,222 0/0:5,0:5:12.04:0,12,143 0/0:3,0:3:6.02:0,6,87 0/0:3,0:3:9.02:0,9,100 0/0:1,0:1:3.01:0,3,40 0/0:3,0:3:9.03:0,9,119 0/0:4,0:4:12.04:0,12,149 0/0:3,0:4:9.03:0,9,108 0/0:4,0:4:12.04:0,12,148 0/0:4,0:4:12.04:0,12,158 0/0:5,0:5:15.04:0,15,177 0/0:11,0:11:27.09:0,27,348 0/0:8,0:8:24.04:0,24,271 0/0:5,0:5:15.04:0,15,185 0/0:5,0:5:12.03:0,12,143 0/0:10,0:10:27.09:0,27,351 0/0:22,0:22:63.18:0,63,795 0/0:24,0:24:63.20:0,63,801 0/0:25,0:25:69.17:0,69,804 0/0:21,0:21:60.16:0,60,732 0/0:13,0:13:39.11:0,39,469 0/0:13,0:13:39.12:0,39,484 0/0:14,0:14:42.12:0,42,501 0/0:13,0:13:39.12:0,39,482 0/0:42,0:42:99:0,114,1372 0/1:4,4:8:90.95:125,0,91 0/0:11,0:11:33.10:0,33,396 0/0:59,0:59:99:0,165,1988 0/0:44,0:44:99:0,123,1524 0/0:35,0:36:93.28:0,93,1148 0/0:29,0:29:84.26:0,84,1055 0/0:12,0:12:27.08:0,27,335 0/0:15,0:15:39.12:0,39,476 0/0:7,0:7:21.06:0,21,252 0/0:11,0:12:33.10:0,33,411 0/0:18,0:18:51.16:0,51,642 0/0:16,0:16:42.13:0,42,515 0/1:13,1:14:2.11:2,0,403 -chr1 977294 . G A 323.25 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.012;DP=2064;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.9641;InbreedingCoeff=-0.0130;MQ=55.98;MQ0=0;MQRankSum=1.642;QD=9.51;ReadPosRankSum=0.377;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|6),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,77 0/0:13,0:13:36.10:0,36,431 0/0:4,0:4:12.04:0,12,152 0/0:3,0:3:9.03:0,9,113 0/0:26,0:26:72.22:0,72,933 0/0:23,0:23:57.15:0,57,695 0/0:36,0:36:99:0,105,1320 0/0:28,0:28:81.23:0,81,1008 0/0:63,0:63:99:0,178,2275 0/0:69,0:69:99:0,178,2261 0/0:18,0:18:51.16:0,51,663 0/0:31,0:31:84.23:0,84,1048 0/0:29,0:29:84.24:0,84,1046 0/0:10,0:10:18.06:0,18,239 0/0:14,0:14:36.09:0,36,448 0/0:4,0:4:12.04:0,12,157 0/0:7,0:7:18.06:0,18,225 0/0:6,0:6:18.06:0,18,233 0/0:15,0:15:42.13:0,42,536 0/0:7,0:8:18.06:0,18,234 0/0:7,0:7:21.06:0,21,265 0/0:9,0:9:27.09:0,27,352 0/0:12,0:12:30.09:0,30,378 0/0:10,0:10:24.07:0,24,303 0/0:8,0:8:21.07:0,21,271 0/0:13,0:13:30.10:0,30,394 0/0:8,0:8:21.07:0,21,285 0/0:7,0:7:21.07:0,21,273 0/0:16,0:17:45.14:0,45,571 0/0:14,0:14:36.11:0,36,467 0/0:17,0:17:42.14:0,42,567 0/0:13,0:13:36.09:0,36,450 0/0:16,0:16:42.12:0,42,540 0/0:10,0:10:27.08:0,27,341 0/0:14,0:14:39.11:0,39,466 0/0:13,0:14:33.08:0,33,389 0/0:7,0:8:21.06:0,21,265 0/0:14,0:14:39.13:0,39,520 0/0:63,0:63:99:0,144,1838 0/0:80,0:80:99:0,214,2711 0/0:61,0:61:99:0,147,1893 0/0:65,0:65:99:0,156,2019 0/0:38,0:39:99:0,99,1270 0/0:46,1:48:99:0,111,1359 0/0:41,0:42:96.30:0,96,1212 0/0:62,0:63:99:0,150,1941 0/0:101,0:103:99:0,238,2968 0/1:17,17:34:99:371,0,477 0/0:65,0:65:99:0,159,2012 0/0:141,0:144:99:0,343,4244 0/0:105,0:106:99:0,262,3215 0/0:72,0:73:99:0,193,2433 0/0:91,1:93:99:0,220,2731 0/0:58,0:60:99:0,135,1714 0/0:52,0:52:99:0,111,1399 0/0:44,0:44:99:0,111,1439 0/0:42,0:42:93.30:0,93,1214 0/0:64,0:64:99:0,141,1835 0/0:46,0:46:96.29:0,96,1243 0/0:54,0:57:99:0,129,1694 -chr1 977330 . T C 75130.94 . AC=107;AF=0.8917;AN=120;BaseQRankSum=4.114;DP=2805;Dels=0.00;FS=1.138;HRun=2;HaplotypeScore=2.7705;InbreedingCoeff=0.2224;MQ=56.35;MQ0=0;MQRankSum=1.859;QD=27.97;ReadPosRankSum=-0.230;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|6),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=splice_region_variant&intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,9:9:21.07:271,21,0 0/1:11,8:19:99:178,0,344 1/1:0,7:7:21.07:281,21,0 1/1:0,9:9:27.08:338,27,0 1/1:0,23:23:66.20:855,66,0 1/1:0,27:27:75.24:993,75,0 1/1:0,52:52:99:1979,150,0 1/1:0,30:30:84.27:1121,84,0 1/1:0,74:74:99:2886,220,0 1/1:0,74:74:99:2807,214,0 1/1:1,30:31:87.27:1141,87,0 0/1:33,16:50:99:404,0,1122 1/1:0,24:24:66.21:848,66,0 1/1:0,18:18:39.12:512,39,0 1/1:0,26:26:66.22:895,66,0 1/1:0,10:10:30.10:398,30,0 1/1:0,18:18:42.13:560,42,0 1/1:0,14:14:36.09:450,36,0 1/1:0,25:25:57.17:751,57,0 1/1:0,11:11:24.07:301,24,0 0/1:8,7:15:99:167,0,227 1/1:0,21:21:54.17:715,54,0 1/1:0,17:17:45.14:572,45,0 1/1:0,11:11:27.08:332,27,0 0/1:3,6:9:65.41:169,0,65 1/1:0,16:16:36.11:462,36,0 1/1:0,15:15:39.13:509,39,0 1/1:0,12:12:21.05:277,21,0 0/1:10,17:27:99:447,0,207 1/1:0,14:14:42.13:535,42,0 1/1:0,28:28:54.17:712,54,0 1/1:0,15:15:42.13:550,42,0 1/1:0,24:24:57.18:744,57,0 1/1:0,21:22:48.15:610,48,0 1/1:0,23:23:51.15:643,51,0 1/1:0,12:12:30.09:381,30,0 1/1:0,12:12:30.09:374,30,0 0/0:36,0:36:84.24:0,84,1082 1/1:0,72:72:99:2115,166,0 1/1:0,119:119:99:3537,274,0 0/1:43,49:92:99:1170,0,1147 0/1:46,37:83:99:922,0,1239 1/1:0,55:55:99:1845,144,0 1/1:0,79:80:99:2418,190,0 1/1:0,66:66:99:1992,153,0 1/1:0,86:87:99:2502,196,0 1/1:0,132:132:99:3884,307,0 1/1:0,46:46:99:1285,102,0 1/1:0,88:88:99:2545,202,0 1/1:0,149:149:99:4616,364,0 1/1:0,131:131:99:3980,316,0 1/1:0,104:105:99:3152,250,0 1/1:0,106:106:99:3067,244,0 1/1:0,83:83:99:2147,169,0 1/1:0,76:76:99:2068,160,0 1/1:0,61:62:99:1867,144,0 0/1:29,30:59:99:761,0,714 0/1:41,42:83:99:1068,0,858 1/1:0,66:66:99:2024,156,0 0/0:80,2:83:81.03:0,81,1972 -chr1 977356 . C T 37.67 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.314;DP=3180;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.0624;InbreedingCoeff=-0.0085;MQ=56.04;MQ0=0;MQRankSum=1.209;QD=3.42;ReadPosRankSum=0.828;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R400W|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=missense_variant|Cgg/Tgg|R/W|ENSG00000188157|AGRN|ENST00000379370|7/36|benign(0.061)|deleterious(0.02)|400/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:9,0:9:24.07:0,24,290 0/0:22,0:22:51.16:0,51,649 0/0:11,0:11:30.10:0,30,395 0/0:12,0:12:36.11:0,36,455 0/0:31,0:31:93.29:0,93,1186 0/0:33,0:33:96.30:0,96,1273 0/0:57,0:57:99:0,147,1938 0/0:27,0:27:78.25:0,78,1040 0/0:77,0:77:99:0,199,2615 0/0:77,0:78:99:0,190,2446 0/0:41,0:43:99:0,108,1398 0/0:44,0:44:99:0,120,1563 0/0:28,0:28:66.20:0,66,827 0/0:24,0:24:54.14:0,54,711 0/0:32,0:32:81.25:0,81,1054 0/0:18,0:18:36.11:0,36,475 0/0:23,0:24:51.16:0,51,670 0/0:20,0:20:48.11:0,48,601 0/0:28,0:28:57.16:0,57,711 0/1:8,3:11:85.43:85,0,274 0/0:17,0:17:36.11:0,36,463 0/0:26,0:26:63.18:0,63,816 0/0:23,0:23:54.10:0,54,644 0/0:12,0:12:30.07:0,30,348 0/0:15,0:15:33.11:0,33,440 0/0:19,0:19:45.13:0,45,587 0/0:23,0:23:54.16:0,54,669 0/0:15,0:15:30.07:0,30,367 0/0:28,0:29:63.18:0,63,802 0/0:14,0:14:33.09:0,33,404 0/0:36,0:36:72.19:0,72,907 0/0:19,0:19:42.11:0,42,523 0/0:30,0:30:66.20:0,66,859 0/0:28,0:28:63.17:0,63,794 0/0:25,0:27:54.16:0,54,706 0/0:15,1:16:42.12:0,42,532 0/0:12,0:12:33.10:0,33,408 0/0:46,0:46:99:0,111,1447 0/0:76,0:77:99:0,165,2036 0/0:138,1:140:99:0,298,3731 0/0:109,0:110:99:0,241,3056 0/0:91,0:91:99:0,214,2725 0/0:62,0:65:99:0,144,1820 0/0:86,0:89:99:0,196,2423 0/0:75,1:79:99:0,159,2024 0/0:97,0:97:99:0,223,2765 0/0:144,0:147:99:0,343,4262 0/0:53,0:55:99:0,114,1433 0/0:105,0:107:99:0,211,2633 0/0:152,1:157:99:0,308,4203 0/0:145,0:148:99:0,331,4093 0/0:116,0:118:99:0,259,3197 0/0:104,0:106:99:0,262,3220 0/0:89,0:93:99:0,190,2369 0/0:78,0:78:99:0,162,2108 0/0:70,0:70:99:0,150,1892 0/0:72,0:72:99:0,162,2067 0/0:91,0:93:99:0,208,2662 0/0:65,0:66:99:0,159,1974 0/0:83,0:85:99:0,174,2226 -chr1 977570 . G A 23442.1 . AC=102;AF=0.8500;AN=120;BaseQRankSum=-2.570;DP=882;Dels=0.00;FS=3.065;HRun=0;HaplotypeScore=1.0563;InbreedingCoeff=0.1840;MQ=56.97;MQ0=0;MQRankSum=1.250;QD=27.84;ReadPosRankSum=-0.551;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,5:5:12.04:144,12,0 0/1:5,1:7:13.68:14,0,82 1/1:0,4:4:12.04:157,12,0 1/1:0,4:4:6.02:74,6,0 1/1:0,16:16:39.12:512,39,0 1/1:0,11:11:30.09:386,30,0 1/1:0,29:29:72.16:840,72,0 1/1:0,16:16:45.12:526,45,0 1/1:0,26:26:66.17:791,66,0 1/1:1,33:34:99:1175,99,0 1/1:0,9:9:27.05:308,27,0 0/1:5,7:13:99:221,0,169 1/1:0,12:12:30.05:339,30,0 1/1:0,5:5:15.05:196,15,0 1/1:0,10:10:27.09:346,27,0 1/1:0,12:12:27.09:367,27,0 1/1:0,7:7:21.06:266,21,0 1/1:0,8:8:24.04:297,24,0 1/1:0,2:2:3.01:41,3,0 1/1:0,7:7:21.07:277,21,0 0/1:6,3:9:93.73:94,0,205 1/1:0,11:11:30.10:393,30,0 1/1:0,7:7:21.07:262,21,0 1/1:0,3:3:6.02:86,6,0 0/1:7,3:10:81.88:82,0,238 1/1:0,5:5:12.01:143,12,0 0/1:3,2:5:48.40:48,0,104 1/1:0,3:3:9.03:112,9,0 0/1:4,2:6:26.54:27,0,105 1/1:0,5:5:15.05:193,15,0 1/1:0,19:19:45.13:577,45,0 1/1:0,11:11:21.07:288,21,0 1/1:0,9:9:21.06:273,21,0 1/1:0,11:11:33.08:422,33,0 1/1:0,3:3:9.03:125,9,0 1/1:0,10:10:21.07:285,21,0 1/1:0,9:9:27.09:348,27,0 0/0:11,0:11:30.10:0,30,402 1/1:0,16:16:42.13:527,42,0 1/1:1,33:34:84.24:1043,84,0 0/1:14,10:24:99:315,0,436 0/1:10,14:24:99:391,0,305 1/1:0,17:17:51.16:660,51,0 1/1:0,14:14:36.11:438,36,0 1/1:0,11:11:27.07:329,27,0 1/1:1,14:15:36.11:453,36,0 1/1:2,40:42:67.70:1337,68,0 0/0:15,0:15:36.11:0,36,448 1/1:1,25:27:69.22:891,69,0 0/1:23,22:46:99:609,0,703 1/1:0,39:39:99:1352,105,0 1/1:2,28:30:72.20:922,72,0 0/1:12,18:31:99:549,0,327 1/1:0,13:13:36.11:442,36,0 1/1:0,16:16:48.14:599,48,0 1/1:1,27:28:63.12:786,63,0 0/1:8,5:13:99:116,0,227 0/1:7,6:13:99:180,0,188 1/1:1,15:16:36.11:469,36,0 0/0:14,0:14:39.13:0,39,520 -chr1 977780 . C T 1896.26 . AC=55;AF=0.833;AN=66;BaseQRankSum=-0.091;DP=70;Dels=0.00;FS=1.840;HRun=0;HaplotypeScore=0.0570;InbreedingCoeff=0.2412;MQ=56.97;MQ0=0;MQRankSum=0.071;QD=30.10;ReadPosRankSum=0.112;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,3:3:9.03:110,9,0 0/0:1,0:1:3.01:0,3,41 1/1:0,3:3:6.02:78,6,0 1/1:0,5:5:12.04:155,12,0 ./. 1/1:0,1:1:3.01:40,3,0 1/1:0,3:3:9.03:119,9,0 1/1:0,3:3:6.02:81,6,0 1/1:0,4:4:12.04:164,12,0 1/1:0,5:5:12.03:140,12,0 1/1:0,2:2:6.02:80,6,0 0/0:1,0:1:3.01:0,3,39 1/1:0,3:3:9.03:111,9,0 ./. 1/1:0,1:1:3.01:32,3,0 ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:37,3,0 ./. 1/1:0,3:3:6.02:83,6,0 1/1:0,2:2:6.02:77,6,0 0/0:2,0:2:3.01:0,3,45 1/1:0,1:1:3.01:42,3,0 ./. 0/1:2,3:5:63.16:94,0,63 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:6.02:79,6,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:39,3,0 ./. 1/1:0,2:2:3.01:31,3,0 0/0:1,0:1:3.01:0,3,42 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:37,3,0 ./. 1/1:0,1:1:3.01:42,3,0 0/0:1,0:1:3.01:0,3,40 1/1:0,3:3:6:61,6,0 ./. 1/1:0,3:3:6.02:80,6,0 ./. ./. ./. ./. -chr1 978183 . C G 34.17 . AC=2;AF=0.043;AN=46;BaseQRankSum=1.339;DP=53;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0869;InbreedingCoeff=0.1027;MQ=58.24;MQ0=0;MQRankSum=1.491;QD=17.09;ReadPosRankSum=0.025;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:3,0:3:3.01:0,3,39 0/0:3,0:3:9.03:0,9,111 0/0:4,0:4:12.04:0,12,159 0/0:4,0:4:9.03:0,9,114 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,80 0/0:4,0:4:12.04:0,12,150 0/0:2,0:2:6.02:0,6,82 0/0:3,0:3:9.03:0,9,116 0/0:6,0:6:18.05:0,18,218 0/0:2,0:2:6.02:0,6,75 0/0:1,0:1:3.01:0,3,39 1/1:0,2:2:6.02:82,6,0 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:3.01:0,3,45 ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,72 ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. 0/0:2,0:2:6.02:0,6,80 ./. 0/0:2,0:2:6.02:0,6,71 -chr1 978193 . G A 202.48 . AC=6;AF=0.125;AN=48;BaseQRankSum=0.284;DP=51;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.0833;InbreedingCoeff=-0.1181;MQ=58.63;MQ0=0;MQRankSum=-0.041;QD=14.46;ReadPosRankSum=0.527;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3:0,3,25 0/0:2,0:2:6.02:0,6,78 0/0:5,0:5:15.04:0,15,184 0/0:4,0:4:9.03:0,9,112 0/0:1,0:1:3.01:0,3,41 0/1:1,1:2:35.21:35,0,35 0/0:4,0:4:12.04:0,12,162 0/0:2,0:2:6.02:0,6,81 0/1:2,2:4:66.54:67,0,67 0/1:2,3:5:59.31:107,0,59 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,82 0/0:2,0:2:6.02:0,6,78 ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. 0/1:1,1:2:27.42:34,0,27 ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. 0/0:1,0:1:3.01:0,3,38 ./. 0/0:2,0:2:6.02:0,6,81 ./. 0/0:1,0:1:3.01:0,3,40 -chr1 978576 . A AG 514.05 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.254;DP=2624;FS=0.000;HRun=7;HaplotypeScore=255.5270;InbreedingCoeff=-0.0227;MQ=57.44;MQ0=0;MQRankSum=-3.300;QD=9.70;ReadPosRankSum=-2.347;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3:0,3,27 0/0:6,0:6:15.01:0,15,140 0/0:7,0:7:12.01:0,12,115 0/0:4,0:4:6.01:0,6,58 0/0:11,0:11:24.03:0,24,232 0/0:6,0:6:12.02:0,12,116 0/0:21,0:21:45.07:0,45,434 0/0:8,0:8:15.02:0,15,145 0/0:24,0:24:63.10:0,63,607 0/0:12,0:12:23.99:0,24,222 0/0:6,0:6:15.02:0,15,145 0/0:9,0:9:15.01:0,15,145 0/1:7,2:9:54.46:54,0,98 0/0:34,0:34:93.15:0,93,895 0/0:53,0:53:99:0,141,1361 0/0:34,0:34:87.13:0,87,839 0/0:41,0:42:92.16:0,92,873 0/1:27,17:44:99:534,0,465 0/0:55,0:55:99:0,153,1473 0/0:45,0:45:99:0,104,1062 0/0:33,0:33:78.12:0,78,753 0/0:57,1:58:99:0,150,1443 0/0:35,0:35:90.08:0,90,865 0/0:43,1:44:74.93:0,75,1006 0/0:32,0:32:87.11:0,87,832 0/0:45,0:45:99:0,99,956 0/0:42,0:42:99:0,117,1130 0/0:33,0:33:90.14:0,90,867 0/0:42,0:42:99:0,107,1021 0/0:44,0:44:99:0,114,1100 0/0:60,0:60:99:0,159,1526 0/0:39,0:39:99:0,105,1010 0/0:66,0:66:99:0,177,1708 0/0:45,0:45:99:0,105,1013 0/0:36,0:36:99:0,102,984 0/0:46,0:46:99:0,123,1188 0/0:64,0:64:99:0,159,1534 0/0:69,0:69:99:0,186,1795 0/0:48,0:48:99:0,120,1154 0/0:102,0:102:99:0,258,2487 0/0:68,0:68:99:0,177,1704 0/0:59,0:60:99:0,143,1366 0/0:53,0:53:99:0,135,1302 0/0:40,1:41:74.91:0,75,1006 0/0:42,1:43:96.13:0,96,927 0/0:71,0:71:99:0,180,1734 0/0:100,0:100:99:0,253,2611 0/0:38,0:38:98.18:0,98,930 0/0:71,0:71:99:0,186,1793 0/0:98,2:100:99:0,183,2328 0/0:85,0:85:99:0,222,2137 0/0:53,0:53:99:0,120,1157 0/0:69,0:69:99:0,150,1727 0/0:70,1:70:99:0,183,1763 0/0:51,0:51:99:0,126,1216 0/0:49,0:49:99:0,117,1130 0/0:32,0:32:84.12:0,84,810 0/0:54,0:54:99:0,119,1386 0/0:50,0:49:99:0,126,1214 0/0:49,0:49:99:0,111,1070 -chr1 978600 . GCC G 17413.56 . AC=61;AF=0.5169;AN=118;BaseQRankSum=43.323;DP=3497;FS=2.177;HRun=4;HaplotypeScore=348.2579;InbreedingCoeff=-0.1331;MQ=57.63;MQ0=0;MQRankSum=3.380;QD=6.27;ReadPosRankSum=3.269;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:1,0:1:2.84:0,3,14 0/1:8,0:9:48.43:48,0,98 0/1:4,0:4:43.67:44,0,44 ./. 0/1:12,0:12:19.15:19,0,235 0/0:6,0:6:15.05:0,15,281 1/1:15,0:15:28.30:135,28,0 0/0:9,0:9:27.09:0,27,504 0/1:21,0:21:84.68:85,0,558 0/1:14,0:15:66.30:66,0,247 1/1:7,0:7:14.43:70,14,0 0/1:8,0:8:17.52:18,0,258 1/1:13,0:13:31.58:153,32,0 0/1:55,0:55:99:229,0,1205 1/1:62,0:62:99:861,159,0 1/1:48,0:48:99:614,109,0 0/1:54,1:55:99:182,0,1441 1/1:55,0:55:99:696,127,0 0/1:73,0:73:99:314,0,1873 0/0:61,0:61:99:0,169,3137 0/1:49,0:49:99:178,0,1324 1/1:66,1:67:99:869,113,0 1/1:45,0:45:99:705,122,0 0/1:59,0:59:99:246,0,1444 0/1:44,0:44:99:246,0,962 0/1:54,1:55:99:384,0,742 0/1:73,0:73:99:249,0,2017 0/1:46,0:46:99:120,0,1362 0/1:65,0:65:99:197,0,1766 1/1:60,1:61:99:929,166,0 0/1:72,0:72:99:327,0,1487 1/1:55,1:56:99:844,149,0 0/1:76,0:76:99:154,0,2324 0/0:56,0:56:99:0,157,2919 0/1:51,0:51:99:172,0,1324 0/1:73,0:73:99:394,0,1478 0/1:80,0:80:99:297,0,2037 0/0:87,0:87:99:0,244,4454 1/1:62,0:62:99:829,129,0 0/1:124,0:125:99:445,0,3126 0/1:81,2:85:99:439,0,1714 0/0:95,0:95:99:0,245,4708 0/0:66,0:66:99:0,193,3598 0/1:69,0:69:99:148,0,2062 0/1:58,1:59:99:280,0,1159 0/1:92,0:92:99:282,0,2370 0/1:144,0:145:99:659,0,3301 0/0:54,0:54:99:0,151,2786 0/1:103,0:103:99:323,0,2923 0/0:126,0:125:99:0,329,6320 0/1:108,0:108:99:476,0,2542 0/1:59,0:60:99:199,0,1666 0/1:92,0:93:99:197,0,2824 1/1:92,1:92:72.21:1106,72,0 1/1:68,0:68:99:973,176,0 1/1:70,0:70:99:822,134,0 0/1:48,0:48:99:136,0,1472 0/0:91,0:91:99:0,232,4636 0/1:72,0:71:99:253,0,1684 0/0:68,0:68:99:0,190,3542 -chr1 978603 . CCT C 71936.99 . AC=63;AF=0.5339;AN=118;BaseQRankSum=27.120;DP=3635;FS=0.415;HRun=0;HaplotypeScore=268.7446;InbreedingCoeff=-0.1355;MQ=57.70;MQ0=0;MQRankSum=-0.052;QD=24.97;ReadPosRankSum=2.237;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:1,0:1:2.94:18,3,0 0/1:8,3:11:99:186,0,146 0/1:1,3:4:48.97:134,0,49 ./. 0/1:7,3:10:99:205,0,216 0/0:6,0:6:15.05:0,15,305 1/1:5,11:16:42.14:643,42,0 0/0:12,0:12:36.12:0,36,629 0/1:15,9:24:99:437,0,668 0/1:9,8:17:99:426,0,295 1/1:2,6:8:24.08:378,24,0 0/1:5,3:8:99:123,0,281 1/1:2,11:13:39.13:609,39,0 0/1:28,27:55:99:1114,0,1357 1/1:9,55:64:99:2869,181,0 1/1:8,43:51:99:2224,144,0 0/1:35,21:56:99:959,0,1648 1/1:7,52:59:99:2470,157,0 0/1:42,34:76:99:1472,0,2074 0/0:62,0:62:99:0,178,3435 0/1:31,21:52:99:875,0,1547 1/1:12,60:72:99:3098,199,0 1/1:2,44:46:99:2141,132,0 0/1:38,24:63:99:1188,0,1679 0/1:22,22:44:99:947,0,1006 0/1:24,30:54:99:1437,0,735 0/1:45,30:75:99:1289,0,2071 0/1:27,18:45:99:700,0,1423 0/1:43,26:69:99:1086,0,2022 1/1:11,55:66:99:3059,196,0 0/1:40,34:74:99:1635,0,1586 1/1:4,53:57:99:2601,163,0 0/1:52,26:78:99:1106,0,2540 0/0:59,0:59:99:0,169,3215 0/1:34,22:56:99:936,0,1481 0/1:36,42:78:99:1902,0,1726 0/1:47,37:84:99:1481,0,2237 0/0:91,0:91:99:0,262,4845 1/1:6,57:63:99:2901,184,0 0/1:78,50:128:99:2076,0,3408 0/1:47,43:90:99:1934,0,1909 0/0:94,1:95:99:0,213,5048 0/0:71,0:71:99:0,208,4022 0/1:50,24:74:99:1003,0,2313 0/1:30,30:60:99:1361,0,1324 0/1:60,38:98:99:1624,0,2678 0/1:87,66:153:99:2955,0,3616 0/0:59,0:59:99:0,169,3221 0/1:66,37:103:99:1586,0,3031 0/0:129,1:129:99:0,303,6889 0/1:59,55:114:99:2349,0,2830 0/1:37,25:62:99:1030,0,1847 0/1:65,29:94:99:1343,0,3014 1/1:11,82:93:99:3854,104,0 1/1:5,64:69:99:3130,196,0 1/1:9,63:72:99:2966,187,0 0/1:34,16:50:99:774,0,1551 0/0:95,2:97:99:0,179,5203 0/1:39,33:72:99:1302,0,1763 0/0:71,0:71:99:0,202,3844 -chr1 978604 . CTG C 22255.35 . AC=63;AF=0.5339;AN=118;BaseQRankSum=42.643;DP=3702;FS=4.247;HRun=0;HaplotypeScore=358.4425;InbreedingCoeff=-0.1343;MQ=57.72;MQ0=0;MQRankSum=2.535;QD=7.58;ReadPosRankSum=3.410;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|7),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:2,0:2:1.24:3,1,0 0/1:11,0:11:57.58:58,0,149 0/1:5,0:5:43.60:55,0,44 ./. 0/1:11,0:11:22.85:23,0,249 0/0:7,0:7:15.94:0,16,274 1/1:15,0:15:34.14:192,34,0 0/0:13,0:13:36.12:0,36,660 0/1:25,0:25:87.58:88,0,598 0/1:18,0:18:99:102,0,339 1/1:9,0:9:18.17:115,18,0 0/1:8,0:8:25.22:25,0,251 1/1:13,0:13:29.61:191,30,0 0/1:57,0:57:99:291,0,1226 1/1:64,1:65:99:973,136,0 1/1:52,1:53:99:769,117,0 0/1:57,0:57:99:206,0,1481 1/1:59,0:59:99:809,106,0 0/1:78,0:78:99:424,0,1849 0/0:62,0:62:99:0,172,3128 0/1:54,0:54:99:238,0,1444 1/1:72,0:72:99:1143,174,0 1/1:47,0:47:99:795,127,0 0/1:62,0:64:99:284,0,1582 0/1:44,0:44:99:319,0,908 0/1:57,0:57:99:437,0,689 0/1:75,0:75:99:334,0,1747 0/1:47,0:47:99:190,0,1277 0/1:69,0:69:99:286,0,1897 1/1:67,0:67:99:1066,169,0 0/1:74,0:74:99:478,0,1388 1/1:57,0:57:99:1028,152,0 0/1:82,0:82:99:250,0,2311 0/0:59,0:59:99:0,160,2908 0/1:57,0:57:99:225,0,1382 0/1:78,0:78:99:518,0,1591 0/1:86,0:86:99:344,0,2167 0/0:90,0:92:99:0,250,4442 1/1:66,0:66:99:986,163,0 0/1:131,0:131:99:672,0,3075 0/1:91,0:91:99:573,0,1798 0/0:96,0:96:99:0,241,4712 0/0:73,0:73:99:0,208,3741 0/1:75,0:75:99:216,0,2098 0/1:60,0:60:99:360,0,1212 0/1:102,0:102:99:391,0,2500 0/1:154,0:154:99:822,0,3401 0/0:59,0:59:99:0,168,2955 0/1:106,0:106:99:372,0,2733 0/0:129,0:128:99:0,332,6253 0/1:116,0:116:99:718,0,2624 0/1:64,0:64:99:362,0,1704 0/1:94,0:94:99:385,0,2669 1/1:93,2:94:99:1425,122,0 1/1:70,0:70:99:1146,178,0 1/1:72,0:73:99:1015,162,0 0/1:50,1:51:99:188,0,1356 0/0:101,0:101:99:0,261,5078 0/1:72,0:72:99:365,0,1556 0/0:74,0:74:99:0,205,3699 -chr1 978762 . G A 3088.0 . AC=4;AF=0.0333;AN=120;BaseQRankSum=0.970;DP=3629;Dels=0.00;FS=0.380;HRun=0;HaplotypeScore=2.3356;InbreedingCoeff=-0.0359;MQ=57.56;MQ0=0;MQRankSum=1.561;QD=14.64;ReadPosRankSum=0.622;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G510S|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|Ggc/Agc|G/S|ENSG00000188157|AGRN|ENST00000379370|8/36|probably_damaging(0.961)|tolerated(0.05)|510/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:8,0:8:21.07:0,21,260 0/0:5,0:5:15.05:0,15,185 0/0:12,0:12:33.09:0,33,399 0/0:4,0:4:9.03:0,9,119 0/0:15,0:15:45.15:0,45,606 0/0:9,0:9:24.08:0,24,317 0/1:6,13:19:99:407,0,147 0/0:7,0:7:21.07:0,21,268 0/0:33,0:33:99:0,99,1294 0/0:39,0:39:99:0,111,1442 0/0:14,0:14:42.14:0,42,556 0/0:17,0:17:51.16:0,51,663 0/0:16,0:16:48.12:0,48,605 0/0:56,0:56:99:0,153,1955 0/0:72,0:72:99:0,169,2219 0/0:49,0:50:99:0,132,1731 0/0:51,0:51:99:0,138,1761 0/0:62,0:63:99:0,160,2091 0/0:75,0:76:99:0,193,2489 0/0:66,0:66:99:0,172,2212 0/0:56,0:56:99:0,141,1834 0/1:35,38:74:99:1262,0,852 0/0:61,0:61:99:0,147,1888 0/0:63,0:63:99:0,162,2113 0/0:67,0:67:99:0,172,2223 0/1:23,27:50:99:832,0,606 0/0:77,0:78:99:0,205,2612 0/0:37,0:37:96.30:0,96,1257 0/0:96,0:96:99:0,238,3114 0/0:65,0:66:99:0,181,2345 0/0:106,0:106:99:0,271,3549 0/0:58,0:58:99:0,150,1912 0/0:75,1:78:99:0,190,2482 0/0:89,0:91:99:0,226,2912 0/0:62,0:62:99:0,160,2087 0/0:67,0:67:99:0,169,2179 0/0:72,0:72:99:0,196,2538 0/0:104,1:106:99:0,224,3352 0/0:63,0:64:99:0,156,2037 0/0:123,0:124:99:0,331,4257 0/0:95,0:95:99:0,244,3073 0/0:91,0:91:99:0,229,2925 0/0:75,0:75:99:0,205,2602 0/0:52,0:52:99:0,141,1803 0/0:48,0:48:99:0,132,1657 0/0:75,0:77:99:0,181,2324 0/0:132,0:132:99:0,334,4280 0/0:38,0:38:90.27:0,90,1117 0/0:80,1:82:99:0,199,2543 0/0:89,0:90:99:0,232,2898 0/0:120,0:120:99:0,289,3722 0/0:80,0:81:99:0,196,2454 0/0:94,0:94:99:0,229,2877 0/0:82,0:82:99:0,199,2551 0/0:58,0:58:99:0,147,1888 0/1:39,27:67:99:680,0,955 0/0:42,0:44:99:0,99,1301 0/0:71,0:72:99:0,181,2262 0/0:69,0:69:99:0,175,2198 0/0:52,0:53:99:0,138,1818 -chr1 978850 . T G 355.87 . AC=13;AF=0.1083;AN=120;BaseQRankSum=-20.130;DP=2142;Dels=0.00;FS=811.949;HRun=3;HaplotypeScore=4.6408;InbreedingCoeff=-0.1393;MQ=53.60;MQ0=0;MQRankSum=-8.269;QD=0.90;ReadPosRankSum=-1.238;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|8),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,25 0/0:8,3:11:0.40:0,0,281 0/0:3,1:4:9.03:0,9,122 0/0:3,2:5:6.01:0,6,63 0/0:15,7:22:8.16:0,8,501 0/1:5,3:8:14.44:14,0,180 0/1:6,16:22:23.32:23,0,221 0/1:4,2:6:18.56:19,0,103 0/1:13,18:31:78.03:78,0,427 0/1:17,16:37:62.41:62,0,609 0/1:2,6:8:23.47:23,0,73 0/1:3,4:7:53.64:54,0,95 0/1:9,15:25:35.84:36,0,295 0/0:29,19:48:6.60:0,7,847 0/1:26,15:41:34.37:34,0,748 0/0:27,9:36:12.92:0,13,687 0/0:34,10:45:51.01:0,51,889 0/0:27,15:42:32.76:0,33,766 0/0:29,12:41:58.30:0,58,932 0/0:33,11:44:57.60:0,58,1037 0/0:22,12:35:57.17:0,57,704 0/0:36,14:50:81.20:0,81,999 0/0:26,8:36:60.19:0,60,766 0/1:28,12:41:46.86:47,0,643 0/0:27,10:38:47.52:0,48,823 0/0:32,19:52:39.38:0,39,956 0/0:38,18:56:87.18:0,87,1062 0/0:18,12:30:25.47:0,25,592 0/0:41,23:65:37.16:0,37,1154 0/0:30,13:43:8.11:0,8,784 0/0:43,14:57:79.61:0,80,1244 0/0:34,6:40:83.05:0,83,981 0/0:33,10:43:44.18:0,44,902 0/0:38,16:54:23.30:0,23,1103 0/0:39,8:47:58.57:0,59,1028 0/0:33,9:44:52.52:0,53,903 0/1:25,25:50:74.50:74,0,840 0/1:46,34:80:45.97:46,0,1442 0/0:28,1:29:75.21:0,75,895 0/0:46,8:54:97.48:0,97,1519 0/0:41,4:45:99:0,120,1514 0/0:29,7:36:81.26:0,81,1049 0/0:29,5:34:53.57:0,54,968 0/0:31,5:37:84.27:0,84,1097 0/0:30,4:36:84.24:0,84,1074 0/0:34,3:37:99:0,99,1249 0/0:50,9:59:92.32:0,92,1757 0/0:13,2:15:33.08:0,33,397 0/0:30,6:36:48.87:0,49,953 0/0:41,3:44:99:0,117,1437 0/0:46,9:56:99:0,99,1484 0/0:42,9:51:71.87:0,72,1180 0/1:29,8:38:10.90:11,0,856 0/0:26,5:31:67.75:0,68,812 0/0:15,6:21:5.88:0,6,432 0/0:25,4:29:67.07:0,67,821 0/0:20,4:24:29.50:0,29,661 0/0:30,3:33:87.27:0,87,1101 0/0:23,3:27:60.19:0,60,774 0/0:19,5:24:54.16:0,54,675 -chr1 978857 . T G 60.53 . AC=8;AF=0.0667;AN=120;BaseQRankSum=-18.263;DP=2025;Dels=0.01;FS=633.354;HRun=4;HaplotypeScore=4.9061;InbreedingCoeff=-0.0867;MQ=53.43;MQ0=0;MQRankSum=-5.927;QD=0.18;ReadPosRankSum=3.709;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|8),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,27 0/0:7,2:9:21.05:0,21,251 0/0:3,0:3:9.03:0,9,119 0/0:5,1:6:12.02:0,12,131 0/0:14,4:18:42.12:0,42,526 0/0:8,1:9:24.07:0,24,311 0/1:3,9:13:17.59:18,0,110 0/0:3,0:3:6.02:0,6,81 0/0:17,10:28:45.14:0,45,578 0/0:20,12:32:51.14:0,51,664 0/0:3,5:8:9.03:0,9,121 0/0:3,2:5:9.03:0,9,117 0/1:10,12:22:6.35:6,0,281 0/1:31,16:47:49.82:50,0,828 0/1:24,18:42:26.30:26,0,709 0/0:25,12:37:14.04:0,14,681 0/0:34,10:44:77.27:0,77,941 0/0:31,14:45:12.15:0,12,894 0/0:31,9:40:15.18:0,15,936 0/0:33,11:44:13.42:0,13,1028 0/0:26,11:37:38.78:0,39,815 0/0:34,12:46:84.26:0,84,1067 0/0:21,9:30:23.71:0,24,639 0/1:26,16:42:9.81:10,0,715 0/1:27,10:37:16.17:16,0,705 0/0:34,19:53:3.55:0,4,948 0/0:37,18:55:27.20:0,27,1065 0/0:18,8:27:45.14:0,45,563 0/0:38,21:59:0.56:0,1,1046 0/0:28,12:41:52.54:0,53,887 0/0:40,16:57:60.98:0,61,1297 0/0:32,5:37:81.20:0,81,956 0/0:31,14:45:46.45:0,46,879 0/0:39,12:51:20.25:0,20,1183 0/0:32,10:43:73.75:0,74,898 0/0:34,12:46:81.21:0,81,985 0/1:30,14:45:41.85:42,0,847 0/1:45,28:73:14.90:15,0,1340 0/0:24,3:27:66.20:0,66,836 0/0:44,4:48:99:0,117,1455 0/0:39,2:41:99:0,111,1398 0/0:24,6:30:69.20:0,69,864 0/0:29,3:32:11.38:0,11,860 0/0:29,7:36:62.56:0,63,1021 0/0:30,3:33:83.93:0,84,1062 0/0:31,1:32:90.28:0,90,1149 0/0:45,4:50:99:0,107,1617 0/0:16,0:16:33.10:0,33,391 0/0:28,5:33:78.20:0,78,938 0/0:42,3:45:99:0,114,1338 0/0:44,8:52:84.82:0,85,1352 0/0:37,6:44:87.23:0,87,1050 0/0:29,7:36:77:0,77,903 0/0:26,3:29:68.18:0,68,787 0/0:13,4:17:39.06:0,39,486 0/0:22,3:25:60.19:0,60,761 0/0:19,3:22:51.16:0,51,663 0/0:28,2:30:75.23:0,75,956 0/0:18,4:22:48.16:0,48,628 0/0:19,4:23:54.17:0,54,683 -chr1 979594 . C T 694.16 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.081;DP=5875;DS;Dels=0.00;FS=21.795;HRun=0;HaplotypeScore=3.6311;InbreedingCoeff=-0.0090;MQ=57.97;MQ0=0;MQRankSum=1.076;QD=13.10;ReadPosRankSum=-2.987;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P702L|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|cCg/cTg|P/L|ENSG00000188157|AGRN|ENST00000379370|11/36|probably_damaging(0.931)|tolerated(0.29)|702/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:7,0:7:21.05:0,21,247 0/0:6,0:6:12.04:0,12,151 0/0:10,0:10:27.08:0,27,326 0/0:10,0:10:27.06:0,27,298 0/0:32,0:32:90.29:0,90,1202 0/0:27,0:27:78.25:0,78,1024 0/1:25,28:53:99:742,0,826 0/0:29,0:29:81.21:0,81,1040 0/0:37,0:37:99:0,105,1388 0/0:42,0:43:99:0,117,1509 0/0:21,0:21:54.17:0,54,716 0/0:22,0:22:60.19:0,60,768 0/0:26,0:26:72.22:0,72,932 0/0:69,0:69:99:0,165,2156 0/0:71,3:74:99:0,133,2211 0/0:49,0:49:99:0,105,1393 0/0:74,0:74:99:0,181,2359 0/0:85,0:85:99:0,187,2478 0/0:78,0:78:99:0,178,2347 0/0:60,0:60:99:0,135,1718 0/0:76,0:76:99:0,169,2215 0/0:96,0:96:99:0,232,3067 0/0:73,0:74:99:0,162,2073 0/0:74,0:74:99:0,184,2406 0/0:59,1:61:99:0,101,1749 0/0:48,0:48:99:0,117,1504 0/0:71,0:71:99:0,156,2088 0/0:59,0:59:99:0,156,2023 0/0:88,0:88:99:0,193,2525 0/0:66,0:66:99:0,162,2072 0/0:71,0:71:99:0,184,2291 0/0:58,0:58:99:0,144,1863 0/0:77,0:77:99:0,184,2412 0/0:98,0:98:99:0,241,3129 0/0:69,0:69:99:0,159,2057 0/0:66,0:67:99:0,138,1816 0/0:90,0:90:99:0,211,2721 0/0:103,0:103:99:0,238,3117 0/0:132,0:133:99:0,319,4100 0/0:243,0:243:99:0,602,7562 0/0:190,1:192:99:0,430,5485 0/0:162,0:165:99:0,361,4714 0/0:105,0:106:99:0,280,3575 0/0:141,1:144:99:0,316,4039 0/0:119,1:121:99:0,304,3872 0/0:201,1:202:99:0,481,6218 0/0:237,0:239:99:0,545,6930 0/0:103,0:104:99:0,238,3089 0/0:208,0:209:99:0,469,6074 0/0:245,1:249:99:0,623,7807 0/0:235,1:237:99:0,545,6950 0/0:186,1:190:99:0,427,5442 0/0:186,0:186:99:0,415,5370 0/0:170,0:170:99:0,397,5113 0/0:145,0:145:99:0,343,4411 0/0:118,1:120:99:0,268,3442 0/0:105,0:106:99:0,262,3273 0/0:174,1:176:99:0,367,5039 0/0:131,0:133:99:0,328,4161 0/0:144,0:144:99:0,322,4209 -chr1 979669 . G A 1676.8 . 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G A 3048.77 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-3.190;DP=3529;Dels=0.00;FS=4.170;HRun=0;HaplotypeScore=1.8409;InbreedingCoeff=-0.0220;MQ=57.08;MQ0=0;MQRankSum=0.399;QD=11.82;ReadPosRankSum=-0.422;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|11),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,76 0/0:2,0:2:6.02:0,6,70 0/0:4,0:4:9.02:0,9,102 0/0:6,0:6:12.04:0,12,155 0/0:10,0:10:30.10:0,30,402 0/0:10,0:10:27.09:0,27,352 0/0:20,0:20:48.16:0,48,633 0/0:12,0:12:27.08:0,27,346 0/0:29,0:30:78.25:0,78,1036 0/0:25,0:25:69.20:0,69,889 0/0:12,0:12:21.07:0,21,270 0/0:13,0:13:36.09:0,36,447 0/0:20,0:20:60.16:0,60,754 0/0:47,0:47:99:0,108,1309 0/0:50,0:51:99:0,123,1544 0/0:30,0:30:72.17:0,72,893 0/0:43,0:43:93.27:0,93,1180 0/0:46,1:47:80.68:0,81,1368 0/0:45,0:45:99:0,102,1290 0/0:37,0:37:90.28:0,90,1167 0/0:40,1:41:65.32:0,65,1283 0/0:56,1:57:99:0,104,1716 0/0:27,1:28:23.95:0,24,759 0/0:42,1:44:99:0,108,1372 0/0:46,0:47:99:0,105,1350 0/0:41,1:42:90.23:0,90,1107 0/0:46,1:47:58.49:0,58,1130 0/0:30,0:30:63.19:0,63,809 0/0:34,0:35:84.22:0,84,1064 0/0:39,0:40:99:0,102,1254 0/0:47,0:48:99:0,102,1325 0/0:39,0:39:84.24:0,84,1079 0/0:52,0:53:99:0,120,1538 0/0:49,0:49:99:0,114,1389 0/0:45,0:45:93.27:0,93,1196 0/0:40,0:40:99:0,102,1287 0/0:66,0:67:99:0,150,1963 0/0:60,0:60:99:0,141,1862 0/0:89,0:89:99:0,217,2738 0/0:148,0:149:99:0,364,4594 0/0:99,1:102:99:0,215,3162 0/0:93,0:94:99:0,223,2848 0/0:65,0:65:99:0,175,2173 0/0:77,0:78:99:0,190,2385 0/0:69,0:69:99:0,166,2112 0/0:110,0:112:99:0,277,3484 0/0:158,0:159:99:0,370,4484 0/0:62,0:62:99:0,150,1906 0/0:98,0:100:99:0,235,2986 0/1:77,77:154:99:2065,0,2006 0/0:146,0:149:99:0,355,4385 0/0:112,0:113:99:0,283,3461 0/1:55,46:103:99:1049,0,1466 0/0:109,1:110:99:0,271,3403 0/0:89,0:89:99:0,220,2736 0/0:90,0:90:99:0,223,2759 0/0:61,0:62:99:0,159,2020 0/0:116,1:122:99:0,283,3600 0/0:87,0:89:99:0,187,2400 0/0:89,0:90:99:0,211,2622 -chr1 979748 . A T 1423.3 . AC=2;AF=0.0167;AN=120;BaseQRankSum=0.288;DP=3261;Dels=0.00;FS=1.119;HRun=0;HaplotypeScore=1.7332;InbreedingCoeff=-0.0175;MQ=58.27;MQ0=0;MQRankSum=0.306;QD=11.21;ReadPosRankSum=1.431;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gTg|E728V|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|gAg/gTg|E/V|ENSG00000188157|AGRN|ENST00000379370|12/36|probably_damaging(0.932)|deleterious(0.02)|728/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.04:0,15,171 0/0:11,0:11:30.07:0,30,367 0/0:6,0:6:18.06:0,18,228 0/0:7,0:7:18.05:0,18,216 0/0:11,0:11:33.10:0,33,409 0/0:12,0:12:36.12:0,36,480 0/0:14,0:14:42.12:0,42,536 0/0:8,0:8:24.08:0,24,322 0/0:29,0:29:84.27:0,84,1111 0/0:28,0:28:81.26:0,81,1070 0/0:14,0:14:42.13:0,42,544 0/0:10,0:10:30.10:0,30,390 0/0:13,0:14:36.07:0,36,431 0/0:43,0:43:99:0,102,1332 0/0:49,0:49:99:0,117,1545 0/0:26,0:26:57.18:0,57,747 0/0:31,0:31:78.21:0,78,976 0/0:31,0:31:78.24:0,78,1023 0/0:49,0:51:99:0,120,1586 0/0:39,0:39:93.24:0,93,1176 0/0:41,0:41:96.30:0,96,1270 0/0:61,0:61:99:0,141,1884 0/0:40,0:40:99:0,99,1311 0/0:43,0:43:87.26:0,87,1176 0/0:48,0:48:99:0,117,1508 0/0:38,0:38:93.29:0,93,1218 0/0:46,0:46:99:0,117,1548 0/0:34,0:35:87.28:0,87,1139 0/0:39,0:39:96.29:0,96,1255 0/0:35,0:36:90.29:0,90,1188 0/0:43,0:43:99:0,102,1338 0/0:17,0:17:51.17:0,51,686 0/0:47,0:47:99:0,108,1459 0/0:51,0:53:99:0,120,1594 0/0:43,0:43:99:0,114,1475 0/0:40,0:40:96.31:0,96,1299 0/1:33,26:60:99:592,0,914 0/0:53,0:53:99:0,138,1834 0/0:87,0:87:99:0,205,2600 0/0:126,0:126:99:0,325,4170 0/0:106,0:108:99:0,256,3379 0/0:72,0:73:99:0,190,2464 0/1:36,31:67:99:896,0,997 0/0:65,0:65:99:0,175,2229 0/0:64,0:64:99:0,166,2199 0/0:101,0:102:99:0,277,3526 0/0:143,0:144:99:0,346,4366 0/0:48,0:48:99:0,111,1449 0/0:95,0:96:99:0,232,3025 0/0:140,0:140:99:0,364,4662 0/0:138,0:140:99:0,346,4485 0/0:102,0:102:99:0,259,3300 0/0:94,0:94:99:0,226,2900 0/0:100,0:101:99:0,250,3237 0/0:67,0:68:99:0,162,2071 0/0:87,0:87:99:0,196,2530 0/0:64,0:64:99:0,166,2125 0/0:87,0:89:99:0,214,2788 0/0:85,0:85:99:0,211,2723 0/0:86,0:88:99:0,196,2589 -chr1 979835 . G A 1973.32 . AC=2;AF=0.0169;AN=118;BaseQRankSum=-1.744;DP=1701;Dels=0.00;FS=1.140;HRun=0;HaplotypeScore=1.2871;InbreedingCoeff=-0.0241;MQ=58.02;MQ0=0;MQRankSum=1.712;QD=14.00;ReadPosRankSum=0.225;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|12),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:9.03:0,9,116 0/0:2,0:2:3.01:0,3,33 0/0:2,0:2:6.01:0,6,63 0/0:8,0:8:24.08:0,24,326 0/0:9,0:9:27.09:0,27,348 0/0:10,0:10:27.09:0,27,353 0/0:4,0:4:9.03:0,9,118 0/0:13,0:13:39.12:0,39,490 0/0:10,0:10:30.10:0,30,408 0/0:6,0:6:18.05:0,18,227 0/0:7,0:7:18.06:0,18,241 0/0:9,0:9:24.08:0,24,320 0/0:15,0:15:39.13:0,39,516 0/0:20,0:20:54.17:0,54,697 0/0:16,0:16:42.14:0,42,552 0/0:17,0:18:39.13:0,39,530 0/0:24,0:24:60.18:0,60,799 0/0:23,0:23:54.17:0,54,703 0/0:20,0:20:48.15:0,48,636 0/0:19,0:19:45.15:0,45,607 0/0:24,0:24:63.20:0,63,841 0/0:23,0:23:60.19:0,60,802 0/0:26,0:26:69.21:0,69,885 0/0:16,0:16:39.13:0,39,526 0/0:9,0:9:27.09:0,27,346 0/0:17,0:17:45.14:0,45,583 0/0:21,0:21:48.16:0,48,645 0/0:41,0:41:99:0,105,1402 0/0:13,0:13:36.12:0,36,476 0/0:27,0:27:69.22:0,69,894 0/0:17,0:17:48.14:0,48,606 0/0:30,0:30:75.21:0,75,988 0/0:22,0:22:57.17:0,57,736 0/0:15,0:15:39.12:0,39,492 0/0:27,0:27:63.21:0,63,851 0/0:19,0:20:54.18:0,54,720 0/0:30,0:30:87.26:0,87,1107 0/0:33,0:34:87.27:0,87,1122 0/0:60,0:60:99:0,166,2099 0/0:60,0:60:99:0,156,1990 0/0:43,0:44:99:0,99,1301 0/0:43,1:44:83.93:0,84,1443 0/0:50,0:50:99:0,120,1556 0/0:27,0:27:75.22:0,75,948 0/0:46,0:46:99:0,120,1513 0/0:80,0:80:99:0,199,2569 0/0:22,0:22:54.17:0,54,702 0/0:46,0:46:99:0,117,1532 0/1:39,37:76:99:1073,0,1085 0/0:86,1:87:99:0,185,2692 0/0:50,1:51:99:0,135,1668 0/1:29,35:65:99:966,0,735 0/0:47,0:47:99:0,105,1332 0/0:51,0:51:99:0,129,1694 0/0:32,0:32:81.26:0,81,1080 0/0:34,0:34:96.28:0,96,1218 0/0:46,0:46:99:0,117,1485 0/0:40,1:41:77.92:0,78,1372 0/0:42,0:42:99:0,102,1387 -chr1 979890 . C T 106.44 . AC=1;AF=0.0085;AN=118;BaseQRankSum=0.494;DP=863;Dels=0.00;FS=2.607;HRun=0;HaplotypeScore=0.6567;InbreedingCoeff=-0.0292;MQ=58.16;MQ0=0;MQRankSum=-0.586;QD=9.68;ReadPosRankSum=0.909;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|12),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,35 0/0:5,0:5:15.05:0,15,191 0/0:4,0:4:12.04:0,12,165 0/0:10,0:11:30.10:0,30,402 0/0:2,0:2:6.02:0,6,77 0/0:12,0:12:36.12:0,36,482 0/0:5,0:5:15.05:0,15,199 0/0:5,0:5:12.04:0,12,156 0/0:2,0:2:6.02:0,6,71 0/0:2,0:2:6.02:0,6,81 0/0:4,0:4:12.04:0,12,161 0/0:6,0:6:18.06:0,18,232 0/0:3,0:3:6.02:0,6,82 0/0:7,0:7:18.06:0,18,228 0/0:14,0:14:39.12:0,39,501 0/0:13,0:13:36.11:0,36,461 0/0:7,0:7:18.04:0,18,221 0/0:5,0:5:15.04:0,15,180 0/0:10,0:12:30.10:0,30,396 0/0:13,0:13:39.12:0,39,491 0/0:6,0:6:18.06:0,18,230 0/0:13,0:13:36.12:0,36,469 0/0:10,0:10:24.06:0,24,310 0/0:12,0:12:27.07:0,27,311 0/0:9,0:9:27.08:0,27,345 0/0:15,0:16:36.08:0,36,442 0/0:8,0:8:21.07:0,21,267 0/0:14,0:14:39.12:0,39,501 0/0:14,0:14:36.10:0,36,457 0/0:15,0:15:39.13:0,39,526 0/0:9,0:9:24.07:0,24,292 0/0:4,0:4:9.03:0,9,122 0/0:6,0:6:18.06:0,18,241 0/0:12,0:12:27.09:0,27,357 0/0:15,0:15:39.11:0,39,481 0/0:21,0:21:60.18:0,60,754 0/0:35,0:35:96.30:0,96,1245 0/0:36,0:36:93.28:0,93,1183 0/0:22,0:22:54.17:0,54,693 0/0:22,0:22:60.19:0,60,790 0/0:20,1:21:14.95:0,15,672 0/0:16,1:17:11.70:0,12,510 0/0:24,0:24:63.18:0,63,769 0/0:42,0:43:99:0,114,1437 0/1:4,6:11:99:154,0,137 0/0:21,0:21:57.17:0,57,735 0/0:42,0:42:99:0,114,1457 0/0:44,1:45:99:0,120,1530 0/0:27,0:27:78.24:0,78,981 0/0:37,0:37:99:0,99,1287 0/0:21,0:22:54.17:0,54,694 0/0:27,0:28:81.24:0,81,1030 0/0:17,0:18:39.11:0,39,469 0/0:15,0:15:45.14:0,45,584 0/0:18,0:18:39.11:0,39,490 0/0:18,0:18:45.14:0,45,562 0/0:21,0:21:51.16:0,51,658 -chr1 980077 . C T 58.05 . AC=1;AF=0.012;AN=86;BaseQRankSum=-0.500;DP=105;Dels=0.00;FS=12.895;HRun=0;HaplotypeScore=0.1629;InbreedingCoeff=-0.1341;MQ=58.00;MQ0=0;MQRankSum=0.378;QD=11.61;ReadPosRankSum=0.765;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|12),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,34 0/0:3,0:3:6.02:0,6,73 0/0:2,0:2:6.02:0,6,75 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,73 0/0:3,0:3:9.02:0,9,109 ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,69 0/0:1,0:1:3.01:0,3,37 ./. ./. 0/0:3,0:3:6.02:0,6,84 0/0:1,0:1:3.01:0,3,32 0/0:3,0:3:9.03:0,9,120 0/0:2,0:2:3.01:0,3,45 ./. 0/0:1,0:1:3.01:0,3,39 ./. 0/0:2,0:2:3.01:0,3,33 0/0:9,0:9:21.07:0,21,275 0/0:2,0:2:3.01:0,3,39 ./. ./. 0/0:1,0:1:3.01:0,3,37 ./. ./. 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,35 ./. 0/0:2,0:2:5.99:0,6,64 ./. 0/0:3,0:3:9.03:0,9,116 0/0:3,0:3:9.03:0,9,125 0/0:1,0:1:3.01:0,3,37 0/0:3,0:3:9.03:0,9,121 0/0:4,0:4:9.03:0,9,118 0/0:4,0:4:9.01:0,9,106 0/0:4,0:4:9.03:0,9,128 ./. ./. 0/0:2,0:2:6.02:0,6,75 0/0:3,0:3:9.01:0,9,102 0/0:3,0:3:9.03:0,9,121 0/0:2,0:2:6.02:0,6,83 0/1:2,3:5:29.72:103,0,30 0/0:6,0:6:18.06:0,18,234 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,40 0/0:3,0:3:6.02:0,6,73 ./. 0/0:1,0:1:3.01:0,3,42 0/0:3,0:3:9.03:0,9,114 0/0:2,0:2:6.01:0,6,68 0/0:3,0:3:9.03:0,9,119 0/0:1,0:1:3:0,3,29 -chr1 980189 . G A 62.31 . AC=2;AF=0.032;AN=62;BaseQRankSum=-0.689;DP=65;Dels=0.00;FS=2.622;HRun=0;HaplotypeScore=0.0923;InbreedingCoeff=0.0483;MQ=58.57;MQ0=0;MQRankSum=-0.262;QD=20.77;ReadPosRankSum=-0.131;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|12),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,75 0/0:4,0:4:9.03:0,9,122 ./. 0/0:7,0:7:18.05:0,18,218 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:9.03:0,9,120 0/0:3,0:3:9.03:0,9,116 ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6:0,6,65 ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/0:3,0:3:6.02:0,6,83 ./. 0/0:2,0:2:6.02:0,6,81 0/0:3,0:3:9.03:0,9,122 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,82 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:3,0:3:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,42 ./. 0/0:3,0:3:9.03:0,9,110 ./. ./. 1/1:0,3:3:9.03:114,9,0 0/0:2,0:2:6.02:0,6,79 ./. 0/0:3,0:3:9.03:0,9,120 ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 ./. -chr1 980276 . C T 58.0 . AC=2;AF=0.021;AN=96;BaseQRankSum=-2.227;DP=125;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1208;InbreedingCoeff=0.0215;MQ=58.51;MQ0=0;MQRankSum=0.682;QD=14.50;ReadPosRankSum=-0.682;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|12),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,119 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:9.03:0,9,118 0/0:4,0:4:12.02:0,12,137 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:12.04:0,12,165 ./. 0/0:10,0:10:27.09:0,27,365 0/0:10,0:10:27.09:0,27,357 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,121 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,84 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,84 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,35 ./. 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:6.02:0,6,80 0/0:7,0:7:18.06:0,18,240 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,37 0/0:3,0:3:6.02:0,6,72 0/0:3,0:3:9.03:0,9,125 0/0:5,0:5:15.05:0,15,196 0/0:2,0:2:3.01:0,3,45 0/0:1,0:1:3.01:0,3,37 0/0:4,0:5:12.04:0,12,151 0/0:1,0:1:3.01:0,3,39 ./. 0/0:2,0:2:6.02:0,6,76 0/0:2,0:2:6.02:0,6,73 0/0:4,0:4:9.03:0,9,123 0/0:1,0:1:3.01:0,3,32 0/0:6,0:6:15.05:0,15,205 ./. 0/0:1,0:1:3.01:0,3,42 1/1:0,4:4:9.03:112,9,0 0/0:4,0:4:12.04:0,12,150 ./. 0/0:3,0:3:9.03:0,9,123 ./. ./. 0/0:3,0:3:6.02:0,6,84 0/0:2,0:2:3.01:0,3,37 ./. 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.01:0,6,69 -chr1 980460 . G A 26594.59 . AC=107;AF=0.8917;AN=120;BaseQRankSum=-2.656;DP=975;Dels=0.00;FS=0.883;HRun=0;HaplotypeScore=0.8473;InbreedingCoeff=0.2169;MQ=58.13;MQ0=0;MQRankSum=-0.492;QD=28.60;ReadPosRankSum=0.989;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|12),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,4:4:12:116,12,0 0/1:6,2:8:17.54:18,0,193 1/1:0,8:8:18.03:199,18,0 1/1:1,5:6:9.03:106,9,0 1/1:0,12:12:36.11:455,36,0 1/1:0,9:9:27.05:305,27,0 1/1:0,19:19:54.16:659,54,0 1/1:0,13:13:30.05:338,30,0 1/1:0,24:24:72.20:873,72,0 1/1:0,26:26:57.16:671,57,0 1/1:0,11:11:33.09:380,33,0 0/1:4,8:12:99:240,0,126 1/1:0,12:12:30.07:358,30,0 1/1:0,17:17:39.13:535,39,0 1/1:1,27:28:63.17:796,63,0 1/1:0,14:14:33.11:432,33,0 1/1:0,20:20:51.12:619,51,0 1/1:1,25:26:63.16:791,63,0 1/1:0,16:16:39.12:510,39,0 1/1:0,22:22:54.18:721,54,0 0/1:12,10:22:99:259,0,348 1/1:1,32:33:90.24:1114,90,0 1/1:0,21:21:54.16:693,54,0 1/1:0,23:23:60.19:758,60,0 0/1:14,8:22:99:202,0,367 1/1:0,19:19:51.14:656,51,0 1/1:0,20:20:48.13:611,48,0 1/1:0,9:9:24.07:304,24,0 0/1:12,14:26:99:342,0,364 1/1:0,20:20:54.17:688,54,0 1/1:1,19:20:54.16:665,54,0 1/1:0,12:12:24.07:303,24,0 1/1:0,18:18:42.13:555,42,0 1/1:0,25:25:60.19:775,60,0 1/1:1,19:20:48.15:615,48,0 1/1:0,14:14:33.10:415,33,0 1/1:0,26:26:72.19:895,72,0 0/0:35,0:35:99:0,99,1285 1/1:0,10:10:21.06:257,21,0 1/1:0,18:18:48.09:566,48,0 0/1:6,4:10:80.61:81,0,202 0/1:5,6:11:99:179,0,138 1/1:0,9:9:24.07:306,24,0 1/1:0,9:9:24.08:317,24,0 1/1:0,12:12:27.09:355,27,0 1/1:0,12:12:27.09:361,27,0 1/1:1,23:24:60.19:780,60,0 1/1:0,7:7:18.06:234,18,0 1/1:0,9:9:21.07:287,21,0 1/1:1,19:20:51.12:629,51,0 1/1:1,13:14:30.10:391,30,0 1/1:1,24:25:60.19:779,60,0 1/1:1,16:17:36.09:447,36,0 1/1:0,10:10:24.08:317,24,0 1/1:0,19:19:39.13:540,39,0 1/1:0,8:8:21.07:270,21,0 0/1:3,6:9:62.75:147,0,63 0/1:6,4:10:90.91:91,0,146 1/1:0,10:10:21.07:290,21,0 0/0:10,0:10:27.09:0,27,352 -chr1 980824 . G C 275.83 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.440;DP=1969;Dels=0.00;FS=12.667;HRun=0;HaplotypeScore=2.5993;InbreedingCoeff=-0.0094;MQ=58.48;MQ0=0;MQRankSum=1.465;QD=11.99;ReadPosRankSum=-0.443;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|1),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G819|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|ggG/ggC|G|ENSG00000188157|AGRN|ENST00000379370|14/36|||819/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000479707|1/4||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12.04:0,12,158 0/0:13,0:13:33.10:0,33,417 0/0:7,0:7:18.06:0,18,228 0/0:10,0:10:21.07:0,21,266 0/0:19,0:19:54.17:0,54,719 0/0:26,0:26:72.23:0,72,952 0/0:34,0:34:99:0,99,1269 0/0:18,0:18:54.16:0,54,673 0/0:41,0:41:99:0,120,1546 0/0:37,0:37:99:0,108,1425 0/0:21,0:21:60.14:0,60,721 0/0:15,0:15:45.09:0,45,529 0/0:28,0:28:78.22:0,78,984 0/0:28,0:28:72.23:0,72,951 0/0:60,0:60:99:0,135,1800 0/0:46,0:46:99:0,111,1469 0/0:45,0:45:99:0,108,1374 0/0:66,0:66:99:0,153,1997 0/0:68,0:68:99:0,169,2193 0/0:47,0:47:99:0,114,1501 0/0:42,0:45:99:0,105,1370 0/0:58,0:58:99:0,144,1906 0/0:32,0:32:75.22:0,75,953 0/0:50,0:50:99:0,117,1550 0/0:52,0:53:99:0,123,1635 0/0:40,0:40:84.28:0,84,1148 0/0:47,0:47:99:0,108,1411 0/0:26,0:26:57.18:0,57,754 0/0:57,0:59:99:0,132,1743 0/0:44,0:45:99:0,111,1448 0/0:60,0:61:99:0,138,1829 0/0:53,0:53:99:0,123,1638 0/0:74,0:75:99:0,181,2303 0/0:52,0:52:99:0,129,1685 0/0:54,0:55:99:0,126,1686 0/0:41,0:41:96.31:0,96,1291 0/0:64,0:64:99:0,153,2044 0/0:81,0:81:99:0,196,2599 0/0:8,0:8:24.08:0,24,313 0/0:36,0:36:90.27:0,90,1149 0/0:17,0:17:51.15:0,51,638 0/0:15,0:15:30.09:0,30,380 0/0:19,0:19:51.17:0,51,681 0/0:10,0:10:30.10:0,30,395 0/0:8,0:16:21.07:0,21,278 0/0:19,0:19:42.12:0,42,549 0/0:32,0:32:81.26:0,81,1055 0/0:8,0:8:18.06:0,18,240 0/0:20,0:20:51.16:0,51,660 0/0:20,0:20:51.16:0,51,670 0/0:24,0:24:51.16:0,51,675 0/0:19,0:19:51.15:0,51,635 0/1:11,11:23:99:324,0,372 0/0:20,0:20:57.19:0,57,758 0/0:11,0:11:30.10:0,30,401 0/0:10,0:10:27.09:0,27,358 0/0:12,0:12:30.10:0,30,397 0/0:25,0:25:63.19:0,63,814 0/0:16,0:17:36.11:0,36,464 0/0:16,0:16:24.08:0,24,309 -chr1 980941 . C T 600.94 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.751;DP=2190;Dels=0.00;FS=4.066;HRun=0;HaplotypeScore=1.5643;InbreedingCoeff=-0.0087;MQ=58.24;MQ0=0;MQRankSum=0.449;QD=12.02;ReadPosRankSum=0.589;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|14),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.05:0,15,186 0/0:19,0:19:45.13:0,45,550 0/0:13,0:13:39.10:0,39,490 0/0:12,0:12:27.07:0,27,328 0/0:28,0:29:81.27:0,81,1094 0/0:28,1:29:84.27:0,84,1089 0/0:40,0:41:99:0,111,1453 0/0:20,0:20:60.18:0,60,768 0/0:42,0:42:99:0,117,1513 0/0:66,0:66:99:0,175,2224 0/0:22,0:22:63.19:0,63,797 0/0:24,0:24:69.23:0,69,918 0/0:36,0:36:99:0,102,1308 0/0:26,0:26:72.22:0,72,947 0/0:41,0:41:99:0,114,1499 0/0:21,0:21:57.14:0,57,709 0/0:25,0:25:69.22:0,69,912 0/0:37,0:37:99:0,102,1359 0/0:38,0:38:96.30:0,96,1269 0/0:36,0:36:96.29:0,96,1247 0/0:31,0:31:87.28:0,87,1161 0/0:36,0:36:93.25:0,93,1214 0/0:33,0:33:81.26:0,81,1083 0/0:23,1:24:66.20:0,66,841 0/0:31,0:31:84.27:0,84,1087 0/0:24,0:24:60.19:0,60,801 0/0:35,0:35:90.28:0,90,1181 0/0:16,0:16:39.13:0,39,518 0/0:43,0:43:99:0,120,1568 0/0:34,0:34:93.30:0,93,1211 0/0:43,0:43:99:0,108,1445 0/0:34,0:35:96.30:0,96,1232 0/0:35,0:35:93.29:0,93,1212 0/0:40,0:40:99:0,108,1417 0/0:34,0:34:93.30:0,93,1237 0/0:46,0:46:99:0,114,1532 0/0:39,0:39:99:0,108,1417 0/0:50,0:50:99:0,132,1754 0/0:32,0:32:75.24:0,75,1014 0/0:71,0:71:99:0,190,2456 0/0:39,1:40:99:0,105,1322 0/0:34,0:34:87.27:0,87,1119 0/0:47,0:47:99:0,117,1506 0/0:33,0:33:78.22:0,78,997 0/0:38,0:38:99:0,99,1323 0/0:52,0:52:99:0,129,1684 0/0:62,0:62:99:0,150,1965 0/0:24,0:24:60.19:0,60,793 0/0:60,0:60:99:0,135,1771 0/0:72,0:73:99:0,190,2495 0/0:44,0:45:99:0,111,1448 0/0:47,0:48:99:0,132,1700 0/1:28,22:50:99:649,0,901 0/0:43,1:45:62.29:0,62,1268 0/0:47,0:47:99:0,117,1519 0/0:40,0:40:93.29:0,93,1226 0/0:20,0:20:51.16:0,51,679 0/0:54,0:55:99:0,126,1658 0/0:27,0:27:66.21:0,66,883 0/0:35,0:36:87.27:0,87,1134 -chr1 980948 . C T 538.98 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.096;DP=2144;Dels=0.00;FS=17.669;HRun=0;HaplotypeScore=2.3599;InbreedingCoeff=-0.0087;MQ=58.24;MQ0=0;MQRankSum=-0.314;QD=17.39;ReadPosRankSum=0.302;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|14),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:5,0:6:15.05:0,15,188 0/0:18,0:18:45.12:0,45,546 0/0:12,0:12:36.10:0,36,441 0/0:9,0:9:24.07:0,24,301 0/0:27,0:27:81.25:0,81,1071 0/0:30,0:30:87.26:0,87,1109 0/0:45,0:45:99:0,129,1704 0/0:24,0:24:66.20:0,66,847 0/0:50,0:50:99:0,141,1817 0/0:65,0:66:99:0,181,2324 0/0:23,0:23:63.19:0,63,805 0/0:29,0:29:84.26:0,84,1108 0/0:40,0:40:99:0,111,1435 0/0:26,0:26:72.23:0,72,945 0/0:38,0:38:99:0,105,1418 0/0:21,0:21:57.18:0,57,753 0/0:26,0:26:72.22:0,72,939 0/0:40,0:40:99:0,108,1402 0/0:37,0:37:99:0,99,1314 0/0:36,0:36:99:0,99,1329 0/0:27,0:27:75.24:0,75,996 0/0:36,0:36:96.31:0,96,1270 0/1:11,19:31:99:587,0,310 0/0:21,0:21:54.17:0,54,701 0/0:27,0:27:78.24:0,78,1003 0/0:25,0:25:72.23:0,72,916 0/0:32,0:32:90.29:0,90,1201 0/0:14,0:14:36.12:0,36,485 0/0:40,0:40:99:0,114,1521 0/0:34,0:34:96.29:0,96,1258 0/0:37,0:38:96.31:0,96,1302 0/0:29,0:29:81.26:0,81,1051 0/0:30,0:30:78.25:0,78,1021 0/0:38,0:38:99:0,102,1365 0/0:33,0:33:93.30:0,93,1241 0/0:39,0:39:99:0,108,1443 0/0:40,0:40:99:0,114,1482 0/0:42,0:42:99:0,114,1536 0/0:32,0:32:75.24:0,75,1001 0/0:67,0:67:99:0,184,2417 0/0:44,0:44:99:0,108,1413 0/0:35,0:35:93.30:0,93,1223 0/0:44,0:44:99:0,114,1471 0/0:29,0:29:75.24:0,75,975 0/0:35,0:35:90.27:0,90,1181 0/0:51,0:51:99:0,129,1696 0/0:63,0:64:99:0,166,2151 0/0:22,0:22:57.18:0,57,749 0/0:57,0:57:99:0,129,1709 0/0:73,0:73:99:0,196,2533 0/0:44,0:44:99:0,111,1446 0/0:49,0:49:99:0,135,1756 0/0:48,0:48:99:0,135,1748 0/0:49,0:49:99:0,111,1481 0/0:48,0:48:99:0,120,1578 0/0:39,0:40:87.26:0,87,1147 0/0:22,0:22:57.18:0,57,761 0/0:51,0:51:99:0,123,1634 0/0:28,0:28:75.20:0,75,952 0/0:32,0:32:81.23:0,81,1036 -chr1 980955 . AC A 1099.14 . AC=2;AF=0.0167;AN=120;BaseQRankSum=8.294;DP=2110;FS=28.545;HRun=5;HaplotypeScore=116.2371;InbreedingCoeff=-0.0170;MQ=58.34;MQ0=0;MQRankSum=-0.585;QD=9.16;ReadPosRankSum=1.829;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|14),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:10,0:10:27.09:0,27,369 0/0:19,0:19:48.16:0,48,643 0/0:13,0:13:33.11:0,33,442 0/0:11,0:11:30.10:0,30,404 0/0:29,0:29:87.29:0,87,1182 0/0:33,0:33:90.29:0,90,1207 0/0:40,0:40:99:0,117,1592 0/0:30,0:30:87.29:0,87,1186 0/0:53,0:53:99:0,141,1875 0/0:70,0:69:99:0,187,2511 0/0:22,0:22:60.20:0,60,814 0/0:30,0:30:81.27:0,81,1104 0/0:42,0:42:99:0,105,1432 0/0:24,0:24:63.21:0,63,855 0/0:39,0:39:99:0,105,1417 0/0:20,0:20:57.19:0,57,779 0/0:23,0:23:63.21:0,63,862 0/0:33,0:33:84.27:0,84,1119 0/0:39,0:39:99:0,105,1399 0/0:37,0:37:99:0,99,1354 0/0:24,0:24:72.22:0,72,950 0/0:33,0:33:96.32:0,96,1305 0/0:29,0:29:78.25:0,78,1053 0/0:20,0:20:57.19:0,57,769 0/0:26,0:26:72.24:0,72,984 0/0:24,0:24:66.22:0,66,903 0/0:28,0:28:81.26:0,81,1089 0/0:13,0:13:30.09:0,30,399 0/0:37,0:37:99:0,99,1355 0/0:34,0:34:99:0,99,1347 0/0:37,0:37:99:0,99,1335 0/0:27,0:27:75.25:0,75,1026 0/0:27,0:27:75.23:0,75,999 0/0:35,0:35:99:0,102,1386 0/0:31,0:31:87.29:0,87,1190 0/0:37,0:37:99:0,99,1344 0/0:37,0:37:99:0,108,1469 0/0:43,0:43:99:0,126,1715 0/0:31,0:31:84.28:0,84,1150 0/0:64,0:64:99:0,181,2464 0/0:44,0:44:99:0,120,1625 0/0:33,0:33:99:0,99,1316 0/0:42,0:42:99:0,123,1676 0/0:26,0:26:72.24:0,72,970 0/0:34,0:34:96.91:0,97,1344 0/0:50,0:50:99:0,135,1847 0/0:66,0:66:99:0,187,2519 0/0:23,0:23:60.19:0,60,806 0/0:57,0:57:99:0,144,1956 0/1:46,28:74:99:683,0,1426 0/0:42,0:42:99:0,110,1476 0/0:49,0:49:99:0,144,1925 0/1:28,18:46:99:490,0,763 0/0:50,1:51:99:0,101,1753 0/0:48,0:48:99:0,138,1855 0/0:40,0:40:99:0,105,1421 0/0:22,0:22:63.03:0,63,809 0/0:52,0:52:99:0,138,1881 0/0:28,0:28:81.27:0,81,1108 0/0:29,0:29:75.25:0,75,1026 -chr1 981087 . A G 111674.9 . AC=105;AF=0.8750;AN=120;BaseQRankSum=2.112;DP=3879;Dels=0.00;FS=2.321;HRun=0;HaplotypeScore=2.2416;InbreedingCoeff=0.1619;MQ=58.40;MQ0=0;MQRankSum=-0.442;QD=29.96;ReadPosRankSum=-1.459;EFF=DOWNSTREAM(MODIFIER|||||AGRN|processed_transcript|CODING|ENST00000477585|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|14),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000477585|||||processed_transcript|1 GT:AD:DP:GQ:PL 1/1:0,15:15:42.09:494,42,0 0/1:15,7:22:99:131,0,513 1/1:0,24:24:69.21:868,69,0 1/1:0,27:27:75.20:918,75,0 1/1:0,53:53:99:2033,156,0 1/1:0,37:37:99:1422,108,0 1/1:0,82:82:99:3079,235,0 1/1:0,39:39:99:1476,114,0 1/1:0,123:123:99:4923,370,0 1/1:0,122:122:99:4525,352,0 1/1:0,48:48:99:1816,138,0 0/1:31,31:62:99:968,0,999 1/1:0,64:64:99:2491,190,0 1/1:0,55:55:99:1756,132,0 1/1:0,70:70:99:2308,175,0 1/1:0,43:43:99:1318,99,0 1/1:0,65:65:99:2243,172,0 1/1:0,52:52:99:1642,129,0 1/1:0,79:79:99:2624,199,0 1/1:0,47:47:99:1433,111,0 0/1:22,34:57:99:865,0,547 1/1:1,69:70:99:2111,127,0 1/1:0,44:44:99:1489,114,0 1/1:0,37:37:84.26:1118,84,0 0/1:34,23:57:99:644,0,819 1/1:0,43:43:99:1420,108,0 0/1:36,26:62:99:718,0,959 1/1:1,48:50:90.83:1591,91,0 0/1:28,40:68:99:1131,0,675 1/1:0,54:54:99:1743,135,0 1/1:0,63:64:99:2054,159,0 1/1:0,61:61:99:1808,141,0 1/1:0,60:60:99:1918,147,0 0/1:27,29:57:99:787,0,715 1/1:0,53:53:99:1643,123,0 1/1:0,58:59:99:1915,144,0 1/1:0,49:49:99:1670,132,0 0/0:93,1:94:99:0,202,3090 1/1:0,62:64:99:1970,150,0 1/1:0,140:140:99:4680,367,0 0/1:48,44:95:99:1257,0,1314 0/1:34,29:63:99:726,0,1009 1/1:0,59:60:99:1909,144,0 1/1:0,59:59:99:1879,144,0 1/1:0,78:78:99:2557,193,0 1/1:0,63:64:99:2186,172,0 1/1:0,116:116:99:3818,298,0 1/1:0,42:42:93.30:1232,93,0 1/1:0,70:70:99:2244,175,0 1/1:0,108:108:99:3717,292,0 1/1:0,126:126:99:4049,310,0 1/1:1,81:82:99:2719,186,0 1/1:1,97:99:99:3211,214,0 1/1:0,76:76:99:2455,193,0 1/1:0,70:72:99:2296,181,0 1/1:0,61:61:99:2199,169,0 0/1:26,22:48:99:539,0,737 0/1:36,30:66:99:823,0,974 1/1:0,64:64:99:2117,160,0 0/0:56,2:58:98.43:0,98,1701 -chr1 981131 . A G 3064.9 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-1.865;DP=5182;Dels=0.00;FS=11.038;HRun=0;HaplotypeScore=2.4921;InbreedingCoeff=-0.0256;MQ=58.34;MQ0=0;MQRankSum=1.546;QD=10.79;ReadPosRankSum=1.415;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000469403|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q852R|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|cAa/cGa|Q/R|ENSG00000188157|AGRN|ENST00000379370|15/36|benign(0.227)|tolerated(0.44)|852/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000479707|2/4||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000469403|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:28,0:28:69.19:0,69,829 0/0:30,0:30:87.25:0,87,1065 0/0:31,0:31:87.27:0,87,1108 0/0:22,0:22:60.16:0,60,750 0/0:84,0:84:99:0,253,3325 0/0:75,0:75:99:0,223,2853 0/0:116,0:116:99:0,343,4477 0/0:59,0:59:99:0,175,2300 0/0:184,0:185:99:0,545,7174 0/0:167,0:168:99:0,488,6394 0/0:77,0:77:99:0,229,3019 0/0:61,0:61:99:0,181,2338 0/0:117,0:117:99:0,343,4304 0/0:82,0:82:99:0,205,2697 0/0:89,0:89:99:0,217,2872 0/0:66,1:67:99:0,163,2159 0/0:94,0:94:99:0,229,3056 0/0:68,0:68:99:0,163,2178 0/0:113,0:113:99:0,274,3661 0/0:77,0:77:99:0,193,2528 0/0:76,1:77:99:0,191,2544 0/0:106,0:106:99:0,250,3340 0/0:70,0:70:99:0,163,2234 0/0:60,0:60:99:0,135,1831 0/0:77,0:77:99:0,184,2464 0/0:57,1:58:99:0,135,1766 0/0:86,0:86:99:0,211,2824 0/0:59,1:60:99:0,135,1781 0/0:87,0:89:99:0,232,3033 0/0:73,0:73:99:0,187,2432 0/0:86,0:86:99:0,214,2831 0/0:80,0:80:99:0,211,2712 0/0:68,0:68:99:0,169,2259 0/0:82,0:82:99:0,199,2581 0/0:68,0:68:99:0,169,2248 0/0:93,0:93:99:0,211,2829 0/0:65,0:65:99:0,175,2303 0/0:113,0:113:99:0,301,4010 0/0:74,0:74:99:0,187,2414 0/0:162,0:164:99:0,424,5486 0/0:112,0:112:99:0,289,3706 0/0:92,0:92:99:0,235,3085 0/0:77,0:78:99:0,190,2483 0/0:64,0:65:99:0,162,2050 0/0:91,0:92:99:0,229,3008 0/0:81,0:81:99:0,220,2765 0/0:151,0:152:99:0,397,5129 0/1:23,26:49:99:670,0,610 0/0:106,0:107:99:0,247,3250 0/1:68,45:113:99:1167,0,1828 0/0:147,0:148:99:0,376,4816 0/0:83,0:84:99:0,223,2769 0/1:74,47:122:99:1308,0,1941 0/0:92,0:92:99:0,247,3147 0/0:88,0:89:99:0,226,2897 0/0:88,1:90:99:0,194,3008 0/0:68,0:68:99:0,163,2138 0/0:94,0:95:99:0,241,3084 0/0:73,0:74:99:0,187,2443 0/0:84,0:85:99:0,205,2722 -chr1 981931 . A G 38481.37 . AC=102;AF=0.8500;AN=120;BaseQRankSum=4.244;DP=1481;Dels=0.00;FS=5.461;HRun=0;HaplotypeScore=0.5832;InbreedingCoeff=0.0829;MQ=57.68;MQ0=0;MQRankSum=2.481;QD=26.85;ReadPosRankSum=-2.762;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S1022|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|tcA/tcG|S|ENSG00000188157|AGRN|ENST00000379370|18/36|||1022/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,7:7:18.06:230,18,0 0/1:6,4:10:99:120,0,172 1/1:0,10:10:30.09:373,30,0 1/1:0,14:14:39.11:458,39,0 1/1:0,22:23:60.18:758,60,0 1/1:0,15:15:45.14:591,45,0 1/1:0,38:38:99:1394,108,0 1/1:0,17:17:51.13:602,51,0 1/1:0,56:56:99:2088,162,0 1/1:0,58:59:99:2187,171,0 1/1:0,20:20:60.20:802,60,0 0/1:16,16:32:99:483,0,455 1/1:0,31:31:81.22:1022,81,0 1/1:0,24:24:57.18:743,57,0 1/1:0,39:39:93.27:1218,93,0 1/1:0,31:31:69.21:909,69,0 1/1:0,15:15:42.10:495,42,0 1/1:0,22:22:57.14:700,57,0 1/1:0,23:23:63.18:771,63,0 1/1:0,26:26:63.20:824,63,0 0/1:18,8:28:99:205,0,428 1/1:0,20:21:51.17:685,51,0 1/1:0,16:16:42.13:535,42,0 1/1:0,23:23:63.19:831,63,0 0/1:10,10:21:99:267,0,243 1/1:0,11:12:30.08:371,30,0 0/1:18,12:30:99:332,0,507 1/1:0,19:19:48.14:589,48,0 0/1:19,7:26:99:181,0,475 1/1:0,35:36:90.27:1152,90,0 1/1:1,29:32:27.46:839,27,0 1/1:1,21:22:21.92:648,22,0 1/1:0,19:19:48.14:607,48,0 0/1:18,8:26:99:165,0,504 1/1:0,21:21:45.12:582,45,0 1/1:0,14:15:39.10:469,39,0 1/1:0,22:22:54.17:695,54,0 0/0:28,0:29:78.19:0,78,962 1/1:0,24:25:57.13:695,57,0 1/1:1,29:30:69.21:856,69,0 0/1:19,19:38:99:521,0,444 0/1:13,12:25:99:332,0,345 1/1:0,16:17:45.12:536,45,0 1/1:0,31:31:75.24:982,75,0 1/1:0,12:12:36.11:458,36,0 1/1:0,14:14:36.09:439,36,0 1/1:1,36:37:84.23:1011,84,0 0/1:6,5:12:99:101,0,138 1/1:0,34:34:69.22:892,69,0 0/1:15,18:33:99:409,0,410 1/1:1,43:45:99:1352,105,0 1/1:2,21:23:9.92:544,10,0 0/1:20,17:37:99:415,0,543 1/1:0,16:16:42.12:526,42,0 1/1:0,21:21:48.15:632,48,0 1/1:0,23:23:51.16:681,51,0 0/1:7,1:8:21.41:21,0,84 0/1:13,13:27:99:354,0,407 1/1:1,23:24:60.19:805,60,0 0/0:18,1:19:39.11:0,39,497 -chr1 982205 . G A 372.27 . AC=1;AF=0.0083;AN=120;BaseQRankSum=1.314;DP=1529;Dels=0.00;FS=1.129;HRun=1;HaplotypeScore=1.1177;InbreedingCoeff=-0.0134;MQ=58.00;MQ0=0;MQRankSum=0.488;QD=14.32;ReadPosRankSum=-0.923;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E1086K|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|Gag/Aag|E/K|ENSG00000188157|AGRN|ENST00000379370|19/36|benign(0.32)|tolerated(0.41)|1086/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,104 0/0:7,0:7:18.05:0,18,223 0/0:7,0:7:21.06:0,21,247 0/0:2,0:2:6.02:0,6,72 0/0:7,0:7:18.05:0,18,222 0/0:4,0:5:9.01:0,9,96 0/0:14,0:15:42.12:0,42,533 0/0:4,0:4:12.04:0,12,154 0/0:25,0:25:69.20:0,69,870 0/0:16,0:17:39.12:0,39,506 0/0:6,0:6:12.04:0,12,157 0/0:7,0:7:21.07:0,21,269 0/0:11,0:12:30.07:0,30,355 0/0:35,0:35:69.20:0,69,930 0/0:32,0:32:78.24:0,78,1006 0/0:17,0:17:45.14:0,45,572 0/0:22,0:22:48.14:0,48,592 0/0:26,0:26:63.19:0,63,790 0/0:31,0:31:69.20:0,69,858 0/0:23,0:23:57.18:0,57,756 0/0:24,0:24:60.19:0,60,774 0/0:33,0:33:78.25:0,78,1025 0/0:23,0:23:51.16:0,51,669 0/0:31,0:32:78.23:0,78,1011 0/0:19,0:20:42.14:0,42,560 0/0:27,0:27:75.20:0,75,945 0/0:28,0:28:66.20:0,66,870 0/0:24,0:24:42.14:0,42,574 0/0:32,0:32:84.24:0,84,1053 0/0:28,0:28:66.20:0,66,882 0/0:35,0:35:81.25:0,81,1043 0/0:10,0:10:27.07:0,27,347 0/0:27,0:27:78.22:0,78,980 0/0:34,0:34:78.24:0,78,1023 0/0:19,0:19:51.16:0,51,659 0/0:29,0:30:78.23:0,78,979 0/0:28,0:28:72.23:0,72,959 0/0:31,0:31:81.25:0,81,1059 0/0:35,0:35:84.24:0,84,1072 0/0:46,0:46:99:0,111,1350 0/0:38,0:38:96.28:0,96,1191 0/0:23,0:24:57.17:0,57,712 0/0:21,0:22:51.13:0,51,624 0/0:31,0:31:66.20:0,66,817 0/1:11,15:26:99:420,0,188 0/0:39,0:40:87.24:0,87,1048 0/0:59,0:59:99:0,153,1823 0/0:22,0:22:48.12:0,48,605 0/0:33,0:33:84.24:0,84,1043 0/0:55,0:55:99:0,132,1630 0/0:42,0:44:99:0,105,1253 0/0:38,0:39:90.20:0,90,1047 0/0:49,0:49:99:0,123,1518 0/0:35,0:35:90.26:0,90,1085 0/0:21,0:21:57.16:0,57,699 0/0:22,0:22:57.15:0,57,704 0/0:18,0:19:45.13:0,45,568 0/0:26,0:27:66.18:0,66,808 0/0:29,0:29:60.17:0,60,743 0/0:25,0:25:54.15:0,54,678 -chr1 982403 . C T 1164.33 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-2.215;DP=1442;Dels=0.00;FS=2.421;HRun=1;HaplotypeScore=0.9843;InbreedingCoeff=-0.0334;MQ=57.51;MQ0=0;MQRankSum=0.119;QD=10.49;ReadPosRankSum=-1.415;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|19),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.04:0,12,146 0/0:2,0:2:6.01:0,6,66 0/0:3,0:3:6.01:0,6,65 0/0:2,0:2:6.01:0,6,65 0/0:4,0:4:12.04:0,12,164 0/0:7,0:7:18.06:0,18,231 0/0:5,0:5:15.05:0,15,202 0/0:6,0:6:15.05:0,15,193 0/0:9,0:9:27.08:0,27,353 0/0:18,0:18:48.15:0,48,629 0/0:4,0:4:12.04:0,12,156 0/1:2,1:3:32.20:32,0,68 0/0:11,0:11:33.11:0,33,425 0/0:12,0:12:33.11:0,33,437 0/0:25,0:25:69.22:0,69,899 0/0:10,0:10:27.09:0,27,344 0/0:9,0:9:21.07:0,21,285 0/0:23,0:24:57.17:0,57,755 0/0:20,0:20:54.16:0,54,695 0/0:12,0:12:30.10:0,30,404 0/0:10,0:10:27.09:0,27,353 0/0:22,0:22:60.16:0,60,758 0/0:10,0:10:27.09:0,27,344 0/0:10,0:10:24.08:0,24,315 0/0:12,0:12:33.11:0,33,437 0/0:17,0:17:45.15:0,45,609 0/0:18,0:18:39.13:0,39,523 0/0:15,0:15:39.12:0,39,510 0/0:17,0:17:51.16:0,51,652 0/0:13,0:13:39.12:0,39,507 0/0:18,0:18:54.17:0,54,690 0/0:11,0:11:30.10:0,30,390 0/0:12,0:12:27.09:0,27,358 0/0:22,0:22:66.21:0,66,845 0/0:14,0:14:42.13:0,42,550 0/0:17,0:17:42.14:0,42,569 0/0:25,0:25:66.20:0,66,856 0/0:14,0:14:36.12:0,36,481 0/0:36,0:36:78.24:0,78,1015 0/0:47,0:48:99:0,111,1422 0/0:39,0:39:99:0,102,1315 0/0:41,0:41:99:0,102,1273 0/0:35,0:36:87.27:0,87,1101 0/0:31,0:32:72.21:0,72,907 0/0:34,0:34:87.28:0,87,1141 0/0:40,0:40:99:0,99,1238 0/0:75,0:76:99:0,190,2411 0/0:23,0:23:48.15:0,48,630 0/0:46,0:46:99:0,114,1482 0/0:84,0:84:99:0,196,2481 0/0:79,0:79:99:0,202,2587 0/1:36,28:64:99:757,0,867 0/0:51,0:51:99:0,138,1737 0/0:49,0:49:99:0,108,1385 0/0:37,0:37:96.27:0,96,1225 0/0:22,0:22:51.16:0,51,667 0/0:31,0:31:78.24:0,78,1003 0/0:36,0:36:93.26:0,93,1163 0/1:25,19:44:99:455,0,638 0/0:27,0:27:66.20:0,66,848 -chr1 982444 . A G 24810.69 . AC=102;AF=0.8500;AN=120;BaseQRankSum=4.056;DP=908;Dels=0.00;FS=0.946;HRun=3;HaplotypeScore=0.5521;InbreedingCoeff=0.0418;MQ=57.33;MQ0=0;MQRankSum=0.383;QD=27.94;ReadPosRankSum=1.506;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|19),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,3:3:6.02:69,6,0 0/1:2,1:3:24.41:24,0,71 1/1:0,3:3:9.02:105,9,0 1/1:0,2:2:6.02:78,6,0 1/1:0,3:3:9.03:122,9,0 1/1:0,1:1:3.01:40,3,0 1/1:0,7:7:21.06:262,21,0 1/1:0,4:4:12.04:157,12,0 1/1:0,9:9:27.09:358,27,0 1/1:0,14:14:42.13:543,42,0 1/1:0,2:2:6.02:81,6,0 0/1:1,2:3:30.98:72,0,31 1/1:0,8:8:24.07:299,24,0 1/1:0,9:10:27.09:350,27,0 1/1:0,12:12:33.08:395,33,0 1/1:0,5:5:12.04:158,12,0 1/1:0,8:8:21.06:258,21,0 1/1:0,14:14:39.11:487,39,0 1/1:0,17:17:48.15:604,48,0 1/1:0,8:8:24.06:295,24,0 0/1:6,4:10:97.22:97,0,190 1/1:0,13:13:33.11:430,33,0 1/1:0,8:8:24.07:301,24,0 1/1:0,7:7:21.06:261,21,0 0/1:6,3:10:62.93:63,0,158 1/1:0,16:16:45.14:592,45,0 0/1:7,8:15:99:217,0,211 1/1:0,9:9:24.08:308,24,0 0/1:7,5:12:99:161,0,227 1/1:0,7:7:21.07:266,21,0 1/1:0,7:7:21.05:249,21,0 1/1:0,8:8:24.08:313,24,0 1/1:0,6:6:15.05:194,15,0 0/1:6,9:15:99:299,0,115 1/1:0,5:5:15.03:183,15,0 1/1:0,6:7:18.06:236,18,0 1/1:0,18:18:51.16:661,51,0 0/0:4,0:4:9.03:0,9,118 1/1:0,27:27:75.20:907,75,0 1/1:0,29:30:75.19:907,75,0 0/1:19,16:35:99:410,0,474 0/1:11,14:25:99:408,0,273 1/1:0,21:21:48.15:614,48,0 1/1:0,16:16:42.12:537,42,0 1/1:0,16:16:45.11:542,45,0 1/1:0,28:28:69.22:889,69,0 1/1:1,48:50:96.63:1660,97,0 0/1:4,10:14:74.03:297,0,74 1/1:1,23:24:66.16:785,66,0 0/1:24,23:49:99:643,0,599 1/1:0,46:46:99:1668,135,0 1/1:0,38:38:93.24:1112,93,0 0/1:14,15:29:99:486,0,399 1/1:0,34:34:90.26:1110,90,0 1/1:0,17:17:42.13:540,42,0 1/1:0,9:9:21.07:274,21,0 0/1:12,5:18:99:148,0,309 0/1:8,16:25:99:396,0,188 1/1:1,26:28:72.19:889,72,0 0/0:15,0:16:42.07:0,42,485 -chr1 982462 . T C 27335.24 . AC=119;AF=0.9917;AN=120;BaseQRankSum=0.923;DP=796;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5400;InbreedingCoeff=-0.0264;MQ=57.04;MQ0=0;MQRankSum=0.157;QD=34.34;ReadPosRankSum=-1.750;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|19),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,2:2:3.01:39,3,0 1/1:0,4:4:9.03:120,9,0 1/1:0,1:1:3.01:39,3,0 1/1:0,2:2:6.02:73,6,0 1/1:0,4:4:12.04:155,12,0 1/1:0,3:3:9.03:122,9,0 1/1:0,8:8:24.07:310,24,0 1/1:0,3:3:9.03:122,9,0 1/1:0,12:12:36.11:450,36,0 1/1:0,13:13:39.13:518,39,0 1/1:0,3:3:6.02:82,6,0 1/1:0,4:4:12.04:158,12,0 1/1:0,5:5:9.03:111,9,0 1/1:0,9:9:24.08:301,24,0 1/1:0,9:9:27.09:360,27,0 1/1:0,5:5:12.03:157,12,0 1/1:0,8:8:24.06:284,24,0 1/1:0,10:10:27.09:371,27,0 1/1:0,20:20:57.18:736,57,0 1/1:0,5:5:12.04:154,12,0 0/1:5,5:10:99:167,0,126 1/1:0,9:9:27.08:335,27,0 1/1:0,8:8:24.06:288,24,0 1/1:0,6:7:18.05:226,18,0 1/1:0,4:4:12.03:143,12,0 1/1:0,18:18:51.16:656,51,0 1/1:0,13:13:36.11:464,36,0 1/1:0,7:7:18.06:231,18,0 1/1:0,10:10:27.09:364,27,0 1/1:0,9:9:21.04:261,21,0 1/1:0,7:7:21.06:265,21,0 1/1:0,5:5:15.05:204,15,0 1/1:0,8:8:24.08:316,24,0 1/1:0,11:11:30.08:379,30,0 1/1:0,3:3:9.03:112,9,0 1/1:0,7:7:21.06:265,21,0 1/1:0,11:11:33.11:438,33,0 1/1:0,4:4:12.02:138,12,0 1/1:0,23:23:66.21:835,66,0 1/1:0,27:27:75.20:911,75,0 1/1:0,28:29:69.16:851,69,0 1/1:0,19:19:54.17:703,54,0 1/1:0,17:17:48.14:600,48,0 1/1:0,9:10:27.08:339,27,0 1/1:0,15:15:45.14:563,45,0 1/1:0,26:26:72.22:926,72,0 1/1:0,44:44:99:1506,117,0 1/1:0,10:10:27.09:343,27,0 1/1:0,18:18:45.11:552,45,0 1/1:0,47:47:99:1600,132,0 1/1:0,38:38:99:1300,102,0 1/1:0,32:32:87.27:1080,87,0 1/1:0,28:28:81.23:998,81,0 1/1:0,28:28:78.22:978,78,0 1/1:0,14:14:39.12:504,39,0 1/1:0,9:9:27.06:331,27,0 1/1:0,18:18:48.11:576,48,0 1/1:0,19:20:42.12:520,42,0 1/1:0,29:29:72.21:918,72,0 1/1:0,14:14:39.12:487,39,0 -chr1 982482 . C T 1093.25 . AC=3;AF=0.0254;AN=118;BaseQRankSum=0.161;DP=714;Dels=0.00;FS=1.368;HRun=0;HaplotypeScore=0.5694;InbreedingCoeff=-0.0414;MQ=57.13;MQ0=0;MQRankSum=0.077;QD=14.20;ReadPosRankSum=3.205;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|19),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:6.02:0,6,74 0/0:4,0:4:12.03:0,12,144 0/0:4,0:4:9:0,9,90 0/0:4,0:4:12.04:0,12,160 0/0:3,0:3:9.03:0,9,113 0/0:6,0:6:18.06:0,18,236 0/0:1,0:1:3.01:0,3,41 0/0:10,0:10:30.09:0,30,380 0/0:14,0:14:42.14:0,42,549 0/0:4,0:4:12.04:0,12,156 0/0:3,0:3:9.03:0,9,113 0/0:4,0:4:9.03:0,9,116 0/0:6,0:6:15.05:0,15,193 0/0:11,0:11:30.10:0,30,402 0/0:6,0:6:18.06:0,18,232 0/0:7,0:7:21.06:0,21,258 0/0:7,0:7:18.06:0,18,241 0/0:18,0:18:48.16:0,48,639 0/0:5,0:5:15.03:0,15,180 0/0:10,0:10:30.07:0,30,369 0/0:6,0:6:18.06:0,18,227 0/0:10,0:10:27.07:0,27,352 0/0:7,0:7:18.04:0,18,220 0/0:4,0:4:12.04:0,12,151 0/0:13,0:13:36.11:0,36,461 0/0:13,0:13:33.11:0,33,432 0/0:3,0:3:9.02:0,9,105 0/0:7,0:7:15.04:0,15,188 0/0:8,0:9:18.05:0,18,235 0/0:10,0:10:24.07:0,24,311 0/0:3,0:3:9.03:0,9,113 0/0:9,0:9:24.06:0,24,283 0/0:10,0:10:27.08:0,27,347 0/0:3,0:3:9.03:0,9,121 0/0:6,0:6:15.05:0,15,196 0/0:10,0:10:27.08:0,27,350 0/0:5,0:5:15.03:0,15,186 0/0:21,0:21:60.18:0,60,758 0/0:21,0:21:54.14:0,54,655 0/0:24,0:25:57.17:0,57,724 0/0:14,0:14:36.10:0,36,465 0/0:17,0:17:42.10:0,42,498 0/0:11,0:11:30.09:0,30,381 0/0:17,0:17:51.16:0,51,647 0/0:21,0:21:57.17:0,57,733 0/0:32,1:33:54.70:0,55,1089 0/1:9,1:10:6.37:6,0,268 0/0:16,0:16:33.10:0,33,419 0/1:20,25:45:99:735,0,560 0/0:37,0:38:87.28:0,87,1154 0/0:26,0:26:60.18:0,60,753 0/1:8,14:22:99:423,0,257 0/0:27,0:27:69.20:0,69,888 0/0:16,0:16:45.14:0,45,578 0/0:5,0:5:12.04:0,12,160 0/0:20,0:20:48.13:0,48,586 0/0:16,0:16:39.10:0,39,481 0/0:22,0:23:57.15:0,57,728 0/0:12,0:12:27.08:0,27,337 -chr1 982484 . C T 1096.42 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.607;DP=707;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5118;InbreedingCoeff=-0.0484;MQ=57.24;MQ0=0;MQRankSum=0.555;QD=14.43;ReadPosRankSum=3.144;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|19),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,30 0/0:3,0:3:9:0,9,102 0/0:4,0:4:9.03:0,9,108 0/0:5,0:5:12.04:0,12,151 0/0:5,0:5:12.03:0,12,150 0/0:6,0:6:18.06:0,18,244 0/0:1,0:1:3.01:0,3,41 0/0:10,0:10:30.09:0,30,385 0/0:14,0:14:39.13:0,39,513 0/0:5,0:5:15.05:0,15,195 0/0:2,0:2:6:0,6,65 0/0:2,0:2:6.02:0,6,81 0/0:6,0:6:15.05:0,15,190 0/0:11,0:11:33.11:0,33,436 0/0:6,0:6:18.05:0,18,228 0/0:7,0:7:21.06:0,21,260 0/0:8,0:8:21.07:0,21,274 0/0:18,0:18:51.16:0,51,656 0/0:5,0:5:15.05:0,15,188 0/0:10,0:10:30.09:0,30,378 0/0:6,0:6:18.06:0,18,229 0/0:10,0:10:27.09:0,27,363 0/0:7,0:7:18.05:0,18,219 0/0:4,0:4:12.03:0,12,149 0/0:12,0:12:36.12:0,36,470 0/0:14,0:15:39.13:0,39,513 0/0:3,0:3:9.02:0,9,105 0/0:7,0:7:15.05:0,15,187 0/0:9,0:9:21.04:0,21,267 0/0:10,0:10:24.08:0,24,326 0/0:2,0:2:6.02:0,6,80 0/0:9,0:9:21.06:0,21,261 0/0:12,0:12:33.11:0,33,431 0/0:3,0:3:9.03:0,9,117 0/0:5,0:5:15.05:0,15,198 0/0:10,0:10:27.08:0,27,339 0/0:5,0:5:15.05:0,15,198 0/0:20,0:20:57.16:0,57,710 0/0:23,0:23:66.19:0,66,804 0/0:23,0:23:54.16:0,54,689 0/0:14,0:14:36.10:0,36,466 0/0:14,0:14:36.11:0,36,437 0/0:11,0:11:30.09:0,30,382 0/0:17,0:17:51.16:0,51,646 0/0:21,0:21:54.17:0,54,700 0/0:31,1:32:51.69:0,52,1039 0/1:8,2:10:44.59:45,0,261 0/0:15,0:15:36.08:0,36,440 0/1:19,25:44:99:711,0,533 0/0:38,0:38:93.30:0,93,1222 0/0:25,0:25:60.14:0,60,724 0/1:8,14:22:99:420,0,251 0/0:27,0:27:72.22:0,72,926 0/0:17,0:17:51.16:0,51,651 0/0:5,0:5:12.04:0,12,158 0/0:20,0:20:48.15:0,48,614 0/0:17,0:17:42.10:0,42,519 0/0:22,0:22:57.18:0,57,737 0/0:11,0:11:27.08:0,27,333 -chr1 982513 . T C 22111.8 . AC=107;AF=0.8917;AN=120;BaseQRankSum=1.897;DP=701;Dels=0.00;FS=6.392;HRun=0;HaplotypeScore=0.5397;InbreedingCoeff=0.3020;MQ=57.59;MQ0=0;MQRankSum=-0.108;QD=32.37;ReadPosRankSum=0.738;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|19),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,3:3:9.03:102,9,0 0/0:4,0:4:12.03:0,12,144 1/1:0,5:5:12.04:159,12,0 1/1:0,3:3:6.02:75,6,0 1/1:0,8:8:24.08:311,24,0 1/1:1,4:5:12.04:156,12,0 1/1:0,6:6:18.06:235,18,0 1/1:0,1:1:3.01:34,3,0 1/1:0,11:11:33.11:447,33,0 1/1:0,14:14:42.14:547,42,0 1/1:0,8:8:24.08:322,24,0 1/1:0,1:1:3.01:41,3,0 1/1:0,6:6:18.06:242,18,0 1/1:0,8:8:24.07:307,24,0 1/1:0,8:8:24.08:308,24,0 1/1:0,5:5:15.05:203,15,0 1/1:0,7:7:21.07:270,21,0 1/1:0,6:6:18.05:225,18,0 1/1:0,13:13:36.09:433,36,0 1/1:0,10:10:27.08:341,27,0 0/1:5,4:10:99:138,0,117 1/1:0,5:5:12.04:165,12,0 1/1:0,8:8:21.07:275,21,0 1/1:0,4:4:9.03:123,9,0 0/1:4,2:6:66.19:66,0,102 1/1:0,7:7:21.07:280,21,0 1/1:0,12:12:36.11:467,36,0 1/1:0,2:2:6.02:79,6,0 0/1:5,6:11:63.71:168,0,64 1/1:0,9:9:21.07:285,21,0 1/1:0,13:13:39.13:511,39,0 1/1:0,3:3:9.03:122,9,0 1/1:0,10:10:21.07:285,21,0 1/1:0,14:14:42.13:536,42,0 1/1:0,2:2:6.02:81,6,0 1/1:0,4:4:12.04:160,12,0 1/1:0,7:7:21.07:270,21,0 0/0:6,0:6:18.06:0,18,230 1/1:0,16:16:48.15:608,48,0 1/1:0,30:31:81.25:1041,81,0 0/1:12,6:19:99:183,0,298 0/1:5,8:13:99:268,0,159 1/1:1,15:16:11.69:493,12,0 1/1:0,10:10:30.10:401,30,0 1/1:0,16:16:45.14:590,45,0 1/1:0,18:18:48.15:615,48,0 1/1:0,35:35:87.27:1103,87,0 1/1:0,9:9:24.07:300,24,0 1/1:0,13:13:36.11:460,36,0 1/1:0,49:49:99:1685,132,0 1/1:1,33:34:87.27:1132,87,0 1/1:0,19:19:57.17:723,57,0 1/1:1,21:22:23.20:672,23,0 1/1:0,21:21:60.17:735,60,0 1/1:0,17:17:51.13:651,51,0 1/1:0,10:10:30.10:392,30,0 0/1:15,8:23:99:244,0,510 0/1:5,16:21:99:464,0,123 1/1:0,16:16:45.14:581,45,0 0/0:8,0:8:18.06:0,18,243 -chr1 982573 . C T 1076.33 . AC=3;AF=0.0250;AN=120;BaseQRankSum=0.536;DP=905;Dels=0.00;FS=13.480;HRun=0;HaplotypeScore=0.6754;InbreedingCoeff=-0.0368;MQ=58.37;MQ0=0;MQRankSum=-0.537;QD=12.23;ReadPosRankSum=1.369;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|19),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,70 0/0:9,0:9:24.08:0,24,311 0/0:2,0:2:3.01:0,3,41 0/0:3,0:3:9.03:0,9,113 0/0:11,0:11:33.11:0,33,438 0/0:8,0:8:24.08:0,24,314 0/0:15,0:15:45.14:0,45,601 0/0:6,0:6:18.06:0,18,247 0/0:12,0:12:33.11:0,33,449 0/0:20,0:20:57.19:0,57,773 0/0:5,0:5:15.05:0,15,204 0/0:4,0:4:12.04:0,12,164 0/0:4,0:4:12.04:0,12,164 0/0:13,0:13:36.12:0,36,487 0/0:15,0:15:36.12:0,36,488 0/0:5,0:5:15.05:0,15,190 0/0:5,0:6:15.05:0,15,181 0/0:9,0:9:24.08:0,24,329 0/0:15,0:15:42.14:0,42,570 0/0:11,0:11:30.10:0,30,396 0/0:8,0:8:18.06:0,18,233 0/0:4,0:4:12.03:0,12,152 0/0:7,0:7:18.06:0,18,250 0/0:4,0:4:12.04:0,12,150 0/0:11,0:11:33.11:0,33,430 0/0:5,0:5:15.05:0,15,208 0/0:13,0:13:33.10:0,33,431 0/0:4,0:4:9.03:0,9,125 0/0:17,0:17:48.14:0,48,623 0/0:13,0:13:39.12:0,39,508 0/0:19,0:19:54.18:0,54,721 0/0:6,0:6:18.06:0,18,233 0/0:16,0:16:39.12:0,39,505 0/0:15,0:15:39.12:0,39,505 0/0:4,0:4:12.04:0,12,146 0/0:7,0:7:21.07:0,21,291 0/0:7,0:7:21.07:0,21,273 0/0:9,0:9:27.09:0,27,368 0/0:20,0:20:51.16:0,51,678 0/0:44,0:44:96.31:0,96,1259 0/0:23,0:23:54.17:0,54,711 0/0:21,0:21:57.17:0,57,751 0/0:23,0:23:60.19:0,60,796 0/0:11,0:11:30.10:0,30,390 0/0:15,0:15:33.11:0,33,440 0/0:26,0:26:60.19:0,60,787 0/0:39,0:39:93.27:0,93,1160 0/1:6,7:13:99:186,0,202 0/0:16,0:16:39.12:0,39,485 0/1:27,25:52:99:708,0,753 0/0:50,0:50:99:0,123,1587 0/0:29,0:29:84.27:0,84,1093 0/1:13,10:23:99:262,0,419 0/0:36,0:36:84.25:0,84,1101 0/0:23,0:23:66.20:0,66,841 0/0:22,0:22:60.19:0,60,772 0/0:17,0:17:45.15:0,45,604 0/0:23,0:23:60.17:0,60,751 0/0:19,0:19:54.15:0,54,666 0/0:15,0:15:45.14:0,45,583 -chr1 982844 . G C 4135.57 . AC=11;AF=0.0917;AN=120;BaseQRankSum=-1.942;DP=1958;Dels=0.00;FS=2.777;HRun=0;HaplotypeScore=1.2617;InbreedingCoeff=-0.1015;MQ=58.19;MQ0=0;MQRankSum=1.346;QD=12.09;ReadPosRankSum=2.109;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|20),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:13,0:13:30.09:0,30,361 0/0:13,0:13:30.09:0,30,368 0/0:23,0:23:63.17:0,63,786 0/0:12,0:12:27.09:0,27,340 0/0:52,0:52:99:0,120,1569 0/0:52,0:52:99:0,126,1653 0/1:30,23:53:99:621,0,867 0/0:51,0:51:99:0,138,1801 0/0:120,0:120:99:0,322,4240 0/0:134,0:134:99:0,331,4303 0/0:51,0:51:99:0,129,1693 0/0:44,0:44:99:0,111,1404 0/0:73,0:73:99:0,202,2610 0/0:44,0:45:99:0,114,1484 0/0:36,0:36:84.27:0,84,1115 0/0:18,0:18:51.16:0,51,644 0/0:35,0:35:90.29:0,90,1197 0/0:30,0:30:84.23:0,84,1060 0/1:24,15:39:99:408,0,675 0/0:46,0:46:99:0,123,1604 0/0:35,0:35:87.28:0,87,1140 0/1:16,16:32:99:423,0,501 0/0:30,0:30:72.21:0,72,912 0/0:33,0:33:93.29:0,93,1190 0/0:35,0:35:84.24:0,84,1059 0/1:10,17:27:99:506,0,215 0/0:48,1:49:99:0,120,1570 0/0:37,0:37:99:0,102,1343 0/0:36,0:36:93.28:0,93,1167 0/1:22,14:37:99:396,0,504 0/1:31,16:48:99:342,0,953 0/0:22,0:22:60.18:0,60,767 0/0:28,0:29:78.25:0,78,1018 0/0:29,0:29:78.25:0,78,1003 0/0:24,0:24:57.19:0,57,758 0/0:36,0:36:96.30:0,96,1255 0/0:32,0:32:75.24:0,75,978 0/0:41,0:41:99:0,117,1510 0/1:9,6:15:99:163,0,202 0/1:11,15:26:99:479,0,264 0/1:14,10:24:99:298,0,364 0/0:19,0:19:51.14:0,51,633 0/0:14,0:14:39.12:0,39,495 0/0:13,0:13:30.09:0,30,378 0/0:13,0:13:33.11:0,33,437 0/0:24,0:24:63.19:0,63,794 0/0:31,0:31:81.25:0,81,1019 0/0:7,0:7:15.02:0,15,173 0/0:9,0:9:18.06:0,18,226 0/0:35,0:36:96.31:0,96,1248 0/1:12,12:24:99:314,0,355 0/0:27,0:27:57.18:0,57,738 0/0:29,0:29:81.24:0,81,1003 0/0:13,0:13:33.09:0,33,420 0/0:15,0:15:45.13:0,45,563 0/1:11,6:17:99:187,0,267 0/0:8,0:8:21.06:0,21,261 0/0:18,0:18:39.12:0,39,507 0/0:12,0:12:30.08:0,30,371 0/0:11,0:11:30.10:0,30,397 -chr1 982865 . A G 36.62 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.110;DP=1923;Dels=0.00;FS=2.301;HRun=0;HaplotypeScore=1.0780;InbreedingCoeff=-0.0085;MQ=58.17;MQ0=0;MQRankSum=-1.323;QD=5.23;ReadPosRankSum=1.132;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|20),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000478677|1/2||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:15,0:16:36.11:0,36,440 0/0:17,0:17:48.12:0,48,548 0/0:29,0:29:81.23:0,81,1020 0/0:10,0:10:27.07:0,27,327 0/0:51,0:51:99:0,147,1828 0/0:63,0:63:99:0,184,2356 0/0:61,0:62:99:0,181,2246 0/0:47,0:47:99:0,135,1727 0/0:111,0:111:99:0,322,4209 0/0:129,0:129:99:0,382,4930 0/0:52,0:52:99:0,156,1999 0/0:45,0:45:99:0,129,1672 0/0:78,1:79:99:0,235,3010 0/0:45,0:45:99:0,132,1662 0/0:33,0:33:96.30:0,96,1205 0/0:20,0:20:54.17:0,54,686 0/0:28,0:28:78.24:0,78,995 0/0:32,0:32:93.30:0,93,1232 0/0:32,0:32:90.26:0,90,1111 0/0:42,0:42:99:0,120,1506 0/0:32,0:33:87.20:0,87,1067 0/0:29,0:30:75.24:0,75,950 0/0:28,0:28:72.22:0,72,928 0/0:31,0:31:87.28:0,87,1119 0/0:28,0:29:75.22:0,75,906 0/0:22,0:22:54.14:0,54,654 0/0:40,0:40:99:0,108,1372 0/0:33,0:33:93.28:0,93,1191 0/0:34,0:35:99:0,99,1215 0/0:31,0:31:84.26:0,84,1051 0/0:38,1:39:99:0,111,1405 0/0:25,0:25:69.22:0,69,883 0/0:30,0:31:84.27:0,84,1091 0/0:33,0:33:84.27:0,84,1121 0/0:21,0:21:57.18:0,57,731 0/0:26,0:26:72.23:0,72,896 0/0:31,0:31:87.25:0,87,1094 0/0:41,0:42:99:0,117,1526 0/0:13,0:13:36.11:0,36,446 0/0:23,0:23:66.18:0,66,799 0/0:28,0:29:72.21:0,72,921 0/0:20,0:20:60.18:0,60,748 0/0:14,0:14:39.10:0,39,498 0/0:13,0:13:30.07:0,30,363 0/0:13,0:13:39.12:0,39,485 0/0:23,0:23:63.20:0,63,826 0/0:33,0:33:81.24:0,81,1016 0/1:4,3:7:84.38:84,0,127 0/0:11,0:11:27.06:0,27,324 0/0:35,0:35:87.27:0,87,1120 0/0:27,0:27:78.24:0,78,971 0/0:26,0:27:69.22:0,69,884 0/0:29,0:30:81.26:0,81,1042 0/0:16,0:16:48.12:0,48,571 0/0:13,0:14:33.11:0,33,428 0/0:18,0:18:48.15:0,48,611 0/0:10,0:10:27.08:0,27,339 0/0:18,0:19:45.12:0,45,568 0/0:12,0:12:33.10:0,33,416 0/0:13,0:13:33.11:0,33,422 -chr1 982906 . G A 170.75 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.574;DP=1942;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.9590;InbreedingCoeff=-0.0085;MQ=58.80;MQ0=0;MQRankSum=0.287;QD=11.38;ReadPosRankSum=-1.149;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|20),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000478677|1/2||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:10,0:10:24.05:0,24,275 0/0:14,0:14:39.10:0,39,463 0/0:21,0:21:60.18:0,60,761 0/0:9,0:9:21.04:0,21,250 0/0:44,0:44:99:0,132,1704 0/0:43,0:43:99:0,120,1609 0/0:53,1:54:99:0,112,1945 0/0:35,0:35:99:0,99,1291 0/0:93,0:93:99:0,265,3462 0/0:101,0:101:99:0,295,3844 0/0:41,0:41:99:0,117,1536 0/0:40,0:40:99:0,108,1404 0/0:44,0:45:99:0,129,1640 0/0:44,0:44:99:0,114,1496 0/0:37,0:37:93.28:0,93,1196 0/0:29,0:29:81.22:0,81,1036 0/0:30,0:30:84.25:0,84,1072 0/0:39,0:39:99:0,105,1358 0/0:39,0:39:99:0,99,1294 0/0:36,0:36:99:0,102,1298 0/0:35,0:35:96.29:0,96,1236 0/0:34,0:34:84.24:0,84,1064 0/0:25,0:25:63.15:0,63,774 0/0:38,0:38:99:0,108,1379 0/0:23,0:23:60.17:0,60,763 0/0:35,1:36:65.59:0,66,1110 0/0:27,0:27:72.20:0,72,903 0/0:31,0:31:84.25:0,84,1070 0/0:41,0:41:99:0,114,1472 0/0:39,0:39:99:0,99,1268 0/0:32,0:32:78.18:0,78,966 0/0:29,0:29:69.22:0,69,897 0/0:33,0:33:87.24:0,87,1104 0/0:35,0:35:87.27:0,87,1136 0/0:17,0:17:39.12:0,39,502 0/0:20,0:20:60.17:0,60,754 0/0:31,0:31:81.22:0,81,1023 0/0:52,0:52:99:0,135,1714 0/0:12,0:12:33.09:0,33,405 0/0:37,0:37:90.28:0,90,1158 0/0:27,1:28:27.59:0,28,746 0/0:27,0:27:72.22:0,72,947 0/0:21,0:21:54.16:0,54,700 0/0:19,0:19:48.13:0,48,603 0/0:18,0:18:48.15:0,48,616 0/0:29,0:29:66.22:0,66,899 0/0:34,0:34:87.23:0,87,1062 0/1:7,8:15:99:219,0,231 0/0:25,0:26:57.16:0,57,727 0/0:58,0:59:99:0,153,1970 0/0:35,0:35:93.29:0,93,1198 0/0:30,0:31:81.24:0,81,1030 0/0:28,1:29:63.20:0,63,832 0/0:19,0:19:51.16:0,51,649 0/0:17,0:17:45.14:0,45,580 0/0:22,0:22:51.16:0,51,663 0/0:15,0:15:30.10:0,30,392 0/0:25,0:25:66.19:0,66,837 0/0:18,0:18:42.10:0,42,526 0/0:22,0:23:54.15:0,54,687 -chr1 982941 . T C 66725.31 . AC=101;AF=0.8417;AN=120;BaseQRankSum=6.926;DP=2345;Dels=0.00;FS=18.520;HRun=3;HaplotypeScore=1.4495;InbreedingCoeff=0.1870;MQ=58.87;MQ0=0;MQRankSum=0.922;QD=29.91;ReadPosRankSum=-2.729;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|20),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000478677|1/2||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,10:10:30.08:349,30,0 0/1:8,2:10:56.56:57,0,154 1/1:0,19:19:54.16:688,54,0 1/1:0,17:17:45.14:563,45,0 1/1:0,45:45:99:1653,126,0 1/1:0,43:43:99:1647,126,0 1/1:0,65:65:99:2562,193,0 1/1:0,31:31:90.29:1188,90,0 1/1:0,109:109:99:4232,322,0 1/1:0,104:104:99:3964,301,0 1/1:0,47:47:99:1722,132,0 0/1:20,29:49:99:972,0,521 1/1:0,55:55:99:2104,166,0 1/1:0,46:46:99:1485,114,0 1/1:0,55:56:99:1855,138,0 1/1:0,30:30:75.23:976,75,0 1/1:0,38:38:93.30:1225,93,0 1/1:0,53:53:99:1612,123,0 1/1:0,49:49:99:1661,126,0 1/1:0,38:38:96.31:1259,96,0 0/1:23,26:49:99:710,0,458 1/1:0,38:38:96.31:1266,96,0 1/1:0,32:32:81.26:1060,81,0 1/1:0,43:43:99:1477,114,0 0/1:18,19:37:99:504,0,467 1/1:0,45:45:99:1492,114,0 0/1:11,26:37:99:790,0,314 1/1:0,31:31:87.28:1141,87,0 0/1:33,17:50:99:423,0,820 1/1:0,43:43:99:1531,117,0 1/1:0,35:35:90.28:1166,90,0 1/1:0,30:30:75.22:954,75,0 1/1:0,37:37:99:1324,102,0 0/1:22,26:48:99:680,0,622 1/1:0,24:25:63.20:815,63,0 1/1:0,23:23:66.22:885,66,0 1/1:0,34:34:81.27:1097,81,0 0/0:65,0:65:99:0,175,2246 1/1:0,22:22:60.19:766,60,0 1/1:0,46:46:99:1596,129,0 0/1:20,14:34:99:427,0,488 0/1:13,23:36:99:583,0,392 1/1:0,35:35:90.29:1177,90,0 1/1:0,27:27:75.24:978,75,0 1/1:0,28:28:72.23:949,72,0 1/1:0,34:35:87.27:1119,87,0 1/1:0,45:45:99:1548,123,0 0/0:16,1:17:42.11:0,42,538 1/1:0,33:33:69.21:898,69,0 0/1:40,31:71:99:824,0,1077 1/1:0,42:42:99:1429,111,0 1/1:0,34:34:72.22:967,72,0 0/1:16,19:35:99:385,0,402 1/1:2,28:30:41.26:936,41,0 1/1:0,26:26:72.22:917,72,0 1/1:0,26:26:69.20:853,69,0 0/1:15,5:21:78.54:79,0,376 0/1:15,17:32:99:388,0,327 1/1:0,22:22:66.15:814,66,0 0/0:32,0:32:72.23:0,72,939 -chr1 982994 . T C 93842.13 . AC=104;AF=0.8667;AN=120;BaseQRankSum=1.394;DP=3268;Dels=0.00;FS=0.376;HRun=1;HaplotypeScore=1.8496;InbreedingCoeff=0.1346;MQ=58.74;MQ0=0;MQRankSum=1.734;QD=30.11;ReadPosRankSum=-2.989;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|2),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|1),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F1186|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000466223|2/3||||retained_intron|1,synonymous_variant|ttT/ttC|F|ENSG00000188157|AGRN|ENST00000379370|21/36|||1186/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000478677|1/2||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,23:23:66.20:828,66,0 0/1:11,11:22:99:311,0,293 1/1:0,26:26:75.23:950,75,0 1/1:0,25:25:75.22:933,75,0 1/1:0,56:56:99:2255,169,0 1/1:0,60:60:99:2385,178,0 1/1:0,95:95:99:3769,286,0 1/1:0,50:50:99:1968,150,0 1/1:0,128:128:99:5030,382,0 1/1:0,131:131:99:5181,388,0 1/1:0,59:59:99:2344,178,0 0/1:34,18:52:99:543,0,1137 1/1:0,78:78:99:2967,229,0 1/1:0,49:49:99:1678,126,0 1/1:0,66:66:99:2030,153,0 1/1:0,35:35:87.26:1148,87,0 1/1:1,56:57:99:1631,126,0 1/1:0,52:52:99:1749,132,0 1/1:0,56:56:99:1787,132,0 1/1:0,64:64:99:2072,159,0 0/1:40,25:65:99:680,0,1081 1/1:0,59:59:99:2002,150,0 1/1:0,36:36:90.29:1189,90,0 1/1:0,60:60:99:1901,144,0 0/1:21,18:39:99:511,0,525 1/1:0,59:59:99:1784,132,0 0/1:30,42:72:99:1169,0,762 1/1:0,43:43:99:1366,102,0 0/1:42,21:63:99:591,0,1120 1/1:0,56:56:99:1888,141,0 1/1:1,60:61:99:1906,141,0 1/1:0,44:44:99:1370,102,0 1/1:0,45:45:99:1470,111,0 0/1:34,34:68:99:904,0,857 1/1:0,42:42:99:1429,108,0 1/1:0,46:46:99:1410,105,0 1/1:0,46:46:99:1512,111,0 0/0:100,0:100:99:0,238,3220 1/1:0,37:37:93.29:1204,93,0 1/1:0,71:71:99:2311,181,0 0/1:27,21:48:99:617,0,804 0/1:22,26:48:99:778,0,530 1/1:0,52:52:99:1725,132,0 1/1:0,43:43:99:1303,99,0 1/1:0,33:33:90.28:1136,90,0 1/1:0,44:44:99:1539,120,0 1/1:0,74:74:99:2366,181,0 0/1:11,13:24:99:376,0,323 1/1:0,37:37:84.26:1124,84,0 1/1:2,90:92:99:2775,187,0 1/1:2,73:75:99:2420,190,0 1/1:0,44:44:99:1332,102,0 1/1:0,62:62:99:2056,156,0 1/1:0,45:45:99:1458,114,0 1/1:0,37:37:90.28:1196,90,0 1/1:0,44:44:96.31:1283,96,0 0/1:18,10:28:99:296,0,491 0/1:22,27:49:99:653,0,527 1/1:0,39:40:96.30:1251,96,0 0/0:51,0:51:99:0,120,1615 -chr1 983005 . G A 980.3 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.923;DP=3454;Dels=0.00;FS=1.269;HRun=0;HaplotypeScore=1.9623;InbreedingCoeff=-0.0084;MQ=58.65;MQ0=0;MQRankSum=1.298;QD=13.62;ReadPosRankSum=2.603;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|2),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R1190H|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000466223|2/3||||retained_intron|1,missense_variant|cGc/cAc|R/H|ENSG00000188157|AGRN|ENST00000379370|21/36|benign(0.252)|tolerated(0.19)|1190/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000478677|1/2||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:18,0:18:39.12:0,39,474 0/0:20,0:20:54.15:0,54,664 0/0:23,0:23:66.21:0,66,844 0/0:23,0:23:66.19:0,66,807 0/0:52,0:52:99:0,153,2006 0/0:49,0:49:99:0,141,1861 0/0:90,0:90:99:0,265,3441 0/0:54,0:54:99:0,153,2026 0/0:117,0:117:99:0,340,4390 0/0:127,0:127:99:0,376,4948 0/0:63,0:63:99:0,184,2386 0/0:48,0:48:99:0,141,1859 0/0:88,0:88:99:0,256,3315 0/0:46,0:46:99:0,120,1589 0/0:73,0:74:99:0,169,2224 0/0:41,0:41:90.29:0,90,1220 0/0:55,0:57:99:0,138,1778 0/0:49,0:51:99:0,120,1592 0/0:56,0:56:99:0,135,1765 0/0:69,0:70:99:0,169,2192 0/0:63,0:63:99:0,156,2047 0/0:68,0:68:99:0,163,2146 0/0:41,0:42:99:0,108,1408 0/0:60,0:60:99:0,147,1900 0/0:48,0:48:99:0,111,1459 0/0:58,0:58:99:0,123,1648 0/0:85,0:85:99:0,196,2590 0/0:46,0:46:99:0,105,1403 0/0:61,0:61:99:0,156,2036 0/0:58,0:58:99:0,141,1891 0/0:61,1:62:99:0,106,1847 0/0:49,0:49:99:0,111,1500 0/0:47,0:47:99:0,108,1443 0/1:35,37:72:99:1028,0,887 0/0:47,0:47:99:0,120,1571 0/0:49,0:49:99:0,114,1522 0/0:45,0:45:99:0,108,1455 0/0:100,0:102:99:0,232,3144 0/0:42,1:44:99:0,111,1426 0/0:74,0:74:99:0,187,2421 0/0:58,0:58:99:0,153,1987 0/0:56,0:56:99:0,144,1896 0/0:58,0:58:99:0,138,1820 0/0:45,0:45:99:0,102,1344 0/0:36,0:36:96.30:0,96,1228 0/0:47,1:48:82.58:0,83,1461 0/0:77,0:77:99:0,196,2500 0/0:30,0:30:72.22:0,72,915 0/0:44,0:44:99:0,108,1408 0/0:95,0:95:99:0,247,3109 0/0:82,0:83:99:0,208,2647 0/0:57,0:57:99:0,135,1788 0/0:78,0:78:99:0,199,2582 0/0:54,1:56:99:0,129,1643 0/0:39,0:39:93.30:0,93,1257 0/0:46,0:46:99:0,105,1384 0/0:36,0:36:90.28:0,90,1167 0/0:54,0:55:99:0,120,1593 0/0:45,0:45:99:0,108,1405 0/0:65,0:65:99:0,157,2099 -chr1 983291 . C G 40.75 . AC=4;AF=0.0333;AN=120;BaseQRankSum=-3.182;DP=508;Dels=0.00;FS=19.277;HRun=1;HaplotypeScore=0.5577;InbreedingCoeff=-0.0586;MQ=54.43;MQ0=0;MQRankSum=-1.088;QD=0.85;ReadPosRankSum=-2.005;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|22),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12.04:0,12,153 0/0:5,2:7:15.04:0,15,181 0/0:3,2:5:9.03:0,9,106 0/0:5,5:10:12.03:0,12,140 0/0:2,1:3:6.02:0,6,82 0/0:9,3:12:24.08:0,24,325 0/0:18,3:21:36.11:0,36,457 0/1:6,6:13:10.59:11,0,175 0/0:12,3:15:24.08:0,24,317 0/0:22,7:29:45.12:0,45,575 0/1:6,4:10:8.65:9,0,138 0/1:3,6:9:24.41:24,0,67 0/1:9,7:16:78.05:78,0,172 0/0:7,0:7:21.05:0,21,249 0/0:9,0:10:18.04:0,18,202 0/0:7,0:7:21.05:0,21,252 0/0:7,0:7:12.04:0,12,151 0/0:6,2:8:18.06:0,18,228 0/0:9,0:9:12.04:0,12,164 0/0:4,0:4:12.04:0,12,151 0/0:4,0:4:9.03:0,9,108 0/0:7,0:7:18.05:0,18,224 0/0:4,0:4:12.03:0,12,139 0/0:2,0:2:2.99:0,3,24 0/0:6,0:6:9.03:0,9,111 0/0:5,0:5:15.03:0,15,169 0/0:7,0:7:18.04:0,18,228 0/0:4,0:4:12.01:0,12,125 0/0:7,0:8:18.06:0,18,225 0/0:12,0:12:27.07:0,27,323 0/0:9,0:9:27.08:0,27,318 0/0:4,0:4:9.03:0,9,116 0/0:8,0:8:21.04:0,21,252 0/0:10,0:10:21.06:0,21,258 0/0:8,1:9:21.06:0,21,254 0/0:1,0:1:3.01:0,3,33 0/0:7,0:8:21.07:0,21,266 0/0:15,0:15:33.11:0,33,426 0/0:11,1:12:27.06:0,27,314 0/0:16,0:16:33.10:0,33,399 0/0:5,0:5:15.04:0,15,172 0/0:9,0:9:27.06:0,27,323 0/0:6,0:6:12.04:0,12,155 0/0:7,0:7:18.05:0,18,212 0/0:7,0:7:12.04:0,12,160 0/0:4,0:4:6.02:0,6,72 0/0:15,1:16:27.06:0,27,327 0/0:6,0:6:12.04:0,12,162 0/0:5,0:5:12.04:0,12,154 0/0:13,1:14:27.08:0,27,333 0/0:14,0:14:36.11:0,36,459 0/0:7,0:8:12.04:0,12,141 0/0:7,0:8:18.05:0,18,222 0/0:6,0:6:18.05:0,18,219 0/0:9,0:9:21.07:0,21,278 0/0:9,0:9:24.07:0,24,292 0/0:3,0:3:9.03:0,9,122 0/0:2,0:2:6.02:0,6,75 0/0:7,0:7:12.04:0,12,156 0/0:5,0:5:12.04:0,12,152 -chr1 984147 . CAAAAAAAAAAA C 4515.7 . AC=46;AF=0.460;AN=100;BaseQRankSum=7.017;DP=179;FS=0.000;HRun=22;HaplotypeScore=47.7401;InbreedingCoeff=0.1656;MQ=37.04;MQ0=0;MQRankSum=-0.993;QD=36.71;ReadPosRankSum=4.302;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|23),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000492947|1/2||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,28 0/0:1,0:2:3.01:0,3,132 1/1:1,0:2:2.91:46,3,0 ./. 0/0:1,0:1:3.01:0,3,148 0/0:1,0:2:6.02:0,6,223 1/1:0,0:1:3.01:67,3,0 ./. 0/1:3,3:7:99:210,0,247 0/0:1,0:1:3.01:0,3,115 0/0:1,0:1:0:0,0,0 0/0:1,0:1:0:0,0,0 1/1:5,1:6:2.50:83,3,0 0/0:5,0:5:12.04:0,12,498 0/1:1,3:4:31.75:240,0,32 1/1:1,1:2:2.67:83,3,0 0/0:1,1:2:0:0,0,0 1/1:4,2:6:5.59:167,6,0 0/1:4,1:7:99:129,0,739 0/0:7,0:7:21.07:0,21,793 0/0:2,0:3:6.02:0,6,294 1/1:2,2:6:11.93:243,12,0 1/1:2,3:7:14.80:343,15,0 0/1:2,2:4:99:133,0,108 0/0:3,0:3:3.01:0,3,161 0/1:3,2:7:99:193,0,523 0/1:2,1:5:99:202,0,176 0/0:1,0:2:6.02:0,6,249 0/1:4,1:5:68.83:69,0,549 1/1:3,2:6:8.71:214,9,0 0/1:3,0:6:99:118,0,325 1/1:1,3:5:11.25:259,11,0 0/1:1,1:3:74.84:75,0,237 0/0:5,0:8:21.07:0,21,832 0/1:2,1:3:60.32:60,0,143 0/1:4,4:10:99:308,0,729 0/1:3,1:4:57.20:57,0,166 0/0:5,0:5:15.05:0,15,733 ./. 1/1:1,1:2:2.96:76,3,0 ./. 0/0:3,0:3:9.03:0,9,450 ./. ./. 0/0:1,0:1:0:0,0,0 1/1:0,1:2:6.02:130,6,0 0/0:1,0:3:6.02:0,6,283 1/1:1,0:1:3.01:43,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,160 ./. 1/1:0,2:2:6.02:168,6,0 1/1:0,2:2:6.02:168,6,0 1/1:0,0:1:3.01:46,3,0 1/1:0,6:6:18.06:501,18,0 1/1:0,1:1:3.01:84,3,0 ./. 0/0:0,0:1:3.01:0,3,129 0/0:1,0:1:3.01:0,3,135 -chr1 984170 . GCA G 2088.76 . AC=73;AF=0.6404;AN=114;BaseQRankSum=8.221;DP=284;FS=0.000;HRun=0;HaplotypeScore=52.8663;InbreedingCoeff=0.0057;MQ=43.30;MQ0=0;MQRankSum=-4.981;QD=8.29;ReadPosRankSum=6.043;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|23),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000492947|1/2||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:2,0:2:3:28,3,0 0/0:2,0:2:3.01:0,3,59 0/1:2,0:2:22.52:23,0,31 0/1:3,0:3:11.03:11,0,53 1/1:2,0:2:3:27,3,0 0/0:1,0:1:3.01:0,3,59 1/1:2,0:2:5.19:20,5,0 0/0:4,0:4:9.03:0,9,175 0/1:9,0:9:19.90:20,0,145 0/1:8,0:8:3.06:3,0,274 ./. 0/1:3,0:3:11.97:12,0,109 1/1:1,0:1:3.01:36,3,0 0/1:5,0:5:37.03:37,0,42 1/1:12,0:12:34.16:206,34,0 1/1:3,0:3:8.83:71,9,0 0/0:2,0:2:3.01:0,3,59 1/1:7,0:7:19.85:109,20,0 0/1:9,0:10:94.09:94,0,127 0/1:10,0:10:11.07:11,0,219 0/1:5,0:5:4.04:4,0,128 1/1:7,0:7:20.38:131,20,0 1/1:7,1:8:23.92:225,24,0 1/1:6,1:7:17.13:108,17,0 0/1:6,0:7:7.38:7,0,218 1/1:9,1:10:12.09:67,12,0 1/1:6,0:6:17.71:150,18,0 0/1:3,0:3:3.58:4,0,53 0/1:8,1:9:6.47:6,0,204 1/1:3,0:3:8.69:48,9,0 0/1:9,0:11:40.55:41,0,101 1/1:5,0:5:10.91:50,11,0 0/1:6,0:6:46.45:59,0,46 0/1:10,1:11:56.73:57,0,131 0/1:7,0:7:51.64:52,0,65 0/1:12,0:12:58.49:58,0,143 0/1:7,0:7:49.29:49,0,103 0/0:9,0:9:10.12:0,10,159 1/1:1,0:1:2.74:12,3,0 1/1:2,0:2:5.97:51,6,0 0/0:1,0:1:3.01:0,3,59 0/0:5,0:5:12.04:0,12,190 ./. 1/1:1,0:1:2.74:12,3,0 1/1:2,0:2:5.49:24,5,0 0/1:4,0:4:40.08:40,0,47 0/1:6,0:6:20.71:21,0,50 ./. 0/1:2,0:2:19.95:20,0,53 0/0:7,0:7:18.06:0,18,351 0/1:6,0:6:4.99:5,0,182 1/1:3,0:3:5.49:24,5,0 0/1:3,0:3:9.97:10,0,88 1/1:4,0:4:11.54:86,12,0 1/1:1,0:1:2.96:19,3,0 1/1:7,0:7:19.72:106,20,0 1/1:1,0:1:2.50:9,2,0 0/0:1,0:1:3.01:0,3,59 1/1:4,0:4:8.56:71,9,0 1/1:1,0:2:0.47:1,0,0 -chr1 984171 . CAG C 6456.64 . AC=72;AF=0.6207;AN=116;BaseQRankSum=5.599;DP=294;FS=0.921;HRun=0;HaplotypeScore=45.6091;InbreedingCoeff=-0.0184;MQ=43.76;MQ0=0;MQRankSum=-4.138;QD=26.03;ReadPosRankSum=5.090;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|23),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000492947|1/2||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:1,1:2:3.01:49,3,0 0/0:2,0:2:3.01:0,3,61 0/1:1,1:2:41.44:41,0,53 0/1:2,1:3:42.94:43,0,55 1/1:1,1:2:3.01:49,3,0 0/0:1,0:1:3.01:0,3,61 1/1:0,2:2:6.02:98,6,0 0/0:4,0:4:9.03:0,9,183 0/1:5,4:9:99:133,0,163 0/1:7,1:8:27.85:28,0,309 ./. 0/1:2,1:3:39.93:40,0,113 1/1:0,1:1:3.01:48,3,0 0/1:3,2:5:51.30:89,0,51 1/1:2,11:13:39.13:632,39,0 1/1:1,2:3:9.03:133,9,0 0/1:2,1:3:38.57:39,0,55 1/1:2,5:8:24.08:387,24,0 0/1:6,4:10:99:165,0,182 0/0:10,0:10:9.84:0,10,241 0/1:4,1:5:36.92:37,0,157 1/1:1,5:7:21.07:330,21,0 1/1:1,7:8:24.08:382,24,0 1/1:2,5:7:20.35:257,20,0 0/1:5,2:7:79.87:80,0,226 1/1:6,4:10:6.24:188,6,0 1/1:0,6:6:18.06:291,18,0 0/0:2,0:3:4.83:0,5,66 0/1:7,2:9:79.86:80,0,218 1/1:1,3:3:9.03:147,9,0 0/1:7,4:11:99:178,0,104 1/1:0,5:5:12.04:196,12,0 0/1:3,3:6:68.56:132,0,69 0/1:9,3:12:99:116,0,212 0/1:3,4:7:85.89:112,0,86 0/1:6,6:12:99:263,0,162 0/1:6,3:9:99:106,0,185 0/0:10,0:10:17.01:0,17,261 1/1:1,1:2:6.02:94,6,0 1/1:0,2:2:6.02:86,6,0 0/0:1,0:1:3.01:0,3,61 0/0:5,0:5:12.04:0,12,216 ./. 1/1:0,1:1:3.01:49,3,0 1/1:0,2:2:6.02:98,6,0 0/1:1,3:4:48.96:135,0,49 0/1:4,2:6:52.01:88,0,52 1/1:1,0:1:3.01:45,3,0 0/1:1,1:2:42.92:43,0,55 0/0:7,0:7:21.07:0,21,405 0/1:4,2:6:34.02:34,0,184 1/1:0,3:3:6.02:98,6,0 0/1:2,1:3:39.91:40,0,111 1/1:0,4:4:12.04:195,12,0 1/1:0,1:1:3.01:49,3,0 1/1:0,7:7:21.07:341,21,0 1/1:0,1:1:3.01:49,3,0 0/0:1,0:1:3.01:0,3,61 1/1:1,3:4:9.03:146,9,0 0/0:2,0:2:2.94:0,3,18 -chr1 984202 . A G 219.31 . AC=2;AF=0.0169;AN=118;BaseQRankSum=-2.549;DP=472;Dels=0.00;FS=8.756;HRun=0;HaplotypeScore=1.0667;InbreedingCoeff=-0.0548;MQ=49.93;MQ0=0;MQRankSum=1.399;QD=7.83;ReadPosRankSum=0.241;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|23),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|1/2||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.01:0,6,62 0/0:4,0:4:12.04:0,12,146 0/0:3,0:3:6.02:0,6,80 0/0:1,0:1:3.01:0,3,35 0/0:4,0:4:12.04:0,12,155 0/0:4,0:4:9.02:0,9,106 0/0:6,0:6:18.06:0,18,236 0/0:13,0:13:36.12:0,36,480 ./. 0/0:7,0:7:21.07:0,21,273 0/0:4,0:4:12.03:0,12,148 0/0:12,0:12:27.08:0,27,331 0/0:18,0:18:54.16:0,54,655 0/0:4,0:4:12.04:0,12,148 0/0:8,0:8:21.07:0,21,269 0/0:16,0:16:45.13:0,45,551 0/0:15,0:15:33.06:0,33,384 0/0:11,0:11:21.06:0,21,256 0/0:9,0:9:21.05:0,21,254 0/0:9,0:9:21.05:0,21,229 0/0:16,0:16:36.09:0,36,408 0/0:14,0:14:33.10:0,33,419 0/0:10,0:10:30.09:0,30,363 0/0:12,0:12:24.07:0,24,276 0/1:6,8:14:99:169,0,123 0/0:6,0:6:12.04:0,12,163 0/0:14,0:14:27.06:0,27,326 0/0:10,0:10:27.08:0,27,335 0/0:14,0:14:24.06:0,24,286 0/0:7,0:7:18.05:0,18,221 0/0:12,0:12:33.06:0,33,381 0/1:8,6:14:99:115,0,139 0/0:8,0:8:15.05:0,15,185 0/0:14,0:14:30.08:0,30,355 0/0:20,0:20:45.14:0,45,571 0/0:17,0:18:33.08:0,33,406 0/0:2,0:2:6.02:0,6,77 0/0:7,0:7:12.04:0,12,160 0/0:7,0:7:21.06:0,21,262 0/0:7,0:7:15.03:0,15,178 0/0:2,0:2:6.02:0,6,75 0/0:2,0:2:6.01:0,6,63 0/0:4,0:4:12.04:0,12,153 0/0:5,0:5:15.04:0,15,178 0/0:11,1:12:27.09:0,27,347 0/0:2,0:2:6.02:0,6,72 0/0:5,0:5:12.03:0,12,141 0/0:11,0:11:33.10:0,33,410 0/0:11,0:11:30.07:0,30,358 0/0:5,0:5:12.04:0,12,153 0/0:6,0:6:18.06:0,18,229 0/0:7,0:7:18.05:0,18,198 0/0:3,0:3:9.03:0,9,111 0/0:11,0:11:30.07:0,30,347 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,38 0/0:4,0:4:9.01:0,9,91 0/0:2,0:2:2.99:0,3,23 -chr1 984257 . C T 182.2 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.337;DP=770;Dels=0.00;FS=9.908;HRun=0;HaplotypeScore=0.4996;InbreedingCoeff=-0.0252;MQ=54.84;MQ0=0;MQRankSum=1.233;QD=12.15;ReadPosRankSum=-0.369;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1372|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|gcC/gcT|A|ENSG00000188157|AGRN|ENST00000379370|24/36|||1372/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|1/2||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:4,0:4:9.03:0,9,108 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,40 0/0:4,0:4:12.04:0,12,146 0/0:3,0:3:9.03:0,9,119 0/0:2,0:2:6.02:0,6,81 0/0:4,0:4:12.04:0,12,162 0/0:4,0:4:12.04:0,12,157 0/0:6,0:6:18.06:0,18,245 0/0:7,0:7:21.07:0,21,284 0/0:4,0:4:12.04:0,12,156 0/0:3,0:3:9.03:0,9,118 0/0:3,0:3:9.02:0,9,100 0/0:23,0:23:57.18:0,57,749 0/0:27,0:27:69.22:0,69,904 0/0:5,0:5:12.03:0,12,148 0/0:12,0:12:33.10:0,33,419 0/0:26,0:26:63.20:0,63,817 0/0:25,0:25:63.19:0,63,782 0/0:13,0:13:27.08:0,27,340 0/1:8,7:15:99:230,0,213 0/0:12,0:12:30.09:0,30,374 0/0:18,0:18:45.13:0,45,548 0/0:23,0:23:54.17:0,54,683 0/0:18,0:18:48.15:0,48,616 0/0:16,0:16:45.14:0,45,544 0/0:23,0:23:54.13:0,54,665 0/0:21,0:21:48.16:0,48,651 0/0:24,0:24:57.17:0,57,736 0/0:20,0:20:51.15:0,51,662 0/0:20,0:20:45.14:0,45,588 0/0:14,0:14:36.11:0,36,471 0/0:16,0:16:30.10:0,30,389 0/0:16,0:16:45.14:0,45,554 0/0:13,0:13:33.10:0,33,427 0/0:22,0:22:51.14:0,51,632 0/0:33,0:33:78.22:0,78,973 0/0:24,0:24:60.18:0,60,762 0/0:7,0:7:18.06:0,18,230 0/0:12,0:12:30.08:0,30,373 0/0:11,0:11:30.09:0,30,373 0/0:12,0:12:30.09:0,30,372 0/0:8,0:8:24.08:0,24,307 0/0:6,0:6:18.05:0,18,212 0/0:9,0:9:15.05:0,15,193 0/0:13,0:13:36.11:0,36,448 0/0:25,0:25:48.15:0,48,632 0/0:7,0:7:15.05:0,15,207 0/0:11,0:11:27.06:0,27,317 0/0:19,0:19:42.11:0,42,518 0/0:15,0:15:39.12:0,39,482 0/0:7,0:7:8.98:0,9,75 0/0:10,0:10:24.08:0,24,303 0/0:13,0:13:33.11:0,33,440 0/0:9,0:9:12.04:0,12,143 0/0:18,0:18:42.13:0,42,523 0/0:5,0:5:15.05:0,15,205 0/0:8,0:8:18.04:0,18,228 0/0:11,0:11:24.08:0,24,315 0/0:9,0:9:24.07:0,24,297 -chr1 984272 . C T 98.86 . AC=2;AF=0.0169;AN=118;BaseQRankSum=-0.517;DP=781;Dels=0.00;FS=1.477;HRun=2;HaplotypeScore=0.5249;InbreedingCoeff=-0.0341;MQ=54.72;MQ0=0;MQRankSum=0.805;QD=3.95;ReadPosRankSum=0.353;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1377|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|ttC/ttT|F|ENSG00000188157|AGRN|ENST00000379370|24/36|||1377/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|1/2||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3.01:0,3,39 0/0:2,0:2:6.02:0,6,75 ./. 0/0:4,0:4:12.04:0,12,148 0/0:4,0:4:12.03:0,12,150 0/0:2,0:2:6.02:0,6,80 0/0:4,0:4:12.04:0,12,156 0/0:4,0:4:12.04:0,12,158 0/0:6,0:6:18.06:0,18,238 0/0:7,0:7:21.07:0,21,281 0/0:4,0:4:12.04:0,12,153 0/0:2,0:2:6.02:0,6,80 0/0:1,0:1:3.01:0,3,41 0/0:27,1:28:23.98:0,24,793 0/0:26,0:26:69.22:0,69,899 0/0:5,0:5:9.03:0,9,120 0/0:14,0:14:36.11:0,36,456 0/0:26,0:26:63.20:0,63,814 0/0:27,0:27:69.20:0,69,853 0/0:11,0:11:30.07:0,30,347 0/0:18,0:18:51.16:0,51,664 0/0:14,0:14:30.09:0,30,374 0/0:18,0:18:48.14:0,48,572 0/0:21,0:21:51.16:0,51,646 0/0:19,0:19:54.17:0,54,709 0/0:18,0:18:51.14:0,51,612 0/0:24,0:24:57.18:0,57,747 0/0:23,0:23:54.18:0,54,734 0/0:22,0:22:60.19:0,60,776 0/0:20,0:20:48.15:0,48,621 0/0:19,0:19:48.13:0,48,597 0/0:16,0:16:45.14:0,45,577 0/0:15,0:15:33.11:0,33,435 0/0:17,0:17:45.14:0,45,563 0/0:13,0:13:36.11:0,36,459 0/0:21,0:21:51.15:0,51,652 0/0:29,0:29:69.21:0,69,894 0/0:28,0:28:66.20:0,66,841 0/0:7,0:7:15.04:0,15,184 0/0:12,1:13:33.10:0,33,426 0/0:12,0:12:36.11:0,36,445 0/0:12,0:13:30.09:0,30,369 0/0:10,0:10:27.09:0,27,358 0/0:7,0:7:21.06:0,21,258 0/0:9,0:9:18.06:0,18,229 0/0:13,0:13:36.10:0,36,453 0/0:24,0:24:45.14:0,45,573 0/0:7,0:7:18.06:0,18,243 0/1:9,1:10:15.38:15,0,183 0/1:10,5:15:99:144,0,276 0/0:12,0:12:30.09:0,30,369 0/0:5,0:5:9.01:0,9,100 0/0:11,0:11:27.09:0,27,349 0/0:15,0:15:39.12:0,39,504 0/0:10,0:10:21.06:0,21,240 0/0:17,0:17:42.12:0,42,505 0/0:7,0:7:18.06:0,18,243 0/0:8,0:8:18.06:0,18,241 0/0:10,0:10:27.08:0,27,351 0/0:12,0:12:33.11:0,33,434 -chr1 984302 . T C 14311.5 . AC=73;AF=0.6186;AN=118;BaseQRankSum=1.074;DP=888;Dels=0.00;FS=38.864;HRun=1;HaplotypeScore=0.6522;InbreedingCoeff=-0.0933;MQ=54.70;MQ0=0;MQRankSum=1.221;QD=18.54;ReadPosRankSum=0.025;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1387|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|acT/acC|T|ENSG00000188157|AGRN|ENST00000379370|24/36|||1387/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|1/2||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3.01:30,3,0 0/0:2,0:2:6.02:0,6,69 1/1:0,1:1:3.01:39,3,0 0/1:2,4:6:47.23:92,0,47 0/0:4,1:5:12.04:0,12,155 1/1:0,1:1:3.01:40,3,0 1/1:0,4:4:12.04:156,12,0 ./. 0/1:8,4:12:99:107,0,240 0/1:12,5:17:99:147,0,365 1/1:0,1:1:3.01:41,3,0 0/1:2,4:6:26.54:93,0,27 1/1:0,9:9:24.07:301,24,0 0/1:10,18:28:99:549,0,183 1/1:0,29:29:69.20:880,69,0 1/1:0,6:6:18.05:224,18,0 0/1:7,5:12:92.47:92,0,197 1/1:0,28:28:66.20:843,66,0 0/1:13,12:25:99:352,0,309 0/0:13,0:13:30.08:0,30,363 0/1:12,9:21:99:221,0,316 1/1:0,20:20:39.11:496,39,0 1/1:0,17:17:45.13:521,45,0 0/1:6,12:18:99:367,0,138 0/1:15,10:25:99:243,0,405 0/1:7,11:18:99:320,0,191 0/1:11,9:20:99:207,0,316 0/1:15,8:23:99:216,0,430 0/1:14,8:22:99:138,0,396 1/1:0,21:21:54.15:669,54,0 0/1:11,7:18:99:213,0,300 1/1:0,19:19:51.15:638,51,0 0/1:11,9:20:99:218,0,252 0/0:23,0:23:48.14:0,48,580 0/1:9,9:18:99:219,0,209 0/1:8,11:19:99:213,0,261 0/1:13,17:30:99:431,0,390 0/0:31,0:31:75.20:0,75,942 1/1:0,14:14:24.08:324,24,0 1/1:0,18:18:48.14:597,48,0 0/1:11,7:18:99:172,0,309 0/0:15,0:15:33.09:0,33,388 0/0:13,0:13:33.10:0,33,423 1/1:0,12:12:30.08:371,30,0 0/1:4,5:9:84.20:129,0,84 0/1:5,9:14:71.78:257,0,72 0/1:19,6:25:65.32:65,0,382 1/1:0,7:7:18.06:236,18,0 0/1:4,6:10:99:141,0,124 0/1:9,7:16:99:187,0,262 0/1:8,7:15:99:156,0,147 1/1:0,4:4:12.04:148,12,0 1/1:0,13:13:36.11:465,36,0 1/1:0,18:18:45.14:566,45,0 1/1:0,12:12:27.07:317,27,0 1/1:0,19:19:48.14:581,48,0 0/1:5,4:9:95.71:96,0,134 0/1:9,2:11:20.70:21,0,236 0/1:7,6:13:99:166,0,168 0/0:14,0:14:36.09:0,36,464 -chr1 984456 . C T 37.75 . AC=2;AF=0.0175;AN=114;BaseQRankSum=0.621;DP=348;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=0.7641;InbreedingCoeff=-0.0607;MQ=53.36;MQ0=0;MQRankSum=0.580;QD=2.90;ReadPosRankSum=-0.096;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,30 0/0:1,0:1:3.01:0,3,41 ./. 0/0:2,0:2:6.02:0,6,82 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.02:0,6,70 0/0:1,0:1:3.01:0,3,41 0/0:10,0:10:27.09:0,27,367 0/0:8,0:8:24.08:0,24,315 0/0:1,0:1:3.01:0,3,40 0/0:3,0:3:9.03:0,9,118 0/0:4,0:4:12.04:0,12,163 0/0:3,0:3:9.03:0,9,115 0/0:6,0:7:15.05:0,15,193 0/0:6,0:6:15.05:0,15,208 0/0:3,0:3:6.02:0,6,83 0/0:9,0:9:18.06:0,18,250 0/0:6,0:6:12.04:0,12,152 0/0:5,0:6:15.04:0,15,189 0/0:7,0:7:21.05:0,21,247 0/0:7,0:7:21.07:0,21,274 ./. 0/0:6,0:6:15.05:0,15,190 0/0:7,0:8:18.04:0,18,224 0/0:2,0:3:6.02:0,6,77 0/0:5,0:5:12.04:0,12,158 0/0:4,0:4:9.03:0,9,120 0/0:5,0:5:9.03:0,9,115 0/0:4,0:4:12.04:0,12,159 0/0:8,0:8:18.05:0,18,218 0/0:3,0:3:9.03:0,9,121 0/0:5,0:6:12.04:0,12,160 0/0:10,0:10:30.09:0,30,357 0/0:6,0:6:12.04:0,12,158 0/0:6,0:6:12.03:0,12,145 0/0:12,0:12:33.10:0,33,423 0/0:8,0:8:24.07:0,24,292 0/0:4,0:4:9.03:0,9,117 0/0:7,0:9:21.06:0,21,250 0/0:10,0:11:24.04:0,24,265 0/0:8,0:8:18.04:0,18,216 0/0:8,0:9:21.06:0,21,253 0/0:6,0:6:12.04:0,12,171 0/0:8,0:8:21.06:0,21,260 0/0:3,0:3:9.03:0,9,122 0/0:10,0:11:27.08:0,27,348 0/1:4,2:7:32.56:33,0,34 0/0:2,0:2:6.02:0,6,69 0/1:4,2:6:67.77:69,0,68 0/0:18,0:18:33.10:0,33,413 0/0:6,0:6:12.03:0,12,137 0/0:4,0:4:12.01:0,12,122 0/0:10,0:11:24.06:0,24,308 0/0:11,0:11:27.08:0,27,339 0/0:3,0:3:9.03:0,9,123 0/0:6,0:6:15.05:0,15,207 0/0:3,0:3:6.02:0,6,80 0/0:7,0:7:18.05:0,18,214 0/0:5,0:5:12.04:0,12,149 -chr1 984476 . T G 35.43 . AC=6;AF=0.060;AN=100;BaseQRankSum=-3.204;DP=227;Dels=0.01;FS=3.373;HRun=3;HaplotypeScore=0.9086;InbreedingCoeff=-0.1488;MQ=48.96;MQ0=0;MQRankSum=-3.544;QD=1.07;ReadPosRankSum=1.813;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:2,0:2:6.02:0,6,76 ./. 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:9.03:0,9,123 0/0:4,0:4:9.02:0,9,101 0/0:1,0:1:2.98:0,3,22 0/0:3,0:3:9.02:0,9,107 0/0:2,0:2:6.02:0,6,78 ./. 0/1:2,2:4:15.67:16,0,69 0/0:3,0:3:9.03:0,9,118 0/0:1,1:2:3.01:0,3,35 0/0:7,0:7:18.06:0,18,240 0/1:1,1:2:19.68:27,0,20 0/0:3,1:4:9.03:0,9,116 0/0:4,0:4:12.04:0,12,162 0/0:4,1:5:12.04:0,12,161 0/0:2,0:2:3.01:0,3,33 0/0:2,0:2:3.01:0,3,39 0/0:4,0:4:12.03:0,12,136 0/0:2,1:3:6.02:0,6,73 0/0:3,0:3:9.03:0,9,122 0/0:2,0:2:6.02:0,6,75 0/1:3,1:4:13.67:14,0,72 ./. 0/0:5,2:7:15.03:0,15,163 0/0:2,0:2:6.02:0,6,81 0/0:1,1:2:3.01:0,3,40 0/1:6,2:8:9.61:10,0,168 0/0:2,0:2:3.01:0,3,41 0/0:1,2:3:3.01:0,3,33 0/0:5,1:6:15.03:0,15,176 0/0:5,0:6:15.04:0,15,176 ./. 0/0:6,1:7:12.04:0,12,158 0/1:6,3:9:51.03:51,0,52 0/0:4,0:4:12.04:0,12,154 0/0:1,3:4:3.01:0,3,33 0/0:2,1:4:6.02:0,6,80 0/0:5,1:6:9.03:0,9,116 0/0:2,2:4:6.02:0,6,74 0/0:6,1:7:18.05:0,18,218 0/0:2,4:6:3.01:0,3,42 0/0:3,1:4:6.02:0,6,76 0/0:2,2:4:3.01:0,3,39 0/0:15,2:18:33.10:0,33,416 0/1:2,2:5:16.67:17,0,59 0/0:4,1:5:12:0,12,111 0/0:8,1:9:15.05:0,15,200 0/0:4,1:5:9.02:0,9,107 ./. 0/0:4,0:4:9.02:0,9,107 ./. 0/0:6,0:6:15.05:0,15,184 0/0:2,1:4:6.02:0,6,73 -chr1 984480 . C G 43.98 . AC=7;AF=0.071;AN=98;BaseQRankSum=-3.119;DP=215;Dels=0.00;FS=2.297;HRun=4;HaplotypeScore=2.0881;InbreedingCoeff=-0.1728;MQ=47.60;MQ0=0;MQRankSum=-4.127;QD=1.47;ReadPosRankSum=3.119;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,80 ./. 0/0:1,0:1:3:0,3,27 0/0:2,0:3:6.02:0,6,81 0/0:3,0:3:6:0,6,65 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,80 0/0:2,0:2:6.02:0,6,82 ./. 0/1:1,2:3:27.42:27,0,35 0/0:3,0:3:6.02:0,6,80 ./. 0/0:7,0:7:15.05:0,15,205 0/1:2,1:3:27.42:27,0,27 0/0:3,1:4:9.02:0,9,107 0/0:3,0:3:9.02:0,9,107 0/0:4,1:5:12.04:0,12,158 0/1:1,1:2:22.63:23,0,27 0/0:2,0:2:3.01:0,3,37 0/0:3,0:3:6.02:0,6,70 0/0:2,1:3:6.02:0,6,74 0/0:3,0:3:9.03:0,9,120 0/0:2,0:2:6.02:0,6,67 0/1:3,1:4:21.40:21,0,97 ./. 0/0:4,2:6:9.03:0,9,110 0/0:2,0:2:6.02:0,6,82 0/0:1,1:2:3.01:0,3,35 0/0:8,0:8:18.05:0,18,216 0/0:2,0:2:3.01:0,3,40 0/1:2,1:3:16.68:17,0,27 0/0:4,1:5:9.03:0,9,117 0/0:6,0:6:15.04:0,15,185 ./. 0/0:3,2:5:9.03:0,9,122 0/1:6,4:10:17.60:18,0,88 0/0:5,0:5:9.03:0,9,119 0/0:2,2:4:3.01:0,3,33 0/0:3,1:5:6.02:0,6,76 0/0:3,2:5:6.02:0,6,83 0/0:2,1:3:3.01:0,3,41 0/0:7,0:7:12.04:0,12,146 0/0:4,2:6:3.01:0,3,42 0/0:5,0:5:9.03:0,9,113 0/0:4,0:4:3.01:0,3,39 0/0:15,1:16:33.10:0,33,406 0/1:4,1:5:20.61:21,0,52 0/0:3,0:5:9.03:0,9,109 0/0:8,1:9:15.05:0,15,193 0/0:4,2:6:9.03:0,9,108 ./. 0/0:3,0:3:6.02:0,6,83 ./. 0/0:3,2:5:9.02:0,9,108 0/0:3,2:5:6.02:0,6,79 -chr1 984485 . A G 61.07 . AC=8;AF=0.083;AN=96;BaseQRankSum=-3.712;DP=196;Dels=0.02;FS=2.293;HRun=4;HaplotypeScore=2.7170;InbreedingCoeff=-0.0981;MQ=45.76;MQ0=0;MQRankSum=-5.008;QD=2.35;ReadPosRankSum=3.158;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,80 ./. 0/0:1,0:1:3.01:0,3,37 0/0:3,0:3:6.02:0,6,81 0/0:2,0:2:3.01:0,3,35 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,81 ./. 0/1:1,2:3:27.42:27,0,34 0/0:2,1:3:6.02:0,6,76 ./. 0/0:7,1:9:15.05:0,15,198 0/1:1,2:3:22.63:27,0,23 0/1:2,1:3:24.41:24,0,68 0/0:3,0:3:9.03:0,9,122 0/0:2,1:3:6.02:0,6,76 0/0:1,1:2:3.01:0,3,33 0/0:2,0:2:6.02:0,6,77 0/0:3,0:3:9.02:0,9,99 0/0:2,0:3:3.01:0,3,41 0/0:3,0:3:9.03:0,9,116 0/0:1,0:1:3.01:0,3,38 0/1:2,1:3:20.66:21,0,33 1/1:0,1:1:3.01:33,3,0 0/0:3,2:5:9.03:0,9,113 0/0:2,0:2:6.02:0,6,80 ./. 0/0:5,0:6:15.01:0,15,164 0/0:1,0:1:3.01:0,3,33 0/1:1,1:3:27.42:27,0,27 0/0:5,1:6:12.04:0,12,155 0/0:5,1:6:15.05:0,15,190 0/0:1,0:1:3.01:0,3,31 0/0:4,1:5:6.02:0,6,79 0/1:5,5:10:9.70:10,0,99 0/0:4,1:5:12.04:0,12,148 0/0:1,3:4:3.01:0,3,33 ./. 0/0:3,2:5:6.02:0,6,83 0/0:2,1:4:3.01:0,3,41 0/0:1,2:3:3.01:0,3,30 0/0:2,2:6:3.01:0,3,42 0/0:3,0:5:9.02:0,9,107 ./. 0/0:7,3:12:18.05:0,18,210 0/0:4,1:5:6.02:0,6,65 0/0:2,3:5:6.02:0,6,67 0/0:5,3:8:12.04:0,12,151 0/0:2,2:5:6.01:0,6,65 ./. 0/0:3,0:3:6.01:0,6,67 ./. 0/0:4,1:5:9.03:0,9,114 0/0:3,1:5:6.02:0,6,75 -chr1 984489 . G T 64.93 . AC=2;AF=0.021;AN=96;BaseQRankSum=1.248;DP=184;Dels=0.00;FS=2.430;HRun=0;HaplotypeScore=2.0202;InbreedingCoeff=0.0358;MQ=44.34;MQ0=0;MQRankSum=0.975;QD=21.64;ReadPosRankSum=-0.342;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,82 ./. 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:6.02:0,6,82 0/0:2,0:2:6.01:0,6,65 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,82 ./. 0/0:2,0:2:3.01:0,3,33 ./. ./. 0/0:9,0:9:15.05:0,15,193 0/0:3,0:3:6.01:0,6,68 0/0:3,0:3:6.02:0,6,79 1/1:0,3:3:9.03:119,9,0 ./. 0/0:2,0:2:6.01:0,6,60 0/0:2,0:2:6.02:0,6,76 0/0:3,0:3:9.02:0,9,97 0/0:3,0:3:6.01:0,6,64 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,32 0/0:3,0:3:9.01:0,9,93 0/0:1,0:1:3.01:0,3,33 0/0:7,0:7:12.04:0,12,155 0/0:1,0:1:3.01:0,3,35 0/0:2,0:2:3.01:0,3,33 0/0:7,0:7:18.05:0,18,205 0/0:2,0:2:3.01:0,3,30 0/0:3,0:3:6:0,6,58 0/0:6,0:6:12.02:0,12,140 0/0:5,0:5:12.04:0,12,159 0/0:2,0:2:6.02:0,6,67 0/0:4,0:5:6.02:0,6,78 0/0:10,0:10:15.02:0,15,151 0/0:3,0:3:6.02:0,6,73 0/0:4,0:4:3.01:0,3,33 ./. 0/0:5,0:5:6.02:0,6,80 0/0:5,0:5:6.01:0,6,66 0/0:3,0:3:6.02:0,6,75 0/0:6,0:6:3.01:0,3,41 0/0:4,0:4:3.01:0,3,40 0/0:4,0:4:3.01:0,3,38 0/0:11,0:11:18.05:0,18,215 0/0:5,0:5:12:0,12,109 0/0:4,0:4:9.03:0,9,102 0/0:7,0:7:12.04:0,12,142 0/0:5,0:5:6.02:0,6,73 ./. 0/0:2,0:2:6.02:0,6,72 ./. 0/0:4,0:4:9.03:0,9,108 0/0:4,0:4:3.01:0,3,34 -chr1 984489 . GAC G 147.88 . AC=19;AF=0.1863;AN=102;BaseQRankSum=5.670;DP=170;FS=16.798;HRun=0;HaplotypeScore=44.7087;InbreedingCoeff=-0.0321;MQ=43.36;MQ0=0;MQRankSum=-5.590;QD=2.39;ReadPosRankSum=-1.803;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,73 0/0:1,0:1:3.01:0,3,58 ./. 0/0:1,0:1:3.01:0,3,56 0/0:3,0:3:6.49:0,6,117 0/0:1,0:1:3.01:0,3,57 0/0:1,0:1:3.01:0,3,72 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.02:0,6,130 ./. 1/1:1,1:2:5.91:48,6,0 0/0:1,0:1:2.74:0,3,12 0/0:1,1:2:2.30:0,2,8 0/1:7,0:8:18.43:18,0,225 0/1:3,0:3:21.51:22,0,51 0/0:3,0:3:7.27:0,7,115 0/0:2,0:2:6.02:0,6,109 1/1:1,0:1:2.37:8,2,0 0/1:2,0:2:15.68:16,0,51 0/0:2,0:2:6.02:0,6,116 0/0:2,0:2:6.02:0,6,116 0/0:3,0:3:3.01:0,3,57 ./. 0/0:1,0:1:3.01:0,3,58 0/0:2,1:3:4.75:0,5,110 1/1:0,1:1:3.01:49,3,0 0/0:7,0:7:12.51:0,13,219 ./. 0/0:2,0:2:3.01:0,3,40 0/1:6,0:6:9.30:9,0,200 0/1:2,0:2:7.69:8,0,51 0/0:3,0:3:5.98:0,6,77 0/0:6,0:6:12.04:0,12,214 0/0:5,0:5:12.04:0,12,231 0/0:2,0:2:6.02:0,6,85 0/0:5,0:5:8.86:0,9,155 0/1:9,1:10:2.86:3,0,297 0/0:2,0:2:3.01:0,3,58 0/1:3,0:3:0:0,0,0 0/1:2,1:3:0:0,0,0 0/0:4,1:5:6.02:0,6,113 0/1:3,1:5:40.92:41,0,52 0/1:3,0:3:18.80:19,0,103 0/0:5,1:6:2.54:0,3,55 0/1:4,0:4:17.92:18,0,61 0/0:4,0:4:6.02:0,6,125 0/0:8,0:9:17.34:0,17,347 0/1:4,1:5:9.71:10,0,66 0/0:3,1:4:9.03:0,9,130 0/0:6,0:6:7.92:0,8,132 0/0:5,0:5:6:0,6,113 ./. 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:2.04:0,2,6 0/1:4,0:4:33.68:34,0,128 0/0:4,0:4:6.02:0,6,83 -chr1 984494 . GC G 1466.1 . AC=57;AF=0.663;AN=86;BaseQRankSum=2.571;DP=152;FS=2.990;HRun=1;HaplotypeScore=47.8858;InbreedingCoeff=0.1367;MQ=40.49;MQ0=0;MQRankSum=-2.751;QD=11.64;ReadPosRankSum=0.066;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. 1/1:1,0:1:2.92:17,3,0 0/0:3,0:3:6:0,6,88 ./. ./. ./. ./. ./. 1/1:2,0:2:5.77:34,6,0 0/0:1,0:1:2.04:0,2,6 1/1:4,0:4:3.98:63,4,0 1/1:6,0:6:8.02:131,8,0 1/1:2,1:3:8.70:91,9,0 1/1:1,1:2:5.75:54,6,0 0/0:2,0:2:6.02:0,6,80 1/1:2,0:2:5.38:41,5,0 1/1:1,1:2:5.93:59,6,0 0/1:1,1:2:35.96:36,0,37 0/0:2,0:2:6.02:0,6,88 ./. ./. 0/0:1,0:1:3:0,3,28 0/1:2,0:2:13.47:13,0,38 1/1:1,0:1:1.25:3,1,0 0/1:6,0:6:48.08:48,0,76 ./. 1/1:2,0:2:2.92:17,3,0 0/1:6,0:6:26.45:26,0,56 1/1:2,0:2:6.01:63,6,0 1/1:3,1:4:8.76:80,9,0 0/1:4,2:6:71.92:72,0,75 0/0:2,0:3:6.02:0,6,88 1/1:0,2:2:6.02:83,6,0 1/1:4,0:4:6.01:70,6,0 0/1:7,4:11:99:114,0,109 0/0:2,0:2:3.01:0,3,44 1/1:3,0:3:2.96:19,3,0 1/1:3,0:3:3:26,3,0 1/1:4,1:5:2.38:53,2,0 0/1:4,1:5:26.26:26,0,38 1/1:1,2:3:4.26:45,4,0 1/1:5,1:6:6.40:51,6,0 0/1:4,0:4:13.25:13,0,42 0/0:5,0:5:9.03:0,9,132 0/1:7,0:7:20.95:21,0,120 1/1:3,2:5:1.77:48,2,0 1/1:3,2:5:1.46:46,1,0 1/1:1,3:4:6.01:70,6,0 1/1:3,1:4:6.46:57,6,0 ./. ./. 0/0:0,1:1:2.60:0,3,10 1/1:2,0:2:5.89:57,6,0 0/0:3,0:3:3:0,3,26 -chr1 984501 . A G 452.7 . AC=26;AF=0.317;AN=82;BaseQRankSum=0.750;DP=155;Dels=0.04;FS=57.535;HRun=7;HaplotypeScore=2.7737;InbreedingCoeff=-0.1078;MQ=40.74;MQ0=0;MQRankSum=-5.758;QD=5.73;ReadPosRankSum=3.176;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:6.02:0,6,82 ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:33,3,0 0/0:1,1:2:3.01:0,3,33 0/0:2,2:4:6:0,6,52 0/1:1,3:5:27.42:27,0,29 0/1:2,1:3:24.41:24,0,60 0/1:1,1:2:27.42:27,0,32 0/0:1,0:1:3.01:0,3,40 0/0:2,1:3:6.02:0,6,69 1/1:1,1:2:3.01:33,3,0 0/0:4,0:4:12.03:0,12,141 0/0:3,0:3:9.03:0,9,107 ./. ./. ./. 0/1:2,1:3:27.42:27,0,34 1/1:0,1:1:3:25,3,0 0/1:3,2:5:13.65:14,0,104 ./. 0/1:1,1:2:20.67:27,0,21 0/1:2,3:5:24.41:55,0,24 0/1:1,1:2:20.67:27,0,21 0/0:2,1:3:6.01:0,6,60 0/0:4,2:6:6.01:0,6,66 0/0:3,0:3:3.01:0,3,40 0/0:2,0:2:6.01:0,6,60 0/0:2,1:4:3.01:0,3,33 0/1:6,4:10:48.83:49,0,107 0/0:2,1:3:6.01:0,6,60 ./. 1/1:0,3:3:3.01:33,3,0 0/0:2,2:4:3:0,3,26 0/1:1,3:5:23.61:27,0,24 1/1:1,1:2:3.01:32,3,0 0/0:2,3:5:6:0,6,61 0/1:1,2:4:20.67:25,0,21 0/0:3,2:5:9.03:0,9,106 0/1:6,2:9:18.40:18,0,118 0/1:2,2:4:27.42:27,0,31 0/0:2,0:4:3:0,3,27 0/0:3,0:3:6.01:0,6,60 1/1:0,3:3:6.01:61,6,0 ./. 0/0:1,0:1:3.01:0,3,36 0/0:2,0:2:3.01:0,3,39 0/1:1,1:2:18.69:19,0,22 ./. -chr1 984510 . C CG 61.68 . AC=13;AF=0.144;AN=90;BaseQRankSum=4.890;DP=164;FS=70.003;HRun=4;HaplotypeScore=50.6057;InbreedingCoeff=-0.0152;MQ=42.03;MQ0=0;MQRankSum=-4.938;QD=1.50;ReadPosRankSum=-1.662;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3:0,3,26 0/0:1,0:1:3.01:0,3,34 0/1:3,0:3:5.04:5,0,34 0/0:3,0:3:2.74:0,3,34 0/0:6,0:6:6.15:0,6,98 0/0:4,1:5:1.94:0,2,62 0/0:3,0:3:5.68:0,6,42 1/1:1,0:1:3.01:36,3,0 ./. 0/1:3,0:3:9.75:10,0,59 0/0:2,0:2:5.50:0,6,43 0/0:3,0:3:9.03:0,9,102 0/0:3,0:3:9.03:0,9,102 0/0:3,0:3:2.87:0,3,15 ./. ./. 0/1:4,0:4:3.55:4,0,85 0/0:3,0:3:5.85:0,6,49 0/0:4,0:4:8.87:0,9,101 0/0:1,0:1:3:0,3,29 0/0:3,0:3:8.86:0,9,81 0/0:9,0:8:17.53:0,18,174 0/0:3,0:3:5.18:0,5,67 0/0:2,0:2:3.01:0,3,34 0/0:5,0:5:8.53:0,9,101 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3.01:0,3,34 0/0:4,0:4:6.02:0,6,68 0/0:11,0:11:3.46:0,3,124 0/0:4,0:4:6.02:0,6,68 0/0:4,0:4:6.01:0,6,63 1/1:1,2:3:3.01:34,3,0 0/0:3,1:4:5.67:0,6,49 0/0:6,0:6:3.89:0,4,36 0/0:4,0:4:5.60:0,6,43 0/0:3,0:3:3.01:0,3,34 0/0:5,1:6:8.05:0,8,129 0/0:6,0:6:9.02:0,9,102 0/1:8,1:9:31.27:31,0,111 0/1:5,0:5:14.91:15,0,26 0/1:5,0:5:29.30:29,0,58 0/0:3,0:3:3.01:0,3,34 0/1:3,2:5:18.30:18,0,46 0/0:3,0:3:8.97:0,9,80 0/0:1,0:1:3.01:0,3,34 0/0:2,0:2:4.56:0,5,38 0/1:1,0:1:0:0,0,0 0/1:1,1:2:0:0,0,0 -chr1 984524 . T G 47.35 . AC=11;AF=0.125;AN=88;BaseQRankSum=-2.019;DP=191;Dels=0.01;FS=48.423;HRun=3;HaplotypeScore=3.1841;InbreedingCoeff=-0.0001;MQ=47.05;MQ0=0;MQRankSum=-3.798;QD=1.01;ReadPosRankSum=3.652;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,81 ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,65 0/0:2,0:2:6.01:0,6,66 0/1:3,1:5:21.42:21,0,78 0/0:5,1:6:12.02:0,12,125 0/1:5,1:7:9.68:10,0,111 0/0:4,0:4:12.03:0,12,134 0/0:1,0:1:3:0,3,27 ./. 0/0:3,0:3:8.98:0,9,84 ./. 0/0:6,0:6:15.04:0,15,171 0/0:4,0:4:12.01:0,12,127 0/0:5,0:5:12.03:0,12,136 0/0:2,0:2:6.02:0,6,70 ./. 0/0:4,0:4:12.02:0,12,134 0/1:3,1:4:13.67:14,0,61 0/0:2,1:3:2.99:0,3,23 0/0:3,0:3:9.03:0,9,108 0/0:4,0:4:12:0,12,113 0/1:8,1:9:9.39:9,0,208 0/0:5,0:5:12.03:0,12,130 0/0:2,0:2:6:0,6,58 0/0:6,1:7:15.04:0,15,175 0/0:4,1:5:12.04:0,12,146 0/0:1,0:1:2.99:0,3,23 0/0:6,0:6:18.05:0,18,203 0/1:6,3:9:21.40:21,0,98 0/0:3,1:4:6:0,6,56 0/0:3,1:4:9:0,9,93 1/1:1,1:2:3:26,3,0 0/1:2,2:4:18.65:19,0,53 0/0:2,2:4:2.99:0,3,23 0/0:1,1:4:3.01:0,3,35 0/0:1,1:2:3.01:0,3,33 0/0:7,0:7:15.04:0,15,174 0/1:4,2:6:18.42:18,0,99 0/0:7,2:9:15.04:0,15,175 0/0:2,2:5:6.02:0,6,72 0/0:4,3:7:9.02:0,9,102 0/0:3,0:3:6.02:0,6,68 0/0:4,0:4:11.98:0,12,110 0/0:3,0:3:6:0,6,56 ./. 0/0:4,0:4:12.03:0,12,133 1/1:0,1:1:3.01:32,3,0 ./. -chr1 984528 . T G 133.69 . AC=15;AF=0.167;AN=90;BaseQRankSum=-2.316;DP=208;Dels=0.01;FS=63.386;HRun=4;HaplotypeScore=2.2156;InbreedingCoeff=-0.0134;MQ=47.68;MQ0=0;MQRankSum=-5.136;QD=2.09;ReadPosRankSum=3.074;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. ./. ./. 0/0:3,0:3:9.03:0,9,109 ./. ./. ./. 0/0:1,0:1:3.01:0,3,37 0/0:2,0:2:6.02:0,6,68 0/0:2,0:2:3.01:0,3,38 0/1:4,1:6:18.56:19,0,91 0/0:5,1:6:9.01:0,9,87 0/0:4,2:6:9.02:0,9,101 0/0:4,0:5:12.03:0,12,140 0/0:1,0:1:3.01:0,3,33 ./. 0/0:3,0:3:2.99:0,3,23 ./. 0/0:6,0:6:15.02:0,15,158 0/0:5,0:5:9.02:0,9,96 0/0:6,1:7:18.05:0,18,206 0/0:2,0:2:6.02:0,6,65 ./. 0/0:4,0:4:9.03:0,9,109 0/1:5,1:6:10.65:11,0,121 0/0:1,2:3:3.01:0,3,30 0/0:3,0:3:9.03:0,9,110 0/0:3,0:3:2.99:0,3,24 0/1:7,2:9:37.05:37,0,164 0/0:4,1:5:9.02:0,9,103 0/0:3,0:3:6.01:0,6,64 0/1:4,2:6:17.59:18,0,93 0/0:6,1:7:18.05:0,18,203 ./. 0/0:7,0:7:21.06:0,21,239 0/1:4,3:8:15.64:16,0,87 0/0:2,0:4:3:0,3,25 0/0:4,1:5:9.03:0,9,102 1/1:0,2:2:3.01:30,3,0 0/1:2,2:4:24.58:27,0,25 1/1:2,2:5:3:29,3,0 0/0:5,0:6:9.03:0,9,101 0/1:1,1:2:19.68:20,0,27 0/0:7,0:7:15.03:0,15,157 0/1:4,2:6:21.42:21,0,71 0/0:8,3:11:21.03:0,21,217 0/0:2,2:5:6.02:0,6,76 0/1:4,3:7:16.67:17,0,64 0/0:2,2:4:6.02:0,6,73 0/0:4,0:4:9.02:0,9,96 0/0:3,0:3:3.01:0,3,33 ./. 0/0:4,0:4:12.02:0,12,128 1/1:0,1:1:3.01:33,3,0 0/0:1,1:2:3.01:0,3,30 -chr1 984533 . T G 92.45 . AC=10;AF=0.111;AN=90;BaseQRankSum=-2.508;DP=221;Dels=0.00;FS=75.206;HRun=4;HaplotypeScore=0.9453;InbreedingCoeff=0.0314;MQ=49.13;MQ0=0;MQRankSum=-5.147;QD=1.71;ReadPosRankSum=0.969;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|24),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|1),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. 0/0:3,0:3:9.03:0,9,105 ./. ./. ./. 0/0:1,0:1:3.01:0,3,37 0/0:2,0:2:6.01:0,6,60 0/0:2,0:2:6.01:0,6,63 0/0:4,1:6:12.02:0,12,129 0/0:5,1:6:9.02:0,9,93 0/0:5,1:6:12:0,12,121 0/0:5,0:5:15.04:0,15,179 0/0:2,0:2:6.02:0,6,68 0/0:2,0:2:6.02:0,6,71 0/0:3,0:3:6.01:0,6,64 ./. 0/0:6,0:6:15.03:0,15,162 0/0:5,0:5:12.01:0,12,123 0/0:6,0:7:18.05:0,18,214 0/0:2,0:2:3.01:0,3,33 ./. 0/0:5,0:5:15.04:0,15,174 0/0:5,1:7:15.04:0,15,163 0/0:3,1:4:6.01:0,6,64 0/0:4,0:4:12.03:0,12,139 0/0:3,0:3:6.01:0,6,58 0/1:9,1:10:7.62:8,0,158 0/0:5,0:5:9.01:0,9,94 0/0:2,1:3:3.01:0,3,40 0/0:6,1:7:12.04:0,12,140 0/0:7,1:8:18.05:0,18,208 ./. 0/0:6,0:6:18.05:0,18,205 0/1:5,5:11:46.93:47,0,119 0/0:2,0:4:3:0,3,25 0/0:4,1:5:9.02:0,9,95 ./. 0/1:2,2:4:18.68:19,0,27 ./. 0/0:6,0:6:12.04:0,12,146 1/1:0,1:1:3:26,3,0 0/0:7,0:7:18.03:0,18,193 0/1:4,2:6:13.68:53,0,14 0/1:10,2:12:8.58:9,0,182 0/0:2,1:5:6.02:0,6,72 0/1:7,2:9:14.58:15,0,127 0/0:5,1:6:9.01:0,9,100 0/0:3,0:3:9.02:0,9,96 0/0:2,0:2:6.01:0,6,59 ./. 0/0:3,0:3:6.01:0,6,62 1/1:0,1:1:3.01:33,3,0 0/0:1,2:3:3.01:0,3,35 -chr1 984711 . G A 778.12 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.444;DP=2749;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.7477;InbreedingCoeff=-0.0101;MQ=58.27;MQ0=0;MQRankSum=-0.471;QD=11.61;ReadPosRankSum=-0.316;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R1465Q|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|cGg/cAg|R/Q|ENSG00000188157|AGRN|ENST00000379370|25/36|benign(0.094)|tolerated(0.53)|1465/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000492947|2/2||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:7,0:7:18.06:0,18,226 0/0:8,0:8:18.04:0,18,209 0/0:5,0:5:12.04:0,12,144 0/0:3,0:3:9.03:0,9,119 0/0:13,0:13:39.13:0,39,524 0/0:21,0:21:60.17:0,60,774 0/0:24,0:24:69.22:0,69,921 0/0:20,0:20:60.19:0,60,780 0/0:32,0:32:93.29:0,93,1221 0/0:46,0:46:99:0,135,1724 0/0:25,0:25:72.23:0,72,947 0/0:13,0:13:39.12:0,39,480 0/0:23,0:23:66.20:0,66,842 0/0:38,0:38:99:0,105,1385 0/0:41,0:41:99:0,108,1391 0/0:34,0:34:87.27:0,87,1142 0/0:42,0:42:99:0,108,1384 0/0:42,0:42:99:0,108,1432 0/0:47,1:49:99:0,126,1673 0/0:44,0:44:99:0,123,1613 0/0:44,0:44:99:0,108,1405 0/0:54,0:56:99:0,132,1762 0/0:38,0:38:90.28:0,90,1172 0/0:49,0:49:99:0,126,1647 0/0:40,0:41:99:0,105,1380 0/0:42,0:44:96.30:0,96,1266 0/0:31,0:32:84.26:0,84,1100 0/0:35,0:35:93.27:0,93,1186 0/0:45,0:45:99:0,114,1515 0/0:46,0:46:99:0,126,1628 0/0:62,0:62:99:0,162,2118 0/0:47,0:47:99:0,120,1583 0/0:59,0:59:99:0,159,2050 0/0:50,0:50:99:0,123,1606 0/0:44,0:44:99:0,114,1488 0/0:47,0:47:99:0,114,1544 0/0:46,0:46:99:0,123,1563 0/0:59,1:60:99:0,118,1969 0/0:43,0:43:99:0,111,1427 0/0:90,0:90:99:0,202,2630 0/1:33,33:67:99:826,0,895 0/0:43,0:43:99:0,108,1380 0/0:40,0:40:96.29:0,96,1229 0/0:41,0:41:99:0,108,1373 0/0:57,0:57:99:0,141,1770 0/0:54,0:55:99:0,135,1763 0/0:83,0:83:99:0,205,2623 0/0:30,0:30:66.21:0,66,857 0/0:64,0:64:99:0,135,1739 0/0:110,0:110:99:0,238,3068 0/0:103,0:103:99:0,247,3087 0/0:86,0:86:99:0,205,2546 0/0:95,0:95:99:0,223,2824 0/0:64,0:65:99:0,156,2005 0/0:53,0:53:99:0,126,1593 0/0:38,0:38:99:0,102,1305 0/0:34,0:34:81.25:0,81,1057 0/0:73,0:73:99:0,175,2268 0/0:54,0:54:99:0,126,1622 0/0:48,0:49:99:0,105,1347 -chr1 984847 . G C 1888.19 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.596;DP=3896;Dels=0.00;FS=5.841;HRun=0;HaplotypeScore=3.8645;InbreedingCoeff=-0.0190;MQ=58.46;MQ0=0;MQRankSum=0.505;QD=13.58;ReadPosRankSum=-1.173;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|25),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,79 0/0:18,0:18:45.13:0,45,555 0/0:9,0:9:24.08:0,24,305 0/0:6,0:6:15.04:0,15,178 0/0:23,0:23:69.23:0,69,935 0/0:29,0:29:84.27:0,84,1107 0/0:27,0:27:78.26:0,78,1052 0/0:18,0:18:54.15:0,54,706 0/0:33,0:33:99:0,99,1324 0/0:44,0:44:99:0,126,1645 0/0:24,0:24:72.22:0,72,940 0/0:16,0:16:48.15:0,48,626 0/0:35,0:35:96.31:0,96,1256 0/0:76,0:76:99:0,181,2363 0/0:68,0:68:99:0,166,2172 0/0:52,0:52:99:0,135,1772 0/0:81,0:81:99:0,187,2454 0/0:86,0:86:99:0,187,2490 0/0:79,0:79:99:0,196,2539 0/0:82,0:82:99:0,205,2682 0/0:60,0:60:99:0,150,1961 0/0:90,0:90:99:0,211,2727 0/0:71,0:72:99:0,184,2390 0/0:78,0:78:99:0,199,2572 0/0:64,0:64:99:0,160,2082 0/0:71,0:71:99:0,175,2254 0/1:25,45:70:99:1220,0,613 0/0:55,0:55:99:0,144,1905 0/0:67,0:67:99:0,166,2187 0/0:70,0:70:99:0,178,2320 0/0:99,0:99:99:0,247,3216 0/0:56,0:56:99:0,144,1874 0/0:68,1:69:99:0,147,2299 0/1:39,30:69:99:734,0,1095 0/0:59,0:60:99:0,153,2031 0/0:75,0:75:99:0,175,2302 0/0:71,0:71:99:0,181,2305 0/0:84,0:84:99:0,214,2747 0/0:62,0:62:99:0,144,1884 0/0:115,0:115:99:0,277,3559 0/0:94,0:94:99:0,232,2943 0/0:67,0:67:99:0,159,2056 0/0:65,0:65:99:0,169,2184 0/0:68,0:68:99:0,181,2307 0/0:80,0:80:99:0,193,2424 0/0:80,0:81:99:0,214,2688 0/0:119,0:119:99:0,283,3685 0/0:38,0:38:99:0,99,1264 0/0:87,0:87:99:0,196,2539 0/0:152,0:152:99:0,370,4781 0/0:102,0:102:99:0,256,3194 0/0:83,0:83:99:0,208,2636 0/0:111,0:111:99:0,289,3718 0/0:82,0:82:99:0,193,2498 0/0:75,0:75:99:0,187,2393 0/0:64,0:64:99:0,166,2180 0/0:56,0:56:99:0,135,1800 0/0:97,0:97:99:0,232,3007 0/0:46,0:46:99:0,114,1472 0/0:63,0:63:99:0,144,1880 -chr1 984888 . A G 1593.23 . AC=2;AF=0.0167;AN=120;BaseQRankSum=0.251;DP=2785;Dels=0.00;FS=2.468;HRun=0;HaplotypeScore=2.4818;InbreedingCoeff=-0.0179;MQ=58.39;MQ0=0;MQRankSum=2.076;QD=14.75;ReadPosRankSum=3.534;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|25),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:5,0:6:15.05:0,15,187 0/0:9,0:9:24.05:0,24,268 0/0:6,0:6:18.05:0,18,216 0/0:4,0:4:12.04:0,12,156 0/0:11,0:11:33.11:0,33,438 0/0:22,0:22:66.21:0,66,855 0/0:23,0:23:69.23:0,69,916 0/0:19,0:19:57.18:0,57,737 0/0:33,0:33:99:0,99,1307 0/0:38,0:38:99:0,114,1469 0/0:14,0:14:42.13:0,42,536 0/0:11,0:11:33.11:0,33,425 0/0:23,0:24:69.22:0,69,890 0/0:50,0:50:99:0,129,1649 0/0:57,0:57:99:0,144,1845 0/0:37,0:37:99:0,102,1313 0/0:48,0:48:99:0,120,1559 0/0:49,0:50:99:0,120,1498 0/0:55,0:55:99:0,147,1903 0/0:59,0:60:99:0,150,1838 0/0:41,0:41:99:0,102,1311 0/0:57,0:57:99:0,150,1888 0/0:48,0:48:99:0,120,1548 0/0:50,1:51:99:0,132,1683 0/0:47,0:48:99:0,117,1500 0/0:45,0:45:99:0,111,1393 0/1:17,38:55:99:1129,0,452 0/0:39,0:40:99:0,102,1325 0/0:48,0:49:99:0,123,1574 0/0:54,0:54:99:0,150,1891 0/0:66,0:66:99:0,175,2209 0/0:31,0:31:84.20:0,84,1033 0/0:53,1:54:99:0,104,1752 0/1:34,19:53:99:530,0,987 0/0:43,0:43:99:0,117,1519 0/0:46,0:46:99:0,126,1611 0/0:57,0:57:99:0,135,1740 0/0:69,0:69:99:0,184,2279 0/0:41,1:42:99:0,111,1396 0/0:87,0:87:99:0,223,2744 0/0:74,1:75:99:0,184,2280 0/0:43,0:43:99:0,108,1351 0/0:43,0:44:99:0,117,1448 0/0:44,0:46:99:0,105,1348 0/0:55,1:57:99:0,141,1783 0/0:56,0:56:99:0,156,1927 0/0:93,0:93:99:0,238,2998 0/0:27,1:29:66.17:0,66,801 0/0:58,0:59:99:0,138,1772 0/0:121,0:121:99:0,307,3830 0/0:68,1:71:99:0,177,2168 0/0:48,0:49:99:0,132,1602 0/0:67,0:67:99:0,190,2393 0/0:58,0:58:99:0,141,1828 0/0:55,0:55:99:0,126,1622 0/0:48,0:48:99:0,123,1571 0/0:45,1:46:99:0,120,1506 0/0:68,0:68:99:0,168,2140 0/0:43,1:44:99:0,105,1332 0/0:42,0:42:99:0,99,1273 -chr1 984957 . G A 998.45 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.493;DP=2152;Dels=0.00;FS=5.524;HRun=0;HaplotypeScore=1.2695;InbreedingCoeff=-0.0190;MQ=58.57;MQ0=0;MQRankSum=-0.059;QD=17.83;ReadPosRankSum=1.102;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R1509Q|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|cGg/cAg|R/Q|ENSG00000188157|AGRN|ENST00000379370|26/36|possibly_damaging(0.459)|tolerated(0.3)|1509/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3.01:0,3,36 0/0:2,0:3:3.01:0,3,41 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3:0,3,29 0/0:16,0:16:39.10:0,39,476 0/0:14,0:14:42.13:0,42,549 0/0:15,0:15:45.15:0,45,599 0/0:8,0:8:21.07:0,21,270 0/0:13,0:13:39.13:0,39,514 0/0:34,0:34:99:0,99,1256 0/0:7,0:7:18.06:0,18,234 0/0:10,0:10:30.10:0,30,383 0/0:19,1:20:54.17:0,54,702 0/0:38,0:38:99:0,105,1309 0/0:52,0:53:99:0,126,1635 0/0:27,0:27:75.24:0,75,989 0/0:51,0:51:99:0,126,1665 0/0:49,0:49:99:0,111,1429 0/0:43,0:43:99:0,120,1524 0/0:51,0:51:99:0,123,1588 0/0:45,0:45:99:0,102,1307 0/0:56,0:57:99:0,144,1897 0/0:43,0:43:99:0,108,1407 0/0:46,0:46:99:0,117,1516 0/0:39,0:39:99:0,99,1269 0/0:34,0:34:81.22:0,81,1033 0/0:32,0:32:78.25:0,78,1021 0/0:35,0:35:93.23:0,93,1134 0/0:46,0:46:99:0,111,1458 0/0:49,1:50:85.12:0,85,1515 0/0:57,0:57:99:0,144,1783 0/0:31,0:31:78.25:0,78,1016 0/0:49,0:50:99:0,132,1736 0/0:49,0:49:99:0,114,1488 0/0:45,0:45:99:0,102,1381 0/0:34,0:34:87.26:0,87,1091 0/0:51,0:51:99:0,129,1660 0/0:75,0:75:99:0,205,2691 0/0:24,0:24:66.18:0,66,824 0/0:61,1:62:99:0,144,1833 0/0:58,0:58:99:0,144,1866 0/0:33,0:33:84.26:0,84,1088 0/0:32,0:32:75.24:0,75,997 0/0:42,0:42:99:0,99,1283 0/0:30,0:30:72.23:0,72,945 0/0:32,0:32:87.28:0,87,1119 0/0:72,0:72:99:0,175,2226 0/0:23,0:23:60.19:0,60,798 0/0:47,0:47:90.25:0,90,1159 0/0:69,0:69:99:0,190,2391 0/1:23,32:56:99:1046,0,588 0/0:39,0:39:99:0,102,1310 0/0:28,0:28:75.17:0,75,918 0/0:26,0:26:63.21:0,63,843 0/0:37,0:37:90.27:0,90,1168 0/0:39,0:40:93.27:0,93,1179 0/0:34,0:34:75.24:0,75,980 0/0:43,0:43:99:0,105,1346 0/0:26,0:26:69.21:0,69,898 0/0:24,0:24:63.20:0,63,804 -chr1 985165 . C T 53.15 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.519;DP=760;Dels=0.00;FS=6.936;HRun=0;HaplotypeScore=0.5648;InbreedingCoeff=-0.0414;MQ=58.09;MQ0=0;MQRankSum=0.442;QD=3.32;ReadPosRankSum=1.429;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1578|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|ccC/ccT|P|ENSG00000188157|AGRN|ENST00000379370|26/36|||1578/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:4:2.99:0,3,24 0/0:3,0:3:9.03:0,9,107 0/0:4,0:4:6.02:0,6,69 0/0:3,0:3:3.01:0,3,38 0/0:14,0:14:39.12:0,39,496 0/0:17,0:17:51.16:0,51,664 0/0:35,0:35:99:0,102,1314 0/0:20,0:20:57.16:0,57,739 0/0:45,0:45:99:0,120,1560 0/0:40,0:40:99:0,120,1557 0/0:16,0:16:48.14:0,48,617 0/0:14,0:14:39.13:0,39,507 0/0:22,0:22:63.20:0,63,796 0/0:11,0:11:24.07:0,24,301 0/0:14,0:14:36.11:0,36,459 0/1:9,1:10:13.72:14,0,254 0/0:11,0:12:30.09:0,30,385 0/0:15,0:15:42.12:0,42,520 0/0:15,0:15:27.08:0,27,356 0/0:20,0:20:54.15:0,54,669 0/0:19,0:19:48.15:0,48,599 0/0:20,0:20:54.18:0,54,717 0/0:17,0:17:48.14:0,48,614 0/0:10,0:10:27.09:0,27,352 0/0:12,0:12:36.12:0,36,481 0/0:21,0:21:48.16:0,48,645 0/0:15,0:15:39.13:0,39,506 0/0:12,0:12:30.10:0,30,394 0/0:15,0:15:42.13:0,42,537 0/0:15,0:15:33.11:0,33,423 0/0:21,0:21:48.13:0,48,604 0/0:15,0:15:42.13:0,42,535 0/0:25,0:25:66.19:0,66,837 0/1:3,3:6:68.30:99,0,68 0/0:14,0:15:30.08:0,30,367 0/0:15,0:15:39.11:0,39,492 0/0:15,0:15:30.10:0,30,384 0/0:32,1:34:47.65:0,48,954 0/0:6,0:6:12.04:0,12,153 0/0:4,0:4:12.02:0,12,131 0/0:7,0:7:18.06:0,18,235 0/0:2,0:2:6.02:0,6,78 0/0:16,0:16:36.10:0,36,453 0/0:3,0:3:9.03:0,9,116 0/0:6,0:6:15.05:0,15,194 0/0:9,0:9:21.07:0,21,274 0/0:12,0:12:30.08:0,30,360 0/0:2,0:2:6.02:0,6,75 0/0:4,0:4:12.04:0,12,142 0/0:10,0:10:27.08:0,27,345 0/0:6,0:6:18.06:0,18,230 0/0:5,0:5:12.04:0,12,147 0/0:5,0:5:6.01:0,6,67 0/0:2,0:2:3.01:0,3,41 0/0:6,0:6:18.06:0,18,231 0/0:3,0:3:6.02:0,6,84 0/0:4,0:4:9.03:0,9,113 0/0:6,0:6:18.06:0,18,238 0/0:4,0:4:12.04:0,12,154 0/0:2,0:2:6.02:0,6,71 -chr1 985239 . C T 170.83 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.190;DP=977;Dels=0.00;FS=9.028;HRun=0;HaplotypeScore=0.4363;InbreedingCoeff=-0.0324;MQ=58.40;MQ0=0;MQRankSum=-0.599;QD=6.57;ReadPosRankSum=0.946;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|26),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.05:0,15,187 0/0:10,0:10:24.06:0,24,289 0/0:10,0:10:30.07:0,30,351 0/0:5,0:5:15.05:0,15,187 0/0:30,0:30:84.24:0,84,1075 0/0:25,0:25:75.24:0,75,988 0/0:43,0:43:99:0,120,1581 0/0:18,0:18:51.16:0,51,655 0/0:85,0:85:99:0,247,3213 0/0:64,0:64:99:0,193,2451 0/0:21,0:21:60.19:0,60,783 0/0:25,0:25:72.21:0,72,896 0/0:43,0:43:99:0,123,1575 0/0:11,0:11:30.08:0,30,366 0/0:16,0:16:33.09:0,33,416 0/0:15,0:15:33.05:0,33,377 0/0:28,0:28:57.14:0,57,687 0/0:24,0:24:51.14:0,51,639 0/0:18,0:18:48.13:0,48,603 0/0:22,1:23:57.18:0,57,735 0/0:18,0:19:42.13:0,42,543 0/0:18,0:18:36.10:0,36,459 0/0:21,0:21:57.14:0,57,691 0/0:8,0:8:18.06:0,18,242 0/0:20,0:20:51.13:0,51,614 0/0:23,0:23:48.16:0,48,671 0/1:9,2:11:39.80:40,0,222 0/0:9,0:9:24.08:0,24,307 0/0:17,0:17:42.13:0,42,543 0/0:17,0:17:45.11:0,45,554 0/0:26,0:27:63.21:0,63,846 0/0:14,0:14:36.11:0,36,464 0/0:28,0:28:66.18:0,66,828 0/1:8,7:15:99:196,0,220 0/0:11,0:11:24.08:0,24,302 0/0:14,0:14:39.12:0,39,497 0/0:21,0:21:45.13:0,45,575 0/0:20,0:20:54.17:0,54,703 0/0:3,0:3:6.02:0,6,67 0/0:7,0:7:18.06:0,18,225 0/0:14,0:14:24.07:0,24,308 0/0:3,0:3:9.02:0,9,102 0/0:14,0:14:36.11:0,36,451 0/0:4,0:4:9.03:0,9,105 0/0:4,0:4:9.02:0,9,110 0/0:6,0:6:15.05:0,15,211 0/0:9,0:9:18.05:0,18,228 0/0:6,0:6:12.04:0,12,166 0/0:9,0:9:18.06:0,18,233 0/0:12,0:12:27.08:0,27,323 0/0:6,0:6:15.04:0,15,170 0/0:6,0:6:12.03:0,12,141 0/0:6,0:6:12.03:0,12,134 0/0:1,0:1:3.01:0,3,37 0/0:8,0:8:18.03:0,18,200 0/0:6,0:6:15.05:0,15,204 0/0:2,0:2:6.02:0,6,70 0/0:10,0:10:18.05:0,18,232 0/0:6,0:6:12.03:0,12,138 0/0:3,0:3:6.02:0,6,83 -chr1 985266 . C T 19790.42 . AC=69;AF=0.5750;AN=120;BaseQRankSum=-0.605;DP=1126;Dels=0.00;FS=27.225;HRun=0;HaplotypeScore=0.6765;InbreedingCoeff=-0.0986;MQ=58.34;MQ0=0;MQRankSum=-0.994;QD=19.93;ReadPosRankSum=-1.430;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|26),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,8:8:21.06:240,21,0 0/1:2,6:8:23.53:122,0,24 0/1:4,5:9:99:127,0,125 0/1:1,6:7:14.46:145,0,14 0/1:19,13:32:99:356,0,516 0/1:18,12:30:99:291,0,631 1/1:0,57:57:99:2064,159,0 0/0:28,0:28:75.24:0,75,987 0/1:44,49:93:99:1543,0,1416 0/1:34,44:78:99:1378,0,998 1/1:0,29:29:84.24:1042,84,0 0/1:14,7:21:99:191,0,476 1/1:0,50:50:99:1857,147,0 0/1:6,13:19:99:346,0,179 1/1:0,17:17:45.14:557,45,0 1/1:0,15:15:39.10:478,39,0 0/1:18,15:33:99:372,0,314 1/1:0,24:24:54.15:691,54,0 0/1:10,9:19:99:235,0,290 0/0:23,0:23:51.17:0,51,690 0/1:12,9:22:99:213,0,239 1/1:0,18:18:48.15:604,48,0 1/1:1,25:26:63.21:849,63,0 0/1:10,3:13:83.28:83,0,279 0/1:16,8:24:99:241,0,412 0/1:15,7:22:99:199,0,332 0/1:5,10:15:94.41:348,0,94 0/1:5,7:12:99:251,0,163 0/1:9,15:24:99:417,0,246 1/1:0,19:19:48.16:636,48,0 0/1:13,12:25:99:295,0,316 1/1:2,16:18:6.88:496,7,0 0/1:18,19:37:99:533,0,383 0/0:17,0:17:42.14:0,42,571 0/1:11,3:14:77.20:77,0,330 0/1:10,7:17:99:205,0,241 0/1:15,12:27:99:291,0,384 0/0:22,0:22:57.18:0,57,767 1/1:0,3:3:6.02:75,6,0 1/1:1,7:8:21.04:245,21,0 0/1:5,5:10:97.10:109,0,97 0/0:3,0:3:6.02:0,6,75 0/0:14,0:14:27.07:0,27,330 1/1:1,5:6:12.04:155,12,0 0/1:1,3:4:27.97:104,0,28 0/1:3,2:5:64.97:67,0,65 0/1:4,3:7:66.83:67,0,99 0/0:7,0:7:15.04:0,15,183 0/1:6,4:10:96.47:96,0,129 0/1:8,5:13:99:139,0,227 0/1:7,3:10:53.73:54,0,206 1/1:1,7:8:18.06:231,18,0 1/1:1,6:7:12.04:147,12,0 1/1:0,1:1:3.01:42,3,0 1/1:0,7:7:18.06:243,18,0 1/1:0,5:5:12.04:161,12,0 0/0:3,0:3:9.03:0,9,117 0/0:9,0:10:24.07:0,24,292 0/1:4,3:7:79.43:79,0,122 0/0:6,0:6:12.04:0,12,156 -chr1 985378 . G A 349.18 . AC=1;AF=0.0083;AN=120;BaseQRankSum=1.347;DP=1151;Dels=0.00;FS=36.082;HRun=1;HaplotypeScore=0.7396;InbreedingCoeff=-0.0111;MQ=57.13;MQ0=0;MQRankSum=0.215;QD=14.55;ReadPosRankSum=1.577;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E1614K|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|);CSQ=downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|Gag/Aag|E/K|ENSG00000188157|AGRN|ENST00000379370|27/36|benign(0.087)|tolerated(0.36)|1614/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.03:0,12,135 0/0:8,0:8:24.06:0,24,291 0/0:4,0:4:12.03:0,12,135 0/0:8,0:8:21.07:0,21,261 0/0:29,0:29:84.27:0,84,1116 0/0:20,0:20:57.16:0,57,731 0/0:45,0:45:99:0,135,1817 0/0:27,0:27:75.25:0,75,1003 0/0:82,0:82:99:0,247,3208 0/0:55,0:55:99:0,163,2115 0/0:27,0:27:78.25:0,78,1034 0/0:26,0:26:75.24:0,75,981 0/0:40,0:40:99:0,114,1489 0/0:13,0:13:39.10:0,39,477 0/0:26,0:26:57.16:0,57,768 0/0:17,0:17:39.13:0,39,512 0/0:15,0:15:36.12:0,36,474 0/0:11,1:12:24.07:0,24,295 0/0:20,0:20:48.15:0,48,622 0/0:15,0:15:33.11:0,33,457 0/0:23,0:23:54.17:0,54,688 0/0:23,0:23:57.18:0,57,749 0/0:26,0:26:69.22:0,69,892 0/0:15,0:15:45.14:0,45,574 0/0:20,0:20:51.17:0,51,688 0/0:6,0:6:18.06:0,18,238 0/0:21,0:21:54.17:0,54,703 0/0:17,0:17:42.13:0,42,552 0/0:16,0:16:42.13:0,42,545 0/0:13,0:13:36.11:0,36,463 0/0:17,0:17:42.14:0,42,557 0/0:21,0:21:51.16:0,51,649 0/0:19,0:19:51.15:0,51,657 0/0:9,0:9:24.08:0,24,321 0/0:16,0:16:45.13:0,45,574 0/0:13,0:13:36.11:0,36,463 0/0:12,0:12:33.10:0,33,399 0/0:38,0:38:90.28:0,90,1185 0/0:12,0:12:30.09:0,30,387 0/0:26,0:26:72.22:0,72,889 0/0:21,0:21:57.18:0,57,720 0/0:14,0:14:36.10:0,36,434 0/0:14,0:14:24.07:0,24,294 0/0:11,0:11:33.10:0,33,426 0/0:6,0:6:12.03:0,12,139 0/0:16,0:16:39.13:0,39,512 0/1:10,14:24:99:397,0,275 0/0:7,0:7:15.05:0,15,182 0/0:11,0:11:30.09:0,30,374 0/0:25,0:25:60.17:0,60,733 0/0:35,0:35:96.30:0,96,1210 0/0:11,0:11:33.10:0,33,418 0/0:14,0:14:42.13:0,42,541 0/0:13,0:13:36.11:0,36,443 0/0:22,0:22:66.21:0,66,833 0/0:10,0:11:30.10:0,30,396 0/0:5,0:5:12.03:0,12,142 0/0:10,0:10:24.08:0,24,316 0/0:10,0:10:27.08:0,27,334 0/0:15,0:15:39.12:0,39,506 -chr1 985443 . AG A 5524.19 . AC=63;AF=0.5250;AN=120;BaseQRankSum=-4.267;DP=1211;FS=1.118;HRun=15;HaplotypeScore=183.6608;InbreedingCoeff=0.2307;MQ=52.69;MQ0=0;MQRankSum=2.703;QD=6.02;ReadPosRankSum=0.541;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:3:0.40:0,0,1 1/1:3,0:3:0.38:1,0,0 0/0:6,0:6:9.58:0,10,53 0/0:4,0:4:5:0,5,26 1/1:8,3:11:8.58:56,9,0 1/1:8,3:11:0.73:29,1,0 1/1:17,7:24:3.99:106,4,0 1/1:2,4:6:11.64:73,12,0 0/1:31,7:38:33.31:127,0,33 1/1:26,11:37:9.34:212,9,0 1/1:9,4:13:3.84:62,4,0 0/0:9,0:9:10.46:0,10,41 0/0:14,0:14:14.82:0,15,46 0/1:4,4:8:10.83:41,0,11 0/0:10,0:10:8.52:0,9,53 0/0:10,0:10:5.67:0,6,24 0/1:8,1:9:7.17:7,0,28 0/0:9,1:10:7.85:0,8,47 0/1:5,8:13:6.32:90,0,6 1/1:4,5:9:13.80:83,14,0 1/1:10,5:15:11.74:74,12,0 0/1:15,1:16:34.59:35,0,54 0/0:14,0:14:8.71:0,9,36 0/0:9,0:9:10.65:0,11,49 0/0:12,0:12:4.91:0,5,33 1/1:4,3:7:1.12:79,1,0 1/1:4,5:9:10.79:88,11,0 1/1:4,3:7:11.40:75,11,0 0/0:16,0:16:30.07:0,30,129 0/0:8,0:8:7.47:0,7,44 0/1:12,5:17:8.38:73,0,8 0/1:10,6:16:25.14:68,0,25 1/1:4,4:8:14.38:94,14,0 1/1:6,5:11:14.73:92,15,0 1/1:2,7:9:14.32:95,14,0 1/1:3,4:7:14.51:90,15,0 1/1:0,12:13:34.52:213,35,0 0/0:18,0:18:13.83:0,14,77 0/1:23,1:24:3.84:4,0,41 0/1:33,13:46:15.49:221,0,15 0/1:43,3:45:6.24:6,0,100 0/1:22,13:35:11.24:192,0,11 1/1:11,13:24:46.46:292,46,0 0/0:23,0:24:26.23:0,26,129 0/1:15,6:21:34.05:99,0,34 0/1:15,12:27:13.40:166,0,13 0/1:32,12:44:27.04:226,0,27 0/1:10,4:14:37.37:37,0,53 1/1:21,11:33:2.86:173,3,0 1/1:25,52:79:99:1019,148,0 0/1:44,16:61:44.77:316,0,45 0/0:35,1:36:28.99:0,29,142 0/1:33,14:47:64.15:205,0,64 1/1:17,17:34:29.23:284,29,0 0/0:41,0:41:19.77:0,20,140 0/0:26,1:27:11.34:0,11,111 0/1:15,2:17:17.44:17,0,51 0/1:12,11:23:12.47:151,0,12 1/1:11,13:24:0.11:151,0,0 0/0:23,0:23:22.43:0,22,109 -chr1 985445 . G GT 4225.58 . AC=52;AF=0.4333;AN=120;BaseQRankSum=0.352;DP=1238;FS=80.878;HRun=0;HaplotypeScore=191.8295;InbreedingCoeff=-0.1480;MQ=52.62;MQ0=0;MQRankSum=2.617;QD=4.70;ReadPosRankSum=-5.379;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:3,0:3:4.03:41,4,0 0/1:3,0:3:10.38:10,0,26 0/1:5,1:6:29.66:30,0,33 0/1:4,0:4:20.12:20,0,55 0/1:10,0:10:80.87:81,0,87 0/1:10,0:10:22.15:22,0,132 0/1:24,0:24:99:193,0,197 0/0:7,0:7:17.49:0,17,145 0/1:39,0:39:99:344,0,193 0/1:36,0:36:99:304,0,309 1/1:13,0:13:33.60:280,34,0 0/1:9,0:9:59.75:60,0,133 0/1:15,0:15:6.08:161,0,6 0/1:7,1:8:35.53:36,0,105 0/1:10,0:10:7.02:118,0,7 1/1:9,1:10:21.70:166,22,0 0/1:9,0:9:52.23:67,0,52 1/1:10,0:10:6.65:83,7,0 0/1:13,0:13:38.41:38,0,151 0/0:9,0:9:21.03:0,21,211 0/0:15,0:15:18.02:0,18,168 0/1:14,0:14:75.06:75,0,181 0/1:14,0:14:12.19:102,0,12 0/1:9,0:9:12.58:67,0,13 0/1:12,0:12:44.89:45,0,173 0/0:7,0:7:20.93:0,21,204 0/0:9,0:9:24.03:0,24,241 0/0:8,0:8:20.96:0,21,188 0/1:15,1:16:36.04:36,0,249 1/1:8,0:8:1.98:79,2,0 0/1:15,0:15:54.07:54,0,114 0/1:15,0:15:11.37:139,0,11 0/0:8,0:8:21.03:0,21,204 0/0:11,0:11:15:0,15,133 0/0:9,0:9:23.99:0,24,216 0/1:7,0:7:26.99:89,0,27 0/0:13,0:13:35.99:0,36,313 0/1:18,0:18:7.65:129,0,8 1/1:24,0:24:20.11:144,20,0 0/1:46,2:48:53.69:54,0,530 0/1:45,1:45:99:147,0,412 0/0:36,0:35:71.20:0,71,728 0/0:26,0:26:63.36:0,63,567 0/1:25,0:25:1.19:106,0,1 0/0:23,0:23:36.43:0,36,385 0/1:26,2:28:41.94:42,0,247 0/1:48,1:49:30.36:30,0,404 0/0:15,0:15:30:0,30,338 0/1:38,0:38:12.62:13,0,281 0/0:83,0:83:99:0,191,1680 0/1:59,2:61:92.33:92,0,544 1/1:36,0:36:2.53:97,3,0 0/1:51,0:51:99:202,0,520 0/0:37,0:37:69.74:0,70,595 1/1:40,1:41:28.11:239,28,0 0/1:26,1:27:28.96:29,0,298 0/1:17,0:17:33.55:34,0,168 0/0:23,0:23:51.08:0,51,528 0/1:23,1:24:0.46:0,0,340 1/1:24,0:24:8.24:124,8,0 -chr1 985446 . G T 10415.52 . AC=55;AF=0.4583;AN=120;BaseQRankSum=-15.323;DP=1238;Dels=0.00;FS=78.688;HRun=0;HaplotypeScore=12.5413;InbreedingCoeff=-0.0418;MQ=52.62;MQ0=0;MQRankSum=3.979;QD=11.59;ReadPosRankSum=-1.572;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,3:3:6.02:78,6,0 0/1:2,1:3:30.96:35,0,31 0/1:2,4:6:18.42:104,0,18 0/1:2,2:4:29.55:54,0,30 0/1:5,5:10:99:145,0,136 0/1:6,4:10:99:123,0,172 0/1:11,13:24:99:366,0,376 0/0:7,0:7:21.05:0,21,264 0/1:14,25:39:99:701,0,400 0/1:17,19:36:99:555,0,502 0/1:4,9:13:97.63:260,0,98 0/1:4,5:9:99:127,0,137 1/1:1,14:15:20.40:427,20,0 0/1:5,3:8:45.18:45,0,163 1/1:1,9:10:21.05:244,21,0 0/1:1,9:10:6.92:281,0,7 0/1:2,7:9:55.92:154,0,56 1/1:1,9:10:24.01:252,24,0 0/1:9,4:13:99:100,0,204 0/0:9,0:9:18.06:0,18,237 0/0:15,0:15:21.06:0,21,262 0/1:8,6:14:99:146,0,177 1/1:6,8:14:18.05:222,18,0 0/1:1,8:9:7.61:172,0,8 0/1:7,5:12:99:125,0,174 0/0:7,0:7:18.06:0,18,242 0/0:9,0:9:24.07:0,24,289 0/0:8,0:8:18.06:0,18,233 0/1:9,7:16:99:132,0,295 1/1:0,8:8:18.05:210,18,0 0/1:6,9:15:99:181,0,153 0/1:9,6:15:99:154,0,155 0/0:8,0:8:21.07:0,21,269 0/0:11,0:11:15.05:0,15,186 0/0:9,0:9:24.06:0,24,275 0/1:6,1:7:22.59:23,0,174 0/0:13,0:13:36.09:0,36,412 1/1:2,16:18:33.09:377,33,0 1/1:4,20:24:14.63:441,15,0 0/1:34,13:48:99:286,0,694 0/1:28,18:46:99:336,0,446 0/0:36,0:36:69.22:0,69,889 0/0:26,0:26:66.20:0,66,821 1/1:4,21:25:45.03:464,45,0 0/0:23,0:23:39.11:0,39,478 0/1:23,5:28:67.98:68,0,449 0/1:37,12:49:99:217,0,720 0/0:15,0:15:30.09:0,30,369 0/1:26,12:38:99:260,0,584 0/0:81,1:83:99:0,196,2448 0/1:39,21:61:99:443,0,839 1/1:8,28:36:29.34:488,29,0 0/1:44,7:51:21.54:22,0,1022 0/0:37,0:37:69.19:0,69,821 1/1:9,32:41:56.29:746,56,0 0/1:15,10:27:99:188,0,324 0/1:11,6:17:99:131,0,200 0/0:23,0:23:51.16:0,51,650 0/1:19,5:24:50.42:50,0,476 1/1:4,19:24:45.08:482,45,0 -chr1 985447 . G T 432.38 . AC=5;AF=0.0417;AN=120;BaseQRankSum=-5.349;DP=1263;Dels=0.00;FS=3.447;HRun=0;HaplotypeScore=12.2057;InbreedingCoeff=-0.0488;MQ=52.38;MQ0=0;MQRankSum=-2.193;QD=3.90;ReadPosRankSum=0.844;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:3:6.02:0,6,81 0/0:3,0:3:6.02:0,6,78 0/0:6,0:6:15.04:0,15,179 0/0:4,0:4:12.03:0,12,143 0/0:9,0:9:27.09:0,27,359 0/0:10,0:10:24.08:0,24,312 0/1:21,2:23:4.29:4,0,730 0/0:7,0:7:21.06:0,21,262 0/0:37,1:38:76.62:0,77,1251 0/0:35,1:36:68.35:0,68,1274 0/1:10,4:14:89.06:89,0,246 0/0:9,0:9:27.08:0,27,338 0/0:15,0:15:39.10:0,39,450 0/0:9,0:9:24.07:0,24,282 0/0:10,0:10:27.07:0,27,321 0/0:10,0:10:30.09:0,30,373 0/0:9,0:9:27.08:0,27,329 0/0:9,1:10:27.05:0,27,310 0/0:13,0:13:30.08:0,30,359 0/0:8,0:8:18.06:0,18,232 0/0:14,0:14:21.06:0,21,261 0/0:12,1:13:30.09:0,30,373 0/0:14,0:14:30.08:0,30,356 0/0:8,0:8:18.05:0,18,206 0/0:12,0:12:33.08:0,33,411 0/0:8,0:8:21.07:0,21,281 0/0:9,0:9:27.08:0,27,321 0/0:8,0:8:18.06:0,18,238 0/0:17,0:17:48.13:0,48,582 0/0:9,0:9:21.06:0,21,257 0/0:15,0:15:39.12:0,39,484 0/1:7,8:15:99:129,0,222 0/0:9,0:9:24.08:0,24,307 0/0:11,0:11:15.04:0,15,183 0/0:9,0:9:24.07:0,24,282 0/1:4,3:7:98.77:99,0,102 0/0:13,0:13:33.10:0,33,393 0/0:17,0:17:39.11:0,39,475 0/0:23,1:24:20.45:0,20,502 0/0:52,0:52:99:0,117,1428 0/0:45,1:46:49.01:0,49,1002 0/0:37,0:37:72.23:0,72,926 0/0:27,0:27:69.22:0,69,866 0/0:25,0:25:48.13:0,48,560 0/0:25,0:25:48.15:0,48,595 0/0:29,1:30:32.51:0,33,668 0/0:54,1:55:78.84:0,79,1282 0/0:15,0:15:30.09:0,30,371 0/0:37,1:38:47.27:0,47,992 0/0:85,0:85:99:0,205,2560 0/0:62,1:63:99:0,108,1617 0/0:35,2:37:66.19:0,66,770 0/1:40,12:52:99:207,0,857 0/0:37,0:37:69.20:0,69,819 0/0:41,0:41:93.23:0,93,1059 0/0:27,1:28:27.68:0,28,670 0/0:17,2:19:5.68:0,6,405 0/0:23,0:23:51.16:0,51,642 0/0:25,1:26:57.18:0,57,712 0/0:24,0:24:54.14:0,54,641 -chr1 985449 . G A 14507.18 . AC=74;AF=0.6167;AN=120;BaseQRankSum=-12.718;DP=1283;Dels=0.00;FS=44.752;HRun=0;HaplotypeScore=13.5390;InbreedingCoeff=-0.3559;MQ=52.41;MQ0=0;MQRankSum=2.768;QD=12.78;ReadPosRankSum=-2.687;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,3:3:6.02:79,6,0 1/1:0,3:3:6.01:64,6,0 1/1:2,4:6:9.01:100,9,0 1/1:0,3:3:9:85,9,0 0/1:4,5:9:92.61:93,0,144 0/1:3,8:11:78.41:246,0,78 0/1:8,13:21:99:441,0,220 0/1:5,2:7:47.83:48,0,177 0/1:10,27:37:99:649,0,311 0/1:14,22:36:99:625,0,382 0/1:4,9:13:99:118,0,101 1/1:0,8:8:21.04:239,21,0 1/1:1,14:15:39.09:443,39,0 0/1:5,5:10:74.39:74,0,125 0/1:2,8:10:6.62:191,0,7 0/1:1,9:10:11.16:292,0,11 0/1:1,8:9:17.20:166,0,17 0/1:1,8:9:11.22:205,0,11 0/1:8,5:13:80.05:80,0,176 0/1:6,2:8:52.37:52,0,166 0/1:12,2:14:14.51:15,0,229 1/1:3,10:13:15.52:188,16,0 1/1:1,13:14:24.06:281,24,0 1/1:1,7:8:15.04:174,15,0 1/1:1,11:12:30.05:340,30,0 0/1:4,4:8:99:103,0,105 0/1:7,3:10:87.68:88,0,163 0/1:7,2:9:18.97:19,0,170 1/1:1,15:16:1.42:385,1,0 1/1:0,9:9:21.04:232,21,0 0/1:5,10:15:99:233,0,119 0/1:9,6:15:99:133,0,183 0/1:6,3:9:18.98:19,0,168 0/0:10,1:11:15.04:0,15,181 0/1:7,1:8:18.97:19,0,172 0/1:6,1:7:21.95:22,0,171 0/0:13,0:13:36.10:0,36,422 1/1:3,13:16:33.06:368,33,0 1/1:5,19:24:11.61:430,12,0 0/1:32,23:56:99:502,0,642 0/1:15,32:48:23.49:777,0,23 0/1:22,15:37:99:203,0,438 0/1:24,5:29:11.55:12,0,750 1/1:3,23:26:11.64:441,12,0 0/1:13,14:27:99:171,0,245 0/1:22,8:31:95.56:96,0,510 0/1:35,25:60:99:410,0,654 0/1:8,9:17:99:132,0,148 0/1:25,14:39:99:293,0,590 0/0:75,10:85:34.27:0,34,2110 0/1:29,31:61:99:557,0,559 1/1:8,30:39:60.16:691,60,0 0/1:24,29:53:99:557,0,454 0/0:33,6:39:31.41:0,31,754 1/1:7,34:41:22.04:771,22,0 0/1:7,20:28:15.80:441,0,16 0/1:5,14:19:19.08:310,0,19 0/1:15,10:25:99:124,0,379 0/1:19,8:27:99:147,0,435 1/1:1,23:24:48.06:532,48,0 -chr1 985450 . G A 9694.98 . AC=38;AF=0.3167;AN=120;BaseQRankSum=-9.217;DP=1307;Dels=0.00;FS=25.729;HRun=0;HaplotypeScore=14.9791;InbreedingCoeff=-0.3897;MQ=52.45;MQ0=0;MQRankSum=4.412;QD=10.72;ReadPosRankSum=2.909;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,113 0/0:3,0:3:9.03:0,9,104 0/0:7,0:7:18.05:0,18,212 0/0:3,0:3:9.03:0,9,107 0/1:4,4:8:99:128,0,129 0/1:8,3:11:67.69:68,0,265 0/1:12,7:20:99:174,0,429 0/1:2,7:9:45.70:243,0,46 0/1:27,10:37:99:270,0,826 0/1:22,15:37:99:471,0,677 0/1:9,5:14:94:94,0,189 0/0:8,0:8:21.07:0,21,276 0/0:15,0:15:42.13:0,42,538 0/1:6,4:10:99:105,0,111 0/0:10,0:10:27.08:0,27,340 0/0:10,0:10:27.09:0,27,350 0/1:8,1:9:4.50:4,0,256 0/1:8,1:9:8.18:8,0,263 0/1:4,8:13:97.70:149,0,98 0/1:2,6:8:49.67:94,0,50 0/1:10,5:15:84.38:129,0,84 0/0:12,1:13:29.43:0,29,330 0/0:13,0:14:33.10:0,33,402 0/0:8,0:8:18.05:0,18,223 0/0:13,0:13:30.10:0,30,384 0/1:4,4:8:80.79:81,0,126 0/1:3,7:10:83.65:184,0,84 0/1:4,6:10:48.29:155,0,48 0/0:16,0:16:45.10:0,45,548 0/0:9,0:9:21.07:0,21,262 0/1:10,5:15:60.82:61,0,301 0/1:6,9:15:99:155,0,181 0/1:4,6:10:44.59:181,0,45 1/1:5,6:11:12.03:137,12,0 0/1:2,6:8:27.99:74,0,28 0/1:2,5:7:21.95:177,0,22 0/1:1,12:13:5.50:303,0,6 0/0:18,0:18:45.14:0,45,554 0/0:23,1:24:14.52:0,15,472 0/1:35,23:58:99:529,0,692 0/0:45,3:48:3.52:0,4,853 0/1:22,14:37:99:359,0,314 0/1:7,23:30:25.28:655,0,25 0/0:26,0:26:45.13:0,45,546 0/1:18,11:29:99:245,0,306 0/1:16,17:33:99:394,0,213 0/1:38,21:60:99:426,0,548 0/1:12,5:17:91.04:91,0,185 0/1:24,16:41:99:425,0,456 0/1:25,60:85:99:1345,0,221 0/1:44,17:62:99:339,0,858 0/0:39,1:41:69.17:0,69,818 0/1:37,17:54:99:285,0,739 0/1:17,22:39:62.44:528,0,62 0/0:42,0:42:78.20:0,78,921 0/0:27,1:28:27.67:0,28,651 0/0:17,2:19:2.67:0,3,357 0/1:13,12:25:99:354,0,159 0/1:12,15:27:99:276,0,256 0/0:25,0:25:60.16:0,60,704 -chr1 985458 . GT G 311.7 . AC=16;AF=0.1333;AN=120;BaseQRankSum=4.206;DP=1448;FS=204.972;HRun=2;HaplotypeScore=201.5164;InbreedingCoeff=-0.1309;MQ=53.65;MQ0=0;MQRankSum=1.914;QD=0.64;ReadPosRankSum=10.293;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/1:3,0:3:10.91:11,0,28 0/0:4,0:4:11.99:0,12,116 0/0:7,0:7:16.26:0,16,157 0/0:4,0:4:11.87:0,12,117 0/0:9,0:9:25.90:0,26,209 0/0:13,0:13:34.39:0,34,324 0/0:17,0:17:35.84:0,36,351 0/0:12,0:12:34.94:0,35,288 0/0:35,1:36:51.53:0,52,790 0/0:35,1:36:87.81:0,88,793 0/0:16,1:17:36.08:0,36,245 0/0:5,0:5:14.25:0,14,146 0/0:15,0:15:40.66:0,41,439 0/0:10,0:10:15.18:0,15,138 0/0:9,0:9:23.60:0,24,216 0/0:9,0:9:24.47:0,24,256 0/0:6,0:6:14.84:0,15,133 0/0:10,0:10:21.99:0,22,241 0/0:13,0:13:21.45:0,21,175 0/1:6,1:7:12:12,0,43 0/0:13,0:14:20.69:0,21,254 0/1:12,1:13:8.60:9,0,286 0/0:13,0:13:29.81:0,30,288 0/0:8,0:8:12.92:0,13,142 0/0:12,0:12:26.12:0,26,256 0/1:8,1:9:2.37:2,0,117 0/0:10,0:10:11.81:0,12,108 0/1:7,1:8:3.12:3,0,70 0/0:16,0:16:47.87:0,48,469 0/0:10,0:10:26.97:0,27,269 0/1:13,1:14:11.76:12,0,227 0/0:14,0:14:15.03:0,15,218 0/1:8,2:10:16.01:16,0,79 0/1:9,1:10:8.07:8,0,17 0/0:8,0:8:13.95:0,14,79 0/0:8,0:8:20.31:0,20,122 0/0:15,0:15:20.58:0,21,151 0/0:18,0:18:31.18:0,31,345 0/0:25,0:25:42.71:0,43,344 0/0:68,3:71:42.27:0,42,1070 0/0:51,0:50:71.31:0,71,654 0/1:39,3:41:0.55:1,0,438 0/1:30,4:34:13.07:13,0,329 0/0:37,0:37:66.13:0,66,609 0/1:31,3:34:1.56:2,0,356 0/1:36,1:37:6.53:7,0,379 0/0:66,3:69:31.52:0,32,947 0/0:25,0:25:17.05:0,17,285 0/0:53,2:55:56.46:0,56,687 0/1:86,7:93:99:221,0,457 0/1:66,7:73:99:99,0,644 0/0:49,1:50:82.26:0,82,674 0/1:51,7:58:44.18:44,0,504 0/1:36,4:40:12.77:13,0,143 0/0:46,2:48:60.67:0,61,659 0/0:32,0:32:48.64:0,49,407 0/0:23,0:23:48.66:0,49,364 0/0:30,1:31:40.17:0,40,387 0/0:38,1:39:57.73:0,58,590 0/0:29,0:29:50.74:0,51,406 -chr1 985460 . T C 3061.71 . AC=16;AF=0.1333;AN=120;BaseQRankSum=-0.490;DP=1456;Dels=0.00;FS=6.540;HRun=0;HaplotypeScore=4.9126;InbreedingCoeff=0.2588;MQ=53.76;MQ0=0;MQRankSum=-0.066;QD=11.78;ReadPosRankSum=0.826;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,112 0/0:5,0:5:15.03:0,15,177 0/0:7,0:7:18.04:0,18,203 0/0:5,0:5:15.04:0,15,185 0/0:9,0:9:27.07:0,27,344 0/0:13,0:13:39.10:0,39,490 0/0:17,0:17:48.15:0,48,618 0/0:12,0:12:36.11:0,36,455 0/0:39,0:39:99:0,111,1468 0/0:34,0:34:96.30:0,96,1242 0/1:8,9:17:99:216,0,192 0/0:5,0:5:15.05:0,15,191 0/0:16,0:16:45.15:0,45,589 0/0:10,0:10:15.01:0,15,168 0/0:9,0:9:21.05:0,21,250 0/0:9,0:9:24.07:0,24,304 0/0:5,0:5:12.04:0,12,153 0/0:10,0:10:24.06:0,24,274 0/0:13,0:13:27.08:0,27,334 0/0:8,0:8:15.04:0,15,174 0/0:13,0:13:33.06:0,33,369 0/0:11,0:13:30.07:0,30,364 0/0:13,0:13:30.04:0,30,315 0/0:7,0:7:15.04:0,15,184 0/0:11,0:12:24.07:0,24,304 0/0:9,0:9:24.02:0,24,248 1/1:0,10:10:27.08:331,27,0 0/1:2,6:8:57.61:128,0,58 0/0:17,0:17:45.11:0,45,531 0/0:10,0:10:27.06:0,27,310 0/0:14,0:14:27.06:0,27,317 0/1:5,9:14:99:184,0,141 0/1:4,6:10:52.04:114,0,52 1/1:1,6:9:12.03:143,12,0 0/1:3,4:8:77.73:99,0,78 0/1:4,4:8:99:127,0,125 0/1:7,9:16:99:265,0,181 0/0:16,0:16:33.09:0,33,391 0/0:25,0:25:51.08:0,51,535 0/0:67,0:71:99:0,153,1704 0/0:52,0:54:96.11:0,96,983 0/0:39,0:42:78.15:0,78,856 0/0:35,0:35:87.16:0,87,926 0/0:35,0:37:72.13:0,72,807 0/1:20,15:35:99:297,0,334 0/0:37,0:38:75.12:0,75,797 0/0:67,0:69:99:0,153,1707 0/1:11,13:26:99:269,0,218 0/0:53,0:56:99:0,117,1294 0/0:87,0:92:99:0,171,1774 0/0:70,0:74:99:0,123,1286 0/0:46,0:47:81.12:0,81,869 0/1:33,26:60:99:275,0,625 1/1:0,35:39:75.15:815,75,0 0/0:44,0:46:96.15:0,96,997 0/0:30,0:32:48.08:0,48,515 0/0:24,0:25:45.09:0,45,495 0/0:29,0:32:72.14:0,72,790 0/0:39,0:39:81.17:0,81,908 0/0:28,0:28:60.09:0,60,618 -chr1 985509 . G A 2780.67 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.579;DP=2940;Dels=0.00;FS=10.079;HRun=0;HaplotypeScore=1.7811;InbreedingCoeff=-0.0096;MQ=56.77;MQ0=0;MQRankSum=2.214;QD=17.60;ReadPosRankSum=0.249;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|27),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:13,0:13:36.11:0,36,436 0/0:10,0:10:27.09:0,27,358 0/0:10,0:10:30.09:0,30,372 0/0:4,0:4:12.04:0,12,144 0/0:23,0:23:69.23:0,69,934 0/0:20,0:20:60.20:0,60,808 0/0:24,0:24:72.24:0,72,963 0/0:21,0:21:63.21:0,63,841 0/0:50,0:50:99:0,150,1996 0/0:57,0:57:99:0,166,2165 0/0:20,0:20:57.19:0,57,763 0/0:23,0:23:66.20:0,66,858 0/0:37,0:37:99:0,111,1474 0/0:12,1:13:15.42:0,15,419 0/0:19,0:19:57.18:0,57,748 0/0:10,0:10:24.08:0,24,311 0/0:17,0:17:48.14:0,48,610 0/0:11,0:12:30.10:0,30,395 0/0:13,0:13:36.11:0,36,463 0/0:25,0:26:60.19:0,60,801 0/0:11,0:11:27.09:0,27,354 0/0:14,0:14:42.14:0,42,562 0/0:15,0:15:42.10:0,42,526 0/0:6,0:6:15.03:0,15,182 0/0:13,0:13:33.11:0,33,431 0/0:13,0:13:36.11:0,36,451 0/0:12,0:12:33.11:0,33,444 0/0:11,0:11:33.10:0,33,424 0/0:17,0:17:45.10:0,45,546 0/0:11,0:11:33.10:0,33,423 0/0:22,0:22:63.20:0,63,823 0/0:15,0:15:42.11:0,42,533 0/0:14,0:14:36.11:0,36,448 0/0:8,0:8:24.08:0,24,312 0/0:11,0:11:30.10:0,30,384 0/0:8,0:8:24.08:0,24,312 0/0:22,0:22:54.16:0,54,703 0/0:20,0:20:57.18:0,57,752 0/0:72,0:73:99:0,169,2219 0/0:163,0:165:99:0,373,4896 0/0:104,0:104:99:0,253,3255 0/0:90,0:93:99:0,211,2718 0/0:92,0:92:99:0,217,2778 0/0:93,0:93:99:0,229,3025 0/0:64,0:65:99:0,150,1917 0/0:104,0:104:99:0,265,3416 0/0:168,0:170:99:0,382,5000 0/0:59,0:59:99:0,120,1525 0/0:131,1:132:99:0,266,3883 0/1:58,100:158:99:2828,0,1109 0/0:144,0:146:99:0,355,4502 0/0:104,1:107:99:0,247,3065 0/0:128,0:129:99:0,292,3738 0/0:90,0:90:99:0,211,2728 0/0:97,0:97:99:0,232,2926 0/0:71,1:72:99:0,162,2086 0/0:66,0:66:99:0,165,2098 0/0:86,0:86:99:0,208,2648 0/0:98,0:98:99:0,211,2759 0/0:74,0:76:99:0,163,2167 -chr1 985662 . C T 105.9 . AC=5;AF=0.0417;AN=120;BaseQRankSum=-11.359;DP=3310;Dels=0.00;FS=122.177;HRun=2;HaplotypeScore=2.7454;InbreedingCoeff=-0.0439;MQ=57.76;MQ0=0;MQRankSum=-6.298;QD=0.47;ReadPosRankSum=-5.444;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1643|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|ttC/ttT|F|ENSG00000188157|AGRN|ENST00000379370|28/36|||1643/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/1:10,3:13:9.36:9,0,242 0/1:9,6:15:35.85:36,0,252 0/0:12,3:15:5.39:0,5,293 0/0:7,1:9:12.04:0,12,158 0/1:31,10:41:98.69:99,0,990 0/0:30,10:40:31.83:0,32,897 0/1:54,14:68:48.64:49,0,1517 0/0:28,4:32:38.51:0,39,763 0/1:72,16:88:7.49:7,0,2063 0/0:80,15:95:52.67:0,53,2300 0/0:28,4:32:46.52:0,47,814 0/0:24,6:30:18.85:0,19,781 0/0:59,12:71:99:0,128,1986 0/0:44,1:45:99:0,102,1286 0/0:58,0:58:99:0,138,1786 0/0:31,0:31:78.24:0,78,995 0/0:41,1:43:99:0,105,1342 0/0:47,2:49:96.31:0,96,1296 0/0:45,0:45:99:0,117,1478 0/0:58,1:59:99:0,147,1908 0/0:57,1:58:99:0,123,1539 0/0:69,1:70:99:0,153,2026 0/0:50,0:50:99:0,114,1527 0/0:43,1:45:96.30:0,96,1265 0/0:43,0:44:99:0,105,1356 0/0:47,0:47:99:0,114,1503 0/0:47,0:47:93.26:0,93,1218 0/0:35,0:35:81.22:0,81,1035 0/0:56,0:56:99:0,117,1505 0/0:47,1:49:99:0,99,1294 0/0:49,0:49:99:0,117,1526 0/0:46,0:46:99:0,99,1255 0/0:55,0:55:99:0,123,1641 0/0:43,0:43:87.22:0,87,1090 0/0:47,0:47:99:0,102,1378 0/0:58,0:58:99:0,123,1645 0/0:60,1:61:99:0,138,1762 0/0:64,1:65:99:0,147,1913 0/0:62,0:62:99:0,166,2127 0/0:86,1:87:99:0,220,2761 0/0:94,1:96:99:0,265,3298 0/0:54,0:54:99:0,138,1762 0/0:54,1:55:99:0,138,1736 0/0:69,0:69:99:0,187,2365 0/0:59,0:59:99:0,156,1973 0/0:78,0:79:99:0,214,2668 0/0:110,0:111:99:0,274,3448 0/0:25,0:25:63.20:0,63,812 0/0:64,0:64:99:0,156,2012 0/0:116,1:117:99:0,298,3799 0/0:95,0:95:99:0,250,3105 0/0:56,1:57:99:0,147,1830 0/0:77,2:79:99:0,199,2439 0/0:67,1:68:99:0,172,2160 0/0:64,0:64:99:0,175,2167 0/0:56,0:56:99:0,147,1866 0/0:50,0:51:99:0,126,1586 0/0:62,0:63:99:0,153,1952 0/0:50,0:50:99:0,126,1526 0/0:45,0:45:99:0,108,1392 -chr1 985797 . A G 944.49 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.428;DP=2302;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.3924;InbreedingCoeff=-0.0171;MQ=57.79;MQ0=0;MQRankSum=2.462;QD=13.12;ReadPosRankSum=0.537;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|28),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:11,0:11:24.07:0,24,299 0/0:15,0:15:39.12:0,39,485 0/0:7,0:7:21.07:0,21,275 0/0:10,0:10:30.09:0,30,361 0/0:37,0:37:99:0,105,1379 0/0:36,0:36:99:0,108,1407 0/0:88,0:88:99:0,259,3410 0/0:22,0:22:57.13:0,57,693 0/0:74,0:74:99:0,214,2781 0/0:79,0:79:99:0,232,3041 0/0:31,0:31:93.28:0,93,1196 0/0:24,0:24:60.19:0,60,792 0/0:43,1:44:99:0,126,1623 0/0:21,0:21:51.16:0,51,664 0/0:27,0:27:72.23:0,72,963 0/0:20,0:20:60.19:0,60,769 0/0:21,0:21:54.15:0,54,708 0/0:20,0:20:45.14:0,45,594 0/0:26,1:27:75.24:0,75,972 0/0:30,0:30:84.27:0,84,1101 0/0:23,0:23:63.20:0,63,828 0/0:20,0:20:54.17:0,54,706 0/0:24,0:24:63.20:0,63,826 0/0:22,0:22:57.18:0,57,739 0/0:27,0:27:60.20:0,60,827 0/0:22,0:22:54.17:0,54,712 0/0:20,0:20:48.16:0,48,637 0/0:24,0:24:63.18:0,63,825 0/0:27,0:27:75.25:0,75,1002 0/0:27,0:27:69.22:0,69,913 0/0:33,0:33:87.28:0,87,1159 0/0:23,0:23:60.19:0,60,793 0/0:14,0:14:42.13:0,42,541 0/0:25,0:25:60.18:0,60,763 0/0:19,0:19:51.17:0,51,676 0/0:30,0:30:72.23:0,72,963 0/1:18,16:34:99:492,0,513 0/0:33,0:33:90.29:0,90,1204 0/0:44,0:44:99:0,117,1520 0/0:81,0:82:99:0,205,2639 0/0:62,1:63:99:0,147,1884 0/0:58,0:58:99:0,138,1837 0/1:18,18:38:99:518,0,516 0/0:44,0:45:99:0,108,1421 0/0:37,0:38:99:0,99,1252 0/0:60,0:62:99:0,150,1943 0/0:81,0:82:99:0,193,2514 0/0:41,0:41:99:0,105,1387 0/0:51,0:51:99:0,129,1667 0/0:86,0:88:99:0,211,2738 0/0:68,0:69:99:0,184,2299 0/0:54,0:54:99:0,135,1648 0/0:56,0:56:99:0,141,1753 0/0:66,0:67:99:0,156,2040 0/0:50,1:51:99:0,132,1693 0/0:50,0:50:99:0,129,1687 0/0:23,0:23:63.20:0,63,827 0/0:68,0:69:99:0,169,2173 0/0:46,0:46:99:0,114,1493 0/0:33,0:33:72.23:0,72,957 -chr1 985826 . G A 438.23 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.507;DP=2255;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.1410;InbreedingCoeff=-0.0085;MQ=57.85;MQ0=0;MQRankSum=0.635;QD=14.61;ReadPosRankSum=-0.381;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V1666I|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|Gtc/Atc|V/I|ENSG00000188157|AGRN|ENST00000379370|29/36|benign(0.119)|tolerated(0.44)|1666/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:11,0:11:24.07:0,24,295 0/0:14,0:14:33.09:0,33,390 0/0:8,0:8:21.05:0,21,243 0/0:14,0:14:42.11:0,42,498 0/0:55,0:55:99:0,160,2108 0/0:28,0:28:81.27:0,81,1087 0/0:63,0:63:99:0,181,2326 0/0:22,0:22:60.16:0,60,769 0/0:77,0:77:99:0,223,2933 0/0:84,0:84:99:0,241,3084 0/0:32,0:32:90.27:0,90,1168 0/0:28,0:28:84.26:0,84,1063 0/0:36,0:36:96.30:0,96,1250 0/0:14,0:14:39.12:0,39,499 0/0:24,0:24:66.21:0,66,852 0/0:15,0:15:39.12:0,39,505 0/0:13,0:13:33.10:0,33,438 0/0:20,0:20:39.12:0,39,530 0/0:23,0:23:57.19:0,57,779 0/0:19,0:20:54.16:0,54,689 0/0:20,0:20:60.20:0,60,804 0/0:15,0:15:39.13:0,39,524 0/0:24,0:24:66.20:0,66,853 0/0:20,0:20:60.17:0,60,769 0/0:23,0:23:51.17:0,51,693 0/0:23,0:23:54.17:0,54,704 0/0:22,0:22:54.15:0,54,675 0/0:22,0:22:60.19:0,60,791 0/0:20,0:20:54.18:0,54,723 0/0:25,0:26:63.20:0,63,840 0/0:29,0:29:84.27:0,84,1112 0/0:27,0:27:57.18:0,57,743 0/0:13,0:14:39.12:0,39,507 0/0:24,0:24:66.21:0,66,869 0/0:25,0:25:63.21:0,63,855 0/0:26,0:26:66.20:0,66,871 0/0:26,0:26:66.21:0,66,886 0/0:32,0:32:75.24:0,75,1006 0/0:46,0:47:99:0,114,1501 0/0:84,0:85:99:0,205,2615 0/0:62,0:63:99:0,153,1967 0/0:57,0:57:99:0,126,1667 0/0:34,0:34:87.27:0,87,1121 0/0:47,0:48:99:0,114,1462 0/1:14,16:30:99:486,0,349 0/0:68,0:68:99:0,172,2246 0/0:88,0:88:99:0,214,2791 0/0:43,0:43:99:0,102,1321 0/0:53,0:53:99:0,132,1699 0/0:82,0:82:99:0,211,2721 0/0:72,0:72:99:0,172,2172 0/0:58,0:58:99:0,138,1752 0/0:59,0:60:99:0,135,1706 0/0:65,0:66:99:0,156,2035 0/0:46,0:46:99:0,114,1504 0/0:53,0:53:99:0,129,1635 0/0:24,0:24:57.15:0,57,740 0/0:71,0:71:99:0,165,2113 0/0:54,0:54:99:0,132,1741 0/0:33,0:33:84.25:0,84,1049 -chr1 985855 . C T 288.16 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.233;DP=2094;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0217;InbreedingCoeff=-0.0087;MQ=58.10;MQ0=0;MQRankSum=0.034;QD=11.53;ReadPosRankSum=-1.888;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G1675|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|ggC/ggT|G|ENSG00000188157|AGRN|ENST00000379370|29/36|||1675/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:8,0:8:15.04:0,15,171 0/0:12,0:12:36.10:0,36,434 0/0:10,0:10:27.08:0,27,337 0/0:9,0:9:24.08:0,24,312 0/0:47,0:47:99:0,132,1642 0/1:13,12:25:99:336,0,394 0/0:52,0:52:99:0,141,1775 0/0:23,0:23:66.19:0,66,841 0/0:85,0:85:99:0,229,2984 0/0:81,0:82:99:0,232,2952 0/0:35,0:35:93.28:0,93,1206 0/0:32,0:33:93.28:0,93,1182 0/0:42,0:42:99:0,114,1422 0/0:12,0:12:27.08:0,27,347 0/0:20,0:20:57.18:0,57,752 0/0:13,0:13:36.11:0,36,462 0/0:14,0:14:33.11:0,33,443 0/0:16,0:16:39.11:0,39,486 0/0:22,0:22:57.17:0,57,718 0/0:20,0:20:57.16:0,57,728 0/0:17,0:17:42.11:0,42,539 0/0:14,0:14:39.11:0,39,470 0/0:29,0:30:81.25:0,81,1037 0/0:19,0:19:48.15:0,48,628 0/0:17,0:17:42.13:0,42,549 0/0:16,1:17:33.07:0,33,405 0/0:19,0:19:54.17:0,54,682 0/0:18,0:18:51.16:0,51,658 0/0:19,0:19:48.15:0,48,631 0/0:25,0:25:60.19:0,60,782 0/0:24,0:24:57.17:0,57,734 0/0:26,0:26:66.20:0,66,833 0/0:20,0:20:54.15:0,54,672 0/0:28,0:28:63.18:0,63,809 0/0:26,0:26:66.19:0,66,837 0/0:26,0:26:66.21:0,66,863 0/0:29,0:29:66.21:0,66,878 0/0:24,0:24:57.17:0,57,740 0/0:38,0:39:99:0,99,1248 0/0:80,0:80:99:0,166,2115 0/0:44,0:44:99:0,102,1285 0/0:59,1:60:93.79:0,94,1616 0/0:38,0:38:90.28:0,90,1151 0/0:45,0:45:99:0,108,1404 0/0:29,0:29:72.20:0,72,899 0/0:53,0:54:99:0,135,1757 0/0:84,0:85:99:0,193,2451 0/0:30,0:31:69.22:0,69,898 0/0:50,0:53:99:0,108,1375 0/0:70,0:73:99:0,178,2272 0/0:66,0:67:99:0,153,1926 0/0:52,0:53:99:0,132,1620 0/0:55,0:55:99:0,123,1487 0/0:51,0:52:99:0,120,1468 0/0:49,0:50:99:0,120,1502 0/0:49,0:51:99:0,120,1486 0/0:20,0:20:45.13:0,45,574 0/0:58,0:58:99:0,135,1692 0/0:44,0:44:99:0,99,1329 0/0:34,1:35:69.20:0,69,882 -chr1 985900 . C T 558.67 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.271;DP=2177;Dels=0.00;FS=1.593;HRun=2;HaplotypeScore=1.0978;InbreedingCoeff=-0.0209;MQ=58.11;MQ0=0;MQRankSum=0.567;QD=10.16;ReadPosRankSum=-1.144;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1690|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|ttC/ttT|F|ENSG00000188157|AGRN|ENST00000379370|29/36|||1690/2045|protein_coding|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:10,0:10:27.07:0,27,332 0/0:19,0:19:48.14:0,48,579 0/0:11,0:11:30.09:0,30,378 0/0:8,0:8:18.05:0,18,212 0/0:31,0:31:87.29:0,87,1169 0/0:31,0:31:84.24:0,84,1067 0/0:70,0:70:99:0,211,2717 0/0:24,0:24:66.21:0,66,842 0/0:83,0:83:99:0,235,3090 0/0:69,0:69:99:0,205,2574 0/0:31,0:31:90.29:0,90,1183 0/0:31,0:31:90.28:0,90,1137 0/0:52,0:52:99:0,150,1958 0/0:8,0:8:21.07:0,21,280 0/0:25,0:25:66.18:0,66,832 0/0:12,0:12:30.09:0,30,388 0/0:16,0:16:39.13:0,39,523 0/0:14,0:14:42.12:0,42,517 0/0:26,1:27:20.19:0,20,727 0/0:20,0:20:51.13:0,51,640 0/0:19,0:19:36.12:0,36,484 0/0:23,0:24:63.20:0,63,810 0/0:27,0:27:57.15:0,57,735 0/0:19,0:19:45.15:0,45,594 0/0:17,0:17:48.15:0,48,616 0/0:15,0:15:33.09:0,33,429 0/1:12,11:23:99:299,0,354 0/0:26,0:26:51.16:0,51,681 0/0:25,0:25:60.18:0,60,778 0/0:16,3:19:1.33:0,1,446 0/0:20,0:20:54.17:0,54,707 0/0:26,0:26:63.19:0,63,795 0/0:24,0:24:54.17:0,54,706 0/1:17,15:32:99:325,0,419 0/0:24,0:24:63.20:0,63,806 0/0:22,0:22:57.16:0,57,717 0/0:27,0:27:69.20:0,69,867 0/0:43,0:43:93.29:0,93,1263 0/0:36,0:36:87.28:0,87,1146 0/0:69,0:69:99:0,181,2283 0/0:49,0:49:99:0,126,1630 0/0:52,0:52:99:0,123,1618 0/0:41,0:41:93.29:0,93,1217 0/0:41,0:41:99:0,102,1323 0/0:32,0:32:72.21:0,72,924 0/0:56,1:57:99:0,135,1764 0/0:86,0:86:99:0,211,2673 0/0:21,0:22:57.18:0,57,710 0/0:60,0:60:99:0,132,1739 0/0:93,0:93:99:0,229,2901 0/0:69,0:69:99:0,169,2143 0/0:52,0:53:99:0,123,1541 0/0:57,0:57:99:0,150,1867 0/0:47,0:47:99:0,114,1466 0/0:56,0:56:99:0,138,1811 0/0:52,0:53:99:0,126,1625 0/0:30,0:30:63.20:0,63,833 0/0:62,0:62:99:0,153,1968 0/0:49,0:49:99:0,114,1503 0/0:38,0:39:96.30:0,96,1210 -chr1 985999 . G T 316.5 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.550;DP=1428;Dels=0.00;FS=4.252;HRun=0;HaplotypeScore=0.7980;InbreedingCoeff=-0.0179;MQ=58.27;MQ0=0;MQRankSum=0.065;QD=8.79;ReadPosRankSum=0.661;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|29),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:6,0:6:15.03:0,15,165 0/0:5,0:5:12.04:0,12,148 0/0:10,0:10:27.08:0,27,318 0/0:9,0:9:24.05:0,24,276 0/0:20,0:20:54.18:0,54,719 0/0:14,0:14:39.13:0,39,516 0/0:41,1:42:99:0,120,1538 0/0:16,0:16:48.15:0,48,621 0/0:65,0:65:99:0,196,2573 0/0:40,0:40:99:0,108,1410 0/0:27,0:27:81.25:0,81,1057 0/0:20,0:20:48.13:0,48,598 0/0:24,0:24:69.19:0,69,843 0/0:20,0:20:48.16:0,48,655 0/0:22,0:22:57.16:0,57,719 0/0:12,0:12:27.08:0,27,343 0/0:7,0:7:21.06:0,21,264 0/0:19,0:19:48.15:0,48,617 0/0:14,0:14:39.12:0,39,502 0/0:17,0:17:42.11:0,42,518 0/0:23,0:23:51.15:0,51,675 0/0:19,0:19:48.15:0,48,625 0/0:26,1:27:66.18:0,66,843 0/0:14,0:14:36.11:0,36,459 0/0:20,0:20:45.15:0,45,612 0/0:19,0:19:42.12:0,42,544 0/1:12,8:20:99:166,0,323 0/0:20,0:20:51.14:0,51,625 0/0:25,0:25:51.16:0,51,669 0/0:10,0:10:27.08:0,27,328 0/0:28,0:28:72.23:0,72,945 0/0:34,0:34:78.25:0,78,1039 0/0:22,0:22:60.19:0,60,775 0/1:9,7:16:99:216,0,261 0/0:24,0:24:54.13:0,54,665 0/0:18,0:18:45.14:0,45,584 0/0:27,0:27:66.17:0,66,833 0/0:26,0:26:75.22:0,75,962 0/0:17,0:17:48.15:0,48,611 0/0:51,0:51:99:0,126,1580 0/0:35,0:35:93.29:0,93,1201 0/0:21,0:21:48.15:0,48,610 0/0:19,0:19:45.12:0,45,542 0/0:28,0:28:60.19:0,60,755 0/0:27,0:28:69.18:0,69,856 0/0:18,0:18:48.12:0,48,588 0/0:43,0:43:99:0,120,1435 0/0:17,0:17:39.12:0,39,502 0/0:36,0:36:84.25:0,84,1040 0/0:51,0:52:99:0,123,1464 0/0:33,0:34:84.25:0,84,1059 0/0:41,0:41:84.21:0,84,1037 0/0:37,0:37:87.22:0,87,1049 0/0:25,0:25:54.16:0,54,669 0/0:34,0:34:87.24:0,87,1087 0/0:21,0:21:45.14:0,45,577 0/0:9,1:10:24.07:0,24,291 0/0:30,0:30:75.22:0,75,933 0/0:13,0:13:33.10:0,33,417 0/0:16,0:16:39.12:0,39,499 -chr1 986038 . G A 80.39 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.606;DP=1099;Dels=0.00;FS=1.750;HRun=0;HaplotypeScore=0.5655;InbreedingCoeff=-0.0135;MQ=57.65;MQ0=0;MQRankSum=0.062;QD=8.04;ReadPosRankSum=0.009;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|29),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,39 0/0:5,0:5:12.04:0,12,149 0/0:5,0:5:12.04:0,12,159 0/0:5,0:5:12.03:0,12,141 0/0:21,0:21:57.17:0,57,739 0/0:14,0:14:42.13:0,42,540 0/0:24,0:25:69.21:0,69,867 0/0:9,0:9:27.09:0,27,351 0/0:47,0:47:99:0,135,1766 0/0:40,0:42:99:0,114,1479 0/0:18,0:18:45.10:0,45,545 0/0:20,0:20:60.17:0,60,753 0/0:29,0:29:84.23:0,84,1034 0/0:19,0:19:42.10:0,42,505 0/0:23,0:24:63.18:0,63,781 0/0:10,0:10:27.09:0,27,353 0/0:7,0:7:21.07:0,21,269 0/0:18,0:18:51.11:0,51,613 0/0:12,0:12:33.08:0,33,403 0/0:16,0:16:42.12:0,42,517 0/0:19,0:19:51.16:0,51,661 0/0:17,0:17:42.12:0,42,517 0/0:22,0:22:51.16:0,51,671 0/0:9,0:9:21.04:0,21,237 0/0:21,0:21:45.12:0,45,573 0/0:15,0:15:45.14:0,45,573 0/0:9,0:9:24.08:0,24,313 0/0:17,0:18:45.13:0,45,571 0/0:17,0:17:51.15:0,51,651 0/0:13,0:13:39.13:0,39,509 0/0:22,0:22:54.15:0,54,670 0/0:13,0:14:33.10:0,33,420 0/0:12,0:12:33.11:0,33,426 0/0:18,0:18:48.15:0,48,631 0/0:20,0:20:51.15:0,51,643 0/0:13,0:13:36.11:0,36,458 0/0:18,0:18:48.14:0,48,589 0/0:25,0:25:63.20:0,63,808 0/0:15,0:15:42.13:0,42,529 0/0:31,0:32:87.20:0,87,1032 0/0:28,0:28:78.24:0,78,988 0/0:18,0:18:42.13:0,42,520 0/0:11,1:12:27.08:0,27,333 0/0:19,0:19:48.14:0,48,598 0/0:16,0:16:42.12:0,42,545 0/0:15,0:15:42.13:0,42,540 0/0:34,0:34:90.26:0,90,1165 0/1:5,5:10:99:128,0,156 0/0:24,0:24:60.19:0,60,759 0/0:49,0:49:99:0,132,1646 0/0:23,0:23:63.19:0,63,779 0/0:30,0:30:78.23:0,78,979 0/0:26,0:26:72.20:0,72,891 0/0:16,0:16:45.14:0,45,583 0/0:21,0:21:60.17:0,60,755 0/0:12,0:12:30.07:0,30,358 0/0:4,0:4:12.04:0,12,148 0/0:25,0:26:66.20:0,66,826 0/0:13,0:13:36.11:0,36,474 0/0:7,0:7:21.07:0,21,266 -chr1 986285 . C T 224.77 . AC=2;AF=0.0169;AN=118;BaseQRankSum=0.797;DP=1956;Dels=0.00;FS=30.697;HRun=0;HaplotypeScore=1.3276;InbreedingCoeff=-0.0312;MQ=54.91;MQ0=0;MQRankSum=2.696;QD=12.49;ReadPosRankSum=-0.681;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|30),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,79 0/0:10,0:10:21.07:0,21,275 0/0:3,0:3:9.02:0,9,100 ./. 0/0:5,0:5:12.04:0,12,149 0/0:4,0:4:9:0,9,95 0/0:12,0:12:33.10:0,33,403 0/0:2,0:2:6.02:0,6,73 0/0:13,0:13:36.11:0,36,454 0/0:12,0:12:36.11:0,36,464 0/0:3,0:3:6.02:0,6,75 0/0:3,0:3:9.03:0,9,108 0/0:4,0:4:9.03:0,9,105 0/0:13,0:13:33.10:0,33,423 0/0:6,0:6:18.05:0,18,223 0/0:6,0:6:15.05:0,15,181 0/0:11,0:11:30.09:0,30,364 0/0:7,0:7:21.06:0,21,263 0/0:6,0:6:18.05:0,18,206 0/0:9,0:9:27.07:0,27,338 0/0:8,0:8:24.06:0,24,259 0/0:15,0:15:39.11:0,39,464 0/0:15,0:15:39.12:0,39,514 0/0:7,0:7:21.06:0,21,255 0/0:7,0:7:18.06:0,18,240 0/0:6,0:6:18.05:0,18,220 0/1:3,4:8:92.71:132,0,93 0/0:8,0:8:21.05:0,21,230 0/0:6,0:6:18.06:0,18,238 0/0:13,0:13:33.10:0,33,420 0/0:4,0:4:12.03:0,12,139 0/0:9,0:9:21.07:0,21,263 0/0:2,0:2:6.02:0,6,76 0/1:5,5:10:99:158,0,142 0/0:7,0:7:21.06:0,21,250 0/0:7,0:7:18.06:0,18,238 0/0:6,0:6:15.04:0,15,181 0/0:16,0:16:42.12:0,42,487 0/0:56,0:56:99:0,132,1630 0/0:107,0:107:99:0,268,3373 0/0:85,0:85:99:0,217,2635 0/0:63,0:63:99:0,141,1824 0/0:61,0:61:99:0,162,2047 0/0:56,0:56:99:0,123,1578 0/0:56,0:56:99:0,132,1680 0/0:68,0:68:99:0,147,1890 0/0:146,1:147:99:0,292,4063 0/0:40,0:40:96.28:0,96,1183 0/0:70,0:70:99:0,156,1961 0/0:120,0:120:99:0,277,3450 0/0:122,0:122:99:0,286,3568 0/0:104,0:104:99:0,235,2907 0/0:111,1:112:99:0,235,2995 0/0:74,0:74:99:0,159,2023 0/0:55,0:55:99:0,144,1826 0/0:61,0:61:99:0,150,1925 0/0:52,0:52:99:0,129,1655 0/0:72,0:72:99:0,147,1926 0/0:53,0:53:99:0,123,1560 0/0:36,0:36:99:0,102,1281 -chr1 986286 . C T 649.39 . AC=1;AF=0.0085;AN=118;BaseQRankSum=-0.566;DP=1981;Dels=0.00;FS=22.049;HRun=0;HaplotypeScore=1.6726;InbreedingCoeff=-0.0217;MQ=54.94;MQ0=0;MQRankSum=4.757;QD=11.39;ReadPosRankSum=1.099;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|30),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,77 0/0:10,0:10:27.09:0,27,344 0/0:3,0:3:9:0,9,92 ./. 0/0:5,0:5:12.04:0,12,149 0/0:5,0:5:12.04:0,12,151 0/0:12,0:12:33.10:0,33,400 0/0:2,0:2:6.02:0,6,73 0/0:13,0:13:36.11:0,36,455 0/0:12,0:12:36.12:0,36,468 0/0:4,0:4:9.03:0,9,115 0/0:3,0:3:9.03:0,9,108 0/0:4,0:4:12.04:0,12,143 0/0:13,0:13:36.11:0,36,457 0/0:6,0:6:18.05:0,18,217 0/0:6,0:6:15.05:0,15,183 0/0:11,0:11:30.09:0,30,364 0/0:7,0:7:21.06:0,21,263 0/0:6,0:6:18.05:0,18,210 0/0:9,0:9:24.08:0,24,312 0/0:8,0:8:24.06:0,24,263 0/0:15,0:15:42.12:0,42,497 0/0:15,0:15:39.13:0,39,518 0/0:7,0:7:21.06:0,21,255 0/0:7,0:7:18.06:0,18,240 0/0:6,0:6:18.05:0,18,219 0/0:8,0:8:21.07:0,21,274 0/0:8,0:8:21.06:0,21,242 0/0:6,0:6:18.06:0,18,236 0/0:14,0:14:36.09:0,36,435 0/0:4,0:4:12.03:0,12,136 0/0:9,0:9:21.06:0,21,261 0/0:1,0:1:3.01:0,3,41 0/0:10,0:10:30.09:0,30,359 0/0:6,0:6:18.05:0,18,216 0/0:7,0:7:21.07:0,21,270 0/0:6,0:6:15.05:0,15,181 0/0:16,0:16:42.12:0,42,489 0/0:58,0:58:99:0,138,1733 0/0:109,0:109:99:0,271,3389 0/0:86,0:86:99:0,217,2687 0/0:65,0:65:99:0,150,1892 0/0:61,0:61:99:0,163,2061 0/0:55,1:56:99:0,123,1596 0/1:29,28:57:99:697,0,714 0/0:69,0:69:99:0,156,1991 0/0:153,0:153:99:0,340,4332 0/0:41,0:41:99:0,99,1222 0/0:70,0:70:99:0,159,1982 0/0:122,0:122:99:0,292,3643 0/0:123,0:123:99:0,292,3669 0/0:103,0:103:99:0,226,2830 0/0:112,0:112:99:0,238,3028 0/0:77,0:77:99:0,168,2116 0/0:55,0:55:99:0,144,1830 0/0:61,0:61:99:0,153,1957 0/0:53,0:53:99:0,135,1731 0/0:73,0:73:99:0,153,1981 0/0:54,0:54:99:0,126,1587 0/0:36,0:36:99:0,99,1226 -chr1 986443 . C T 41215.18 . AC=100;AF=0.8621;AN=116;BaseQRankSum=0.781;DP=1363;Dels=0.00;FS=2.212;HRun=0;HaplotypeScore=0.8018;InbreedingCoeff=0.1240;MQ=57.18;MQ0=0;MQRankSum=-1.053;QD=31.27;ReadPosRankSum=-1.007;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000479707|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|30),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000479707|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. 0/1:3,1:4:27.97:28,0,88 0/1:2,2:4:59.04:59,0,69 ./. 1/1:0,1:1:3:25,3,0 1/1:0,5:5:9.03:112,9,0 1/1:0,2:2:6.02:78,6,0 1/1:0,2:2:6.02:80,6,0 1/1:0,4:4:12.03:148,12,0 1/1:0,7:7:21.07:269,21,0 1/1:0,5:5:15.05:197,15,0 0/0:1,0:1:3.01:0,3,33 1/1:0,5:5:12.04:161,12,0 1/1:0,4:4:9.03:124,9,0 1/1:0,3:3:9.03:119,9,0 1/1:0,5:5:15.05:189,15,0 1/1:0,5:5:15.04:187,15,0 1/1:0,3:3:6.02:83,6,0 1/1:0,4:4:12.04:157,12,0 1/1:0,3:3:6.02:85,6,0 0/1:1,3:4:29.19:109,0,29 1/1:0,4:4:12.04:150,12,0 1/1:0,5:5:12.04:155,12,0 1/1:0,2:2:6.02:81,6,0 1/1:0,1:1:3.01:42,3,0 1/1:0,2:2:3.01:45,3,0 0/1:3,3:6:98.88:99,0,108 1/1:0,3:3:9.03:121,9,0 1/1:0,2:2:6.02:78,6,0 1/1:0,2:2:6.02:77,6,0 1/1:0,5:5:15.05:187,15,0 1/1:0,9:9:27.08:330,27,0 1/1:0,5:5:15.05:191,15,0 0/1:1,3:4:26.22:75,0,26 1/1:0,2:2:6.02:68,6,0 1/1:0,1:1:3.01:42,3,0 1/1:0,9:9:24.08:315,24,0 0/0:5,0:5:15.04:0,15,187 1/1:0,45:45:99:1653,129,0 1/1:0,79:80:99:2891,226,0 0/1:37,32:70:99:818,0,1107 0/1:23,23:46:99:643,0,745 1/1:0,41:41:99:1517,117,0 1/1:1,53:54:99:1918,147,0 0/1:18,28:46:99:908,0,457 1/1:1,49:50:99:1757,102,0 1/1:0,99:100:99:3524,277,0 1/1:0,33:33:96.27:1174,96,0 1/1:0,60:60:99:2006,159,0 1/1:0,69:69:99:2398,193,0 1/1:1,69:70:99:2397,187,0 1/1:0,45:45:99:1604,126,0 1/1:0,64:64:99:2325,181,0 1/1:0,71:72:99:2306,184,0 1/1:0,59:59:99:2125,169,0 1/1:0,60:60:99:2093,165,0 0/1:16,19:35:99:649,0,394 0/1:21,20:41:99:572,0,621 1/1:0,46:46:99:1673,132,0 0/0:38,0:38:99:0,102,1295 -chr1 986737 . T C 414.03 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-2.032;DP=1137;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7186;InbreedingCoeff=-0.0327;MQ=58.21;MQ0=0;MQRankSum=1.287;QD=8.63;ReadPosRankSum=2.285;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G1786|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|ggT/ggC|G|ENSG00000188157|AGRN|ENST00000379370|31/36|||1786/2045|protein_coding|1,synonymous_variant|ggT/ggC|G|ENSG00000188157|AGRN|ENST00000419249|4/9|||89/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6:0,6,58 0/0:1,0:2:3.01:0,3,38 0/0:2,0:2:6.02:0,6,78 0/0:4,0:4:12.04:0,12,149 0/0:1,0:1:3.01:0,3,39 0/0:14,0:14:39.12:0,39,496 0/0:13,0:13:36.08:0,36,418 0/0:15,0:16:45.13:0,45,536 0/0:10,0:10:24.06:0,24,288 0/0:8,0:8:21.04:0,21,239 0/0:3,0:3:6.02:0,6,80 0/0:6,0:6:15.05:0,15,197 0/0:19,1:20:51.16:0,51,670 0/0:34,0:34:81.26:0,81,1063 0/0:12,0:12:36.10:0,36,442 0/0:32,0:32:81.23:0,81,1028 0/0:19,0:19:48.15:0,48,615 0/0:24,0:24:60.19:0,60,786 0/0:25,0:25:63.20:0,63,839 0/0:35,0:36:72.23:0,72,955 0/0:27,0:27:57.18:0,57,749 0/0:19,0:19:45.14:0,45,593 0/0:22,1:23:48.13:0,48,619 0/0:27,0:27:75.21:0,75,937 0/0:28,0:28:69.19:0,69,868 0/1:10,9:19:99:240,0,330 0/0:21,0:21:54.17:0,54,696 0/0:32,0:32:78.23:0,78,988 0/0:35,0:35:84.26:0,84,1107 0/0:34,0:35:78.22:0,78,1013 0/0:26,0:26:72.23:0,72,944 0/0:24,0:24:57.15:0,57,717 0/1:20,9:29:99:239,0,595 0/0:20,0:20:54.17:0,54,692 0/0:22,0:22:51.16:0,51,664 0/0:45,1:47:99:0,105,1341 0/0:26,0:28:69.22:0,69,892 0/0:15,0:15:39.12:0,39,507 0/0:35,0:35:78.24:0,78,1014 0/0:22,0:23:63.19:0,63,778 0/0:13,0:13:33.10:0,33,421 0/0:18,1:19:42.13:0,42,532 0/0:17,0:17:45.14:0,45,563 0/0:12,0:12:33.08:0,33,406 0/0:20,0:21:48.15:0,48,627 0/0:32,0:33:78.24:0,78,972 0/0:4,0:4:12.04:0,12,151 0/0:7,0:7:18.04:0,18,218 0/0:29,0:31:81.25:0,81,1009 0/0:33,1:34:90.26:0,90,1117 0/0:15,0:16:36.11:0,36,447 0/0:18,0:19:51.13:0,51,632 0/0:17,0:17:33.09:0,33,401 0/0:13,0:14:30.09:0,30,380 0/0:5,0:6:15.05:0,15,197 0/0:15,0:15:42.14:0,42,555 0/0:18,0:18:48.11:0,48,570 0/0:10,0:10:27.09:0,27,350 0/0:11,0:11:33.10:0,33,423 -chr1 986885 . T G 155.26 . AC=7;AF=0.0593;AN=118;BaseQRankSum=-10.562;DP=745;Dels=0.00;FS=53.331;HRun=2;HaplotypeScore=0.5798;InbreedingCoeff=-0.0971;MQ=57.41;MQ0=0;MQRankSum=1.830;QD=1.14;ReadPosRankSum=-2.492;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V1808G|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,missense_variant|gTg/gGg|V/G|ENSG00000188157|AGRN|ENST00000379370|32/36|possibly_damaging(0.727)|tolerated(0.14)|1808/2045|protein_coding|1,missense_variant|gTg/gGg|V/G|ENSG00000188157|AGRN|ENST00000419249|5/9|possibly_damaging(0.723)|tolerated(0.1)|111/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL ./. 0/0:5,2:7:12.03:0,12,140 0/0:2,2:4:6.02:0,6,73 0/0:3,2:5:9.02:0,9,99 0/1:7,8:15:36.01:36,0,222 0/1:10,9:19:29.10:29,0,259 0/1:7,10:18:16.30:16,0,169 0/0:10,6:16:3.41:0,3,317 0/1:12,10:22:16.14:16,0,383 0/1:12,13:26:41.70:42,0,370 0/0:5,3:8:9.03:0,9,113 0/1:9,8:17:95.07:95,0,288 0/1:9,10:19:41.24:41,0,272 0/0:5,0:5:9.03:0,9,123 0/0:23,1:24:51.09:0,51,595 0/0:9,1:10:24.07:0,24,306 0/0:17,2:19:36.12:0,36,478 0/0:20,3:23:54.07:0,54,605 0/0:15,1:16:33.08:0,33,372 0/0:13,0:13:27.07:0,27,322 0/0:20,3:23:51.16:0,51,665 0/0:22,2:24:57.16:0,57,711 0/0:16,2:19:33.06:0,33,397 0/0:10,2:12:21.06:0,21,269 0/0:21,2:23:51.13:0,51,610 0/0:21,1:22:54.11:0,54,651 0/0:10,2:12:24.07:0,24,299 0/0:14,3:17:36.07:0,36,414 0/0:15,1:16:17.41:0,17,439 0/0:13,2:15:27.06:0,27,322 0/0:14,3:17:33.10:0,33,406 0/0:10,0:11:24.04:0,24,287 0/0:15,1:16:33.07:0,33,391 0/0:14,1:15:33.10:0,33,414 0/0:20,2:22:48.10:0,48,568 0/0:18,2:20:45.06:0,45,487 0/0:20,1:21:39.06:0,39,441 0/0:20,0:21:45.05:0,45,521 0/0:4,0:4:12.04:0,12,141 0/0:8,1:9:21.05:0,21,233 0/0:8,0:8:18.03:0,18,210 0/0:2,1:3:6.01:0,6,66 0/0:4,0:4:9.02:0,9,105 0/0:4,1:5:12.03:0,12,132 0/0:5,0:5:12.01:0,12,145 0/0:5,1:6:15.04:0,15,178 0/0:13,0:13:24.06:0,24,280 0/0:2,0:2:6.02:0,6,65 0/0:1,0:1:3.01:0,3,35 0/0:13,1:14:39.10:0,39,451 0/0:10,1:11:1.52:0,2,328 0/0:7,1:8:18.05:0,18,226 0/0:9,1:10:21.06:0,21,254 0/0:8,0:8:21.05:0,21,235 0/0:3,0:3:9.02:0,9,95 0/0:3,1:4:5.99:0,6,53 0/0:3,0:3:9.03:0,9,113 0/0:2,0:2:6.02:0,6,77 0/0:2,0:2:6.02:0,6,76 0/0:4,0:4:6.02:0,6,71 -chr1 986920 . C A 169.9 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.934;DP=839;Dels=0.00;FS=1.422;HRun=0;HaplotypeScore=0.7669;InbreedingCoeff=-0.0288;MQ=58.26;MQ0=0;MQRankSum=0.709;QD=10.62;ReadPosRankSum=2.238;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),SYNONYMOUS_CODING(LOW|SILENT|Cgg/Agg|R1820|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,synonymous_variant|Cgg/Agg|R|ENSG00000188157|AGRN|ENST00000379370|32/36|||1820/2045|protein_coding|1,synonymous_variant|Cgg/Agg|R|ENSG00000188157|AGRN|ENST00000419249|5/9|||123/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:3:3.01:0,3,39 0/0:3,0:3:3.01:0,3,40 0/0:3,0:4:9.03:0,9,119 0/0:7,0:7:21.06:0,21,259 0/0:11,0:11:27.09:0,27,363 0/0:15,0:15:30.10:0,30,393 0/0:31,0:31:90.28:0,90,1156 0/0:9,0:9:21.07:0,21,277 0/0:38,0:39:99:0,105,1402 0/0:34,1:35:49.02:0,49,1072 0/0:13,0:13:36.11:0,36,454 0/0:19,0:19:57.17:0,57,707 0/0:12,0:12:36.11:0,36,460 0/0:9,0:9:24.08:0,24,319 0/0:15,0:15:42.10:0,42,514 0/0:8,0:8:24.08:0,24,303 0/0:18,0:18:51.15:0,51,671 0/0:29,0:29:60.18:0,60,767 0/0:21,0:21:57.18:0,57,757 0/1:9,7:16:99:217,0,224 0/0:20,0:20:48.15:0,48,627 0/0:27,0:27:69.22:0,69,918 0/0:19,0:19:48.15:0,48,618 0/0:14,0:14:36.10:0,36,434 0/0:21,0:22:51.16:0,51,659 0/0:28,0:28:63.18:0,63,818 0/0:18,0:18:45.14:0,45,598 0/0:18,1:19:45.14:0,45,575 0/0:15,0:15:42.12:0,42,532 0/0:27,0:27:66.20:0,66,881 0/0:20,0:20:51.16:0,51,682 0/0:17,0:17:33.11:0,33,456 0/0:17,0:17:45.12:0,45,578 0/0:24,0:25:51.17:0,51,703 0/0:17,0:17:42.12:0,42,555 0/0:22,0:22:57.16:0,57,722 0/0:24,0:24:60.18:0,60,748 0/0:27,0:27:63.21:0,63,847 0/0:6,0:6:15.05:0,15,190 0/0:9,0:9:12.04:0,12,166 0/0:8,0:8:21.07:0,21,280 0/0:2,0:2:6.02:0,6,77 0/0:5,0:5:15.04:0,15,173 0/0:6,0:6:15.05:0,15,187 0/0:5,0:5:12.04:0,12,158 0/0:7,0:7:18.06:0,18,235 0/0:14,0:14:36.10:0,36,441 0/0:2,0:2:6.02:0,6,70 0/0:1,0:1:3.01:0,3,37 0/0:15,0:15:45.14:0,45,592 0/0:9,0:9:27.08:0,27,332 0/0:9,0:9:27.08:0,27,350 0/0:9,0:9:27.08:0,27,344 0/0:10,0:10:27.09:0,27,355 0/0:5,0:6:9.03:0,9,119 0/0:6,0:6:15.05:0,15,197 0/0:4,0:4:9.03:0,9,124 0/0:3,0:3:6.02:0,6,78 0/0:3,0:3:9.03:0,9,123 0/0:5,0:5:15.05:0,15,179 -chr1 987200 . C T 92501.43 . AC=100;AF=0.8333;AN=120;BaseQRankSum=1.193;DP=3392;Dels=0.00;FS=27.772;HRun=0;HaplotypeScore=2.0645;InbreedingCoeff=0.1600;MQ=56.45;MQ0=0;MQRankSum=1.254;QD=28.89;ReadPosRankSum=-2.661;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,18:18:45.12:535,45,0 0/1:6,16:22:99:518,0,126 0/1:12,3:15:65.97:66,0,367 0/1:11,7:18:99:163,0,367 1/1:0,42:42:99:1603,123,0 1/1:0,42:42:99:1652,126,0 1/1:0,49:49:99:1894,144,0 1/1:0,34:34:99:1320,102,0 1/1:0,88:88:99:3348,256,0 1/1:0,88:88:99:3386,256,0 1/1:0,37:37:99:1412,108,0 0/1:22,22:44:99:718,0,681 1/1:0,48:48:99:1754,135,0 1/1:0,66:66:99:1967,150,0 1/1:0,59:59:99:1748,129,0 1/1:0,35:35:81.25:1068,81,0 1/1:0,48:49:99:1517,114,0 1/1:0,42:42:99:1353,105,0 1/1:0,51:51:99:1704,132,0 1/1:0,53:53:99:1678,129,0 0/1:22,19:41:99:488,0,704 1/1:0,57:57:99:1840,141,0 1/1:0,35:35:87.27:1128,87,0 1/1:0,55:55:99:1907,144,0 0/1:20,22:42:99:601,0,498 1/1:0,55:55:99:1709,132,0 0/1:27,22:49:99:626,0,687 1/1:0,38:38:90.27:1177,90,0 0/1:24,29:53:99:696,0,711 1/1:0,48:49:99:1498,114,0 1/1:0,62:62:99:2102,163,0 1/1:0,41:41:99:1359,102,0 1/1:0,52:52:99:1548,114,0 0/0:64,0:64:99:0,159,2057 1/1:0,56:56:99:1777,138,0 1/1:0,61:61:99:1860,141,0 1/1:0,67:67:99:2232,172,0 0/0:73,0:73:99:0,175,2267 1/1:0,44:44:99:1343,105,0 1/1:0,101:101:99:3377,274,0 0/1:47,31:78:99:864,0,1353 0/1:37,34:71:99:933,0,1084 1/1:2,47:49:81.63:1547,82,0 1/1:0,48:48:99:1405,111,0 0/1:21,25:46:99:758,0,464 1/1:0,69:69:99:2293,181,0 1/1:0,115:115:99:3652,289,0 0/1:21,18:39:99:526,0,544 1/1:0,67:67:99:2047,159,0 1/1:0,117:118:99:3716,301,0 1/1:0,113:113:99:3709,298,0 1/1:0,95:95:99:3044,244,0 1/1:0,95:96:99:3123,253,0 1/1:0,69:70:99:2138,171,0 1/1:0,47:48:99:1453,117,0 1/1:0,46:46:99:1471,114,0 0/1:23,20:43:99:447,0,621 0/1:38,37:77:99:936,0,915 1/1:0,55:55:99:1766,138,0 0/0:50,3:53:94.58:0,95,1598 -chr1 987253 . C T 635.19 . AC=4;AF=0.0333;AN=120;BaseQRankSum=0.926;DP=2121;Dels=0.00;FS=5.063;HRun=0;HaplotypeScore=1.9053;InbreedingCoeff=-0.0356;MQ=53.70;MQ0=0;MQRankSum=0.039;QD=7.22;ReadPosRankSum=-2.083;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:13,0:13:33.09:0,33,403 0/0:14,0:14:36.10:0,36,449 0/0:7,0:7:18.06:0,18,227 0/0:3,0:3:9.03:0,9,117 0/0:20,0:21:60.20:0,60,804 0/0:20,0:20:60.20:0,60,797 0/0:38,0:38:99:0,114,1521 0/1:14,10:24:99:332,0,480 0/0:44,0:44:99:0,126,1688 0/0:41,0:41:99:0,120,1560 0/0:20,0:20:57.16:0,57,712 0/0:26,0:26:72.24:0,72,955 0/0:26,0:26:75.23:0,75,967 0/0:27,0:27:72.19:0,72,903 0/0:24,0:24:63.18:0,63,793 0/0:22,0:22:51.16:0,51,662 0/0:22,0:22:51.15:0,51,663 0/0:18,0:18:36.10:0,36,446 0/1:20,3:23:40.85:41,0,572 0/0:23,0:23:57.17:0,57,733 0/0:19,0:19:39.12:0,39,495 0/0:20,0:20:45.11:0,45,556 0/0:13,0:13:36.10:0,36,435 0/0:19,0:19:54.17:0,54,706 0/0:19,0:20:33.09:0,33,402 0/0:29,0:29:60.19:0,60,785 0/0:33,0:33:63.19:0,63,804 0/1:12,7:19:99:178,0,308 0/0:29,0:30:72.22:0,72,908 0/0:25,0:25:66.19:0,66,832 0/0:27,0:27:63.19:0,63,803 0/0:15,0:15:42.10:0,42,514 0/1:15,6:22:99:177,0,406 0/0:28,0:28:51.16:0,51,657 0/0:23,0:23:54.17:0,54,690 0/0:25,0:25:60.18:0,60,775 0/0:29,0:30:63.18:0,63,789 0/0:40,0:40:90.27:0,90,1168 0/0:34,0:34:78.22:0,78,957 0/0:80,0:80:99:0,178,2190 0/0:71,2:74:95.62:0,96,1866 0/0:52,0:53:99:0,108,1344 0/0:36,0:36:78.25:0,78,998 0/0:35,0:35:81.24:0,81,1000 0/0:37,0:37:84.24:0,84,1007 0/0:56,0:57:99:0,120,1490 0/0:88,1:89:99:0,174,2454 0/0:32,0:33:60.14:0,60,725 0/0:50,0:50:99:0,117,1425 0/0:92,0:95:99:0,190,2256 0/0:83,0:84:99:0,202,2431 0/0:81,0:82:99:0,202,2429 0/0:80,0:80:99:0,159,1967 0/0:54,0:54:99:0,99,1225 0/0:55,0:56:99:0,126,1513 0/0:43,0:43:99:0,99,1248 0/0:28,0:29:54.16:0,54,649 0/0:59,0:59:99:0,123,1509 0/0:37,1:38:40.01:0,40,922 0/0:30,0:30:66.20:0,66,794 -chr1 987311 . T C 44.81 . AC=8;AF=0.0667;AN=120;BaseQRankSum=-7.260;DP=1543;Dels=0.00;FS=87.443;HRun=3;HaplotypeScore=1.4824;InbreedingCoeff=0.0204;MQ=46.77;MQ0=0;MQRankSum=0.941;QD=0.41;ReadPosRankSum=-2.570;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,2:5:3.01:0,3,39 0/0:1,3:4:3.01:0,3,41 0/0:2,1:3:6.02:0,6,76 0/0:2,4:6:6.02:0,6,76 0/0:5,4:9:9.03:0,9,121 0/0:6,8:14:6:0,6,57 0/1:8,11:19:36.76:37,0,219 0/0:4,1:5:9.03:0,9,124 0/1:11,14:25:49.92:50,0,225 0/0:14,12:26:21.06:0,21,273 0/0:8,3:11:21.07:0,21,275 0/0:6,3:9:12.04:0,12,159 0/0:5,6:11:3.01:0,3,41 0/0:5,6:12:9.02:0,9,101 0/1:6,7:13:6.68:7,0,126 0/0:4,5:9:9.01:0,9,83 0/0:12,2:14:36.08:0,36,413 0/0:8,3:12:15.03:0,15,165 0/0:5,5:10:9.02:0,9,103 0/0:5,6:11:6.02:0,6,72 0/0:8,5:13:18.03:0,18,198 0/0:6,6:13:9.02:0,9,96 0/0:5,4:9:9.03:0,9,112 0/0:7,6:13:18.04:0,18,217 0/0:4,8:12:6:0,6,53 0/1:10,3:13:9.62:10,0,153 0/0:9,5:14:18.05:0,18,203 0/0:8,1:9:6.02:0,6,72 0/0:7,5:12:9.03:0,9,113 0/1:5,6:11:9.65:10,0,127 0/0:9,7:16:12.04:0,12,152 0/0:4,4:8:9.03:0,9,108 0/0:7,4:12:9.03:0,9,111 0/1:9,9:18:20.23:20,0,113 1/1:4,5:9:3:25,3,0 0/0:5,1:7:6.02:0,6,80 0/0:8,6:14:12:0,12,118 0/0:12,3:15:12.01:0,12,136 0/0:27,7:34:57.15:0,57,691 0/0:55,16:72:99:0,105,1242 0/0:46,23:69:43.30:0,43,1126 0/0:36,19:55:77.90:0,78,935 0/0:18,9:27:36.08:0,36,429 0/0:16,11:27:32.91:0,33,345 0/0:21,16:37:17.42:0,17,442 0/0:34,14:48:75.22:0,75,916 0/0:43,18:61:99:0,99,1151 0/0:17,6:23:36.06:0,36,385 0/0:37,19:56:55.52:0,56,904 0/0:48,27:77:1.27:0,1,824 0/0:61,20:81:99:0,109,1556 0/0:46,22:69:99:0,111,1336 0/0:56,17:73:90.25:0,90,1086 0/0:38,10:49:63.18:0,63,782 0/0:46,19:66:99:0,104,1254 0/0:23,12:35:46.69:0,47,555 0/0:17,8:25:36.09:0,36,434 0/0:36,14:51:53.41:0,53,845 0/0:23,12:35:42.10:0,42,495 0/0:19,8:27:33.07:0,33,375 -chr1 987341 . C T 217.82 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.265;DP=1310;Dels=0.00;FS=10.232;HRun=0;HaplotypeScore=1.1876;InbreedingCoeff=-0.0145;MQ=48.15;MQ0=0;MQRankSum=2.296;QD=7.03;ReadPosRankSum=0.839;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:6,0:6:12.04:0,12,155 0/0:10,0:10:21.06:0,21,258 0/0:3,0:3:9.02:0,9,100 0/0:5,0:5:12.03:0,12,141 0/0:9,0:9:27.09:0,27,350 0/0:6,0:6:18.05:0,18,221 0/0:18,0:18:54.17:0,54,681 0/0:3,0:3:6.01:0,6,66 0/0:12,0:12:36.12:0,36,487 0/0:24,0:24:72.23:0,72,918 0/0:6,0:6:18.06:0,18,234 0/0:9,0:9:27.09:0,27,348 0/0:8,0:8:24.06:0,24,272 0/0:9,0:9:27.08:0,27,310 0/0:8,0:8:24.07:0,24,273 0/0:6,0:6:15.04:0,15,167 0/0:7,0:7:15.04:0,15,177 0/0:8,0:8:21.06:0,21,239 0/0:8,0:8:24.07:0,24,289 0/0:13,0:13:39.09:0,39,428 0/0:9,0:9:24.07:0,24,278 0/0:11,0:11:33.09:0,33,371 0/0:5,0:5:15.04:0,15,172 0/0:7,0:7:21.06:0,21,234 0/0:10,0:10:27.07:0,27,299 0/0:6,0:6:15.04:0,15,172 0/0:8,0:8:24.07:0,24,267 0/0:6,0:6:15.04:0,15,183 0/0:6,0:6:15.04:0,15,167 0/0:10,0:10:30.09:0,30,358 0/0:14,0:14:36.11:0,36,428 0/0:10,0:10:30.09:0,30,358 0/0:11,0:11:30.08:0,30,334 0/0:11,0:11:30.08:0,30,350 0/0:9,0:9:27.08:0,27,320 0/0:7,0:7:21.06:0,21,244 0/0:8,0:8:21.06:0,21,244 0/0:10,0:10:30.09:0,30,349 0/1:19,12:31:99:266,0,562 0/0:61,0:61:99:0,156,1877 0/0:62,0:62:99:0,162,1958 0/0:50,0:50:99:0,111,1425 0/0:25,0:25:75.23:0,75,915 0/0:28,0:28:66.19:0,66,781 0/0:38,0:38:96.27:0,96,1146 0/0:42,0:42:99:0,111,1378 0/0:53,1:54:99:0,138,1677 0/0:22,0:22:51.15:0,51,629 0/0:56,0:56:99:0,135,1652 0/0:58,0:58:99:0,159,1877 0/0:67,0:67:99:0,159,1955 0/0:60,0:60:99:0,141,1722 0/0:71,0:71:99:0,174,2081 0/0:37,0:37:99:0,102,1225 0/0:57,0:57:99:0,135,1660 0/0:28,0:28:72.22:0,72,896 0/0:18,0:18:54.16:0,54,648 0/0:48,0:48:99:0,117,1452 0/0:35,0:35:93.27:0,93,1121 0/0:26,0:26:69.20:0,69,831 -chr1 987342 . G A 259.15 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-4.057;DP=1247;Dels=0.00;FS=1.217;HRun=0;HaplotypeScore=1.1837;InbreedingCoeff=-0.0234;MQ=48.33;MQ0=0;MQRankSum=1.716;QD=5.76;ReadPosRankSum=0.808;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,upstream_gene_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:6,0:6:12.04:0,12,152 0/0:10,0:10:24.08:0,24,303 0/0:3,0:3:9:0,9,94 0/0:5,0:5:12.04:0,12,143 0/0:8,0:8:24.08:0,24,308 0/0:4,0:4:12.04:0,12,148 0/0:15,0:15:42.13:0,42,532 0/0:3,0:3:6.02:0,6,74 0/0:11,0:11:33.11:0,33,445 0/0:20,0:20:60.18:0,60,732 0/0:5,0:5:15.05:0,15,197 0/0:10,0:10:30.09:0,30,380 0/0:8,0:8:21.06:0,21,248 0/1:8,1:9:6.37:6,0,244 0/0:7,0:7:18.05:0,18,206 0/0:5,0:5:15.04:0,15,167 0/0:6,0:6:9.03:0,9,111 0/0:7,0:7:18.05:0,18,206 0/0:8,0:8:24.07:0,24,284 0/0:12,0:12:36.07:0,36,392 0/0:8,0:8:21.06:0,21,242 0/0:10,0:10:30.09:0,30,343 0/0:5,0:5:12.03:0,12,139 0/0:7,0:7:21.06:0,21,231 0/0:9,0:9:24.06:0,24,261 0/0:6,0:6:18.04:0,18,195 0/0:8,0:8:24.07:0,24,266 0/0:5,0:5:12.04:0,12,149 0/0:6,0:6:18.05:0,18,204 0/0:9,0:9:27.06:0,27,315 0/0:14,0:14:36.11:0,36,429 0/0:8,0:8:24.07:0,24,294 0/0:11,0:11:30.08:0,30,343 0/0:10,0:10:27.08:0,27,319 0/0:8,0:8:24.07:0,24,285 0/0:7,0:7:21.06:0,21,243 0/0:7,0:7:18.05:0,18,206 0/0:7,0:7:21.06:0,21,241 0/0:31,0:31:78.23:0,78,954 0/0:59,0:59:99:0,150,1804 0/0:62,0:63:99:0,156,1911 0/0:47,0:49:99:0,105,1344 0/0:25,0:25:75.20:0,75,885 0/0:29,0:29:72.21:0,72,853 0/1:21,14:36:99:307,0,528 0/0:42,0:42:99:0,105,1304 0/0:52,0:52:99:0,132,1623 0/0:20,0:20:42.13:0,42,528 0/0:54,0:54:99:0,117,1456 0/0:53,0:53:99:0,147,1689 0/0:63,0:66:99:0,150,1820 0/0:55,0:57:99:0,126,1548 0/0:67,0:67:99:0,162,1930 0/0:36,0:36:99:0,99,1214 0/0:55,0:55:99:0,129,1597 0/0:27,0:27:69.20:0,69,849 0/0:17,0:17:45.13:0,45,539 0/0:45,0:46:99:0,108,1320 0/0:31,0:31:84.23:0,84,998 0/0:24,0:24:60.18:0,60,729 -chr1 987436 . A G 63.69 . AC=9;AF=0.0865;AN=104;BaseQRankSum=2.297;DP=458;Dels=0.00;FS=20.190;HRun=0;HaplotypeScore=0.9717;InbreedingCoeff=-0.0835;MQ=56.48;MQ0=0;MQRankSum=-5.343;QD=0.49;ReadPosRankSum=-3.854;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3.01:0,3,32 ./. 0/0:1,0:2:3.01:0,3,41 0/0:2,0:2:3.01:0,3,30 0/0:2,0:2:5.99:0,6,58 ./. ./. 0/0:1,0:1:3.01:0,3,35 0/0:3,0:3:9.03:0,9,122 0/0:7,0:7:18.05:0,18,222 0/0:1,0:1:3.01:0,3,41 ./. 0/0:2,0:2:6.01:0,6,65 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:2.99:0,3,23 ./. 0/0:3,0:3:9.02:0,9,101 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9:0,9,95 ./. 0/0:7,0:7:15.04:0,15,196 0/0:3,0:3:6.02:0,6,83 0/0:1,0:1:3.01:0,3,40 0/0:4,0:4:9.01:0,9,101 0/0:2,0:2:6.02:0,6,76 0/0:2,0:2:6.02:0,6,73 ./. 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.01:0,6,66 0/0:3,0:4:9.02:0,9,95 0/0:2,0:2:5.99:0,6,58 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3.01:0,3,36 ./. 0/0:1,0:1:3.01:0,3,38 1/1:0,1:1:3.01:33,3,0 0/1:21,3:25:12.74:13,0,534 0/0:22,1:24:23.70:0,24,596 0/1:21,2:23:9.71:10,0,540 0/0:12,0:13:30.07:0,30,327 0/0:10,1:12:8.39:0,8,310 0/0:10,0:10:21.07:0,21,280 0/1:4,3:8:51.82:52,0,102 0/0:18,1:19:42.10:0,42,492 0/0:25,0:26:63.17:0,63,719 0/0:11,0:12:24.07:0,24,287 0/1:18,2:21:18.79:19,0,418 0/0:22,1:23:20.66:0,21,538 0/0:27,3:32:2.28:0,2,642 0/0:17,1:18:7.50:0,8,348 0/1:14,2:17:36.78:37,0,256 0/1:14,2:18:6.38:6,0,254 0/0:16,0:17:36.10:0,36,420 0/1:12,1:16:3.35:3,0,306 0/0:13,0:13:30.09:0,30,375 0/0:18,0:18:42.01:0,42,430 0/0:12,1:14:2.66:0,3,361 0/0:13,0:13:21.07:0,21,266 -chr1 987670 . T G 1282.33 . AC=44;AF=0.846;AN=52;BaseQRankSum=-0.078;DP=47;Dels=0.00;FS=6.479;HRun=0;HaplotypeScore=0.0222;InbreedingCoeff=0.1213;MQ=59.01;MQ0=0;MQRankSum=-1.300;QD=30.53;ReadPosRankSum=0.391;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000466223|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000478677|),DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000466223|||||retained_intron|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000478677|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,3:3:9.03:120,9,0 0/1:1,2:3:31.62:71,0,32 1/1:0,2:2:6.02:69,6,0 0/1:1,1:2:31.78:32,0,33 ./. ./. ./. ./. ./. 1/1:0,7:7:21.07:276,21,0 ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:45,3,0 ./. 1/1:0,2:2:3.01:36,3,0 ./. ./. 1/1:0,2:2:3.01:45,3,0 1/1:0,1:1:3:29,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:37,3,0 0/0:2,0:2:6.02:0,6,80 1/1:0,1:1:3.01:40,3,0 ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,36 1/1:0,1:1:3.01:34,3,0 1/1:0,2:2:6.02:77,6,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:32,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:39,3,0 1/1:0,2:2:6.02:81,6,0 ./. 1/1:0,2:2:6.02:82,6,0 1/1:0,1:1:3.01:39,3,0 ./. 0/0:2,0:2:6.02:0,6,78 -chr1 988932 . G C 36554.37 . AC=79;AF=0.7596;AN=104;BaseQRankSum=-0.433;DP=1556;Dels=0.00;FS=2.118;HRun=3;HaplotypeScore=0.6684;InbreedingCoeff=0.1833;MQ=57.12;MQ0=0;MQRankSum=-1.108;QD=26.28;ReadPosRankSum=-0.844;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|1),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|33),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,intron_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,2:2:6.02:75,6,0 0/1:6,5:11:99:104,0,174 0/1:3,1:4:30.98:31,0,63 0/1:3,3:6:90.38:100,0,90 1/1:0,4:4:12.04:161,12,0 1/1:0,2:2:6.02:82,6,0 1/1:0,2:2:6.02:81,6,0 1/1:0,1:1:3.01:39,3,0 0/1:1,6:7:20.16:224,0,20 0/1:4,2:6:54.52:55,0,107 1/1:0,1:1:3.01:41,3,0 0/0:2,0:2:6.02:0,6,78 ./. 1/1:0,1:1:3.01:42,3,0 1/1:0,3:3:9.03:125,9,0 1/1:0,1:1:3.01:37,3,0 1/1:0,1:1:3.01:39,3,0 ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:40,3,0 ./. ./. 1/1:0,2:2:6.02:74,6,0 1/1:0,1:1:3.01:40,3,0 ./. 1/1:0,2:2:6.02:79,6,0 ./. 1/1:0,1:1:3.01:37,3,0 0/0:1,0:1:3.01:0,3,39 1/1:0,1:1:3.01:42,3,0 0/0:1,0:1:3.01:0,3,42 1/1:0,4:4:9.03:120,9,0 1/1:0,1:1:3.01:41,3,0 0/0:3,0:3:9.03:0,9,122 ./. 1/1:0,3:3:9.03:112,9,0 ./. 0/0:6,0:6:12.04:0,12,163 1/1:0,54:54:99:1772,135,0 1/1:0,103:103:99:3166,241,0 0/1:34,31:65:99:877,0,896 0/0:67,3:70:99:0,115,1989 1/1:0,56:56:99:1829,141,0 1/1:0,40:40:99:1297,99,0 0/1:43,28:72:99:647,0,1230 1/1:0,64:64:99:2099,163,0 1/1:0,104:104:99:3290,256,0 0/1:23,18:41:99:507,0,661 1/1:0,68:68:99:1909,147,0 1/1:0,94:94:99:3020,232,0 1/1:0,100:101:99:3381,265,0 1/1:0,53:53:99:1699,135,0 1/1:0,60:60:99:1944,150,0 1/1:0,57:57:99:1704,129,0 1/1:0,59:59:99:1782,135,0 1/1:0,53:53:99:1511,114,0 0/1:31,17:48:99:486,0,850 0/1:42,27:69:99:735,0,1124 0/1:24,37:61:99:1036,0,637 0/0:79,3:82:82.50:0,82,2052 -chr1 989423 . G A 1179.93 . AC=6;AF=0.0500;AN=120;BaseQRankSum=-0.586;DP=696;Dels=0.00;FS=1.039;HRun=0;HaplotypeScore=0.3917;InbreedingCoeff=0.5564;MQ=58.43;MQ0=0;MQRankSum=0.139;QD=23.14;ReadPosRankSum=-0.143;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|34),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|1),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,40 0/0:7,0:7:18.05:0,18,220 0/0:8,0:8:21.06:0,21,262 0/0:7,0:7:21.07:0,21,261 0/0:5,0:5:15.05:0,15,202 0/0:7,0:7:21.06:0,21,260 0/0:9,0:9:24.08:0,24,312 0/0:6,0:6:18.05:0,18,228 0/0:16,0:16:48.16:0,48,636 0/0:12,0:13:36.11:0,36,454 0/0:3,0:3:9.03:0,9,121 0/1:3,7:10:58.50:227,0,58 0/0:8,0:8:21.07:0,21,279 0/0:11,0:11:30.10:0,30,389 0/0:11,0:11:30.09:0,30,386 0/0:7,0:7:21.07:0,21,285 0/0:8,0:8:21.07:0,21,279 0/0:5,0:5:15.05:0,15,194 0/0:8,0:8:24.07:0,24,303 0/0:15,0:15:39.13:0,39,521 0/0:12,0:12:33.10:0,33,419 0/0:11,0:11:30.06:0,30,365 0/0:7,0:7:18.06:0,18,238 0/0:13,0:13:33.11:0,33,440 0/0:7,0:7:21.07:0,21,272 0/0:11,0:11:27.09:0,27,364 0/0:8,0:8:15.05:0,15,201 0/0:14,0:14:33.10:0,33,430 0/0:17,0:17:42.12:0,42,545 0/0:7,0:7:18.05:0,18,224 0/0:20,0:20:54.17:0,54,723 0/0:4,0:4:12.04:0,12,166 0/0:12,0:12:33.11:0,33,433 0/0:3,0:3:9.03:0,9,108 0/0:11,0:11:27.09:0,27,364 0/0:11,0:11:33.11:0,33,438 0/0:13,0:13:33.10:0,33,421 1/1:0,11:11:27.09:350,27,0 0/0:8,0:8:21.06:0,21,262 0/0:21,0:21:57.18:0,57,743 0/0:13,0:13:33.11:0,33,429 0/0:17,0:18:39.12:0,39,517 0/0:17,0:17:51.15:0,51,664 0/0:12,0:12:33.10:0,33,426 0/0:8,0:8:24.08:0,24,309 0/0:8,0:8:24.07:0,24,303 0/0:17,0:17:42.13:0,42,533 0/0:7,0:7:21.06:0,21,259 0/0:19,0:19:54.16:0,54,695 0/0:26,0:27:66.21:0,66,863 0/0:29,0:30:69.22:0,69,913 0/0:19,0:19:48.16:0,48,658 0/0:14,0:14:39.13:0,39,531 0/0:13,0:13:36.10:0,36,466 0/0:23,0:23:60.19:0,60,785 0/0:14,0:14:33.10:0,33,433 0/0:9,0:9:24.08:0,24,329 0/1:8,3:11:85.23:85,0,225 0/0:11,0:11:27.09:0,27,347 1/1:0,19:19:51.14:644,51,0 -chr1 989461 . G A 47.93 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.647;DP=465;Dels=0.00;FS=5.710;HRun=0;HaplotypeScore=0.2114;InbreedingCoeff=-0.0294;MQ=58.14;MQ0=0;MQRankSum=-0.206;QD=5.99;ReadPosRankSum=1.402;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|34),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|1),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,75 0/0:3,0:3:9.01:0,9,91 0/0:6,0:6:15.05:0,15,187 0/0:2,0:2:6.02:0,6,74 0/0:5,0:5:15.05:0,15,193 0/0:11,0:11:33.11:0,33,432 0/0:12,0:12:36.08:0,36,428 0/0:8,0:8:24.08:0,24,325 0/0:10,0:10:30.09:0,30,375 0/0:15,0:15:42.12:0,42,519 0/0:6,0:6:18.04:0,18,204 0/0:7,0:7:15.04:0,15,189 0/0:4,0:4:12.04:0,12,164 0/0:9,0:10:27.09:0,27,359 0/0:9,0:9:27.08:0,27,342 0/0:4,0:4:12.04:0,12,164 0/0:5,0:5:15.05:0,15,205 0/0:3,0:3:6.02:0,6,81 0/0:3,0:3:9.03:0,9,114 0/0:8,0:8:24.06:0,24,289 0/0:4,0:4:12.04:0,12,156 0/0:11,0:11:27.09:0,27,352 0/0:6,0:6:18.06:0,18,234 0/0:9,0:9:24.08:0,24,320 0/0:6,0:6:18.06:0,18,243 0/0:11,0:11:27.09:0,27,355 0/0:5,0:5:12.04:0,12,156 0/0:10,0:11:27.08:0,27,344 0/0:11,0:11:27.07:0,27,322 0/0:2,0:2:6.01:0,6,66 0/0:13,2:15:7.41:0,7,384 0/0:1,0:1:3.01:0,3,42 0/0:6,0:6:18.06:0,18,226 0/0:5,0:5:15.05:0,15,191 0/0:4,0:4:12.03:0,12,148 0/0:4,0:4:12.04:0,12,160 0/0:9,0:9:24.02:0,24,254 0/0:6,0:6:18.06:0,18,232 0/0:7,0:7:21.06:0,21,270 0/0:10,0:10:30.10:0,30,405 0/0:8,0:8:24.07:0,24,304 0/0:11,0:12:33.10:0,33,407 0/0:8,0:8:24.08:0,24,304 0/0:8,0:8:15.05:0,15,191 0/1:4,4:8:95.48:95,0,142 0/0:5,0:5:12.04:0,12,155 0/0:11,0:11:33.11:0,33,428 0/0:4,0:4:12.04:0,12,150 0/0:11,0:11:33.10:0,33,398 0/0:15,0:15:42.13:0,42,528 0/0:13,0:13:36.11:0,36,461 0/0:11,0:11:33.11:0,33,436 0/0:16,0:16:33.10:0,33,421 0/0:8,0:8:12.04:0,12,154 0/0:13,0:13:36.12:0,36,473 0/0:8,0:9:21.07:0,21,276 0/0:5,0:5:15.05:0,15,202 0/0:7,0:7:18.06:0,18,233 0/0:11,0:11:30.10:0,30,391 0/0:6,0:6:15.05:0,15,200 -chr1 989500 . G A 537.75 . AC=8;AF=0.0678;AN=118;BaseQRankSum=0.771;DP=317;Dels=0.00;FS=1.526;HRun=1;HaplotypeScore=0.4247;InbreedingCoeff=0.2291;MQ=57.86;MQ0=0;MQRankSum=1.486;QD=19.21;ReadPosRankSum=-0.692;EFF=DOWNSTREAM(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000492947|),INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|34),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|1),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000492947|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,41 0/0:6,0:6:15.05:0,15,195 0/0:3,0:3:9.03:0,9,115 1/1:0,3:3:9.03:119,9,0 0/0:6,0:6:18.06:0,18,241 0/1:1,4:5:24.96:148,0,25 0/0:7,0:7:21.07:0,21,286 0/0:6,0:6:18.04:0,18,224 0/0:9,0:9:27.09:0,27,366 0/0:13,0:13:39.12:0,39,514 0/1:3,4:7:91.03:138,0,91 0/0:5,0:5:15.05:0,15,204 0/1:2,2:4:67.28:70,0,67 0/0:10,0:10:27.09:0,27,359 0/1:4,3:7:60.21:109,0,60 0/0:2,0:2:6.02:0,6,76 0/0:4,0:4:12.04:0,12,164 1/1:0,2:2:6.02:80,6,0 0/0:5,0:5:15.05:0,15,200 0/0:4,0:4:12.04:0,12,151 0/0:4,0:4:12.04:0,12,152 0/0:8,0:8:21.07:0,21,284 0/0:7,0:7:21.07:0,21,269 0/0:5,0:5:15.05:0,15,203 0/0:4,0:4:12.04:0,12,166 0/0:8,0:8:24.08:0,24,312 0/0:6,0:6:18.06:0,18,232 0/0:6,0:6:18.06:0,18,241 0/0:5,0:5:15.05:0,15,206 0/0:1,0:1:3.01:0,3,41 0/0:6,0:6:18.06:0,18,238 ./. 0/0:4,0:4:12.04:0,12,158 0/0:3,0:3:9.03:0,9,115 0/0:3,0:3:9.03:0,9,124 0/0:2,0:2:6.02:0,6,82 0/0:7,0:7:21.07:0,21,280 0/0:6,0:6:18.06:0,18,238 0/0:2,0:2:6.02:0,6,72 0/0:5,0:5:15.05:0,15,203 0/0:6,0:6:18.05:0,18,218 0/0:7,0:7:18.06:0,18,241 0/0:2,0:2:6.02:0,6,76 0/0:6,0:6:9.03:0,9,116 0/0:5,0:5:12.04:0,12,160 0/0:5,0:5:15.05:0,15,200 0/0:7,0:7:21.07:0,21,289 0/0:2,0:2:6.02:0,6,67 0/0:6,0:6:18.05:0,18,215 0/0:8,0:8:24.05:0,24,283 0/0:10,0:10:24.08:0,24,318 0/0:5,0:5:9.03:0,9,119 0/0:12,0:12:30.09:0,30,383 0/0:6,0:6:15.04:0,15,175 0/0:6,0:6:18.06:0,18,238 0/0:9,0:9:27.08:0,27,347 0/0:4,0:4:12.04:0,12,151 0/0:2,0:2:6.02:0,6,80 0/0:6,0:6:18.06:0,18,237 0/0:2,0:2:6.02:0,6,84 -chr1 989811 . C A 1223.0 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-3.075;DP=1715;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.1951;InbreedingCoeff=-0.0226;MQ=58.98;MQ0=0;MQRankSum=0.887;QD=11.87;ReadPosRankSum=-0.484;EFF=INTRON(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|34),INTRON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|1),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,intron_variant|||ENSG00000188157|AGRN|ENST00000379370||||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,114 0/0:5,0:5:15.05:0,15,192 0/0:5,0:5:15.05:0,15,195 0/0:1,0:1:3.01:0,3,41 0/0:5,0:5:15.04:0,15,174 0/0:6,0:6:18.05:0,18,227 0/0:14,0:14:36.11:0,36,459 0/0:5,0:5:15.05:0,15,205 0/0:20,0:20:60.20:0,60,821 0/0:8,0:8:24.08:0,24,321 0/0:11,0:11:30.09:0,30,395 0/0:4,0:4:12.03:0,12,139 0/0:12,0:12:36.10:0,36,449 0/1:24,24:48:99:606,0,676 0/0:39,0:39:99:0,105,1413 0/0:29,0:29:69.23:0,69,935 0/0:32,0:32:81.26:0,81,1083 0/0:52,0:52:99:0,111,1491 0/0:52,0:52:99:0,102,1380 0/0:58,0:58:99:0,135,1843 0/0:35,0:35:78.24:0,78,1039 0/0:55,0:55:99:0,132,1708 0/0:44,0:44:90.30:0,90,1263 0/0:38,0:38:93.29:0,93,1229 0/0:33,0:34:81.25:0,81,1048 0/0:32,0:32:87.27:0,87,1125 0/0:51,0:51:99:0,120,1579 0/0:49,0:49:99:0,108,1486 0/0:50,0:50:99:0,120,1633 0/0:53,0:53:99:0,135,1760 0/0:61,0:61:99:0,147,1936 0/0:30,0:30:69.22:0,69,918 0/1:28,27:55:99:682,0,762 0/0:54,0:54:99:0,141,1807 0/0:41,0:41:96.31:0,96,1276 0/0:53,0:54:99:0,129,1698 0/0:59,0:59:99:0,150,2028 0/0:89,0:89:99:0,202,2691 0/0:18,0:18:54.17:0,54,706 0/0:39,0:39:99:0,99,1290 0/0:25,0:25:69.19:0,69,882 0/0:16,0:16:48.15:0,48,611 0/0:16,0:16:42.12:0,42,535 0/0:13,0:13:39.13:0,39,517 0/0:16,0:16:39.13:0,39,529 0/0:15,0:15:36.10:0,36,454 0/0:23,0:24:54.17:0,54,714 0/0:11,0:11:27.08:0,27,349 0/0:13,0:13:27.08:0,27,353 0/0:30,0:30:75.23:0,75,963 0/0:40,0:40:99:0,117,1508 0/0:27,0:27:66.20:0,66,827 0/0:24,0:24:60.19:0,60,791 0/0:18,0:18:54.17:0,54,705 0/0:15,0:15:45.15:0,45,595 0/0:13,0:13:30.09:0,30,382 0/0:17,0:17:39.12:0,39,501 0/0:9,0:9:24.08:0,24,328 0/0:12,0:12:33.10:0,33,409 0/0:11,0:11:24.07:0,24,320 -chr1 989847 . C T 704.05 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.110;DP=2200;Dels=0.00;FS=6.860;HRun=1;HaplotypeScore=1.7382;InbreedingCoeff=-0.0131;MQ=58.83;MQ0=0;MQRankSum=-0.133;QD=10.67;ReadPosRankSum=0.559;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|2),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L1966|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,synonymous_variant|Ctg/Ttg|L|ENSG00000188157|AGRN|ENST00000379370|35/36|||1966/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|2/3||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:7,0:7:18.06:0,18,221 0/0:4,0:4:12.04:0,12,149 0/0:1,0:1:3.01:0,3,36 0/0:3,0:3:9.03:0,9,115 0/0:6,0:6:18.06:0,18,237 0/0:12,0:12:36.11:0,36,471 0/0:17,0:17:48.16:0,48,642 0/0:5,0:5:15.05:0,15,203 0/0:19,0:19:57.19:0,57,774 0/0:18,0:18:54.18:0,54,734 0/0:10,0:10:30.10:0,30,394 0/0:7,0:7:21.06:0,21,267 0/0:20,0:20:57.18:0,57,735 0/0:52,0:52:99:0,138,1816 0/0:52,0:52:99:0,120,1622 0/0:34,0:34:90.29:0,90,1179 0/0:34,0:34:78.21:0,78,1029 0/0:57,0:57:99:0,138,1845 0/0:63,0:63:99:0,156,2016 0/0:74,0:74:99:0,175,2385 0/0:48,0:48:99:0,114,1539 0/0:71,0:71:99:0,169,2254 0/0:53,0:53:99:0,117,1571 0/0:46,0:46:99:0,114,1538 0/0:55,0:55:99:0,114,1550 0/0:44,0:44:99:0,114,1520 0/0:71,0:71:99:0,169,2261 0/0:55,0:55:99:0,126,1747 0/0:67,0:67:99:0,163,2171 0/0:56,0:56:99:0,132,1730 0/0:74,0:74:99:0,178,2372 0/0:37,0:37:93.29:0,93,1220 0/0:64,0:64:99:0,144,1962 0/1:38,27:66:99:752,0,1074 0/0:59,1:60:99:0,129,1767 0/0:70,0:70:99:0,160,2172 0/0:71,0:71:99:0,181,2386 0/0:102,0:102:99:0,235,3179 0/0:33,0:33:90.29:0,90,1185 0/0:49,0:49:99:0,138,1794 0/0:35,0:35:96.30:0,96,1245 0/0:26,0:26:69.22:0,69,911 0/0:17,0:17:45.15:0,45,602 0/0:18,0:18:51.16:0,51,665 0/0:23,0:23:63.19:0,63,806 0/0:21,0:21:57.18:0,57,751 0/0:29,0:30:75.23:0,75,963 0/0:14,0:14:33.11:0,33,434 0/0:24,0:24:60.19:0,60,796 0/0:44,0:44:99:0,126,1575 0/0:57,0:57:99:0,153,1997 0/0:36,0:36:93.29:0,93,1206 0/0:22,0:22:63.20:0,63,811 0/0:27,0:27:78.24:0,78,1002 0/0:19,0:19:51.16:0,51,652 0/0:25,0:25:72.23:0,72,923 0/0:19,0:19:54.16:0,54,690 0/0:17,0:17:48.16:0,48,660 0/0:20,0:20:60.19:0,60,780 0/0:19,0:19:45.15:0,45,619 -chr1 990213 . C T 965.08 . AC=1;AF=0.0085;AN=118;BaseQRankSum=0.966;DP=1603;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.3432;InbreedingCoeff=-0.0258;MQ=58.45;MQ0=0;MQRankSum=0.239;QD=15.57;ReadPosRankSum=-0.735;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P1997L|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,missense_variant|cCg/cTg|P/L|ENSG00000188157|AGRN|ENST00000379370|36/36|possibly_damaging(0.612)|deleterious(0.04)|1997/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:3:6.02:0,6,72 0/0:4,0:4:12.04:0,12,148 0/0:1,0:1:3.01:0,3,32 ./. 0/0:6,0:6:15.05:0,15,195 0/0:2,0:2:6.02:0,6,79 0/0:9,0:9:24.08:0,24,321 0/0:2,0:2:6.02:0,6,82 0/0:5,0:5:12.03:0,12,150 0/0:3,0:3:6.02:0,6,80 0/0:2,0:2:3.01:0,3,41 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.03:0,12,143 0/0:14,0:14:27.09:0,27,361 0/0:18,0:18:36.12:0,36,489 0/0:19,0:20:42.14:0,42,577 0/0:17,0:17:42.14:0,42,564 0/0:22,0:22:51.14:0,51,663 0/0:25,0:25:54.17:0,54,728 0/0:24,0:24:54.17:0,54,734 0/0:22,0:22:51.15:0,51,674 0/0:26,0:26:72.23:0,72,927 0/0:11,0:11:30.07:0,30,388 0/0:23,0:23:51.17:0,51,707 0/0:16,0:16:39.13:0,39,513 0/0:36,0:36:81.23:0,81,1050 0/0:30,0:30:72.23:0,72,950 0/0:23,0:23:48.16:0,48,652 0/0:26,0:26:69.21:0,69,922 0/0:24,0:24:54.16:0,54,708 0/0:22,0:22:51.16:0,51,673 0/0:29,0:29:72.23:0,72,949 0/0:23,0:23:51.17:0,51,692 0/0:12,0:12:36.11:0,36,460 0/0:18,0:18:39.13:0,39,516 0/0:17,0:17:27.09:0,27,373 0/0:34,0:34:72.23:0,72,998 0/0:37,0:37:87.28:0,87,1185 0/0:42,0:42:99:0,105,1380 0/0:52,0:53:99:0,129,1648 0/0:49,0:49:99:0,120,1596 0/0:43,0:43:99:0,108,1413 0/0:35,0:35:87.28:0,87,1144 0/0:32,0:32:81.25:0,81,1066 0/0:31,0:31:81.25:0,81,1057 0/0:47,0:47:99:0,123,1585 0/0:60,0:60:99:0,150,1943 0/0:18,0:18:51.15:0,51,635 0/1:24,38:62:99:1013,0,608 0/0:78,0:78:99:0,202,2559 0/0:78,0:78:99:0,190,2416 0/0:36,0:36:96.28:0,96,1265 0/0:53,0:53:99:0,132,1703 0/0:36,0:36:81.26:0,81,1093 0/0:49,0:50:99:0,114,1467 0/0:46,0:46:99:0,108,1459 0/0:25,0:25:63.20:0,63,831 0/0:37,0:37:78.26:0,78,1069 0/0:30,0:30:66.22:0,66,906 0/0:51,0:51:99:0,117,1556 -chr1 990280 . C T 40484.94 . AC=89;AF=0.7672;AN=116;BaseQRankSum=-1.914;DP=1861;Dels=0.00;FS=0.408;HRun=0;HaplotypeScore=1.6608;InbreedingCoeff=-0.0422;MQ=58.21;MQ0=0;MQRankSum=1.964;QD=23.35;ReadPosRankSum=-2.688;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D2019|2045|AGRN|protein_coding|CODING|ENST00000379370|),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,synonymous_variant|gaC/gaT|D|ENSG00000188157|AGRN|ENST00000379370|36/36|||2019/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3.01:37,3,0 ./. 1/1:0,2:2:6.02:77,6,0 1/1:0,3:3:9.03:123,9,0 0/1:1,1:2:35.21:35,0,35 1/1:0,8:8:24.08:323,24,0 0/1:3,1:4:27.97:28,0,98 1/1:0,5:5:15.05:189,15,0 1/1:0,2:2:6.02:82,6,0 1/1:0,2:2:6.02:66,6,0 1/1:0,3:3:9.03:107,9,0 1/1:0,3:3:9.03:105,9,0 0/1:2,11:13:36.44:366,0,36 1/1:0,23:23:63.16:785,63,0 1/1:0,15:15:36.11:468,36,0 0/1:12,10:22:99:193,0,318 1/1:0,23:23:63.20:819,63,0 0/1:8,13:21:99:311,0,198 0/0:27,0:27:63.19:0,63,825 0/1:7,11:18:99:288,0,226 1/1:0,29:29:66.20:839,66,0 1/1:0,18:18:36.12:478,36,0 0/1:7,9:16:99:270,0,200 1/1:0,17:17:45.15:590,45,0 0/1:3,21:24:60.26:603,0,60 1/1:0,31:31:78.25:1035,78,0 0/1:11,9:20:99:236,0,227 1/1:0,26:26:63.18:819,63,0 1/1:0,19:19:39.09:473,39,0 1/1:0,19:19:48.13:595,48,0 1/1:0,28:28:60.19:789,60,0 0/1:9,6:15:99:115,0,211 1/1:0,23:23:39.12:526,39,0 0/1:5,10:15:81.98:259,0,82 0/1:11,2:13:45.66:46,0,324 0/1:15,15:30:99:310,0,368 1/1:0,34:35:81.21:1023,81,0 1/1:1,60:62:99:1808,138,0 1/1:0,87:88:99:2949,232,0 1/1:0,67:68:99:2092,168,0 1/1:0,49:50:99:1547,123,0 0/0:44,0:44:99:0,111,1407 1/1:0,37:37:99:1235,102,0 0/1:24,26:50:99:759,0,597 0/1:31,28:59:99:659,0,850 0/1:42,38:81:99:1096,0,1132 0/1:12,15:27:99:343,0,330 0/1:42,47:89:99:1114,0,1021 0/1:46,34:80:99:732,0,1214 0/1:37,44:81:99:1167,0,979 1/1:1,43:44:83.90:1379,84,0 1/1:0,76:76:99:2353,187,0 1/1:0,48:48:99:1312,102,0 0/0:51,0:52:99:0,111,1437 1/1:0,61:64:99:1921,147,0 1/1:0,35:35:87.25:1123,87,0 0/1:28,25:53:99:646,0,729 1/1:0,41:42:99:1400,108,0 1/1:0,50:51:99:1445,111,0 -chr1 990380 . C T 8429.21 . AC=25;AF=0.2119;AN=118;BaseQRankSum=-1.731;DP=1638;Dels=0.00;FS=19.219;HRun=0;HaplotypeScore=0.9542;InbreedingCoeff=0.0822;MQ=58.01;MQ0=0;MQRankSum=-0.121;QD=14.79;ReadPosRankSum=1.180;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UPSTREAM(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=upstream_gene_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:9.02:0,9,97 0/0:3,0:3:6.02:0,6,79 0/0:2,0:2:6.02:0,6,75 0/0:4,0:4:12.04:0,12,163 1/1:0,1:1:3.01:41,3,0 0/0:4,0:4:12.04:0,12,162 0/1:2,2:4:32.20:32,0,72 0/0:8,0:8:24.08:0,24,317 0/0:4,0:4:12.04:0,12,150 0/0:3,0:3:9.03:0,9,119 0/0:1,0:1:3.01:0,3,39 0/0:5,0:5:15.05:0,15,198 0/1:2,3:5:66.54:74,0,67 0/0:16,0:16:45.14:0,45,586 0/0:13,0:13:33.11:0,33,449 0/1:3,8:11:92.44:232,0,92 0/0:16,0:17:48.15:0,48,623 0/1:8,7:15:99:207,0,272 1/1:0,9:9:21.07:275,21,0 0/0:11,0:11:27.09:0,27,376 0/0:18,0:18:48.15:0,48,624 0/0:11,0:11:27.09:0,27,355 0/1:9,2:11:55.79:56,0,254 0/0:16,0:16:39.13:0,39,537 0/1:9,3:12:73.69:74,0,325 0/0:7,0:7:21.07:0,21,281 0/1:6,8:14:99:231,0,128 0/0:11,0:11:30.10:0,30,409 0/0:14,0:14:36.11:0,36,456 0/0:10,0:10:27.08:0,27,348 0/0:20,0:20:51.16:0,51,666 0/1:5,8:13:99:216,0,136 0/1:5,7:12:99:188,0,165 0/1:4,2:6:65.94:66,0,124 0/1:3,3:6:89.39:89,0,104 0/1:4,9:13:90.88:273,0,91 0/0:15,0:15:42.13:0,42,544 0/0:60,0:60:99:0,150,2014 0/0:101,0:101:99:0,241,3143 0/0:66,0:66:99:0,175,2218 0/0:43,0:43:99:0,111,1444 1/1:2,44:46:69.56:1394,70,0 0/0:42,0:42:99:0,117,1506 0/0:52,0:52:99:0,138,1775 0/1:33,30:63:99:860,0,834 0/1:63,39:102:99:896,0,1597 0/0:29,0:29:78.25:0,78,1016 0/1:24,36:61:99:883,0,631 0/0:88,0:88:99:0,226,2926 0/1:58,28:86:99:591,0,1637 0/0:76,0:76:99:0,178,2365 0/0:78,0:78:99:0,220,2796 0/0:57,0:57:99:0,129,1676 1/1:2,39:41:99:1271,99,0 0/0:57,1:58:99:0,103,1787 0/0:36,0:36:84.26:0,84,1083 0/1:21,18:39:99:481,0,564 0/0:28,0:28:69.23:0,69,925 0/0:37,0:37:90.29:0,90,1215 -chr1 990417 . T C 8344.97 . AC=27;AF=0.2328;AN=116;BaseQRankSum=-1.168;DP=1150;Dels=0.00;FS=1.555;HRun=0;HaplotypeScore=0.4386;InbreedingCoeff=0.0986;MQ=57.95;MQ0=0;MQRankSum=-0.663;QD=16.33;ReadPosRankSum=-1.059;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),EXON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|1/2||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.02:0,6,81 0/0:6,0:6:18.06:0,18,224 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,39 1/1:0,1:1:3.01:41,3,0 ./. ./. 0/0:5,0:5:15.05:0,15,199 0/0:5,0:5:15.05:0,15,205 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,107 0/0:3,0:3:9.03:0,9,121 0/0:3,0:3:9.03:0,9,122 0/0:7,0:7:18.06:0,18,230 0/0:7,0:7:21.07:0,21,285 0/1:3,6:9:82.70:181,0,83 0/0:9,0:9:24.08:0,24,319 0/1:5,3:8:94.78:95,0,181 1/1:0,6:6:18.06:238,18,0 0/0:3,0:3:6.02:0,6,87 0/0:7,0:7:21.07:0,21,273 0/0:5,0:5:15.05:0,15,200 0/1:5,1:6:21.95:22,0,178 0/0:8,0:8:21.07:0,21,291 0/1:4,1:5:29.72:30,0,111 0/0:4,0:4:12.04:0,12,154 0/1:3,4:7:96.28:142,0,96 0/0:4,0:4:9.03:0,9,125 0/0:7,0:7:15.05:0,15,201 0/0:7,0:7:21.07:0,21,272 0/0:7,0:7:15.05:0,15,209 0/1:2,5:7:29.72:141,0,30 0/1:2,3:5:67.36:102,0,67 0/1:3,2:5:63.53:64,0,103 0/1:2,1:3:27.95:28,0,72 0/1:5,4:9:99:128,0,167 0/0:10,0:10:27.08:0,27,332 0/0:39,0:39:93.29:0,93,1216 0/0:77,0:77:99:0,196,2561 0/0:47,0:47:99:0,129,1688 0/0:38,0:38:87.28:0,87,1176 1/1:1,32:33:29.98:866,30,0 0/0:29,0:29:81.26:0,81,1078 0/1:19,17:36:99:469,0,554 0/1:23,23:46:99:616,0,618 0/1:55,29:84:99:690,0,1648 0/1:10,7:17:99:153,0,351 0/1:21,20:41:99:533,0,531 1/1:1,62:63:99:2079,129,0 0/1:42,19:61:99:484,0,1321 0/0:55,0:55:99:0,126,1701 0/0:61,0:61:99:0,175,2271 0/0:43,0:43:99:0,102,1356 1/1:1,27:28:63.20:845,63,0 0/0:50,2:52:78.64:0,79,1576 0/0:30,0:30:69.22:0,69,902 0/1:17,14:31:99:399,0,468 0/0:23,0:23:66.22:0,66,885 0/0:27,0:27:57.19:0,57,794 -chr1 990517 . C T 9650.24 . AC=75;AF=0.798;AN=94;BaseQRankSum=1.624;DP=348;Dels=0.00;FS=0.641;HRun=0;HaplotypeScore=0.4773;InbreedingCoeff=0.1734;MQ=57.98;MQ0=0;MQRankSum=0.522;QD=30.54;ReadPosRankSum=1.100;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),EXON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|1/2||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3.01:32,3,0 0/1:1,4:5:24.27:143,0,24 ./. 0/1:1,2:3:15.67:67,0,16 ./. ./. 1/1:0,2:2:6.02:81,6,0 ./. 1/1:0,1:1:3.01:41,3,0 0/1:1,1:2:34.63:35,0,35 ./. ./. 1/1:0,2:2:6.02:81,6,0 1/1:0,1:1:3.01:42,3,0 1/1:0,2:2:6.02:84,6,0 1/1:0,2:2:6.02:79,6,0 1/1:0,2:2:6.02:69,6,0 1/1:0,2:2:6.02:74,6,0 1/1:0,5:5:15.05:203,15,0 ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 1/1:0,2:2:6.02:83,6,0 0/0:1,0:1:3.01:0,3,40 1/1:0,3:3:6.01:69,6,0 ./. 1/1:0,1:1:3.01:40,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,40 1/1:0,6:6:15.05:203,15,0 1/1:0,1:1:3.01:39,3,0 1/1:0,1:1:3.01:39,3,0 ./. 1/1:0,1:1:3.01:42,3,0 1/1:0,3:3:6.02:80,6,0 0/0:5,0:5:15.04:0,15,182 1/1:0,15:15:42.13:532,42,0 1/1:0,15:16:42.14:558,42,0 0/1:9,11:20:99:362,0,293 0/0:17,0:17:48.14:0,48,596 1/1:0,9:9:24.05:287,24,0 1/1:0,12:12:36.12:488,36,0 1/1:0,17:17:48.15:624,48,0 1/1:0,17:17:45.14:586,45,0 1/1:0,27:27:72.23:929,72,0 0/1:4,4:8:99:99,0,138 1/1:0,7:7:18.06:235,18,0 0/1:8,8:16:99:212,0,218 1/1:0,19:19:57.17:708,57,0 1/1:0,12:12:33.11:443,33,0 1/1:0,23:24:63.19:806,63,0 1/1:0,10:10:27.08:322,27,0 1/1:0,4:4:12.04:161,12,0 1/1:0,8:8:24.07:306,24,0 0/1:6,2:8:21.17:21,0,196 0/1:4,6:10:99:179,0,126 0/1:4,4:8:99:124,0,139 0/0:5,0:5:15.05:0,15,186 -chr1 990557 . C T 59.21 . AC=1;AF=0.011;AN=90;BaseQRankSum=2.271;DP=279;Dels=0.00;FS=2.553;HRun=0;HaplotypeScore=0.3165;InbreedingCoeff=-0.0942;MQ=57.30;MQ0=0;MQRankSum=0.765;QD=8.46;ReadPosRankSum=-0.239;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),EXON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|1/2||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,30 ./. 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/0:2,0:2:6.02:0,6,82 ./. 0/0:1,0:1:3:0,3,29 ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,38 ./. ./. 0/0:1,0:2:3.01:0,3,39 0/0:2,0:2:6.02:0,6,77 0/0:1,0:1:3.01:0,3,35 0/0:3,0:4:6.02:0,6,83 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.01:0,6,68 0/0:1,0:1:2.98:0,3,22 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,32 ./. ./. 0/0:5,0:5:12.04:0,12,160 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:2,0:2:6.02:0,6,81 0/0:4,0:4:9.03:0,9,124 0/0:12,0:12:33.10:0,33,406 0/0:12,0:12:30.10:0,30,401 0/0:12,0:12:33.11:0,33,441 0/0:17,0:18:51.16:0,51,663 0/0:5,0:5:15.05:0,15,198 0/0:6,0:6:15.05:0,15,200 0/0:15,0:15:42.10:0,42,516 0/0:11,0:11:30.10:0,30,392 0/0:21,0:21:51.14:0,51,659 0/1:4,3:7:99:105,0,145 0/0:7,0:7:18.06:0,18,238 0/0:19,0:19:54.17:0,54,684 0/0:16,0:16:42.10:0,42,503 0/0:7,0:7:18.06:0,18,223 0/0:21,0:21:54.17:0,54,688 0/0:9,0:9:24.07:0,24,297 0/0:2,0:2:6.02:0,6,77 0/0:8,0:8:18.06:0,18,220 0/0:11,0:11:30.08:0,30,358 0/0:6,0:6:15.04:0,15,178 0/0:6,0:6:18.06:0,18,217 0/0:6,0:6:15.05:0,15,195 -chr1 990773 . C T 25625.67 . AC=51;AF=0.689;AN=74;BaseQRankSum=-0.671;DP=1023;Dels=0.00;FS=8.374;HRun=0;HaplotypeScore=0.7685;InbreedingCoeff=0.2919;MQ=57.82;MQ0=0;MQRankSum=0.992;QD=27.26;ReadPosRankSum=1.535;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),INTRON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=intron_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3:25,3,0 ./. 0/1:1,2:3:31.62:62,0,32 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,40 ./. 1/1:0,1:1:3.01:41,3,0 ./. 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,41 1/1:0,1:1:3.01:41,3,0 ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,3:3:6.02:85,6,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. 1/1:0,1:1:3.01:35,3,0 ./. 0/0:1,0:1:3.01:0,3,40 ./. 1/1:0,1:1:3.01:38,3,0 ./. ./. 1/1:1,44:45:99:1393,105,0 1/1:1,65:66:99:2099,159,0 0/1:38,15:53:99:380,0,1148 0/0:36,0:36:99:0,102,1308 1/1:1,38:39:93.30:1253,93,0 1/1:0,30:30:78.24:1010,78,0 0/1:13,16:29:99:455,0,384 1/1:1,41:42:99:1327,102,0 1/1:0,84:84:99:2551,193,0 0/1:14,6:20:99:157,0,391 1/1:0,37:37:96.29:1242,96,0 1/1:0,81:81:99:2595,202,0 1/1:0,46:46:99:1504,117,0 1/1:0,47:47:99:1514,114,0 1/1:2,79:81:99:2638,205,0 1/1:0,38:38:99:1309,99,0 1/1:1,36:37:93.28:1189,93,0 1/1:1,42:43:99:1429,108,0 0/1:20,10:30:99:205,0,563 0/1:23,18:41:99:519,0,480 0/1:18,20:38:99:452,0,546 0/0:40,0:40:84.27:0,84,1120 -chr1 990806 . G A 25266.48 . AC=55;AF=0.764;AN=72;BaseQRankSum=-2.112;DP=1071;Dels=0.00;FS=2.830;HRun=0;HaplotypeScore=0.8208;InbreedingCoeff=0.2300;MQ=58.13;MQ0=0;MQRankSum=-0.461;QD=25.63;ReadPosRankSum=0.166;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),INTRON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=intron_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. 0/1:2,2:4:63.52:67,0,64 0/0:1,0:1:3:0,3,27 0/0:3,0:3:9.01:0,9,101 ./. 1/1:0,1:1:3.01:39,3,0 1/1:0,1:1:3.01:33,3,0 ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:39,3,0 ./. 1/1:0,1:1:3.01:36,3,0 ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. ./. 1/1:0,4:4:9.03:127,9,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. 1/1:0,2:2:3.01:45,3,0 ./. ./. ./. 1/1:0,1:1:3.01:34,3,0 ./. ./. 1/1:0,39:40:99:1244,99,0 1/1:1,61:63:99:2011,162,0 0/1:47,18:67:99:483,0,1176 0/0:36,0:37:90.28:0,90,1159 1/1:0,45:46:99:1520,120,0 1/1:0,37:37:93.30:1228,93,0 0/1:13,16:30:99:423,0,388 1/1:0,46:49:99:1561,123,0 1/1:0,87:88:99:2681,208,0 0/1:11,7:18:99:160,0,356 1/1:0,41:43:99:1281,99,0 1/1:1,70:72:99:2064,168,0 1/1:0,45:47:99:1485,120,0 1/1:2,47:51:99:1355,108,0 1/1:1,72:75:99:2088,168,0 1/1:0,38:39:99:1298,105,0 1/1:0,43:45:99:1306,102,0 1/1:1,42:43:96.26:1250,96,0 0/1:21,13:34:99:310,0,593 0/1:21,19:40:99:523,0,526 0/1:23,17:41:99:454,0,664 0/0:41,0:41:99:0,102,1296 -chr1 990839 . C T 1668.45 . AC=2;AF=0.029;AN=70;BaseQRankSum=1.196;DP=1096;Dels=0.00;FS=1.633;HRun=2;HaplotypeScore=0.6892;InbreedingCoeff=-0.0818;MQ=58.31;MQ0=0;MQRankSum=1.390;QD=12.27;ReadPosRankSum=-2.018;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),INTRON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=intron_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,34 ./. 0/0:3,0:3:9.03:0,9,113 0/0:5,0:5:9.03:0,9,112 0/0:3,0:3:9.03:0,9,124 ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,32 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. 0/0:3,0:3:9.01:0,9,105 ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. ./. 0/0:36,0:36:99:0,102,1320 0/0:61,0:61:99:0,150,2003 0/0:67,0:67:99:0,162,2100 0/0:45,0:45:99:0,111,1470 0/0:51,0:51:99:0,135,1777 0/0:35,0:35:96.30:0,96,1256 0/0:36,0:36:99:0,102,1342 0/0:52,0:52:99:0,126,1644 0/0:94,0:94:99:0,232,3055 0/0:20,0:20:48.16:0,48,648 0/0:57,0:57:99:0,132,1800 0/1:38,34:72:99:980,0,1151 0/0:48,0:48:99:0,141,1846 0/0:47,0:47:99:0,114,1507 0/1:39,25:64:99:748,0,1051 0/0:38,0:39:96.30:0,96,1258 0/0:39,0:39:93.30:0,93,1262 0/0:45,0:45:99:0,108,1446 0/0:34,0:34:87.25:0,87,1126 0/0:44,0:44:99:0,105,1431 0/0:38,0:38:96.31:0,96,1278 0/0:44,0:44:99:0,105,1396 -chr1 990943 . G C 216.41 . AC=1;AF=0.019;AN=52;BaseQRankSum=-0.081;DP=536;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6541;InbreedingCoeff=-0.0441;MQ=58.64;MQ0=0;MQRankSum=-0.296;QD=10.31;ReadPosRankSum=-0.366;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),INTRON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=intron_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. 0/0:2,0:2:6.02:0,6,80 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/0:10,0:10:27.09:0,27,375 0/0:36,0:36:99:0,99,1297 0/0:31,0:31:90.28:0,90,1139 0/0:21,0:22:57.19:0,57,766 0/0:18,0:18:48.15:0,48,640 0/0:17,0:17:48.13:0,48,622 0/1:13,8:21:99:260,0,319 0/0:18,0:18:54.17:0,54,687 0/0:40,0:40:99:0,105,1386 0/0:11,0:11:24.07:0,24,307 0/0:27,0:27:72.23:0,72,941 0/0:33,0:33:84.21:0,84,1058 0/0:25,0:25:75.24:0,75,960 0/0:14,0:14:36.12:0,36,480 0/0:41,0:41:99:0,99,1308 0/0:32,0:32:81.26:0,81,1087 0/0:21,0:21:54.18:0,54,731 0/0:20,0:20:54.17:0,54,721 0/0:18,0:19:45.15:0,45,599 0/0:31,0:31:81.25:0,81,1049 0/0:18,0:18:45.12:0,45,590 0/0:26,0:26:60.19:0,60,800 -chr1 990984 . G A 3835.45 . AC=33;AF=0.786;AN=42;BaseQRankSum=-0.791;DP=131;Dels=0.00;FS=7.195;HRun=0;HaplotypeScore=0.1328;InbreedingCoeff=0.2454;MQ=58.69;MQ0=0;MQRankSum=-2.076;QD=32.78;ReadPosRankSum=-1.157;EFF=EXON(MODIFIER|||||AGRN|retained_intron|CODING|ENST00000461111|3),INTRON(MODIFIER|||||RP11-54O7.14|processed_transcript|NON_CODING|ENST00000418300|1),UPSTREAM(MODIFIER|||||RP11-465B22.3|processed_transcript|NON_CODING|ENST00000427998|),UTR_3_PRIME(MODIFIER||||2045|AGRN|protein_coding|CODING|ENST00000379370|36);CSQ=intron_variant&nc_transcript_variant|||ENSG00000242590|RP11-54O7.14|ENST00000418300|||||sense_intronic|1,3_prime_UTR_variant|||ENSG00000188157|AGRN|ENST00000379370|36/36|||-/2045|protein_coding|1,downstream_gene_variant|||ENSG00000188157|AGRN|ENST00000419249||||-/271|protein_coding|1,upstream_gene_variant|||ENSG00000217801|RP11-465B22.3|ENST00000427998|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000188157|AGRN|ENST00000461111|3/3||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,9:9:27.09:349,27,0 0/1:3,3:6:61.40:64,0,61 0/0:9,0:9:27.08:0,27,353 1/1:0,2:2:6.02:79,6,0 1/1:0,7:7:18.06:234,18,0 1/1:0,7:7:15.05:203,15,0 1/1:0,3:3:9.03:116,9,0 1/1:0,10:10:30.10:395,30,0 0/1:2,1:3:26.22:26,0,73 1/1:0,8:8:24.08:307,24,0 1/1:0,13:13:33.10:391,33,0 1/1:0,7:7:21.06:268,21,0 1/1:0,5:5:15.05:202,15,0 1/1:0,8:8:24.08:323,24,0 1/1:0,6:6:18.06:232,18,0 1/1:0,4:4:12.04:156,12,0 1/1:0,5:5:15.05:204,15,0 0/1:1,1:2:35.21:35,0,36 0/1:3,4:8:98.95:142,0,99 0/1:1,3:4:30.19:109,0,30 0/0:5,0:5:15.05:0,15,199 -chr1 1102069 . A G 744.18 . AC=36;AF=0.900;AN=40;BaseQRankSum=-0.783;DP=29;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0800;InbreedingCoeff=0.1040;MQ=56.74;MQ0=0;MQRankSum=0.679;QD=32.36;ReadPosRankSum=1.410;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=upstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:6.01:66,6,0 1/1:0,1:1:3.01:40,3,0 1/1:0,1:1:3.01:40,3,0 ./. ./. 1/1:0,2:2:6.02:80,6,0 1/1:0,2:2:3.01:36,3,0 1/1:0,1:1:3.01:39,3,0 ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:34,3,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. 1/1:0,3:3:9.03:115,9,0 ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. 1/1:0,1:1:3.01:31,3,0 ./. ./. 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:42,3,0 1/1:0,1:1:3.01:42,3,0 1/1:0,1:1:3.01:42,3,0 1/1:0,1:1:2.99:23,3,0 ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. -chr1 1102296 . G A 783.47 . AC=4;AF=0.0357;AN=112;BaseQRankSum=-0.578;DP=498;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.2286;InbreedingCoeff=0.2474;MQ=55.59;MQ0=0;MQRankSum=0.771;QD=18.22;ReadPosRankSum=0.212;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=upstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL ./. ./. ./. 0/0:2,0:2:6.02:0,6,73 0/0:3,0:3:9.03:0,9,120 0/0:2,0:2:6.02:0,6,76 0/0:7,0:7:21.07:0,21,283 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:9.03:0,9,120 0/0:13,0:13:39.12:0,39,492 ./. 0/0:5,0:5:15.04:0,15,185 0/0:6,0:6:18.06:0,18,240 0/0:4,0:4:12.04:0,12,160 0/0:11,0:11:33.10:0,33,419 0/0:8,0:8:21.07:0,21,287 0/0:5,0:5:12.04:0,12,167 0/0:5,0:5:15.04:0,15,189 0/0:5,0:5:6.01:0,6,65 0/0:5,0:5:9.03:0,9,110 0/0:1,0:1:3.01:0,3,42 0/0:7,0:7:21.07:0,21,270 0/0:2,0:2:6.02:0,6,82 0/0:4,0:4:12.04:0,12,154 0/0:6,0:6:15.05:0,15,196 0/0:4,0:4:9.03:0,9,112 0/0:8,0:8:21.07:0,21,272 0/0:7,0:7:18.06:0,18,223 0/0:7,0:7:18.06:0,18,250 0/0:2,0:2:6.02:0,6,77 0/0:6,0:6:15.04:0,15,179 0/0:6,0:6:18.06:0,18,231 0/0:4,0:4:12.04:0,12,154 0/0:3,0:3:9.03:0,9,123 0/0:4,0:4:9.03:0,9,118 0/0:6,0:6:18.06:0,18,237 0/0:8,0:8:21.07:0,21,269 0/0:10,0:11:30.09:0,30,373 0/0:7,0:7:9.03:0,9,111 0/0:22,0:22:54.17:0,54,699 0/0:15,0:15:39.12:0,39,507 0/0:13,0:13:36.11:0,36,448 0/0:11,0:12:30.09:0,30,392 0/1:9,1:10:5.16:5,0,312 0/0:11,0:11:27.09:0,27,364 0/0:9,0:9:27.09:0,27,359 0/0:19,0:20:48.15:0,48,618 0/1:6,2:8:56.26:56,0,197 0/0:13,0:13:30.10:0,30,385 1/1:1,24:25:63.20:811,63,0 0/0:29,1:31:50.80:0,51,970 0/0:18,0:19:42.12:0,42,520 0/0:32,0:32:81.25:0,81,1030 0/0:7,0:7:15.05:0,15,190 0/0:15,0:15:45.13:0,45,556 0/0:6,0:6:12.03:0,12,146 0/0:8,0:8:21.07:0,21,282 0/0:10,0:10:30.09:0,30,376 0/0:16,0:16:42.14:0,42,562 0/0:5,0:5:15.05:0,15,207 -chr1 1102360 . T G 216.82 . AC=16;AF=0.1379;AN=116;BaseQRankSum=-10.289;DP=1092;Dels=0.00;FS=25.292;HRun=4;HaplotypeScore=1.6139;InbreedingCoeff=-0.2074;MQ=53.49;MQ0=0;MQRankSum=2.414;QD=0.71;ReadPosRankSum=7.754;EFF=INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=upstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,40 0/0:2,2:4:3:0,3,26 0/0:1,0:1:3.01:0,3,33 0/0:2,4:6:3.01:0,3,41 0/0:2,1:3:3.01:0,3,41 0/0:3,1:4:6.02:0,6,77 0/0:1,2:3:3.01:0,3,37 0/0:3,6:9:6.02:0,6,72 0/0:3,6:9:9.02:0,9,107 0/1:2,5:7:17.68:18,0,42 ./. 0/0:3,7:10:6.01:0,6,64 0/1:6,3:9:18.65:19,0,55 0/1:10,13:23:10.53:11,0,166 0/0:2,9:11:6.01:0,6,63 0/1:6,4:10:38.34:38,0,66 0/1:4,7:11:15.68:16,0,59 0/1:8,6:14:55.84:56,0,130 0/0:8,7:15:15.03:0,15,159 0/0:4,4:8:12.04:0,12,147 0/0:12,6:18:12.01:0,12,121 0/0:4,4:8:3.01:0,3,39 0/0:6,4:10:9.02:0,9,106 0/1:8,3:11:42.09:42,0,106 0/0:9,5:14:18.03:0,18,194 0/0:9,9:18:18.03:0,18,204 0/1:7,6:13:7.65:8,0,140 0/0:8,4:12:15.03:0,15,169 0/0:9,4:13:18.06:0,18,222 0/0:14,2:17:33.09:0,33,375 0/0:9,4:14:15.02:0,15,155 0/0:7,4:11:12.02:0,12,135 0/1:5,8:13:48.82:49,0,118 0/1:3,5:9:44.18:50,0,44 0/1:7,3:10:18.56:19,0,93 0/0:5,5:11:6.01:0,6,66 0/0:9,11:20:18.01:0,18,185 0/0:14,13:28:7.38:0,7,308 0/0:37,15:52:72.11:0,72,812 0/0:23,4:27:24.89:0,25,632 0/1:16,9:25:0.34:0,0,315 0/1:19,14:35:7.28:7,0,391 0/0:19,5:24:30.06:0,30,332 0/0:14,5:19:33.06:0,33,360 0/0:15,10:26:4.53:0,5,339 0/1:23,18:41:25.51:26,0,513 0/1:10,10:21:1.70:2,0,147 0/0:16,9:25:27.07:0,27,310 0/0:49,17:68:99:0,102,1116 0/1:34,18:53:17.59:18,0,669 0/0:39,13:53:62.43:0,62,899 0/0:40,14:54:43.62:0,44,780 0/0:15,7:23:4.42:0,4,303 0/0:15,13:28:2.62:0,3,324 0/0:12,4:16:21.03:0,21,224 0/0:7,6:13:15.05:0,15,182 0/0:18,13:32:10.36:0,10,328 0/0:15,9:25:5.49:0,5,360 0/0:15,5:20:15.04:0,15,183 -chr1 1102563 . G A 1052.38 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.152;DP=4513;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.2999;InbreedingCoeff=-0.0179;MQ=56.60;MQ0=0;MQRankSum=2.502;QD=14.03;ReadPosRankSum=-0.938;EFF=EXON(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|1),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000207730|MIR200B|ENST00000384997|1/1||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL 0/0:9,0:9:24.05:0,24,284 0/0:5,0:5:15.04:0,15,189 0/0:7,0:7:18.05:0,18,220 0/0:5,0:5:12.04:0,12,149 0/0:20,0:20:54.16:0,54,692 0/0:15,0:15:45.14:0,45,576 0/0:30,0:30:87.28:0,87,1127 0/1:8,9:17:99:267,0,269 0/0:32,0:32:90.29:0,90,1181 0/0:39,0:39:99:0,111,1442 0/0:15,0:15:45.15:0,45,601 0/0:10,0:10:30.09:0,30,377 0/0:18,0:18:51.13:0,51,621 0/0:47,0:47:87.21:0,87,1133 0/0:63,0:63:99:0,144,1863 0/0:54,0:54:99:0,126,1644 0/0:71,0:73:99:0,165,2154 0/0:68,0:68:99:0,169,2206 0/0:67,0:68:99:0,162,2083 0/0:56,0:58:99:0,129,1710 0/0:57,0:57:99:0,141,1823 0/0:75,0:76:99:0,166,2166 0/0:70,0:70:99:0,150,1980 0/0:45,1:47:99:0,99,1293 0/1:26,32:58:99:851,0,664 0/0:63,0:63:99:0,147,1962 0/0:55,0:55:99:0,126,1674 0/0:61,0:61:99:0,132,1687 0/0:61,0:61:99:0,129,1718 0/0:71,0:71:99:0,144,1941 0/0:115,0:115:99:0,250,3294 0/0:55,0:55:99:0,129,1709 0/0:82,0:82:99:0,178,2290 0/0:76,0:77:99:0,160,2093 0/0:49,0:49:99:0,108,1436 0/0:69,0:69:99:0,162,2108 0/0:61,0:62:99:0,144,1882 0/0:84,0:84:99:0,190,2454 0/0:93,0:93:99:0,241,2980 0/0:170,0:171:99:0,400,5119 0/0:148,0:148:99:0,361,4620 0/0:99,1:100:99:0,229,2947 0/0:106,1:107:99:0,221,3041 0/0:94,0:94:99:0,226,2901 0/0:102,0:103:99:0,256,3283 0/0:120,0:120:99:0,277,3534 0/0:183,0:184:99:0,421,5377 0/0:89,0:90:99:0,202,2576 0/0:130,0:131:99:0,301,3867 0/0:187,1:189:99:0,390,5343 0/0:190,0:190:99:0,469,5895 0/0:118,0:118:99:0,286,3684 0/0:168,0:168:99:0,373,4814 0/0:105,0:105:99:0,253,3205 0/0:113,0:113:99:0,244,3087 0/0:78,0:79:99:0,175,2277 0/0:60,0:60:99:0,141,1814 0/0:117,1:119:99:0,277,3507 0/0:87,0:87:99:0,196,2520 0/0:78,0:79:99:0,181,2318 -chr1 1102657 . C T 464.41 . AC=2;AF=0.0169;AN=118;BaseQRankSum=0.429;DP=1409;Dels=0.00;FS=2.023;HRun=0;HaplotypeScore=1.5640;InbreedingCoeff=-0.0230;MQ=53.83;MQ0=0;MQRankSum=0.937;QD=12.90;ReadPosRankSum=0.639;EFF=DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:6.02:0,6,79 0/0:5,0:5:15.04:0,15,182 0/0:4,0:4:12.03:0,12,140 0/0:9,0:9:27.09:0,27,361 0/0:9,0:9:27.09:0,27,349 0/0:12,0:12:36.12:0,36,483 0/0:6,0:6:18.06:0,18,238 0/0:17,0:17:51.17:0,51,673 0/0:18,0:18:54.17:0,54,697 0/0:5,0:5:15.05:0,15,194 0/0:9,0:9:27.08:0,27,340 0/0:2,0:2:6.02:0,6,79 0/0:3,0:3:9.03:0,9,120 0/0:17,0:17:42.13:0,42,549 0/0:12,0:12:33.10:0,33,422 0/0:16,0:16:48.15:0,48,623 0/0:18,0:19:51.15:0,51,633 0/0:18,0:18:51.16:0,51,633 0/1:5,6:11:99:202,0,156 0/0:12,0:12:33.09:0,33,399 0/0:21,0:21:60.18:0,60,734 0/0:21,0:21:57.18:0,57,717 0/0:17,0:17:48.15:0,48,622 0/0:17,0:17:51.16:0,51,641 0/0:15,0:15:42.13:0,42,552 0/0:11,0:11:30.10:0,30,394 0/0:15,0:15:45.14:0,45,572 0/0:16,0:16:36.11:0,36,479 0/0:16,0:16:45.13:0,45,573 0/0:27,0:27:75.22:0,75,930 0/0:15,0:15:39.13:0,39,514 0/0:24,0:24:57.16:0,57,700 0/0:23,0:23:69.18:0,69,847 0/0:21,0:21:60.18:0,60,741 0/1:14,11:25:99:328,0,462 0/0:27,0:27:75.23:0,75,934 0/0:16,0:16:48.15:0,48,609 0/0:29,0:29:78.23:0,78,949 0/0:73,0:73:99:0,205,2506 0/0:54,0:54:99:0,141,1719 0/0:27,0:27:75.23:0,75,933 0/0:31,0:31:69.21:0,69,860 0/0:26,0:26:72.22:0,72,871 0/0:32,0:32:90.27:0,90,1103 0/0:38,0:38:99:0,99,1214 0/0:60,0:60:99:0,162,1957 0/0:27,0:27:66.19:0,66,800 0/0:29,0:29:72.21:0,72,878 0/0:66,0:66:99:0,174,2089 0/0:84,0:84:99:0,223,2693 0/0:41,0:41:99:0,111,1327 0/0:51,0:51:99:0,132,1611 0/0:35,0:35:99:0,99,1190 0/0:40,0:40:99:0,111,1322 0/0:21,0:21:57.17:0,57,709 0/0:14,0:14:36.11:0,36,442 0/0:39,0:39:99:0,108,1293 0/0:32,0:32:87.23:0,87,1069 0/0:27,0:27:72.21:0,72,883 -chr1 1102674 . G A 964.97 . AC=2;AF=0.0172;AN=116;BaseQRankSum=0.337;DP=1131;Dels=0.00;FS=1.614;HRun=0;HaplotypeScore=1.4083;InbreedingCoeff=-0.0229;MQ=55.34;MQ0=0;MQRankSum=1.906;QD=12.21;ReadPosRankSum=1.395;EFF=DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL ./. 0/0:4,0:4:12.04:0,12,152 0/0:4,0:4:12.04:0,12,153 0/0:4,0:4:12.03:0,12,138 0/0:8,0:8:24.08:0,24,326 0/0:8,0:8:24.08:0,24,315 0/0:12,0:12:33.11:0,33,442 0/0:8,0:8:24.08:0,24,317 0/0:16,0:16:48.16:0,48,638 0/0:18,0:18:54.18:0,54,721 0/0:7,0:7:18.06:0,18,240 0/0:3,0:3:9.03:0,9,121 0/0:3,0:3:9.03:0,9,108 ./. 0/0:12,0:12:30.10:0,30,401 0/0:9,0:9:24.08:0,24,308 0/0:14,0:14:42.14:0,42,558 0/0:17,0:17:51.17:0,51,681 0/0:11,0:11:33.10:0,33,422 0/0:9,1:10:7.40:0,7,317 0/0:14,0:14:39.11:0,39,500 0/0:16,0:17:45.14:0,45,582 0/0:16,0:16:42.13:0,42,533 0/0:11,0:11:30.10:0,30,400 0/0:15,0:15:45.14:0,45,598 0/0:11,0:11:33.11:0,33,436 0/0:8,0:8:24.05:0,24,296 0/0:8,0:8:24.07:0,24,308 0/0:13,0:13:33.10:0,33,429 0/0:11,0:11:33.10:0,33,429 0/0:19,0:19:54.14:0,54,675 0/0:12,0:12:30.10:0,30,400 0/0:18,0:18:51.10:0,51,591 0/0:15,0:15:45.14:0,45,578 0/0:13,0:13:39.12:0,39,514 0/0:20,0:20:60.19:0,60,795 0/0:22,0:22:60.17:0,60,765 0/0:8,0:8:24.08:0,24,316 0/0:25,0:25:69.21:0,69,852 0/0:52,0:52:99:0,150,1943 0/0:39,0:39:99:0,99,1264 0/0:24,0:24:60.19:0,60,777 0/0:26,0:26:63.20:0,63,806 0/0:21,0:21:60.19:0,60,782 0/0:30,0:30:81.24:0,81,1007 0/0:30,0:30:81.25:0,81,1020 0/0:55,0:55:99:0,141,1794 0/1:16,11:28:99:338,0,455 0/0:23,0:24:63.19:0,63,781 0/1:28,22:51:99:692,0,861 0/0:70,0:70:99:0,196,2463 0/0:33,0:33:90.29:0,90,1188 0/0:43,0:43:99:0,114,1427 0/0:26,0:26:78.25:0,78,1028 0/0:29,0:29:81.23:0,81,1018 0/0:18,0:18:51.16:0,51,671 0/0:13,0:13:33.10:0,33,414 0/0:30,0:30:87.26:0,87,1084 0/0:22,0:22:60.19:0,60,769 0/0:23,0:23:60.19:0,60,789 -chr1 1102717 . C T 175.26 . AC=1;AF=0.0083;AN=120;BaseQRankSum=1.432;DP=649;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.6822;InbreedingCoeff=-0.0345;MQ=56.83;MQ0=0;MQRankSum=1.021;QD=9.22;ReadPosRankSum=1.763;EFF=DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,36 0/0:3,0:3:9.03:0,9,119 0/0:3,0:3:9.03:0,9,118 0/0:2,0:2:6.02:0,6,73 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,38 0/0:12,0:12:33.10:0,33,413 0/0:7,0:7:21.07:0,21,278 0/0:10,0:10:30.09:0,30,376 0/0:18,0:18:54.17:0,54,714 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,32 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3:0,3,29 0/0:9,0:9:24.07:0,24,301 0/0:8,0:8:18.06:0,18,230 0/0:6,0:6:18.06:0,18,231 0/0:13,0:13:33.11:0,33,443 0/0:7,0:7:18.06:0,18,233 0/0:4,0:4:12.02:0,12,143 0/0:11,0:11:30.08:0,30,375 0/0:14,0:14:42.14:0,42,541 0/0:9,0:9:24.07:0,24,300 0/0:3,0:3:9.03:0,9,121 0/0:7,0:7:18.06:0,18,229 0/0:8,0:8:21.07:0,21,273 0/0:8,0:8:18.06:0,18,229 0/0:3,0:3:9.03:0,9,114 0/0:8,0:8:24.06:0,24,294 0/0:5,0:5:15.05:0,15,191 0/0:11,0:11:27.06:0,27,334 0/0:5,0:5:15.05:0,15,191 0/0:10,0:10:30.08:0,30,367 0/0:9,0:9:21.07:0,21,280 0/0:5,0:5:15.05:0,15,186 0/0:7,0:7:21.03:0,21,246 0/0:11,0:11:30.08:0,30,353 0/0:2,0:2:6.02:0,6,76 0/0:19,0:19:51.16:0,51,659 0/0:24,0:24:66.19:0,66,797 0/0:29,0:29:84.24:0,84,1004 0/0:18,0:18:54.16:0,54,660 0/0:18,0:18:48.15:0,48,597 0/0:8,0:8:24.08:0,24,309 0/0:24,0:25:60.17:0,60,746 0/0:26,0:26:66.19:0,66,835 0/0:26,0:28:75.20:0,75,920 0/1:11,8:19:99:223,0,351 0/0:9,0:10:24.08:0,24,306 0/0:27,0:27:75.23:0,75,928 0/0:36,0:36:90.27:0,90,1137 0/0:16,0:16:48.14:0,48,597 0/0:23,0:23:63.17:0,63,754 0/0:6,0:6:18.06:0,18,237 0/0:12,0:12:33.10:0,33,390 0/0:8,0:8:24.05:0,24,264 0/0:12,0:12:33.09:0,33,402 0/0:15,0:15:45.11:0,45,544 0/0:14,0:14:39.09:0,39,461 0/0:7,0:7:21.05:0,21,255 -chr1 1103049 . C T 201.32 . AC=1;AF=0.0085;AN=118;BaseQRankSum=0.756;DP=465;Dels=0.00;FS=3.302;HRun=0;HaplotypeScore=0.3840;InbreedingCoeff=-0.0481;MQ=57.23;MQ0=0;MQRankSum=0.101;QD=9.15;ReadPosRankSum=-0.265;EFF=DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6:0,6,64 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,82 0/0:2,0:2:6.02:0,6,74 0/0:3,0:3:9.03:0,9,123 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,122 0/0:4,0:4:12.04:0,12,156 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,81 0/0:2,0:2:6.02:0,6,82 0/0:5,0:5:15.05:0,15,185 0/0:2,0:2:6.02:0,6,71 0/0:5,0:5:12.04:0,12,155 0/0:7,0:7:21.07:0,21,271 0/0:5,0:5:15.05:0,15,192 0/0:11,0:11:30.09:0,30,380 0/0:6,0:6:15.05:0,15,193 0/0:7,0:7:18.06:0,18,226 0/0:3,0:3:9.03:0,9,111 0/0:2,0:2:6.02:0,6,68 0/0:5,0:5:12.03:0,12,138 0/0:2,0:2:6.02:0,6,75 0/0:4,0:4:12.03:0,12,139 0/0:2,0:2:6.02:0,6,83 0/0:4,0:4:12.04:0,12,157 0/0:4,0:4:12.04:0,12,156 0/0:5,0:6:12.03:0,12,150 0/0:4,0:4:12.03:0,12,141 0/0:7,0:7:21.06:0,21,256 0/0:4,0:4:12.04:0,12,151 0/0:8,0:8:21.07:0,21,274 0/0:5,0:5:12.04:0,12,162 0/0:4,0:4:12.04:0,12,162 0/0:6,0:6:15.05:0,15,191 0/0:8,0:8:21.07:0,21,288 0/0:5,0:5:12.03:0,12,142 0/0:18,0:18:45.11:0,45,530 0/0:20,0:20:54.16:0,54,678 0/0:13,0:13:36.12:0,36,473 0/0:12,0:12:33.10:0,33,425 0/0:10,0:10:24.08:0,24,313 0/0:12,0:12:33.10:0,33,426 0/0:8,0:8:21.07:0,21,271 0/0:26,0:26:69.22:0,69,895 0/0:5,0:5:15.05:0,15,194 0/0:12,0:12:33.11:0,33,431 0/1:14,8:22:99:249,0,414 0/0:32,0:32:90.26:0,90,1143 0/0:11,0:11:24.07:0,24,298 0/0:26,0:26:66.21:0,66,884 0/0:9,0:9:27.09:0,27,357 0/0:14,0:14:36.12:0,36,486 0/0:8,0:8:15.05:0,15,194 0/0:11,0:11:30.10:0,30,395 0/0:16,0:16:36.12:0,36,481 0/0:11,0:11:33.11:0,33,432 0/0:13,0:13:36.12:0,36,478 -chr1 1103150 . G A 13784.17 . AC=26;AF=0.2281;AN=114;BaseQRankSum=2.288;DP=1923;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.8331;InbreedingCoeff=0.0633;MQ=56.95;MQ0=0;MQRankSum=6.711;QD=19.50;ReadPosRankSum=1.282;EFF=DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,115 ./. ./. ./. 0/0:4,0:4:12.04:0,12,164 0/0:2,0:2:6.02:0,6,73 1/1:0,2:2:3.01:31,3,0 0/1:2,1:3:31.62:32,0,72 0/1:3,2:5:29.19:29,0,110 0/1:2,4:6:51.51:141,0,52 0/0:3,0:3:9.03:0,9,109 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,41 0/0:20,1:21:17.94:0,18,708 0/0:28,0:28:78.25:0,78,1025 0/0:9,0:9:27.08:0,27,327 0/1:8,14:22:99:454,0,259 0/0:23,0:23:66.20:0,66,829 0/0:26,0:26:75.24:0,75,960 0/0:30,0:30:81.26:0,81,1059 0/1:9,6:16:99:188,0,304 0/0:34,0:34:96.31:0,96,1280 0/0:21,0:21:54.18:0,54,722 0/1:11,15:26:99:518,0,276 0/1:6,15:21:99:497,0,160 0/1:12,7:19:99:176,0,353 0/1:15,12:27:99:399,0,448 0/1:11,8:19:99:260,0,342 0/0:22,0:22:57.18:0,57,749 0/0:24,0:24:69.22:0,69,895 0/1:11,12:24:99:400,0,360 0/0:18,0:18:48.15:0,48,620 0/0:17,0:17:48.15:0,48,620 0/1:15,18:33:99:578,0,417 0/0:26,0:26:75.24:0,75,963 0/0:18,0:18:54.17:0,54,710 0/0:24,0:24:72.23:0,72,943 1/1:0,37:37:99:1395,105,0 0/1:16,15:34:99:364,0,457 0/1:56,40:99:99:1015,0,1504 1/1:1,66:67:99:2276,178,0 0/0:53,1:54:97.79:0,98,1699 0/1:30,21:52:99:590,0,923 0/0:47,0:47:96.30:0,96,1244 0/1:20,25:45:99:788,0,562 0/0:60,1:61:99:0,121,1993 0/0:100,0:102:99:0,250,3129 0/0:29,0:29:69.21:0,69,867 0/1:23,25:48:99:661,0,609 0/0:91,0:96:99:0,217,2735 0/0:90,1:92:99:0,232,2972 0/0:58,0:60:99:0,138,1718 0/0:81,0:82:99:0,202,2551 0/0:65,0:66:99:0,168,2100 0/0:52,0:52:99:0,141,1845 0/0:41,0:41:93.23:0,93,1165 0/0:31,0:32:78.23:0,78,966 0/1:4,54:58:6.34:1585,0,6 0/0:47,0:47:99:0,117,1512 1/1:0,43:43:99:1406,108,0 -chr1 1103231 . C G 920.65 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.613;DP=4071;Dels=0.00;FS=1.295;HRun=0;HaplotypeScore=2.5754;InbreedingCoeff=-0.0143;MQ=57.14;MQ0=0;MQRankSum=0.020;QD=9.59;ReadPosRankSum=1.029;EFF=DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,upstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL 0/0:4,0:4:9.03:0,9,111 0/0:6,0:6:15.05:0,15,192 0/0:4,0:4:12.04:0,12,161 0/0:6,0:6:12.04:0,12,153 0/0:9,0:9:24.08:0,24,322 0/0:9,0:9:27.08:0,27,341 0/0:5,0:5:15.05:0,15,191 0/0:1,0:1:3.01:0,3,35 0/0:25,0:25:75.25:0,75,999 0/0:19,0:19:57.19:0,57,754 0/0:6,0:6:15.05:0,15,195 0/0:9,0:9:27.09:0,27,357 0/0:4,0:4:12.04:0,12,145 0/0:60,0:60:99:0,141,1851 0/0:62,0:62:99:0,141,1862 0/0:31,0:32:78.24:0,78,982 0/0:52,0:52:99:0,120,1594 0/0:63,0:63:99:0,144,1853 0/0:63,0:64:99:0,147,1952 0/0:61,0:61:99:0,150,1916 0/0:55,0:55:99:0,138,1800 0/0:68,0:68:99:0,162,2136 0/0:55,0:55:99:0,120,1598 0/0:57,0:57:99:0,129,1700 0/0:59,0:59:99:0,135,1805 0/0:53,0:53:99:0,117,1578 0/0:65,0:65:99:0,147,1921 0/0:58,2:60:99:0,100,1754 0/0:66,0:66:99:0,147,1964 0/0:46,0:46:99:0,102,1333 0/0:62,0:62:99:0,138,1845 0/0:69,0:69:99:0,166,2209 0/0:58,0:58:99:0,135,1786 0/0:69,0:69:99:0,162,2091 0/0:41,0:41:93.28:0,93,1179 0/0:60,0:60:99:0,132,1742 0/0:73,0:73:99:0,163,2147 0/0:76,0:76:99:0,175,2303 0/0:67,0:67:99:0,162,2062 0/0:173,0:174:99:0,424,5372 0/0:129,0:129:99:0,298,3781 0/0:110,0:110:99:0,283,3622 0/0:99,0:99:99:0,253,3127 0/0:82,0:82:99:0,190,2407 0/0:116,0:116:99:0,259,3350 0/0:113,0:114:99:0,256,3246 0/0:175,0:175:99:0,445,5623 0/0:54,0:54:99:0,135,1604 0/0:118,0:118:99:0,262,3417 0/0:149,0:150:99:0,382,4650 0/0:144,1:145:99:0,341,4487 0/0:108,0:108:99:0,268,3393 0/0:117,0:117:99:0,289,3639 0/0:116,1:117:99:0,244,3479 0/0:109,1:110:99:0,242,3351 0/1:50,46:96:99:968,0,1224 0/0:64,1:65:99:0,147,1863 0/0:115,0:116:99:0,274,3426 0/0:103,0:103:99:0,241,3112 0/0:113,0:113:99:0,259,3315 -chr1 1103423 . GA G 310.03 . AC=11;AF=0.0932;AN=118;BaseQRankSum=3.186;DP=1367;FS=7.032;HRun=1;HaplotypeScore=112.5777;InbreedingCoeff=-0.1319;MQ=56.78;MQ0=0;MQRankSum=-1.054;QD=1.13;ReadPosRankSum=-12.462;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,48 ./. 0/0:1,0:1:3.01:0,3,48 0/0:2,0:2:6.02:0,6,86 0/0:1,0:1:3.01:0,3,48 0/0:1,0:1:3.01:0,3,48 0/0:2,0:2:6.02:0,6,96 0/0:4,0:4:12.04:0,12,192 0/0:8,0:8:24.08:0,24,373 0/0:2,0:2:6.02:0,6,95 0/0:4,0:4:12.04:0,12,180 0/0:2,0:2:6.02:0,6,96 0/0:11,0:11:27.09:0,27,432 0/0:21,0:21:21.44:0,21,889 0/0:10,0:10:27.09:0,27,432 0/0:20,0:20:60.20:0,60,935 0/0:16,0:16:0.59:0,1,577 0/0:26,0:26:27.31:0,27,999 0/1:16,0:16:17.55:18,0,596 0/0:9,0:9:27.09:0,27,415 0/1:19,0:19:47.24:47,0,666 0/1:12,0:12:8.54:9,0,416 0/0:16,1:17:17.48:0,17,720 0/1:16,0:16:1.26:1,0,551 0/0:20,0:20:26.79:0,27,819 0/0:17,0:17:45.14:0,45,670 0/0:12,0:12:36.12:0,36,522 0/0:15,0:15:44.18:0,44,663 0/0:14,0:14:39.12:0,39,575 0/0:21,0:21:31.09:0,31,899 0/1:18,0:18:19.90:20,0,640 0/0:12,0:12:36.12:0,36,559 0/0:24,0:24:34.10:0,34,947 0/0:18,0:18:27.59:0,28,707 0/0:12,0:12:32.59:0,33,447 0/1:22,1:23:29.72:30,0,658 0/0:18,0:18:51.17:0,51,801 0/1:31,0:31:35.43:35,0,1004 0/1:53,0:53:55.70:56,0,1711 0/0:48,1:49:46.42:0,46,1784 0/1:40,0:40:99:104,0,1312 0/0:30,0:30:43.50:0,43,1221 0/0:34,0:33:81.19:0,81,1287 0/0:32,0:32:18.96:0,19,1145 0/0:44,1:45:75.31:0,75,1679 0/0:72,1:73:99:0,129,2984 0/1:24,1:25:85.75:86,0,726 0/0:32,0:32:6.78:0,7,1083 0/0:42,0:42:99:0,111,1720 0/0:65,0:65:99:0,131,2558 0/0:60,0:60:99:0,127,2329 0/0:39,0:39:76.11:0,76,1548 0/0:41,1:42:34.59:0,35,1524 0/0:51,0:51:99:0,141,2186 0/0:37,0:37:12.48:0,12,1274 0/1:22,0:22:56.81:57,0,713 0/0:40,0:40:80.65:0,81,1598 0/0:41,0:41:77.19:0,77,1747 0/0:37,1:38:26.39:0,26,1270 -chr1 1103424 . A G 291.86 . AC=11;AF=0.0932;AN=118;BaseQRankSum=-4.363;DP=1367;Dels=0.01;FS=12.595;HRun=3;HaplotypeScore=1.1874;InbreedingCoeff=-0.1339;MQ=56.78;MQ0=0;MQRankSum=-0.884;QD=0.96;ReadPosRankSum=-10.797;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,81 0/0:4,0:4:12.04:0,12,161 0/0:8,0:8:24.08:0,24,320 0/0:2,0:2:6.02:0,6,81 0/0:4,0:4:12.04:0,12,149 0/0:2,0:2:6.02:0,6,76 0/0:10,1:11:27.09:0,27,355 0/0:20,1:21:20.20:0,20,662 0/0:10,0:10:27.09:0,27,350 0/0:20,0:20:57.19:0,57,759 0/0:13,3:16:7.54:0,8,415 0/0:25,1:26:30.59:0,31,786 0/1:14,2:16:19.07:19,0,509 0/0:9,0:9:27.09:0,27,347 0/1:15,4:19:61.56:62,0,535 0/1:11,1:12:3.90:4,0,339 0/0:16,0:16:48.15:0,48,607 0/0:15,1:16:3.56:0,4,463 0/0:19,1:20:15.91:0,16,607 0/0:16,1:17:45.13:0,45,561 0/0:12,0:12:33.08:0,33,403 0/0:15,0:15:45.13:0,45,578 0/0:14,0:14:36.12:0,36,477 0/0:20,1:21:23.21:0,23,704 0/0:16,2:18:7.84:0,8,467 0/0:12,0:12:33.10:0,33,425 0/0:22,1:23:26.22:0,26,750 0/0:17,1:18:17.18:0,17,609 0/0:12,0:12:30.09:0,30,389 0/1:20,2:22:21.38:21,0,590 0/0:17,1:18:51.14:0,51,658 0/1:24,7:31:59.96:60,0,738 0/1:45,7:53:37.82:38,0,1396 0/0:43,4:48:97.73:0,98,1525 0/1:30,10:40:99:141,0,1011 0/0:28,2:30:42.67:0,43,980 0/0:31,3:34:50.82:0,51,1016 0/1:28,4:32:13.41:13,0,895 0/0:40,4:44:83.89:0,84,1399 0/0:69,3:72:99:0,129,2350 0/1:20,4:24:41.73:42,0,635 0/1:29,3:32:18.72:19,0,936 0/0:40,2:42:99:0,117,1466 0/0:63,2:65:99:0,130,1934 0/0:56,4:60:99:0,115,1739 0/0:38,1:39:66.71:0,67,1259 0/0:36,5:41:32.76:0,33,1191 0/0:51,0:51:99:0,123,1511 0/0:30,7:37:12.03:0,12,947 0/1:19,3:22:19.12:19,0,547 0/0:37,3:40:71.36:0,71,1325 0/0:39,2:41:69.75:0,70,1288 0/0:36,1:37:60.73:0,61,1178 -chr1 1103436 . C T 253.89 . AC=1;AF=0.0094;AN=106;BaseQRankSum=1.346;DP=1176;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0420;InbreedingCoeff=-0.0281;MQ=56.38;MQ0=0;MQRankSum=-1.314;QD=7.25;ReadPosRankSum=-3.184;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,81 ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,40 0/0:9,0:9:21.07:0,21,275 0/0:15,0:15:39.13:0,39,519 0/0:7,0:7:18.06:0,18,238 0/0:14,0:14:39.13:0,39,513 0/0:16,0:16:36.10:0,36,471 0/0:23,0:23:63.18:0,63,811 0/0:13,0:13:39.12:0,39,502 0/0:9,0:9:24.08:0,24,311 0/0:20,0:20:54.16:0,54,692 0/0:7,0:7:18.05:0,18,225 0/0:17,0:17:48.11:0,48,575 0/0:14,0:14:36.11:0,36,467 0/0:15,0:15:45.15:0,45,603 0/0:12,0:12:33.10:0,33,424 0/0:8,0:8:18.06:0,18,236 0/0:14,0:14:42.10:0,42,515 0/0:10,0:10:27.09:0,27,360 0/0:19,0:19:51.16:0,51,666 0/0:15,0:15:42.14:0,42,558 0/0:10,0:10:27.08:0,27,346 0/0:17,0:18:51.15:0,51,652 0/0:9,0:9:24.08:0,24,315 0/0:11,0:11:27.08:0,27,338 0/0:14,0:14:39.11:0,39,503 0/0:16,0:16:45.15:0,45,592 0/0:28,0:29:72.21:0,72,889 0/0:48,0:51:99:0,126,1558 0/0:37,0:39:93.26:0,93,1171 0/0:37,0:37:96.29:0,96,1200 0/0:27,0:28:78.25:0,78,1036 0/0:28,0:29:78.25:0,78,1021 0/0:34,0:34:93.26:0,93,1154 0/0:36,0:37:90.28:0,90,1156 0/0:75,0:75:99:0,178,2253 0/0:24,0:24:60.19:0,60,772 0/0:29,1:30:69.21:0,69,872 0/1:21,12:35:99:301,0,662 0/0:61,0:62:99:0,144,1769 0/0:56,0:57:99:0,135,1687 0/0:34,0:34:90.28:0,90,1163 0/0:39,0:40:84.25:0,84,1046 0/0:44,0:46:99:0,114,1445 0/0:29,1:32:69.20:0,69,863 0/0:24,0:25:63.17:0,63,798 0/0:28,0:28:69.21:0,69,892 0/0:31,0:31:84.25:0,84,1069 0/0:31,0:31:81.25:0,81,1041 -chr1 1103471 . C T 3129.31 . AC=41;AF=0.3596;AN=114;BaseQRankSum=7.298;DP=802;Dels=0.00;FS=25.877;HRun=0;HaplotypeScore=0.4705;InbreedingCoeff=-0.6199;MQ=56.31;MQ0=0;MQRankSum=4.884;QD=4.53;ReadPosRankSum=-15.448;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:6.02:0,6,77 0/0:3,0:3:9.03:0,9,115 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,38 0/0:2,0:2:6.02:0,6,72 0/0:2,0:2:6.02:0,6,74 ./. 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6:0,6,56 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,71 ./. 0/0:4,0:4:9.02:0,9,101 0/1:3,3:6:83.79:93,0,84 0/1:3,1:4:30.98:31,0,63 0/1:3,3:6:62.10:103,0,62 0/1:7,2:9:58.95:59,0,153 0/1:9,1:10:9.93:10,0,297 0/1:4,2:6:55:55,0,120 0/1:2,2:4:26.22:26,0,72 0/1:11,5:16:99:111,0,308 0/1:5,1:6:20.52:21,0,161 0/1:4,5:9:76.18:180,0,76 0/1:6,3:9:94.51:95,0,170 0/1:4,4:8:99:135,0,101 0/1:8,4:12:99:119,0,228 0/1:3,2:6:59.33:59,0,89 0/1:9,1:10:15.93:16,0,244 0/0:2,0:2:6.01:0,6,65 0/1:11,3:14:80.30:80,0,269 0/1:8,5:13:99:147,0,265 0/1:1,1:2:21.65:34,0,22 0/1:11,1:12:4.26:4,0,306 0/1:7,2:9:45.56:46,0,193 0/0:3,0:3:9.03:0,9,113 0/1:8,4:12:99:114,0,238 0/1:5,4:9:99:129,0,141 0/1:12,6:20:99:175,0,279 0/1:28,5:34:99:105,0,625 0/1:23,3:28:54.63:55,0,597 0/1:23,3:27:50.82:51,0,642 0/1:15,5:21:99:132,0,394 0/1:16,2:18:33.48:33,0,389 0/1:20,5:25:90.09:90,0,513 0/1:22,4:26:99:104,0,443 0/1:43,8:53:99:181,0,1046 0/1:14,2:16:35.68:36,0,374 0/0:17,1:18:6.51:0,7,461 0/1:26,3:33:52.07:52,0,606 0/1:49,6:56:98.79:99,0,1299 0/0:34,1:36:56.27:0,56,1097 0/1:18,2:21:22.72:23,0,477 0/1:22,7:29:99:192,0,582 0/0:31,0:31:90.23:0,90,1102 0/1:21,5:26:99:123,0,533 0/1:11,2:13:43.93:44,0,293 0/1:14,5:20:99:125,0,394 0/1:14,2:16:35.22:35,0,353 0/1:15,2:17:25.29:25,0,464 -chr1 1103479 . G C 231.39 . AC=9;AF=0.0804;AN=112;BaseQRankSum=-1.555;DP=715;Dels=0.00;FS=4.645;HRun=2;HaplotypeScore=0.4522;InbreedingCoeff=-0.1256;MQ=56.12;MQ0=0;MQRankSum=1.010;QD=2.22;ReadPosRankSum=-8.435;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:6.02:0,6,80 0/0:4,0:4:12.04:0,12,146 0/0:1,0:1:3.01:0,3,30 0/0:1,0:1:3.01:0,3,32 0/0:2,0:2:6:0,6,58 0/0:2,0:2:6.02:0,6,74 ./. 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:9.03:0,9,107 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,80 ./. 0/0:4,0:4:12.04:0,12,151 0/1:3,1:4:26.23:26,0,60 0/0:3,0:3:9.03:0,9,105 0/0:2,0:3:3.01:0,3,39 0/0:7,0:7:15.04:0,15,180 0/0:8,0:8:24.07:0,24,300 0/0:4,0:4:12.04:0,12,154 0/0:2,0:2:3.01:0,3,42 0/1:11,1:12:7.70:8,0,327 0/1:5,1:6:17.20:17,0,160 0/1:6,4:10:99:116,0,189 0/0:6,0:6:15.05:0,15,198 0/1:5,2:7:57.53:58,0,142 0/0:8,0:8:18.06:0,18,221 0/0:2,1:3:6.02:0,6,76 0/0:9,0:9:21.07:0,21,270 0/0:2,0:2:6.02:0,6,74 0/0:11,0:11:33.08:0,33,391 0/1:9,1:10:8.17:8,0,292 ./. 0/0:11,0:11:30.09:0,30,376 0/0:7,0:7:18.05:0,18,218 0/0:3,0:3:9.02:0,9,103 0/1:8,1:9:9.36:9,0,245 0/0:5,0:5:15.05:0,15,188 0/1:15,2:18:33.93:34,0,378 0/0:29,1:30:72.22:0,72,894 0/0:30,0:30:69.19:0,69,854 0/0:26,0:26:69.20:0,69,861 0/0:19,1:20:20.73:0,21,589 0/0:20,0:20:42.13:0,42,502 0/0:21,1:22:19.37:0,19,619 0/0:22,1:24:19.36:0,19,602 0/0:47,1:48:79.53:0,80,1343 0/0:14,0:14:33.09:0,33,385 0/0:18,1:19:14.46:0,14,474 0/0:31,2:34:34.40:0,34,758 0/0:50,1:51:99:0,100,1561 0/0:32,0:32:87.26:0,87,1067 0/0:17,0:17:39.12:0,39,483 0/1:24,4:28:81.99:82,0,615 0/0:27,0:27:75.22:0,75,929 0/0:22,1:24:22.38:0,22,650 0/0:11,0:11:30.09:0,30,376 0/0:16,0:16:45.13:0,45,554 0/0:15,0:15:42.13:0,42,537 0/0:16,0:16:39.12:0,39,471 -chr1 1103537 . C T 42.98 . AC=4;AF=0.0364;AN=110;BaseQRankSum=-0.058;DP=526;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3527;InbreedingCoeff=0.3068;MQ=56.99;MQ0=0;MQRankSum=1.015;QD=14.33;ReadPosRankSum=0.313;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:9.03:0,9,108 0/0:1,0:1:3.01:0,3,36 0/0:1,0:1:3.01:0,3,41 ./. 0/0:6,0:6:15.03:0,15,175 0/0:2,0:2:6.02:0,6,77 0/0:4,0:4:12.04:0,12,164 0/0:2,0:2:6.02:0,6,79 ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,37 0/0:4,0:4:9.03:0,9,124 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:6.02:0,6,70 0/0:4,0:4:12.02:0,12,131 0/0:2,0:2:6.02:0,6,82 1/1:0,1:1:3.01:35,3,0 ./. 0/0:5,0:5:12.04:0,12,158 0/0:4,0:4:12.04:0,12,158 0/0:3,0:3:9.03:0,9,115 0/0:3,0:3:6.02:0,6,83 0/0:4,0:4:9.03:0,9,124 0/0:7,0:7:15.04:0,15,190 0/0:2,0:2:6.02:0,6,75 0/0:9,0:9:21.07:0,21,281 0/0:1,0:1:3.01:0,3,40 0/0:6,0:6:18.06:0,18,238 0/0:6,0:6:15.05:0,15,204 ./. 0/0:7,0:7:18.06:0,18,243 0/0:7,0:7:18.06:0,18,235 1/1:0,2:2:6.02:80,6,0 0/0:8,0:8:15.05:0,15,213 0/0:4,0:4:12.04:0,12,166 0/0:6,0:6:15.05:0,15,201 0/0:20,0:20:48.15:0,48,630 0/0:28,0:28:78.24:0,78,975 0/0:15,0:15:39.12:0,39,496 0/0:15,0:15:42.09:0,42,495 0/0:25,0:25:72.18:0,72,855 0/0:21,0:21:51.14:0,51,637 0/0:17,0:18:42.14:0,42,549 0/0:37,0:37:99:0,102,1321 0/0:7,0:7:15.04:0,15,184 0/0:12,0:12:30.10:0,30,391 0/0:34,0:34:81.21:0,81,963 0/0:35,0:35:90.27:0,90,1120 0/0:24,0:24:66.20:0,66,848 0/0:16,0:16:48.13:0,48,586 0/0:18,0:18:42.12:0,42,530 0/0:9,0:9:24.08:0,24,316 0/0:17,0:17:42.11:0,42,513 0/0:10,0:10:24.08:0,24,307 0/0:16,0:16:39.11:0,39,481 0/0:11,0:11:30.09:0,30,379 0/0:13,1:14:39.11:0,39,480 -chr1 1103542 . T C 13387.36 . AC=101;AF=0.9182;AN=110;BaseQRankSum=2.524;DP=466;Dels=0.00;FS=6.051;HRun=2;HaplotypeScore=0.2267;InbreedingCoeff=0.0050;MQ=57.11;MQ0=0;MQRankSum=1.977;QD=29.29;ReadPosRankSum=-2.662;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3.01:33,3,0 1/1:0,3:3:9.01:95,9,0 1/1:0,2:2:6.02:79,6,0 1/1:0,1:1:3.01:39,3,0 1/1:0,2:2:3.01:30,3,0 1/1:0,5:5:12.04:150,12,0 1/1:0,2:2:6.02:73,6,0 1/1:0,4:4:12.04:162,12,0 1/1:0,2:2:6.02:80,6,0 ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:39,3,0 1/1:0,1:1:3.01:41,3,0 1/1:0,4:4:9.01:106,9,0 1/1:0,2:2:6.02:81,6,0 1/1:0,2:2:3.01:39,3,0 1/1:0,4:4:12.04:154,12,0 1/1:0,2:2:6.02:71,6,0 ./. ./. 1/1:0,4:4:12.03:147,12,0 1/1:0,3:3:9.03:117,9,0 1/1:0,3:3:9.02:105,9,0 1/1:0,2:2:6.02:84,6,0 1/1:0,3:3:6.02:87,6,0 0/1:4,3:7:66.19:66,0,112 1/1:0,1:1:3.01:40,3,0 1/1:0,7:7:15.05:198,15,0 1/1:0,1:1:3.01:39,3,0 1/1:0,4:4:12.04:156,12,0 1/1:0,5:5:12.04:167,12,0 ./. 1/1:0,3:3:9.03:124,9,0 0/1:1,3:4:9.65:104,0,10 1/1:0,2:2:6.02:78,6,0 0/1:3,4:8:74.51:75,0,84 1/1:0,5:5:15.05:203,15,0 1/1:0,5:5:12.03:143,12,0 1/1:0,20:20:51.13:641,51,0 1/1:0,25:25:72.22:903,72,0 1/1:0,12:12:30.09:382,30,0 1/1:0,11:12:33.10:418,33,0 1/1:0,25:25:66.17:791,66,0 1/1:0,17:17:45.13:561,45,0 1/1:0,16:16:42.13:543,42,0 1/1:0,32:32:93.30:1209,93,0 1/1:0,6:7:15.04:179,15,0 1/1:1,9:10:24.08:317,24,0 1/1:0,28:29:72.22:906,72,0 0/1:16,12:28:99:337,0,411 0/1:12,13:25:99:317,0,356 0/1:4,11:15:85.42:366,0,85 1/1:1,15:18:42.13:530,42,0 0/0:9,0:9:24.07:0,24,307 1/1:0,13:13:33.10:415,33,0 1/1:0,9:9:21.07:273,21,0 1/1:0,15:15:42.12:513,42,0 0/1:4,7:11:99:156,0,131 1/1:0,12:12:30.09:388,30,0 -chr1 1103690 . T TCA 4213.79 . AC=60;AF=0.909;AN=66;BaseQRankSum=-2.219;DP=87;FS=4.960;HRun=0;HaplotypeScore=8.2650;InbreedingCoeff=0.2982;MQ=60.22;MQ0=0;MQRankSum=-0.386;QD=52.02;ReadPosRankSum=-1.623;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL 1/1:0,4:4:9.03:167,9,0 1/1:0,3:3:9.03:168,9,0 1/1:0,5:6:18.06:333,18,0 1/1:1,4:5:12:190,12,0 1/1:0,3:3:9.03:171,9,0 ./. 1/1:0,3:3:9.03:172,9,0 ./. 1/1:1,4:5:12.04:230,12,0 1/1:1,2:3:6.02:113,6,0 1/1:0,2:2:6.02:115,6,0 ./. 1/1:0,2:2:6.02:115,6,0 ./. ./. ./. ./. 1/1:0,1:2:6.02:106,6,0 1/1:0,1:1:3.01:57,3,0 ./. ./. ./. 1/1:0,2:2:6.02:91,6,0 1/1:0,1:1:3.01:57,3,0 1/1:0,1:1:3.01:57,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:57,3,0 ./. ./. ./. ./. 1/1:0,2:2:6.02:115,6,0 1/1:0,6:6:18.06:336,18,0 1/1:1,2:3:9.03:166,9,0 1/1:0,3:3:9.03:172,9,0 1/1:0,1:1:3.01:57,3,0 1/1:0,3:3:9.03:172,9,0 1/1:0,2:2:6.02:91,6,0 1/1:0,4:4:12.04:230,12,0 ./. 1/1:0,2:2:6.02:115,6,0 ./. 0/0:1,0:1:3.01:0,3,46 1/1:0,3:3:9.03:171,9,0 0/0:2,0:2:6.02:0,6,92 1/1:0,2:2:6.02:104,6,0 0/0:1,0:1:3.01:0,3,46 1/1:0,3:3:6.02:115,6,0 ./. 1/1:0,2:2:6.02:111,6,0 ./. 1/1:0,1:1:3.01:57,3,0 -chr1 1103958 . T G 972.47 . AC=38;AF=0.905;AN=42;BaseQRankSum=0.039;DP=33;Dels=0.00;FS=2.722;HRun=0;HaplotypeScore=0.0376;InbreedingCoeff=0.1168;MQ=59.30;MQ0=0;MQRankSum=0.973;QD=31.37;ReadPosRankSum=-0.195;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1 GT:AD:DP:GQ:PL ./. ./. 1/1:0,3:3:9.03:119,9,0 1/1:0,3:3:9.03:114,9,0 1/1:0,1:1:3.01:32,3,0 1/1:0,2:2:6.02:82,6,0 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:41,3,0 ./. 1/1:0,1:1:3.01:39,3,0 ./. 0/0:1,0:1:3.01:0,3,41 1/1:0,2:2:6.02:82,6,0 ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:39,3,0 1/1:0,2:2:3.01:45,3,0 ./. ./. 1/1:0,1:1:3.01:40,3,0 ./. 1/1:0,2:2:3.01:45,3,0 ./. ./. ./. ./. 1/1:0,2:2:3.01:45,3,0 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:45,3,0 ./. ./. 1/1:0,2:2:6.01:66,6,0 ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. 0/0:1,0:1:3.01:0,3,39 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. -chr1 1104406 . C CCAGA 1690.42 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-4.911;DP=3757;FS=4.900;HRun=0;HaplotypeScore=321.6033;InbreedingCoeff=-0.0086;MQ=57.98;MQ0=0;MQRankSum=-8.640;QD=27.71;ReadPosRankSum=0.563;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),EXON(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|1),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant&feature_elongation|||ENSG00000198976|MIR429|ENST00000362106|1/1||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1 GT:AD:DP:GQ:PL 0/0:11,0:11:21.07:0,21,382 0/0:7,0:7:18.06:0,18,316 0/0:9,0:9:27.09:0,27,457 0/0:11,0:11:24.08:0,24,437 0/0:28,0:28:78.27:0,78,1380 0/0:25,0:25:57.20:0,57,1026 0/0:53,0:53:99:0,144,2551 0/0:25,0:25:63.21:0,63,1101 0/0:81,0:81:99:0,208,3667 0/0:76,0:76:99:0,172,2998 0/0:50,0:50:99:0,129,2296 0/0:28,0:28:66.22:0,66,1161 0/0:49,0:49:99:0,117,2106 0/0:50,0:50:99:0,135,2414 0/0:77,0:77:99:0,214,3844 0/0:37,0:37:99:0,105,1890 0/0:40,0:40:99:0,105,1868 0/0:50,0:50:99:0,126,2254 0/0:62,0:62:99:0,172,3077 0/0:54,0:54:99:0,154,2728 0/0:65,0:64:99:0,175,3164 0/0:59,0:59:99:0,151,2698 0/0:42,0:42:99:0,114,2020 0/0:60,0:60:99:0,175,3109 0/0:48,0:48:99:0,129,2326 0/0:52,0:52:99:0,138,2503 0/0:55,1:56:99:0,150,2637 0/0:41,0:41:99:0,117,2099 0/0:46,0:46:99:0,129,2336 0/0:47,0:47:99:0,129,2326 0/0:79,0:79:99:0,211,3747 0/0:26,0:26:75.26:0,75,1365 0/0:51,0:50:99:0,126,2255 0/1:40,21:61:99:1747,0,1626 0/0:55,0:55:99:0,157,2838 0/0:48,0:48:99:0,138,2489 0/0:67,0:67:99:0,187,3360 0/0:71,0:71:99:0,187,3348 0/0:85,0:85:99:0,226,4049 0/0:132,0:132:99:0,349,6289 0/0:79,0:79:99:0,202,3565 0/0:81,0:81:99:0,220,3912 0/0:80,0:80:99:0,211,3751 0/0:66,0:66:99:0,184,3274 0/0:63,0:63:99:0,142,2926 0/0:79,0:79:99:0,220,3911 0/0:148,0:148:99:0,391,6978 0/0:57,0:57:99:0,160,2843 0/0:98,0:98:99:0,274,4929 0/0:125,0:125:99:0,325,5895 0/0:124,0:124:99:0,322,5838 0/0:107,0:106:99:0,289,5140 0/0:111,0:111:99:0,298,5383 0/0:93,0:93:99:0,247,4430 0/0:79,0:79:99:0,220,3953 0/0:78,0:78:99:0,202,3604 0/0:45,0:45:99:0,120,2128 0/0:73,0:73:99:0,202,3643 0/0:84,0:84:99:0,232,4161 0/0:73,0:73:99:0,214,3864 -chr1 1104418 . A C 1306.94 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.348;DP=3836;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.7746;InbreedingCoeff=-0.0084;MQ=57.98;MQ0=0;MQRankSum=-0.429;QD=15.38;ReadPosRankSum=1.041;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),EXON(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|1),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000198976|MIR429|ENST00000362106|1/1||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1 GT:AD:DP:GQ:PL 0/0:11,0:11:30.09:0,30,378 0/0:13,0:13:33.11:0,33,423 0/0:13,0:13:36.11:0,36,453 0/0:13,0:13:39.12:0,39,501 0/0:29,0:29:87.28:0,87,1163 0/0:24,0:24:69.23:0,69,932 0/0:68,0:68:99:0,199,2605 0/0:23,0:23:69.18:0,69,871 0/0:89,0:89:99:0,256,3370 0/0:69,0:69:99:0,190,2482 0/0:40,0:40:99:0,117,1533 0/0:27,0:27:78.23:0,78,992 0/0:47,0:47:99:0,141,1854 0/0:52,0:52:99:0,123,1625 0/0:76,0:76:99:0,175,2373 0/0:42,0:42:96.27:0,96,1273 0/0:40,0:40:93.30:0,93,1229 0/0:49,0:49:99:0,120,1560 0/0:64,0:64:99:0,162,2140 0/0:57,2:59:99:0,104,1792 0/0:64,0:64:99:0,147,1935 0/0:62,0:62:99:0,135,1783 0/0:39,0:39:99:0,99,1290 0/0:60,0:60:99:0,144,1911 0/0:56,0:56:99:0,120,1601 0/0:53,0:53:99:0,135,1796 0/0:55,0:55:99:0,132,1718 0/0:42,0:42:96.31:0,96,1280 0/0:47,0:47:99:0,120,1567 0/0:44,0:44:99:0,120,1594 0/0:76,0:76:99:0,180,2320 0/0:30,0:30:75.21:0,75,953 0/0:48,0:48:99:0,120,1593 0/0:67,0:67:99:0,159,1993 0/0:54,0:54:99:0,129,1725 0/0:48,0:48:99:0,114,1519 0/0:73,0:73:99:0,196,2531 0/0:72,0:72:99:0,181,2384 0/1:34,51:85:99:1355,0,807 0/0:133,0:133:99:0,331,4328 0/0:75,1:77:99:0,184,2326 0/0:76,0:76:99:0,184,2410 0/0:79,2:82:99:0,187,2388 0/0:61,0:61:99:0,153,1956 0/0:67,0:67:99:0,175,2220 0/0:79,0:79:99:0,202,2656 0/0:151,0:151:99:0,355,4535 0/0:57,0:57:99:0,135,1742 0/0:99,0:99:99:0,223,2961 0/0:129,0:131:99:0,319,4010 0/0:126,3:129:99:0,240,3899 0/0:112,0:113:99:0,280,3549 0/0:112,0:112:99:0,286,3683 0/0:98,0:98:99:0,226,2904 0/0:84,0:84:99:0,199,2605 0/0:76,1:78:99:0,181,2333 0/0:47,0:48:99:0,117,1535 0/0:75,0:76:99:0,160,2131 0/0:84,0:84:99:0,199,2583 0/0:78,0:78:99:0,163,2189 -chr1 1104584 . T C 2225.46 . AC=7;AF=0.0583;AN=120;BaseQRankSum=-1.668;DP=1142;Dels=0.00;FS=2.698;HRun=0;HaplotypeScore=0.5785;InbreedingCoeff=0.5329;MQ=58.24;MQ0=0;MQRankSum=1.566;QD=23.93;ReadPosRankSum=1.120;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1,downstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:21.07:0,21,272 0/0:10,0:11:30.08:0,30,365 0/0:8,0:9:15.05:0,15,195 0/0:4,0:4:12.04:0,12,159 0/0:9,0:9:27.09:0,27,366 0/0:15,0:15:45.14:0,45,578 0/0:31,0:31:90.28:0,90,1177 0/0:16,0:16:45.13:0,45,583 0/0:35,0:35:99:0,105,1385 0/0:28,0:28:81.24:0,81,1041 0/0:21,0:22:60.19:0,60,789 0/0:11,0:11:33.11:0,33,429 0/0:22,0:23:63.20:0,63,825 0/0:14,0:14:42.13:0,42,530 0/0:16,0:16:48.14:0,48,608 0/0:10,0:10:30.10:0,30,393 0/0:14,0:14:33.10:0,33,425 0/0:9,0:9:21.07:0,21,284 0/0:17,0:17:51.17:0,51,672 1/1:0,15:15:42.14:562,42,0 0/0:14,0:15:39.13:0,39,526 0/0:17,0:17:45.15:0,45,590 0/0:9,0:9:27.09:0,27,346 0/0:13,0:13:33.09:0,33,422 0/0:14,0:14:39.11:0,39,491 0/1:8,8:16:99:204,0,220 0/0:18,0:18:48.13:0,48,605 0/0:6,0:6:18.06:0,18,238 0/0:20,0:20:57.17:0,57,726 0/0:14,0:14:39.12:0,39,510 0/0:15,0:15:45.15:0,45,592 0/0:7,0:8:21.06:0,21,265 0/0:10,0:10:30.10:0,30,390 0/0:13,0:13:36.11:0,36,455 0/0:18,0:18:51.16:0,51,665 0/1:5,1:6:23.70:24,0,177 0/0:17,0:17:45.14:0,45,586 0/0:19,0:19:57.16:0,57,727 0/0:16,0:16:36.11:0,36,463 0/0:40,0:40:99:0,108,1419 0/0:27,0:27:66.21:0,66,860 0/0:25,0:25:75.20:0,75,931 0/0:28,0:28:75.24:0,75,981 0/0:14,0:14:36.12:0,36,472 0/0:26,0:26:69.22:0,69,875 0/0:23,1:24:54.18:0,54,715 0/0:43,0:43:99:0,114,1433 0/1:6,7:13:99:222,0,193 0/0:15,0:15:39.13:0,39,507 1/1:1,42:43:80.90:1350,81,0 0/0:42,0:42:99:0,114,1420 0/0:38,0:39:93.27:0,93,1170 0/0:28,1:29:72.23:0,72,949 0/0:20,0:21:60.18:0,60,770 0/0:32,0:32:93.30:0,93,1204 0/0:22,0:23:63.20:0,63,794 0/0:12,0:12:33.11:0,33,441 0/0:21,0:21:57.14:0,57,705 0/0:28,0:28:78.25:0,78,1006 0/0:16,0:16:42.13:0,42,538 -chr1 1104624 . C T 353.09 . AC=2;AF=0.0167;AN=120;BaseQRankSum=1.668;DP=653;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.6949;InbreedingCoeff=-0.0240;MQ=57.96;MQ0=0;MQRankSum=0.018;QD=15.35;ReadPosRankSum=0.448;EFF=DOWNSTREAM(MODIFIER|||||MIR200A|miRNA|NON_CODING|ENST00000384875|),DOWNSTREAM(MODIFIER|||||MIR200B|miRNA|NON_CODING|ENST00000384997|),DOWNSTREAM(MODIFIER|||||MIR429|miRNA|NON_CODING|ENST00000362106|),DOWNSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|),UPSTREAM(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|);CSQ=downstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,downstream_gene_variant|||ENSG00000207730|MIR200B|ENST00000384997|||||miRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1,downstream_gene_variant|||ENSG00000198976|MIR429|ENST00000362106|||||miRNA|1,downstream_gene_variant|||ENSG00000207607|MIR200A|ENST00000384875|||||miRNA|1,upstream_gene_variant|||ENSG00000272141|RP11-465B22.8|ENST00000606993|||||lincRNA|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12.01:0,12,135 0/0:4,0:4:9.03:0,9,118 0/0:4,0:4:9.03:0,9,112 0/0:5,0:5:15.03:0,15,184 0/0:6,0:6:18.06:0,18,239 0/0:5,0:5:15.05:0,15,203 0/0:11,0:11:30.10:0,30,408 0/0:7,0:7:18.05:0,18,232 0/0:17,0:17:51.17:0,51,693 0/0:17,0:17:51.16:0,51,666 0/0:11,0:11:30.10:0,30,396 0/0:9,0:9:27.08:0,27,353 0/0:12,0:12:36.12:0,36,475 0/0:11,0:11:27.08:0,27,339 0/0:6,0:6:18.06:0,18,243 0/0:6,0:6:15.05:0,15,195 0/0:9,0:9:27.06:0,27,320 0/0:7,0:7:21.07:0,21,271 0/0:6,0:6:18.06:0,18,241 0/0:4,0:4:12.04:0,12,160 0/0:10,0:10:21.07:0,21,281 0/0:8,0:8:21.07:0,21,285 0/0:11,0:11:24.08:0,24,308 0/0:8,0:8:24.07:0,24,291 0/0:8,0:8:18.06:0,18,226 0/0:14,0:14:42.13:0,42,525 0/1:5,6:11:99:210,0,111 0/0:4,0:4:12.04:0,12,162 0/0:10,0:10:27.09:0,27,345 0/0:8,0:8:21.07:0,21,280 0/0:9,0:9:24.08:0,24,316 0/0:11,0:11:33.10:0,33,410 0/0:5,0:5:15.05:0,15,190 0/0:9,0:9:27.01:0,27,293 0/0:10,0:10:24.08:0,24,316 0/0:3,0:3:9.02:0,9,97 0/0:12,0:12:36.11:0,36,451 0/0:9,0:9:27.09:0,27,349 0/0:12,0:12:36.11:0,36,458 0/0:19,0:19:57.16:0,57,720 0/0:21,0:21:60.17:0,60,740 0/0:17,0:17:51.15:0,51,645 0/0:13,0:13:39.12:0,39,519 0/0:10,0:10:30.10:0,30,394 0/1:6,6:12:99:209,0,203 0/0:11,0:11:33.11:0,33,432 0/0:24,0:24:72.22:0,72,907 0/0:9,0:9:27.09:0,27,344 0/0:9,0:9:27.09:0,27,356 0/0:28,0:28:78.24:0,78,986 0/0:32,0:32:90.28:0,90,1153 0/0:33,0:33:87.28:0,87,1143 0/0:15,0:15:39.12:0,39,494 0/0:9,0:9:27.08:0,27,346 0/0:12,0:12:33.11:0,33,428 0/0:16,0:16:42.13:0,42,529 0/0:6,0:6:18.06:0,18,237 0/0:8,0:8:24.08:0,24,307 0/0:9,0:9:24.08:0,24,331 0/0:6,0:6:18.06:0,18,239 -chr1 1115086 . C T 1455.37 . AC=1;AF=0.0086;AN=116;BaseQRankSum=-2.311;DP=1823;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0613;InbreedingCoeff=-0.0319;MQ=58.20;MQ0=0;MQRankSum=0.635;QD=14.13;ReadPosRankSum=-1.886;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G56|673|TTLL10|protein_coding|CODING|ENST00000379289|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G56|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),UTR_5_PRIME(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|1);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,synonymous_variant|ggC/ggT|G|ENSG00000162571|TTLL10|ENST00000379289|5/16|||56/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,synonymous_variant|ggC/ggT|G|ENSG00000162571|TTLL10|ENST00000379290|5/16|||56/673|protein_coding|1,5_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|1/9|||-/404|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,76 0/0:1,0:1:3.01:0,3,31 0/0:1,0:1:3.01:0,3,32 0/0:3,0:3:9.03:0,9,107 0/0:1,0:1:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,36 ./. 0/0:4,0:4:12.03:0,12,152 0/0:4,0:4:12.04:0,12,148 0/0:2,0:2:3.01:0,3,36 0/0:2,0:2:6.01:0,6,59 0/0:2,0:2:3.01:0,3,41 0/0:23,0:23:60.18:0,60,774 0/0:38,0:38:99:0,99,1273 0/0:26,0:26:63.19:0,63,797 0/0:23,0:23:45.15:0,45,613 0/0:37,0:37:90.28:0,90,1199 0/0:27,0:28:60.17:0,60,796 0/0:35,0:35:72.22:0,72,983 0/0:29,0:29:78.24:0,78,1030 0/0:34,0:34:75.22:0,75,988 0/0:22,1:23:14.18:0,14,597 0/0:19,0:19:42.12:0,42,546 0/0:31,0:31:69.20:0,69,889 0/0:31,0:31:81.22:0,81,999 0/0:22,0:22:60.16:0,60,744 0/0:14,0:14:33.11:0,33,454 0/0:14,0:14:33.10:0,33,430 0/0:23,0:23:57.18:0,57,759 0/0:40,0:40:96.31:0,96,1300 0/0:21,0:21:54.16:0,54,703 0/0:38,0:38:99:0,108,1389 0/0:35,0:35:75.22:0,75,990 0/0:29,0:29:66.21:0,66,894 0/0:18,0:18:39.13:0,39,536 0/0:28,0:28:66.21:0,66,857 0/0:35,0:35:81.25:0,81,1073 0/0:29,0:29:75.22:0,75,992 0/0:73,0:73:99:0,181,2342 0/0:60,0:61:99:0,138,1794 0/0:54,0:54:99:0,129,1637 0/0:47,0:47:99:0,120,1538 0/0:24,0:24:60.19:0,60,796 0/0:34,0:34:93.27:0,93,1160 0/0:34,0:34:90.29:0,90,1180 0/0:87,0:87:99:0,199,2566 0/0:31,0:31:81.22:0,81,976 0/0:47,0:47:99:0,108,1409 0/0:77,0:77:99:0,199,2559 0/1:42,61:103:99:1503,0,1001 0/0:49,1:50:79.96:0,80,1353 0/0:60,0:60:99:0,138,1778 0/0:51,0:51:99:0,126,1642 0/0:58,0:58:99:0,129,1741 0/0:41,0:41:93.27:0,93,1206 0/0:30,0:30:54.17:0,54,736 0/0:41,0:41:99:0,117,1498 0/0:24,0:24:54.16:0,54,687 0/0:50,0:50:99:0,114,1503 -chr1 1115187 . C T 128.35 . AC=1;AF=0.0085;AN=118;BaseQRankSum=0.636;DP=678;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5936;InbreedingCoeff=-0.0317;MQ=57.89;MQ0=0;MQRankSum=0.815;QD=14.26;ReadPosRankSum=0.228;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|5),START_GAINED(LOW||||404|TTLL10|protein_coding|CODING|ENST00000379288|1),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,5_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|1/9|||-/404|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,73 0/0:1,0:1:3.01:0,3,33 0/0:4,0:4:12.04:0,12,158 0/0:1,0:1:3.01:0,3,32 ./. 0/0:4,0:4:12.04:0,12,159 0/0:2,0:2:3.01:0,3,41 0/0:2,0:2:6.02:0,6,82 0/0:2,0:2:6.02:0,6,82 0/0:4,0:4:12.04:0,12,157 0/0:3,0:3:9.03:0,9,120 0/0:1,0:1:3.01:0,3,30 0/0:1,0:1:3.01:0,3,41 0/1:4,5:9:93.72:176,0,94 0/0:15,0:15:42.14:0,42,558 0/0:7,0:7:21.07:0,21,275 0/0:12,0:12:33.10:0,33,420 0/0:18,0:18:51.15:0,51,642 0/0:13,0:13:36.08:0,36,436 0/0:12,0:12:36.12:0,36,466 0/0:13,0:13:36.11:0,36,463 0/0:15,0:15:42.13:0,42,534 0/0:13,0:13:39.13:0,39,526 0/0:11,0:11:27.09:0,27,359 0/0:11,0:11:33.10:0,33,423 0/0:14,0:14:39.12:0,39,505 0/0:10,0:10:30.10:0,30,390 0/0:7,0:7:18.06:0,18,246 0/0:6,0:6:15.02:0,15,192 0/0:8,0:8:24.08:0,24,315 0/0:10,0:10:24.07:0,24,289 0/0:11,0:11:24.08:0,24,314 0/0:19,0:19:54.17:0,54,716 0/0:12,0:12:30.10:0,30,405 0/0:5,0:5:15.05:0,15,196 0/0:6,0:6:18.06:0,18,229 0/0:17,0:17:42.14:0,42,565 0/0:9,0:9:24.07:0,24,304 0/0:9,0:9:24.08:0,24,313 0/0:17,0:17:45.12:0,45,569 0/0:16,0:16:39.12:0,39,504 0/0:23,0:23:60.19:0,60,790 0/0:13,0:13:39.12:0,39,489 0/0:8,0:8:24.07:0,24,302 0/0:15,0:15:45.15:0,45,587 0/0:11,0:11:33.11:0,33,425 0/0:25,0:25:63.19:0,63,783 0/0:14,0:14:42.12:0,42,539 0/0:12,0:12:33.10:0,33,413 0/0:23,0:23:63.20:0,63,825 0/0:34,0:34:99:0,99,1258 0/0:15,0:15:39.12:0,39,487 0/0:25,0:25:69.21:0,69,886 0/0:19,0:19:51.14:0,51,639 0/0:19,0:19:54.17:0,54,706 0/0:14,0:15:33.08:0,33,402 0/0:5,0:5:15.04:0,15,185 0/0:14,0:14:39.12:0,39,502 0/0:12,0:12:36.10:0,36,443 0/0:24,0:24:63.19:0,63,768 -chr1 1115210 . G A 3468.51 . AC=23;AF=0.1983;AN=116;BaseQRankSum=-0.114;DP=539;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6710;InbreedingCoeff=0.0851;MQ=58.05;MQ0=0;MQRankSum=-0.518;QD=16.84;ReadPosRankSum=-1.559;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|5),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),UTR_5_PRIME(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|1);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,5_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|1/9|||-/404|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,40 0/0:3,0:3:9.03:0,9,111 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:9.03:0,9,115 ./. 0/1:1,1:2:32.56:33,0,33 1/1:0,1:1:3.01:41,3,0 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.04:0,12,159 0/0:5,0:5:15.05:0,15,193 ./. 1/1:0,1:1:3.01:40,3,0 0/0:3,0:3:6.02:0,6,81 1/1:0,10:10:24.08:321,24,0 0/0:17,0:17:48.16:0,48,640 0/0:6,0:6:18.06:0,18,245 0/0:11,0:11:27.09:0,27,354 0/0:12,0:12:33.10:0,33,423 0/0:6,0:7:15.05:0,15,193 0/0:11,0:11:33.10:0,33,413 0/0:8,0:8:24.07:0,24,307 0/1:6,5:11:99:142,0,191 0/0:11,0:11:30.10:0,30,407 0/0:7,0:7:12.04:0,12,161 0/0:10,0:11:27.08:0,27,351 0/0:11,0:11:30.10:0,30,390 0/1:4,5:9:94.61:130,0,95 0/1:1,3:4:30.19:99,0,30 0/0:5,0:5:15.05:0,15,203 0/0:6,0:6:18.06:0,18,248 0/1:6,5:11:99:122,0,175 0/0:8,0:8:24.07:0,24,299 0/1:8,8:16:99:243,0,274 0/0:10,0:10:27.09:0,27,363 0/1:1,3:4:26.56:87,0,27 0/0:4,0:4:12.04:0,12,147 0/1:3,4:7:99:107,0,100 0/0:12,0:12:27.09:0,27,352 0/0:4,0:4:12.04:0,12,161 0/0:14,0:14:39.12:0,39,498 0/1:9,8:17:99:264,0,195 0/0:15,0:15:45.14:0,45,592 0/0:10,0:10:30.09:0,30,382 0/0:7,0:7:18.06:0,18,232 0/0:11,0:11:33.11:0,33,437 0/0:7,0:7:21.07:0,21,293 0/0:20,0:20:51.13:0,51,627 0/1:7,7:14:99:233,0,236 0/0:12,0:12:33.09:0,33,411 0/1:8,10:18:99:308,0,263 0/1:23,9:32:99:267,0,727 0/0:17,0:17:42.13:0,42,545 1/1:0,18:18:54.17:687,54,0 0/0:11,0:11:30.10:0,30,394 0/0:10,0:10:30.10:0,30,412 0/1:9,3:12:80.83:81,0,237 0/0:6,0:6:18.06:0,18,231 0/1:7,6:13:99:165,0,237 0/1:3,3:6:88.43:98,0,88 0/0:11,0:11:27.08:0,27,326 -chr1 1115213 . G T 2687.22 . AC=21;AF=0.1810;AN=116;BaseQRankSum=0.184;DP=530;Dels=0.00;FS=4.737;HRun=1;HaplotypeScore=0.7398;InbreedingCoeff=0.1254;MQ=58.19;MQ0=0;MQRankSum=0.107;QD=15.10;ReadPosRankSum=-1.774;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|5),START_GAINED(LOW||||404|TTLL10|protein_coding|CODING|ENST00000379288|1),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,5_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|1/9|||-/404|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:6.02:0,6,78 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.01:0,6,59 ./. 0/0:1,0:1:3.01:0,3,39 1/1:0,1:1:3.01:41,3,0 0/0:1,0:1:3.01:0,3,36 0/0:4,0:4:12.04:0,12,158 0/0:4,0:4:12.03:0,12,149 0/0:1,0:1:3.01:0,3,41 1/1:0,1:1:3.01:41,3,0 0/0:3,0:3:6.02:0,6,82 1/1:0,9:9:24.05:300,24,0 0/0:16,0:16:45.14:0,45,573 0/0:7,0:7:21.07:0,21,273 0/0:11,0:11:27.09:0,27,354 0/0:13,0:13:33.09:0,33,407 0/1:6,1:7:20.52:21,0,174 0/0:9,0:9:27.09:0,27,346 0/0:8,0:8:24.07:0,24,290 0/1:6,6:12:99:157,0,175 0/0:11,0:11:30.10:0,30,404 0/0:7,0:7:12.04:0,12,163 0/0:10,0:10:24.07:0,24,311 0/0:11,0:11:27.07:0,27,334 0/1:4,5:9:87.32:160,0,87 0/1:1,3:4:29.19:102,0,29 0/0:5,0:5:15.05:0,15,199 0/0:6,0:6:18.06:0,18,243 0/1:6,5:11:99:125,0,161 0/0:8,0:8:24.07:0,24,286 0/1:8,8:16:99:232,0,271 0/0:10,0:10:27.09:0,27,356 0/1:2,3:5:25.76:105,0,26 0/0:4,0:4:12.04:0,12,160 0/1:3,4:7:98.88:106,0,99 0/0:11,0:11:27.08:0,27,342 0/0:4,0:4:12.04:0,12,153 0/0:13,0:13:36.11:0,36,447 0/1:9,9:18:99:294,0,235 0/0:15,0:15:45.15:0,45,589 0/0:10,0:10:30.09:0,30,379 0/0:6,0:6:15.05:0,15,193 0/0:11,0:11:33.11:0,33,430 0/0:7,0:7:21.07:0,21,293 0/0:19,0:19:54.17:0,54,679 0/0:14,0:14:39.12:0,39,496 0/0:12,0:12:33.09:0,33,407 0/0:19,0:19:54.17:0,54,680 0/1:23,9:32:99:230,0,687 0/0:18,0:18:42.13:0,42,542 1/1:0,17:17:51.16:633,51,0 0/0:11,0:11:30.10:0,30,392 0/0:10,0:10:30.10:0,30,403 0/1:8,3:12:84.15:84,0,233 0/0:6,0:6:18.06:0,18,231 0/1:6,6:12:99:169,0,186 0/1:2,3:5:41.09:100,0,41 0/0:9,0:9:21.05:0,21,247 -chr1 1115222 . C T 45.39 . AC=1;AF=0.0085;AN=118;BaseQRankSum=-0.693;DP=471;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3240;InbreedingCoeff=-0.0359;MQ=58.17;MQ0=0;MQRankSum=0.038;QD=5.67;ReadPosRankSum=-1.442;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|5),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),UTR_5_PRIME(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|1);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,5_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|1/9|||-/404|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:6.02:0,6,69 0/0:2,0:2:6.02:0,6,81 0/0:2,0:2:6.02:0,6,72 0/0:2,0:2:6.02:0,6,80 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:9.03:0,9,122 0/0:1,0:1:3.01:0,3,38 0/0:8,0:8:24.08:0,24,320 0/0:4,0:4:12.04:0,12,162 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,82 0/0:3,0:3:9.03:0,9,120 0/0:8,0:8:18.06:0,18,245 0/0:16,0:17:42.12:0,42,545 0/0:6,0:6:18.04:0,18,226 0/0:10,0:10:27.08:0,27,328 0/0:13,0:13:36.12:0,36,469 0/0:5,0:5:15.05:0,15,190 0/0:9,0:9:27.08:0,27,334 0/0:5,0:5:15.05:0,15,201 0/0:10,0:10:27.09:0,27,342 0/0:10,0:10:27.09:0,27,368 0/0:5,0:5:6.02:0,6,83 0/0:10,0:10:24.08:0,24,320 0/0:10,0:10:30.08:0,30,381 0/0:6,0:6:18.06:0,18,225 0/0:5,0:5:15.05:0,15,187 0/0:4,0:4:12.04:0,12,163 0/0:7,0:7:21.07:0,21,285 0/0:11,0:11:27.08:0,27,349 0/0:9,0:9:27.09:0,27,345 0/0:12,0:13:33.11:0,33,441 0/1:5,3:8:92.77:93,0,134 0/0:5,0:5:15.05:0,15,194 0/0:5,0:5:12.04:0,12,151 0/0:6,0:6:15.05:0,15,204 0/0:9,0:9:21.07:0,21,278 0/0:4,0:4:12.04:0,12,154 0/0:14,0:14:39.11:0,39,466 0/0:18,0:18:51.15:0,51,651 0/0:12,0:12:30.09:0,30,385 0/0:9,0:9:27.09:0,27,342 0/0:4,0:4:12.04:0,12,160 0/0:7,0:7:21.06:0,21,272 0/0:6,0:6:18.06:0,18,248 0/0:16,0:16:45.14:0,45,565 0/0:12,0:12:33.10:0,33,433 0/0:11,0:11:30.07:0,30,369 0/0:18,0:18:48.15:0,48,625 0/0:27,0:27:72.23:0,72,943 0/0:12,0:12:27.09:0,27,346 0/0:11,0:11:33.10:0,33,414 0/0:11,0:11:30.08:0,30,380 0/0:8,0:8:24.08:0,24,325 0/0:9,0:9:24.05:0,24,288 0/0:5,0:5:15.05:0,15,197 0/0:9,0:9:27.08:0,27,340 0/0:4,0:4:12.04:0,12,150 0/0:7,0:7:18.06:0,18,227 -chr1 1115379 . G A 616.46 . AC=5;AF=0.0417;AN=120;BaseQRankSum=0.553;DP=584;Dels=0.00;FS=2.233;HRun=0;HaplotypeScore=0.3425;InbreedingCoeff=-0.0782;MQ=58.20;MQ0=0;MQRankSum=1.750;QD=9.94;ReadPosRankSum=0.385;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|processed_transcript|CODING|ENST00000506177|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|1),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|5),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000506177|||||processed_transcript|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,41 0/0:5,0:5:15.04:0,15,179 0/0:8,0:8:21.07:0,21,283 0/0:3,0:3:9.02:0,9,100 0/1:5,2:7:59.48:59,0,175 0/0:12,0:12:36.11:0,36,449 0/0:13,0:13:36.12:0,36,479 0/1:3,5:8:86.10:171,0,86 0/0:22,0:22:60.18:0,60,762 0/0:22,0:22:66.18:0,66,841 0/0:12,0:12:27.09:0,27,366 0/0:6,0:6:18.06:0,18,232 0/0:14,0:14:42.13:0,42,529 0/0:11,0:11:30.09:0,30,387 0/0:23,0:23:57.18:0,57,742 0/0:8,0:8:24.08:0,24,312 0/0:14,0:14:30.08:0,30,390 0/0:13,0:13:33.10:0,33,423 0/0:19,0:19:51.16:0,51,656 0/1:7,13:20:99:360,0,158 0/0:14,0:15:36.12:0,36,479 0/0:17,0:18:45.15:0,45,604 0/0:9,0:9:24.08:0,24,318 0/0:7,0:8:21.06:0,21,261 0/0:12,0:12:27.08:0,27,356 0/0:20,0:20:51.17:0,51,671 0/0:17,0:17:45.14:0,45,584 0/0:10,0:10:30.09:0,30,383 0/1:9,5:14:99:117,0,304 0/0:12,0:12:30.09:0,30,382 0/0:19,0:19:48.14:0,48,634 0/1:12,1:13:3.34:3,0,326 0/0:13,0:13:36.11:0,36,460 0/0:13,0:13:36.09:0,36,462 0/0:8,0:8:24.08:0,24,307 0/0:20,0:20:51.16:0,51,662 0/0:22,0:22:57.18:0,57,758 0/0:26,0:27:60.19:0,60,803 0/0:4,0:5:9.03:0,9,116 0/0:6,0:6:18.05:0,18,220 0/0:1,0:1:3.01:0,3,33 0/0:5,0:5:9.03:0,9,104 0/0:6,0:6:15.05:0,15,196 0/0:4,0:4:12.04:0,12,164 0/0:2,0:2:6.02:0,6,84 0/0:4,0:4:12.04:0,12,166 0/0:5,0:5:12.03:0,12,144 0/0:2,0:2:6.02:0,6,79 0/0:4,0:4:12.04:0,12,155 0/0:1,0:1:3.01:0,3,39 0/0:5,0:5:15.05:0,15,187 0/0:2,0:2:6.02:0,6,70 0/0:1,0:1:3.01:0,3,37 0/0:7,0:7:12.04:0,12,164 0/0:2,0:2:6.02:0,6,78 0/0:4,0:4:12.04:0,12,145 0/0:2,0:2:6.02:0,6,75 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:3.01:0,3,33 -chr1 1115415 . C T 177.42 . AC=1;AF=0.0085;AN=118;BaseQRankSum=-1.248;DP=752;Dels=0.00;FS=3.560;HRun=0;HaplotypeScore=0.6217;InbreedingCoeff=-0.0287;MQ=58.39;MQ0=0;MQRankSum=1.308;QD=8.06;ReadPosRankSum=-0.853;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G67|673|TTLL10|protein_coding|CODING|ENST00000379289|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G67|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),UTR_5_PRIME(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|2);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,splice_region_variant&synonymous_variant|ggC/ggT|G|ENSG00000162571|TTLL10|ENST00000379289|6/16|||67/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,splice_region_variant&synonymous_variant|ggC/ggT|G|ENSG00000162571|TTLL10|ENST00000379290|6/16|||67/673|protein_coding|1,splice_region_variant&5_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|2/9|||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.01:0,6,63 0/0:9,0:9:24.07:0,24,306 0/0:7,0:7:21.06:0,21,261 0/0:6,0:6:15.04:0,15,181 0/0:12,0:12:36.10:0,36,466 0/0:11,0:11:24.07:0,24,311 0/0:21,0:21:60.20:0,60,806 0/0:6,0:6:15.05:0,15,198 0/0:30,0:30:87.26:0,87,1121 0/0:26,0:26:75.24:0,75,996 0/0:14,0:14:39.13:0,39,523 0/0:8,0:8:24.07:0,24,299 0/0:23,0:23:63.17:0,63,764 0/0:12,0:12:30.09:0,30,385 0/0:25,0:26:48.15:0,48,621 0/0:11,0:11:33.10:0,33,409 0/0:17,0:17:36.12:0,36,484 0/0:16,0:16:33.10:0,33,409 0/0:20,0:20:48.11:0,48,588 0/0:20,0:21:48.15:0,48,622 0/0:16,0:16:42.14:0,42,548 0/0:19,0:19:45.14:0,45,579 0/0:16,0:16:33.10:0,33,435 0/0:14,0:14:36.10:0,36,440 0/0:20,0:20:42.14:0,42,571 0/0:24,0:24:54.16:0,54,682 0/0:21,0:21:39.11:0,39,487 0/0:18,0:18:36.12:0,36,503 0/0:17,0:17:42.13:0,42,536 0/0:15,0:15:27.09:0,27,360 0/0:24,0:24:60.19:0,60,796 0/0:22,0:22:45.14:0,45,609 0/0:16,0:16:39.12:0,39,500 0/1:13,9:22:99:225,0,298 0/0:9,0:9:27.09:0,27,353 0/0:29,0:29:63.20:0,63,827 0/0:27,0:27:60.18:0,60,774 0/0:30,0:30:72.22:0,72,926 0/0:6,0:6:15.05:0,15,195 0/0:6,0:6:12.03:0,12,133 0/0:5,0:5:12.04:0,12,144 0/0:8,0:8:21.06:0,21,254 0/0:6,0:6:12.04:0,12,161 0/0:4,0:4:9.03:0,9,121 0/0:3,0:3:9.02:0,9,107 0/0:4,0:4:9.03:0,9,116 0/0:7,0:7:18.06:0,18,229 0/0:2,0:2:6.02:0,6,74 0/0:5,0:5:12.04:0,12,141 0/0:3,0:3:9.03:0,9,112 0/0:4,0:4:8.99:0,9,82 0/0:4,0:4:9.02:0,9,94 0/0:4,0:4:12.04:0,12,156 0/0:5,0:5:9.02:0,9,114 0/0:1,0:1:3.01:0,3,39 0/0:5,0:5:15.05:0,15,185 0/0:2,0:2:6.02:0,6,76 0/0:5,0:5:12.04:0,12,158 ./. 0/0:5,0:5:12.04:0,12,151 -chr1 1115461 . C T 331.7 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.166;DP=949;Dels=0.00;FS=1.152;HRun=0;HaplotypeScore=0.9760;InbreedingCoeff=-0.0264;MQ=58.65;MQ0=0;MQRankSum=1.177;QD=12.76;ReadPosRankSum=1.958;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R10W|404|TTLL10|protein_coding|CODING|ENST00000379288|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R83W|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R83W|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,missense_variant|Cgg/Tgg|R/W|ENSG00000162571|TTLL10|ENST00000379289|6/16|benign(0.28)|tolerated(0.08)|83/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,missense_variant|Cgg/Tgg|R/W|ENSG00000162571|TTLL10|ENST00000379290|6/16|benign(0.28)|tolerated(0.08)|83/673|protein_coding|1,missense_variant|Cgg/Tgg|R/W|ENSG00000162571|TTLL10|ENST00000379288|2/9|benign(0.365)|deleterious(0.03)|10/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3.01:0,3,33 0/0:7,0:8:18.05:0,18,229 0/0:7,0:7:15.05:0,15,196 0/0:2,0:2:6.02:0,6,80 0/0:14,0:14:33.11:0,33,444 0/0:7,0:10:21.07:0,21,268 0/0:30,0:30:75.22:0,75,972 0/0:16,0:16:36.12:0,36,469 0/0:44,0:44:90.27:0,90,1180 0/0:38,0:39:84.27:0,84,1101 0/0:26,0:26:60.18:0,60,770 0/0:9,0:11:21.04:0,21,245 0/0:25,0:25:66.19:0,66,860 0/0:21,0:21:48.16:0,48,636 0/0:27,0:27:69.20:0,69,884 0/0:13,0:13:30.08:0,30,385 0/0:25,0:26:57.16:0,57,731 0/0:24,0:25:66.20:0,66,847 0/0:19,0:19:45.14:0,45,560 0/0:29,0:30:69.21:0,69,894 0/0:19,0:19:51.15:0,51,649 0/0:27,0:28:63.20:0,63,816 0/0:19,0:19:45.15:0,45,593 0/0:21,0:21:42.13:0,42,532 0/0:21,0:21:54.15:0,54,682 0/0:24,0:24:66.19:0,66,850 0/0:16,0:16:30.08:0,30,391 0/0:15,0:15:39.12:0,39,496 0/0:21,0:21:51.14:0,51,616 0/0:21,0:21:48.14:0,48,608 0/0:33,0:33:72.23:0,72,940 0/0:28,0:28:60.19:0,60,804 0/0:20,0:20:48.12:0,48,595 0/1:11,14:26:99:379,0,288 0/0:13,0:13:33.11:0,33,437 0/0:36,0:36:81.26:0,81,1064 0/0:33,0:33:87.27:0,87,1140 0/0:31,0:31:81.25:0,81,1063 0/0:4,0:4:12.03:0,12,141 0/0:4,0:4:9.02:0,9,96 0/0:7,0:7:12.04:0,12,156 0/0:11,0:11:30.09:0,30,377 0/0:4,0:4:12.03:0,12,138 0/0:5,0:6:15.05:0,15,202 0/0:4,0:4:9.03:0,9,113 0/0:5,0:5:15.05:0,15,189 0/0:12,0:12:21.06:0,21,263 0/0:5,0:5:12.04:0,12,163 0/0:4,0:4:9.03:0,9,113 0/0:9,0:9:27.09:0,27,351 0/0:5,0:6:9.03:0,9,124 0/0:5,0:5:12.02:0,12,140 0/0:5,0:5:12.04:0,12,153 0/0:9,0:9:27.09:0,27,354 0/0:2,0:3:6.02:0,6,82 0/0:5,0:6:12.04:0,12,158 0/0:3,0:3:6.02:0,6,78 0/0:6,0:6:12.04:0,12,153 0/0:4,0:4:9.03:0,9,120 0/0:7,0:7:18.06:0,18,231 -chr1 1115503 . T C 1171.08 . AC=4;AF=0.0333;AN=120;BaseQRankSum=1.533;DP=1103;Dels=0.00;FS=7.100;HRun=1;HaplotypeScore=0.5750;InbreedingCoeff=-0.0426;MQ=59.00;MQ0=0;MQRankSum=1.371;QD=12.59;ReadPosRankSum=-1.312;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C24R|404|TTLL10|protein_coding|CODING|ENST00000379288|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C97R|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C97R|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,missense_variant|Tgt/Cgt|C/R|ENSG00000162571|TTLL10|ENST00000379289|6/16|benign(0.004)|tolerated(0.53)|97/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,missense_variant|Tgt/Cgt|C/R|ENSG00000162571|TTLL10|ENST00000379290|6/16|benign(0.004)|tolerated(0.53)|97/673|protein_coding|1,missense_variant|Tgt/Cgt|C/R|ENSG00000162571|TTLL10|ENST00000379288|2/9|benign(0.016)|tolerated(0.27)|24/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.04:0,12,143 0/0:9,0:9:21.06:0,21,265 0/0:10,0:10:27.08:0,27,328 0/0:8,0:8:24.07:0,24,290 0/1:11,4:15:99:111,0,396 0/0:17,0:17:45.14:0,45,587 0/0:27,0:27:78.25:0,78,1031 0/1:11,12:23:99:383,0,363 0/0:54,0:54:99:0,153,1980 0/0:47,0:47:99:0,135,1730 0/0:21,0:21:57.18:0,57,757 0/0:22,0:22:63.17:0,63,782 0/0:33,0:33:93.29:0,93,1193 0/0:28,0:29:72.22:0,72,942 0/0:30,0:30:78.25:0,78,1017 0/0:10,0:10:27.08:0,27,334 0/0:33,0:33:72.23:0,72,959 0/0:30,0:30:72.23:0,72,966 0/0:16,0:16:39.13:0,39,522 0/1:12,14:26:99:423,0,367 0/0:26,0:26:60.17:0,60,765 0/0:26,0:26:66.21:0,66,860 0/0:20,0:20:48.16:0,48,646 0/0:20,0:20:51.15:0,51,655 0/0:22,0:22:51.16:0,51,669 0/0:21,0:21:57.16:0,57,699 0/0:14,0:14:39.12:0,39,499 0/0:15,0:15:42.11:0,42,515 0/1:17,12:29:99:346,0,547 0/0:23,0:23:60.19:0,60,807 0/0:39,0:39:90.30:0,90,1224 0/0:22,0:22:57.19:0,57,758 0/0:21,0:21:45.15:0,45,599 0/0:32,0:32:78.25:0,78,1026 0/0:19,0:19:42.14:0,42,564 0/0:44,0:44:99:0,99,1309 0/0:26,0:26:72.18:0,72,892 0/0:27,0:27:69.23:0,69,927 0/0:4,0:4:12.04:0,12,156 0/0:12,0:12:33.10:0,33,419 0/0:7,0:7:21.07:0,21,269 0/0:12,0:12:27.09:0,27,361 0/0:5,0:5:12.04:0,12,157 0/0:7,0:7:21.06:0,21,259 0/0:5,0:5:12.04:0,12,159 0/0:10,0:10:27.09:0,27,362 0/0:22,0:22:45.14:0,45,572 0/0:4,0:4:12.04:0,12,152 0/0:12,0:12:24.06:0,24,302 0/0:15,0:15:36.12:0,36,479 0/0:12,0:12:27.09:0,27,349 0/0:7,0:7:15.04:0,15,195 0/0:4,0:4:12.04:0,12,153 0/0:10,0:10:21.07:0,21,277 0/0:4,0:4:9.03:0,9,118 0/0:12,0:12:24.08:0,24,314 0/0:1,0:1:3.01:0,3,42 0/0:8,0:9:24.08:0,24,305 0/0:12,0:12:24.08:0,24,317 0/0:7,0:7:18.06:0,18,241 -chr1 1115601 . C T 368.82 . AC=1;AF=0.0085;AN=118;BaseQRankSum=-0.437;DP=1078;Dels=0.00;FS=12.205;HRun=0;HaplotypeScore=0.6665;InbreedingCoeff=-0.0165;MQ=58.97;MQ0=0;MQRankSum=0.473;QD=12.29;ReadPosRankSum=2.503;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N129|673|TTLL10|protein_coding|CODING|ENST00000379289|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N129|673|TTLL10|protein_coding|CODING|ENST00000379290|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N56|404|TTLL10|protein_coding|CODING|ENST00000379288|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,synonymous_variant|aaC/aaT|N|ENSG00000162571|TTLL10|ENST00000379289|6/16|||129/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,synonymous_variant|aaC/aaT|N|ENSG00000162571|TTLL10|ENST00000379290|6/16|||129/673|protein_coding|1,synonymous_variant|aaC/aaT|N|ENSG00000162571|TTLL10|ENST00000379288|2/9|||56/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:3.01:0,3,39 0/0:10,0:10:24.06:0,24,284 0/0:7,0:7:15.04:0,15,182 0/0:6,0:6:15.05:0,15,193 0/0:20,0:20:60.16:0,60,747 0/0:8,0:8:21.05:0,21,250 0/0:24,0:25:66.21:0,66,869 0/0:14,0:14:42.12:0,42,529 0/0:35,0:35:99:0,105,1377 0/0:38,0:38:99:0,105,1365 0/0:22,0:22:66.22:0,66,869 0/0:13,0:13:33.10:0,33,418 0/0:26,0:26:75.23:0,75,963 0/0:33,0:33:87.27:0,87,1113 0/0:36,0:37:90.29:0,90,1164 0/0:16,0:16:45.13:0,45,564 0/0:29,0:29:66.19:0,66,834 0/0:35,0:35:81.25:0,81,1039 0/0:17,0:18:42.12:0,42,528 0/0:28,0:28:72.18:0,72,907 0/0:27,0:27:72.23:0,72,962 0/0:34,0:34:75.23:0,75,1000 0/0:16,0:16:42.14:0,42,550 0/1:14,16:30:99:416,0,329 0/0:23,0:24:51.16:0,51,685 0/0:33,0:33:81.24:0,81,1058 0/0:28,0:28:69.19:0,69,869 0/0:18,0:18:39.12:0,39,522 0/0:24,0:24:66.20:0,66,833 0/0:21,0:21:54.17:0,54,693 0/0:42,0:42:99:0,102,1318 0/0:26,0:26:69.22:0,69,895 0/0:24,0:24:60.17:0,60,753 0/0:23,0:23:57.19:0,57,763 0/0:24,0:24:57.17:0,57,738 0/0:25,0:25:60.18:0,60,774 0/0:35,0:35:87.28:0,87,1132 0/0:24,0:24:63.19:0,63,826 0/0:5,0:5:12.04:0,12,161 0/0:15,0:15:30.10:0,30,386 0/0:9,0:9:21.04:0,21,248 0/0:10,0:10:30.10:0,30,386 0/0:5,0:5:12.04:0,12,149 0/0:6,0:6:18.05:0,18,216 0/0:5,0:5:15.05:0,15,186 0/0:9,0:9:27.09:0,27,346 0/0:13,0:13:27.08:0,27,337 0/0:4,0:4:12.04:0,12,152 0/0:10,0:10:27.08:0,27,342 0/0:13,0:13:30.10:0,30,388 0/0:11,0:11:30.10:0,30,383 0/0:9,0:9:21.03:0,21,232 0/0:13,0:13:33.09:0,33,417 0/0:8,0:8:18.06:0,18,249 0/0:2,0:2:6.02:0,6,80 0/0:9,0:9:24.05:0,24,296 ./. 0/0:10,0:10:27.09:0,27,351 0/0:5,0:5:15.04:0,15,171 0/0:6,0:6:18.05:0,18,217 -chr1 1115605 . G T 78.84 . AC=1;AF=0.0085;AN=118;BaseQRankSum=0.557;DP=1031;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6145;InbreedingCoeff=-0.0171;MQ=58.95;MQ0=0;MQRankSum=0.835;QD=4.93;ReadPosRankSum=0.136;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Tcc|A131S|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Tcc|A131S|673|TTLL10|protein_coding|CODING|ENST00000379290|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Tcc|A58S|404|TTLL10|protein_coding|CODING|ENST00000379288|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,missense_variant|Gcc/Tcc|A/S|ENSG00000162571|TTLL10|ENST00000379289|6/16|benign(0.021)|tolerated(0.07)|131/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,missense_variant|Gcc/Tcc|A/S|ENSG00000162571|TTLL10|ENST00000379290|6/16|benign(0.021)|tolerated(0.07)|131/673|protein_coding|1,missense_variant|Gcc/Tcc|A/S|ENSG00000162571|TTLL10|ENST00000379288|2/9|benign(0.087)|tolerated(0.07)|58/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,72 0/0:5,1:6:15.03:0,15,178 0/0:7,0:7:18.05:0,18,216 0/0:4,0:4:9.03:0,9,121 0/0:17,0:17:51.15:0,51,651 0/0:8,0:8:21.07:0,21,272 0/0:23,0:23:66.21:0,66,858 0/0:14,0:14:39.13:0,39,516 0/0:34,0:34:96.31:0,96,1257 0/0:30,0:30:81.24:0,81,1022 0/0:19,0:19:57.18:0,57,744 0/0:14,0:14:39.12:0,39,492 0/0:21,0:21:63.19:0,63,795 0/0:31,0:31:84.25:0,84,1058 0/0:34,0:34:78.25:0,78,1015 0/0:16,0:16:45.13:0,45,562 0/0:29,0:29:66.19:0,66,836 0/0:34,0:34:78.21:0,78,1000 0/0:18,0:18:39.11:0,39,487 0/0:27,0:27:69.20:0,69,878 0/0:28,0:28:72.23:0,72,970 0/0:32,0:32:72.23:0,72,972 0/0:16,0:16:39.13:0,39,514 0/0:30,0:30:69.21:0,69,892 0/0:21,0:21:48.15:0,48,636 0/0:33,0:33:78.25:0,78,1047 0/0:29,0:29:66.19:0,66,841 0/0:19,0:19:39.12:0,39,512 0/0:25,0:25:63.20:0,63,820 0/0:22,0:22:54.16:0,54,704 0/0:39,0:39:93.30:0,93,1243 0/0:27,0:27:66.19:0,66,812 0/0:23,0:23:54.17:0,54,703 0/0:20,0:20:51.16:0,51,675 0/0:22,1:23:22.61:0,23,624 0/0:21,0:21:51.17:0,51,685 0/0:33,0:33:78.24:0,78,1002 0/0:22,0:23:54.17:0,54,720 0/0:5,0:5:9.03:0,9,122 0/1:9,6:16:99:126,0,239 0/0:10,0:10:24.08:0,24,302 0/0:10,0:10:30.10:0,30,394 0/0:6,0:6:15.05:0,15,199 0/0:6,0:6:18.06:0,18,230 0/0:5,0:5:9.03:0,9,117 0/0:9,0:9:24.08:0,24,315 0/0:12,0:12:30.09:0,30,368 0/0:4,0:4:12.04:0,12,162 0/0:8,0:8:21.06:0,21,255 0/0:14,0:14:30.09:0,30,378 0/0:11,0:11:30.09:0,30,374 0/0:8,0:8:21.05:0,21,243 0/0:13,0:13:36.10:0,36,458 0/0:8,0:8:18.06:0,18,248 0/0:2,0:2:6.02:0,6,80 0/0:10,0:10:27.08:0,27,342 ./. 0/0:9,0:9:27.08:0,27,339 0/0:7,0:7:21.06:0,21,258 0/0:5,0:5:15.04:0,15,184 -chr1 1115739 . C T 563.52 . AC=1;AF=0.0085;AN=118;BaseQRankSum=-0.563;DP=900;Dels=0.00;FS=2.949;HRun=0;HaplotypeScore=0.6729;InbreedingCoeff=-0.0307;MQ=58.26;MQ0=0;MQRankSum=1.624;QD=17.61;ReadPosRankSum=1.518;EFF=INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|2),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|6),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|6),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,36 0/0:2,0:2:6.01:0,6,64 ./. 0/0:2,0:2:6.01:0,6,61 0/0:4,0:4:9.03:0,9,123 0/0:7,0:7:15.04:0,15,183 0/0:12,0:12:33.10:0,33,416 0/0:1,0:1:3.01:0,3,39 0/0:17,0:17:48.12:0,48,592 0/0:14,0:14:42.13:0,42,533 0/0:2,0:2:6:0,6,65 0/0:4,0:4:9.03:0,9,106 0/0:10,0:10:27.08:0,27,342 0/0:17,0:17:45.12:0,45,568 0/0:27,0:27:72.21:0,72,902 0/0:18,0:18:48.10:0,48,564 0/0:16,0:16:39.12:0,39,495 0/0:22,0:23:57.16:0,57,734 0/0:32,0:32:72.20:0,72,932 0/0:17,0:17:45.14:0,45,588 0/0:31,0:31:81.16:0,81,974 0/0:23,0:23:57.16:0,57,708 0/0:19,0:19:48.14:0,48,603 0/0:22,0:22:51.16:0,51,639 0/0:17,0:17:48.15:0,48,600 0/0:23,0:24:60.19:0,60,774 0/0:29,0:29:72.23:0,72,926 0/0:20,0:20:51.13:0,51,617 0/0:31,0:31:72.22:0,72,934 0/0:34,0:34:84.19:0,84,1039 0/0:31,1:32:59.85:0,60,1105 0/0:23,0:24:60.19:0,60,770 0/0:24,0:24:69.22:0,69,905 0/1:11,21:32:99:611,0,310 0/0:26,0:26:69.20:0,69,887 0/0:22,0:22:57.17:0,57,741 0/0:34,0:36:93.30:0,93,1202 0/0:23,0:24:63.21:0,63,838 0/0:3,0:3:6.02:0,6,72 0/0:4,0:4:12.04:0,12,153 0/0:10,0:10:30.09:0,30,369 0/0:6,0:6:18.06:0,18,231 0/0:5,0:5:9.03:0,9,112 0/0:8,0:8:18.05:0,18,222 0/0:7,0:7:15.03:0,15,183 0/0:6,0:6:9.03:0,9,117 0/0:19,0:20:48.14:0,48,603 0/0:9,0:9:24.07:0,24,291 0/0:14,0:14:30.09:0,30,377 0/0:13,0:13:36.11:0,36,455 0/0:16,0:16:36.11:0,36,461 0/0:15,0:16:33.11:0,33,448 0/0:16,0:16:33.10:0,33,402 0/0:8,0:8:15.05:0,15,212 0/0:14,0:14:30.10:0,30,391 0/0:5,0:5:12.02:0,12,140 0/0:1,0:1:3.01:0,3,33 0/0:6,0:6:15.05:0,15,188 0/0:9,0:9:21.06:0,21,253 0/0:8,0:8:18.04:0,18,211 -chr1 1115840 . AC A 723.63 . AC=2;AF=0.0175;AN=114;BaseQRankSum=1.500;DP=1665;FS=3.486;HRun=5;HaplotypeScore=137.9849;InbreedingCoeff=-0.0404;MQ=57.81;MQ0=0;MQRankSum=1.153;QD=10.19;ReadPosRankSum=1.601;EFF=INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|2),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|6),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|6),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),UPSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:9.03:0,9,123 0/0:1,0:1:3.01:0,3,41 ./. 0/0:6,0:6:18.05:0,18,229 0/0:6,0:6:18.06:0,18,246 0/0:6,0:6:15.05:0,15,205 0/0:4,0:4:12.03:0,12,141 0/0:10,0:10:27.08:0,27,358 0/0:12,0:12:24.08:0,24,328 0/0:3,0:3:6.02:0,6,82 0/0:2,0:2:6.02:0,6,82 0/0:6,0:6:18.06:0,18,246 0/0:55,0:55:99:0,144,1904 0/0:57,0:57:99:0,144,1945 0/0:41,0:41:99:0,99,1354 0/0:46,0:46:99:0,117,1591 0/0:78,0:78:99:0,208,2791 0/0:68,0:68:99:0,187,2503 0/0:50,0:50:99:0,135,1831 0/0:51,0:51:99:0,132,1806 0/0:62,0:62:99:0,160,2164 0/0:66,0:66:99:0,163,2200 0/0:55,0:55:99:0,132,1791 0/0:62,0:62:99:0,174,2303 0/0:46,0:46:99:0,122,1606 0/0:68,0:68:99:0,171,2269 0/0:46,0:46:99:0,123,1673 0/0:62,0:62:99:0,162,2139 0/0:51,0:51:99:0,126,1722 0/0:81,1:81:99:0,208,2794 0/0:41,0:41:99:0,105,1416 0/0:65,0:65:99:0,166,2234 0/1:37,28:65:99:777,0,971 0/0:56,0:56:99:0,141,1898 0/0:42,0:42:99:0,108,1467 0/0:71,0:71:99:0,190,2537 0/0:69,0:69:99:0,181,2423 0/0:5,0:5:15.05:0,15,205 0/0:7,0:7:18.06:0,18,246 0/0:7,0:8:20.93:0,21,241 0/0:7,0:7:18.06:0,18,246 0/0:7,0:7:12.04:0,12,164 0/0:4,0:4:12.04:0,12,164 0/0:4,0:4:12.04:0,12,164 0/0:8,0:8:21.07:0,21,278 0/0:10,0:10:30.10:0,30,410 ./. 0/0:8,0:8:15.05:0,15,205 0/0:11,0:11:29.31:0,29,376 0/0:11,0:11:27.09:0,27,360 0/0:10,0:10:30.10:0,30,407 0/0:9,0:9:18.05:0,18,226 0/0:6,0:6:12.04:0,12,164 0/0:14,0:14:39.13:0,39,530 0/0:3,0:3:3.01:0,3,41 ./. 0/1:5,1:6:17.02:17,0,141 0/0:2,0:2:3.01:0,3,41 0/0:7,0:7:9.03:0,9,123 -chr1 1115994 . G A 10204.82 . AC=24;AF=0.2000;AN=120;BaseQRankSum=-0.160;DP=1696;Dels=0.00;FS=0.223;HRun=0;HaplotypeScore=1.0682;InbreedingCoeff=0.0308;MQ=58.03;MQ0=0;MQRankSum=0.094;QD=16.57;ReadPosRankSum=1.260;EFF=EXON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|1),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|3),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|7),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|1),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|1/5||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,2:2:6.01:64,6,0 0/0:3,0:3:9.01:0,9,99 0/0:1,0:1:3.01:0,3,36 0/1:2,2:4:60.89:63,0,61 0/0:3,0:3:9.03:0,9,116 0/0:10,0:10:27.07:0,27,340 0/0:14,0:14:36.11:0,36,463 0/0:5,0:5:12.04:0,12,156 0/0:18,0:18:42.13:0,42,546 0/1:9,5:15:99:114,0,234 0/0:8,0:8:21.07:0,21,275 0/0:7,0:7:12.04:0,12,160 0/0:8,0:8:21.06:0,21,258 0/1:13,25:39:99:748,0,358 0/1:14,28:43:99:810,0,346 0/0:35,1:36:60.73:0,61,1203 0/1:18,20:38:99:618,0,460 0/0:56,0:56:99:0,153,1996 0/1:32,15:47:99:330,0,1057 0/1:15,15:30:99:443,0,327 0/0:49,0:49:99:0,129,1680 0/0:53,0:53:99:0,126,1619 0/0:41,0:41:99:0,102,1315 0/1:20,15:35:99:420,0,578 0/0:54,0:54:99:0,138,1761 0/0:36,0:36:87.28:0,87,1142 0/1:18,23:41:99:686,0,581 0/0:26,0:26:72.23:0,72,935 0/0:45,0:45:99:0,114,1445 0/1:16,23:39:99:664,0,430 0/0:57,0:57:99:0,144,1851 0/0:48,0:49:99:0,126,1590 0/0:41,0:41:99:0,102,1352 0/0:48,0:48:99:0,120,1606 0/1:24,21:45:99:632,0,764 1/1:0,43:43:99:1393,108,0 0/0:48,0:48:99:0,132,1661 0/0:52,0:52:99:0,135,1717 0/1:11,11:22:99:314,0,359 0/1:17,9:26:99:230,0,359 0/0:27,0:27:72.23:0,72,924 0/0:26,0:26:75.24:0,75,968 0/0:19,0:19:51.16:0,51,627 0/0:10,0:10:27.08:0,27,330 0/1:8,7:15:99:194,0,263 0/0:27,0:27:66.18:0,66,808 0/0:41,0:41:96.28:0,96,1193 0/1:5,7:12:51.13:223,0,51 0/0:23,0:23:51.16:0,51,654 0/1:25,23:48:99:607,0,684 0/1:16,13:29:99:415,0,452 0/0:28,0:28:75.21:0,75,930 0/0:31,0:31:90.28:0,90,1137 0/0:20,0:20:51.15:0,51,644 1/1:0,32:32:84.24:1065,84,0 0/0:13,0:13:36.11:0,36,462 0/0:13,0:14:36.11:0,36,447 0/0:23,0:23:54.17:0,54,683 0/1:4,6:10:89.07:172,0,89 0/0:10,0:10:30.10:0,30,396 -chr1 1116005 . C T 537.05 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.435;DP=1666;Dels=0.00;FS=14.791;HRun=0;HaplotypeScore=1.1478;InbreedingCoeff=-0.0145;MQ=58.06;MQ0=0;MQRankSum=1.799;QD=13.43;ReadPosRankSum=-0.495;EFF=EXON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|1),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|3),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|7),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|1),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|1/5||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:9.03:0,9,108 0/0:3,0:3:9.01:0,9,93 0/0:5,0:5:15.04:0,15,178 0/0:6,0:6:18.06:0,18,226 0/0:11,0:11:27.08:0,27,342 0/0:15,0:15:39.12:0,39,508 0/0:5,0:5:15.04:0,15,182 0/0:18,0:18:45.13:0,45,551 0/0:11,0:11:33.09:0,33,399 0/0:7,0:7:21.07:0,21,281 0/0:5,0:5:12.04:0,12,160 0/0:7,0:7:18.05:0,18,221 0/0:36,0:36:99:0,102,1322 0/0:47,0:47:99:0,120,1528 0/0:35,0:35:93.26:0,93,1164 0/0:34,0:34:93.29:0,93,1191 0/0:55,0:55:99:0,147,1883 0/0:43,0:43:99:0,114,1501 0/0:24,0:26:66.20:0,66,839 0/0:45,0:45:99:0,120,1566 0/0:45,0:45:99:0,120,1499 0/0:35,0:36:90.28:0,90,1151 0/0:35,0:35:90.29:0,90,1196 0/0:54,0:54:99:0,138,1775 0/0:34,0:34:84.27:0,84,1095 0/1:18,21:40:99:585,0,556 0/0:26,0:26:72.23:0,72,933 0/0:46,0:46:99:0,123,1559 0/0:36,0:36:96.29:0,96,1218 0/0:51,0:52:99:0,135,1731 0/0:45,0:45:99:0,120,1559 0/0:37,0:37:99:0,102,1343 0/0:44,0:44:99:0,120,1563 0/0:42,0:42:99:0,117,1481 0/0:40,0:40:99:0,105,1366 0/0:52,0:52:99:0,135,1742 0/0:49,0:49:99:0,135,1746 0/0:25,0:25:72.20:0,72,902 0/0:19,1:20:54.17:0,54,707 0/0:25,0:25:63.19:0,63,808 0/0:29,0:29:84.26:0,84,1072 0/0:18,0:18:48.13:0,48,564 0/0:11,0:12:24.08:0,24,317 0/0:15,0:15:42.13:0,42,531 0/0:30,0:30:69.20:0,69,856 0/0:41,0:42:93.29:0,93,1175 0/0:14,0:14:33.10:0,33,409 0/0:27,0:27:63.20:0,63,829 0/0:52,0:52:99:0,123,1533 0/0:35,0:35:99:0,105,1334 0/0:30,0:30:78.23:0,78,963 0/0:35,0:35:93.29:0,93,1186 0/0:21,0:21:54.17:0,54,685 0/0:29,0:30:66.20:0,66,835 0/0:14,0:14:36.11:0,36,458 0/0:14,0:14:36.11:0,36,452 0/0:23,0:23:45.14:0,45,584 0/0:13,0:13:24.06:0,24,292 0/0:10,0:10:30.10:0,30,396 -chr1 1116231 . T C 4814.31 . AC=14;AF=0.1167;AN=120;BaseQRankSum=2.445;DP=1389;Dels=0.00;FS=6.355;HRun=2;HaplotypeScore=1.7202;InbreedingCoeff=0.1639;MQ=56.15;MQ0=0;MQRankSum=1.206;QD=15.28;ReadPosRankSum=0.519;EFF=EXON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|1),EXON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V176A|404|TTLL10|protein_coding|CODING|ENST00000379288|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V249A|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V249A|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,missense_variant|gTc/gCc|V/A|ENSG00000162571|TTLL10|ENST00000379289|8/16|benign(0)|tolerated(1)|249/673|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|1/5||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000514695|2/2||||retained_intron|1,missense_variant|gTc/gCc|V/A|ENSG00000162571|TTLL10|ENST00000379290|8/16|benign(0)|tolerated(1)|249/673|protein_coding|1,missense_variant|gTc/gCc|V/A|ENSG00000162571|TTLL10|ENST00000379288|4/9|benign(0)|tolerated(1)|176/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,112 0/0:2,0:2:6:0,6,56 0/0:2,0:2:6.02:0,6,81 0/0:5,0:5:12.03:0,12,139 0/1:6,6:12:99:205,0,189 0/0:14,0:14:39.11:0,39,500 0/0:19,0:19:51.11:0,51,615 0/1:3,7:10:94.16:189,0,94 0/0:18,0:18:51.16:0,51,666 0/0:16,0:16:45.14:0,45,557 0/0:4,0:4:9.03:0,9,107 0/0:8,0:8:24.08:0,24,312 0/0:4,0:4:12.02:0,12,135 0/0:25,0:26:60.16:0,60,744 0/1:21,7:28:99:117,0,611 0/0:16,2:18:6.55:0,7,465 0/0:22,2:24:60.19:0,60,755 0/0:26,2:30:51.14:0,51,626 0/0:27,2:29:72.22:0,72,940 1/1:0,33:33:87.26:1094,87,0 0/0:24,1:27:63.15:0,63,776 0/0:27,2:30:57.11:0,57,653 0/0:23,2:25:60.18:0,60,753 0/1:7,7:14:99:205,0,205 0/0:23,1:24:63.16:0,63,765 0/0:20,0:21:45.12:0,45,576 0/1:15,15:30:99:364,0,339 0/0:13,1:14:27.07:0,27,318 0/1:18,17:35:99:474,0,460 0/0:31,0:31:63.15:0,63,761 0/0:33,2:36:81.21:0,81,976 0/0:19,0:19:48.16:0,48,633 0/0:25,3:30:69.20:0,69,833 0/0:24,1:25:60.13:0,60,731 0/0:23,1:24:63.16:0,63,747 0/1:10,12:22:99:390,0,255 0/0:35,3:39:87.20:0,87,1027 0/0:36,0:38:84.21:0,84,1069 0/0:16,0:16:39.11:0,39,487 0/0:41,2:44:61.41:0,61,1069 0/0:22,1:24:57.18:0,57,704 0/0:32,1:34:90.22:0,90,1059 0/0:15,0:15:42.10:0,42,470 0/0:21,0:21:51.15:0,51,609 0/0:21,0:21:57.18:0,57,732 0/0:28,0:28:66.15:0,66,753 0/0:39,0:40:96.26:0,96,1145 0/1:8,10:18:99:188,0,136 0/0:26,0:27:63.19:0,63,788 0/1:24,22:46:99:484,0,631 0/1:25,23:48:99:556,0,613 0/0:39,3:45:99:0,105,1211 0/0:43,1:45:90.24:0,90,1078 0/0:18,1:19:45.13:0,45,542 1/1:0,18:18:45.14:550,45,0 0/0:19,0:19:48.11:0,48,565 0/0:14,0:14:27.06:0,27,299 0/0:18,0:18:42.12:0,42,517 0/0:15,2:17:39.07:0,39,464 0/0:20,0:21:45.14:0,45,576 -chr1 1116311 . A G 3493.8 . AC=48;AF=0.4706;AN=102;BaseQRankSum=7.547;DP=286;Dels=0.01;FS=2.211;HRun=0;HaplotypeScore=0.9639;InbreedingCoeff=0.0983;MQ=52.73;MQ0=0;MQRankSum=0.694;QD=18.89;ReadPosRankSum=0.096;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|4),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|8),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|1),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3:0,3,28 ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:37,3,0 0/0:4,0:4:9.02:0,9,102 0/0:2,0:2:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 ./. ./. 1/1:0,3:3:9.03:115,9,0 0/1:3,1:4:21.44:21,0,68 0/1:1,1:2:29.23:34,0,29 1/1:0,1:1:3.01:40,3,0 0/1:2,5:8:50.32:163,0,50 0/1:3,2:5:53.36:53,0,80 ./. 0/0:6,0:6:15.02:0,15,157 0/1:5,2:7:56.97:57,0,85 0/0:6,0:6:15:0,15,147 1/1:0,1:1:3.01:37,3,0 0/0:2,0:2:6.01:0,6,65 0/0:2,0:2:6.02:0,6,68 1/1:0,4:4:12.04:152,12,0 0/1:1,1:2:19.67:33,0,20 0/1:3,1:4:27.97:28,0,46 0/1:1,2:3:26.22:69,0,26 0/1:2,1:3:30.98:31,0,58 0/1:1,1:2:27.42:27,0,27 0/1:4,2:6:47.65:48,0,118 1/1:0,1:1:3.01:37,3,0 1/1:0,4:4:12.04:153,12,0 ./. 0/1:6,3:9:48.06:84,0,48 0/0:6,0:7:15.03:0,15,175 0/1:3,2:5:15.67:70,0,16 0/1:4,3:7:90.98:91,0,106 0/1:5,3:10:88.76:89,0,110 0/0:3,0:3:9.02:0,9,99 1/1:1,2:5:6.02:71,6,0 0/0:1,0:3:2.99:0,3,23 1/1:0,5:5:15.04:176,15,0 0/0:4,0:7:9.01:0,9,86 0/0:9,0:13:21.02:0,21,234 1/1:0,7:7:18.06:233,18,0 0/0:5,0:6:12.01:0,12,121 0/1:5,9:17:80.64:218,0,81 1/1:0,19:22:42.12:492,42,0 0/0:15,0:18:33.05:0,33,346 1/1:0,16:16:36.10:443,36,0 0/0:4,1:6:6.02:0,6,75 1/1:0,5:5:12.02:128,12,0 0/1:2,3:6:21.41:90,0,21 0/0:8,0:8:12.02:0,12,122 0/1:1,1:2:32.56:33,0,33 1/1:0,4:4:9.03:109,9,0 0/0:4,0:4:6.01:0,6,67 -chr1 1117111 . T C 797.3 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.679;DP=2103;Dels=0.00;FS=1.613;HRun=4;HaplotypeScore=1.6462;InbreedingCoeff=-0.0099;MQ=57.76;MQ0=0;MQRankSum=1.258;QD=16.61;ReadPosRankSum=-0.652;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|4),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|8),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|1),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:15.03:0,15,166 0/0:4,0:4:12.04:0,12,143 0/0:11,0:11:33.10:0,33,407 0/0:8,0:8:24.08:0,24,310 0/0:4,0:4:12.04:0,12,158 0/0:6,0:6:18.06:0,18,239 0/0:16,0:16:45.14:0,45,590 0/0:10,0:10:27.09:0,27,350 0/0:22,0:22:66.21:0,66,868 0/0:21,0:21:60.19:0,60,792 0/0:7,0:7:21.07:0,21,282 0/0:9,0:9:24.08:0,24,306 0/0:12,0:12:33.10:0,33,408 0/0:25,0:25:60.18:0,60,770 0/0:41,0:41:96.30:0,96,1245 0/0:32,1:33:75.23:0,75,985 0/0:31,1:32:72.23:0,72,983 0/0:32,0:32:78.25:0,78,1040 0/0:25,0:25:69.20:0,69,895 0/0:28,0:28:78.23:0,78,940 0/0:21,0:21:48.13:0,48,622 0/0:34,0:34:78.26:0,78,1072 0/0:30,0:30:66.22:0,66,901 0/0:31,0:31:72.23:0,72,958 0/0:33,0:33:78.23:0,78,1032 0/0:17,0:17:48.16:0,48,640 0/0:29,0:29:75.18:0,75,950 0/0:22,0:22:57.16:0,57,737 0/0:28,0:28:69.18:0,69,853 0/0:27,1:29:69.21:0,69,888 0/0:43,0:43:99:0,105,1383 0/0:35,0:35:90.26:0,90,1162 0/0:41,0:41:99:0,99,1298 0/1:17,31:48:99:845,0,359 0/0:39,0:39:90.29:0,90,1210 0/0:26,1:27:66.21:0,66,865 0/0:26,0:26:69.22:0,69,912 0/0:40,0:40:99:0,102,1328 0/0:52,0:52:99:0,147,1827 0/0:97,0:98:99:0,256,3259 0/0:60,1:62:99:0,147,1851 0/0:47,1:48:99:0,123,1534 0/0:47,0:47:99:0,123,1535 0/0:28,0:28:72.22:0,72,911 0/0:43,0:43:99:0,117,1465 0/0:50,0:50:99:0,123,1560 0/0:99,2:102:99:0,259,3210 0/0:23,0:23:66.20:0,66,838 0/0:65,2:67:99:0,138,1757 0/0:60,0:60:99:0,163,2102 0/0:60,0:60:99:0,156,1992 0/0:27,0:27:69.19:0,69,875 0/0:39,1:40:96.30:0,96,1240 0/0:55,1:56:99:0,144,1852 0/0:68,0:68:99:0,177,2203 0/0:38,1:39:99:0,99,1278 0/0:32,0:34:69.19:0,69,876 0/0:64,0:65:99:0,138,1793 0/0:56,1:57:99:0,132,1682 0/0:50,0:50:99:0,123,1586 -chr1 1117200 . A ACTCAG 2202.05 . AC=4;AF=0.0333;AN=120;BaseQRankSum=-4.680;DP=3092;FS=21.350;HRun=0;HaplotypeScore=287.1827;InbreedingCoeff=-0.0395;MQ=57.35;MQ0=0;MQRankSum=-7.883;QD=28.60;ReadPosRankSum=-0.894;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|9),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|9),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|2),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,splice_region_variant&intron_variant&feature_elongation|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,splice_region_variant&intron_variant&feature_elongation|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,splice_region_variant&intron_variant&feature_elongation|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:15.05:0,15,308 0/0:4,0:4:12.04:0,12,233 0/0:9,0:9:24.08:0,24,443 0/0:4,0:4:3.01:0,3,61 0/1:5,1:6:99:171,0,111 0/0:8,0:8:18.06:0,18,356 0/0:17,0:17:39.13:0,39,778 0/1:11,1:12:99:282,0,205 0/0:21,0:21:57.19:0,57,1032 0/0:21,0:21:39.13:0,39,789 0/0:8,0:8:24.07:0,24,390 0/0:4,0:4:9.03:0,9,185 0/0:23,0:23:54.16:0,54,884 0/0:31,0:31:90.30:0,90,1753 0/0:48,0:48:99:0,132,2627 0/0:21,0:21:54.18:0,54,1024 0/0:40,0:40:99:0,114,2200 0/0:47,0:47:99:0,126,2411 0/0:39,0:39:99:0,102,2079 0/1:23,9:32:99:1021,0,746 0/0:32,0:32:84.28:0,84,1692 0/0:34,0:33:93.32:0,93,1878 0/0:25,0:25:75.25:0,75,1461 0/0:29,0:29:78.26:0,78,1540 0/0:37,0:36:93.32:0,93,1909 0/0:24,0:24:66.22:0,66,1295 0/0:24,0:24:66.22:0,66,1327 0/0:37,0:37:99:0,105,2072 0/1:17,10:27:99:829,0,769 0/0:31,0:31:78.26:0,78,1491 0/0:49,0:49:99:0,135,2687 0/0:31,0:31:81.28:0,81,1662 0/0:37,0:37:99:0,111,2146 0/0:50,0:50:99:0,147,2875 0/0:29,0:29:72.24:0,72,1401 0/0:28,0:28:81.28:0,81,1659 0/0:46,0:46:99:0,129,2541 0/0:52,0:52:99:0,138,2777 0/0:87,0:88:99:0,226,4277 0/0:132,0:132:99:0,346,6936 0/0:117,0:117:99:0,304,6012 0/0:89,0:89:99:0,235,4661 0/0:87,0:87:99:0,226,4455 0/0:71,0:71:99:0,184,3513 0/0:98,0:98:99:0,262,5122 0/0:108,0:108:99:0,280,5547 0/0:150,0:150:99:0,400,7936 0/0:62,0:62:99:0,175,3490 0/0:91,0:91:99:0,229,4589 0/0:97,0:97:99:0,271,5396 0/0:110,0:110:99:0,307,6096 0/0:76,0:76:99:0,220,4405 0/0:79,0:79:99:0,229,4373 0/0:120,0:120:99:0,331,6418 0/0:99,0:99:99:0,256,5093 0/0:74,0:73:99:0,187,3607 0/0:60,0:60:99:0,169,3433 0/0:101,0:101:99:0,274,5330 0/0:72,0:72:99:0,196,3938 0/0:87,0:86:99:0,229,4549 -chr1 1117398 . A G 8833.57 . AC=60;AF=0.5172;AN=116;BaseQRankSum=3.163;DP=557;Dels=0.00;FS=2.617;HRun=0;HaplotypeScore=0.4621;InbreedingCoeff=0.0835;MQ=57.86;MQ0=0;MQRankSum=1.868;QD=22.25;ReadPosRankSum=0.084;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|9),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|9),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|2),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:9.03:0,9,111 1/1:0,1:1:3.01:39,3,0 0/1:2,2:4:31.62:58,0,32 0/1:2,2:4:33.30:33,0,34 0/1:2,2:4:32.21:32,0,59 0/1:1,1:2:29.23:29,0,35 ./. 0/0:3,0:3:6.02:0,6,80 0/1:3,4:7:24.27:141,0,24 1/1:0,2:2:3.01:41,3,0 1/1:0,3:3:6.01:61,6,0 0/1:2,3:5:52.90:56,0,53 1/1:0,5:5:12.04:158,12,0 0/1:2,4:6:29.20:96,0,29 0/0:1,1:2:3.01:0,3,39 0/1:2,1:3:30.11:35,0,30 1/1:0,3:3:6.02:79,6,0 0/1:4,3:8:53.61:54,0,100 1/1:0,4:4:9.02:104,9,0 0/0:4,0:4:6.02:0,6,74 0/1:2,1:3:29.55:30,0,72 0/0:1,0:1:3.01:0,3,40 0/1:3,3:6:49.60:50,0,92 0/0:2,0:2:6.01:0,6,63 0/0:4,0:5:6.02:0,6,77 1/1:0,1:1:3.01:40,3,0 1/1:0,2:2:6:55,6,0 0/1:1,1:2:34.63:35,0,35 0/0:1,1:2:3.01:0,3,40 0/1:4,3:7:16.61:108,0,17 0/1:2,2:4:29.55:59,0,30 0/1:3,1:4:24.94:25,0,104 1/1:0,3:3:9.01:102,9,0 1/1:0,4:4:9.03:112,9,0 1/1:0,3:3:9.03:116,9,0 1/1:1,1:2:3.01:35,3,0 0/0:2,0:2:6.02:0,6,74 0/1:10,10:21:99:304,0,152 0/1:14,18:32:99:526,0,415 0/1:11,11:22:99:340,0,306 0/1:8,10:20:99:253,0,203 0/1:9,10:19:99:253,0,252 0/0:14,0:15:42.09:0,42,485 1/1:0,19:19:54.16:667,54,0 0/0:16,0:16:30.10:0,30,388 0/0:45,1:47:99:0,111,1318 1/1:0,16:16:42.14:552,42,0 0/0:10,0:10:27.08:0,27,344 1/1:0,36:36:93.27:1170,93,0 1/1:0,32:32:75.22:921,75,0 0/0:18,0:21:42.11:0,42,502 1/1:1,22:23:60.15:753,60,0 0/0:11,0:11:33.09:0,33,389 1/1:0,20:20:54.16:682,54,0 0/1:7,4:11:99:121,0,180 0/0:7,0:7:21.06:0,21,251 0/1:5,5:11:93.73:94,0,165 1/1:0,13:13:33.10:413,33,0 0/0:9,0:9:15.05:0,15,191 -chr1 1117486 . A G 1272.34 . AC=17;AF=0.1441;AN=118;BaseQRankSum=-1.118;DP=292;Dels=0.00;FS=2.091;HRun=0;HaplotypeScore=0.1964;InbreedingCoeff=-0.1365;MQ=57.43;MQ0=0;MQRankSum=0.534;QD=14.14;ReadPosRankSum=0.569;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|9),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|9),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|2),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/1:2,2:4:30.29:60,0,30 0/0:3,0:4:6.02:0,6,74 0/0:1,1:2:3.01:0,3,36 0/1:2,3:5:63.86:65,0,64 0/0:4,0:4:9.03:0,9,115 0/0:3,0:3:9.03:0,9,119 0/0:5,0:5:15.05:0,15,193 0/0:5,0:5:15.04:0,15,177 0/0:10,0:10:30.10:0,30,396 0/1:8,5:13:99:120,0,276 0/0:5,0:5:15.05:0,15,184 0/0:3,0:3:9.03:0,9,122 0/0:7,0:7:21.07:0,21,274 0/0:4,0:4:12.04:0,12,157 0/1:2,1:3:26.22:26,0,74 0/0:3,0:3:6.02:0,6,81 0/1:1,2:3:27.10:65,0,27 0/0:2,0:2:6.02:0,6,73 0/0:4,0:4:12.04:0,12,151 0/0:2,0:2:6.02:0,6,83 0/0:3,0:3:9.03:0,9,121 0/0:3,0:4:9.03:0,9,120 0/0:3,0:3:9.03:0,9,115 0/1:2,2:4:64.95:65,0,66 0/0:2,0:2:6.02:0,6,80 0/0:5,0:5:15.05:0,15,195 0/1:1,3:4:32.56:39,0,33 0/0:2,0:2:6.02:0,6,81 0/0:3,0:3:9.03:0,9,123 0/1:1,5:6:21.95:186,0,22 0/0:10,0:10:30.10:0,30,398 0/0:3,0:3:6.02:0,6,87 0/0:2,0:2:6.02:0,6,80 0/0:3,0:3:9.03:0,9,113 0/1:4,6:10:99:169,0,127 ./. 0/0:4,0:4:9.03:0,9,122 0/0:2,0:2:6:0,6,55 0/1:4,4:8:99:122,0,120 0/1:2,4:6:54.70:129,0,55 0/0:10,0:10:24.08:0,24,312 0/0:8,0:8:21.06:0,21,264 0/0:8,0:8:24.07:0,24,304 0/0:6,0:6:12.04:0,12,149 0/1:1,2:3:27.42:33,0,27 0/0:6,0:6:15.05:0,15,194 0/0:13,0:13:33.10:0,33,409 1/1:0,1:1:3.01:42,3,0 0/0:1,0:1:3.01:0,3,38 0/1:6,5:11:99:170,0,184 0/1:3,2:5:62.63:63,0,69 0/0:7,0:7:18.06:0,18,228 0/0:6,0:6:18.05:0,18,229 0/0:6,0:6:15.05:0,15,200 0/0:6,0:6:18.06:0,18,226 0/0:4,0:4:12.04:0,12,156 0/0:4,0:4:9.03:0,9,115 0/0:3,0:3:9.03:0,9,117 0/1:1,3:4:30.19:102,0,30 0/0:5,0:5:12.04:0,12,144 -chr1 1117529 . A C 317.04 . AC=5;AF=0.0424;AN=118;BaseQRankSum=-1.360;DP=362;Dels=0.00;FS=1.548;HRun=1;HaplotypeScore=0.4341;InbreedingCoeff=-0.0846;MQ=57.60;MQ0=0;MQRankSum=0.707;QD=9.61;ReadPosRankSum=0.810;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|9),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|9),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|2),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:3.01:0,3,34 0/0:4,0:4:9.03:0,9,111 0/0:4,0:4:12.04:0,12,152 0/0:1,0:1:3.01:0,3,35 0/1:3,3:6:97.50:99,0,98 0/0:5,0:5:15.04:0,15,178 0/0:9,0:9:27.08:0,27,339 0/1:4,5:9:99:122,0,139 0/0:21,0:21:60.17:0,60,755 0/0:18,0:18:45.13:0,45,558 0/0:4,0:4:12.04:0,12,156 0/0:2,0:2:6:0,6,60 0/0:7,0:7:21.05:0,21,259 0/0:7,0:7:21.07:0,21,267 0/0:5,0:5:15.03:0,15,171 0/0:5,0:5:15.05:0,15,190 0/0:3,0:3:9.02:0,9,107 0/0:8,0:8:21.07:0,21,266 ./. 0/1:2,2:4:38.30:38,0,65 0/0:7,0:7:18.04:0,18,223 0/0:6,0:6:15.04:0,15,183 0/0:6,0:6:18.05:0,18,218 0/0:2,0:2:6.02:0,6,66 0/0:5,0:5:15.05:0,15,188 0/0:6,0:6:15.05:0,15,195 0/0:8,0:8:18.06:0,18,226 0/0:6,0:6:18.05:0,18,220 0/1:4,2:6:63.54:64,0,89 0/0:11,0:11:27.07:0,27,311 0/0:12,0:12:33.10:0,33,411 0/0:5,0:5:15.05:0,15,194 0/0:3,0:3:9.03:0,9,110 0/0:4,0:4:12.04:0,12,143 0/0:9,0:9:24.08:0,24,299 0/0:7,0:7:18.04:0,18,223 0/0:6,1:7:18.06:0,18,232 0/0:4,0:4:6.02:0,6,71 0/0:2,0:2:6.02:0,6,72 0/0:4,0:5:9.03:0,9,116 0/0:7,0:7:18.04:0,18,210 0/0:1,1:2:3.01:0,3,41 0/0:10,0:10:21.07:0,21,267 0/0:2,0:2:3.01:0,3,38 0/0:7,0:7:21.04:0,21,246 0/0:5,0:5:15.05:0,15,185 0/0:15,0:15:33.10:0,33,405 0/0:2,0:2:3.01:0,3,36 0/0:4,0:4:12.01:0,12,137 0/1:4,4:8:96.26:96,0,110 0/0:4,0:4:9.03:0,9,111 0/0:7,0:7:15.02:0,15,174 0/0:7,0:7:21.06:0,21,255 0/0:5,0:5:15.03:0,15,175 0/0:7,0:7:18.05:0,18,215 0/0:6,0:6:15.05:0,15,194 0/0:5,0:5:9.03:0,9,107 0/0:3,0:3:6.02:0,6,80 0/0:5,0:5:15.05:0,15,197 0/0:3,0:3:9.03:0,9,111 -chr1 1117709 . G A 2986.58 . AC=4;AF=0.0333;AN=120;BaseQRankSum=1.592;DP=3059;Dels=0.00;FS=8.817;HRun=1;HaplotypeScore=1.5659;InbreedingCoeff=-0.0345;MQ=59.00;MQ0=0;MQRankSum=-1.150;QD=12.82;ReadPosRankSum=-4.568;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|5),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|9),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|9),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|2),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:24,0:24:66.19:0,66,816 0/0:18,0:18:42.10:0,42,520 0/0:24,0:24:69.22:0,69,871 0/0:12,0:12:33.08:0,33,390 0/1:27,28:55:99:957,0,914 0/0:42,0:42:99:0,126,1646 0/0:73,0:73:99:0,214,2808 0/1:21,16:37:99:473,0,728 0/0:95,0:95:99:0,283,3755 0/0:95,1:96:99:0,277,3639 0/0:46,0:46:99:0,138,1779 0/0:52,0:52:99:0,156,2023 0/0:51,0:51:99:0,150,1947 0/0:83,0:83:99:0,211,2781 0/0:81,0:81:99:0,184,2420 0/0:47,0:47:99:0,126,1614 0/0:58,0:59:99:0,144,1889 0/0:71,0:71:99:0,184,2359 0/0:59,0:59:99:0,160,2080 0/1:40,30:70:99:738,0,1129 0/0:47,0:47:99:0,117,1501 0/0:80,0:80:99:0,193,2596 0/0:57,0:58:99:0,135,1800 0/0:84,0:84:99:0,208,2744 0/0:56,0:56:99:0,135,1762 0/0:52,0:52:99:0,129,1683 0/0:69,0:69:99:0,172,2229 0/0:51,0:51:99:0,117,1549 0/1:40,31:71:99:911,0,1051 0/0:68,0:68:99:0,175,2264 0/0:71,0:71:99:0,187,2398 0/0:67,0:67:99:0,153,2023 0/0:72,0:72:99:0,175,2270 0/0:55,0:55:99:0,138,1802 0/0:54,0:54:99:0,135,1741 0/0:65,0:65:99:0,156,2064 0/0:67,0:67:99:0,159,2117 0/0:76,0:76:99:0,190,2540 0/0:26,0:26:69.22:0,69,888 0/0:44,0:44:99:0,108,1395 0/0:47,0:49:99:0,120,1546 0/0:25,0:25:63.21:0,63,843 0/0:31,0:31:78.21:0,78,952 0/0:22,0:22:45.15:0,45,605 0/0:38,0:38:84.27:0,84,1084 0/0:37,0:37:99:0,99,1278 0/0:69,0:69:99:0,169,2136 0/0:17,0:17:39.12:0,39,507 0/0:39,1:40:87.27:0,87,1125 0/0:59,0:59:99:0,144,1837 0/0:34,0:34:81.25:0,81,1030 0/0:28,0:28:75.24:0,75,958 0/0:55,0:55:99:0,126,1585 0/0:37,0:37:87.27:0,87,1121 0/0:45,0:45:99:0,114,1455 0/0:39,0:39:96.31:0,96,1270 0/0:25,0:25:69.21:0,69,870 0/0:32,0:32:81.25:0,81,1024 0/0:26,0:26:63.20:0,63,824 0/0:23,0:23:54.15:0,54,674 -chr1 1117795 . C G 1423.49 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.182;DP=4738;Dels=0.00;FS=1.073;HRun=1;HaplotypeScore=2.2289;InbreedingCoeff=-0.0084;MQ=59.08;MQ0=0;MQRankSum=-0.250;QD=14.53;ReadPosRankSum=2.714;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),EXON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caG|H222Q|404|TTLL10|protein_coding|CODING|ENST00000379288|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caG|H295Q|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caC/caG|H295Q|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,missense_variant|caC/caG|H/Q|ENSG00000162571|TTLL10|ENST00000379289|10/16|benign(0.046)|tolerated(0.21)|295/673|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|3/5||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,missense_variant|caC/caG|H/Q|ENSG00000162571|TTLL10|ENST00000379290|10/16|benign(0.046)|tolerated(0.21)|295/673|protein_coding|1,missense_variant|caC/caG|H/Q|ENSG00000162571|TTLL10|ENST00000379288|6/9|benign(0.085)|tolerated(0.23)|222/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:35,0:35:90.28:0,90,1135 0/0:49,0:49:99:0,141,1811 0/0:45,0:45:99:0,132,1705 0/0:22,0:22:63.19:0,63,798 0/0:95,0:95:99:0,277,3650 0/0:86,0:86:99:0,259,3472 0/0:134,0:135:99:0,400,5351 0/0:64,0:65:99:0,193,2589 0/0:166,0:167:99:0,488,6542 0/0:175,0:175:99:0,512,6795 0/0:68,0:68:99:0,202,2692 0/0:76,0:76:99:0,223,2956 0/0:94,0:94:99:0,277,3671 0/0:79,0:79:99:0,199,2658 0/0:114,0:114:99:0,286,3818 0/0:64,0:64:99:0,156,2094 0/0:79,0:79:99:0,184,2471 0/0:83,0:83:99:0,229,3014 0/0:101,0:101:99:0,226,3138 0/0:101,0:101:99:0,244,3309 0/0:99,1:100:99:0,226,3086 0/0:100,1:101:99:0,241,3270 0/0:75,0:75:99:0,178,2375 0/0:122,0:122:99:0,277,3737 0/1:44,53:98:99:1471,0,1200 0/0:92,0:92:99:0,205,2789 0/0:106,0:106:99:0,262,3515 0/0:59,0:59:99:0,141,1902 0/0:95,0:95:99:0,235,3165 0/0:99,1:100:99:0,244,3307 0/0:105,0:108:99:0,259,3504 0/0:82,0:82:99:0,202,2759 0/0:99,0:100:99:0,250,3364 0/0:93,0:93:99:0,214,2891 0/0:89,0:89:99:0,223,3025 0/0:95,0:95:99:0,232,3111 0/0:94,0:94:99:0,226,3048 0/0:99,0:99:99:0,247,3338 0/0:36,2:38:96.29:0,96,1258 0/0:86,0:86:99:0,220,2874 0/0:70,0:70:99:0,166,2225 0/0:47,0:47:99:0,117,1579 0/0:60,0:60:99:0,135,1729 0/0:54,0:54:99:0,135,1788 0/0:56,0:56:99:0,135,1809 0/0:60,0:60:99:0,147,1954 0/0:96,0:97:99:0,235,3019 0/0:34,0:34:96.31:0,96,1279 0/0:66,1:67:99:0,153,2025 0/0:85,0:85:99:0,205,2712 0/0:57,0:57:99:0,144,1868 0/0:43,0:43:99:0,111,1422 0/0:72,0:72:99:0,181,2375 0/0:70,0:70:99:0,147,1939 0/0:57,0:57:99:0,144,1859 0/0:58,0:58:99:0,141,1848 0/0:50,0:50:99:0,105,1438 0/0:56,1:57:99:0,144,1926 0/0:42,0:42:99:0,102,1381 0/0:37,0:37:90.28:0,90,1179 -chr1 1118119 . G A 94.5 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.954;DP=605;Dels=0.00;FS=6.112;HRun=0;HaplotypeScore=0.5514;InbreedingCoeff=-0.0360;MQ=57.50;MQ0=0;MQRankSum=0.026;QD=15.75;ReadPosRankSum=-0.231;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|6),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|10),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|10),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|3),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.02:0,6,80 0/0:4,0:4:12.04:0,12,156 0/0:2,0:2:6.02:0,6,79 0/0:8,0:8:24.08:0,24,327 0/0:6,0:6:18.06:0,18,246 0/0:10,0:10:30.10:0,30,393 0/0:3,0:3:9.03:0,9,116 0/0:13,0:13:36.12:0,36,477 0/0:14,0:14:42.13:0,42,548 0/0:3,0:3:9.03:0,9,122 0/0:3,0:3:9.03:0,9,116 0/0:4,0:4:9.03:0,9,118 0/0:2,0:2:6.02:0,6,80 0/0:6,0:6:18.06:0,18,231 0/0:3,0:3:9.03:0,9,116 0/0:5,0:5:15.05:0,15,189 0/0:5,0:5:15.05:0,15,184 0/0:10,0:10:24.08:0,24,324 0/1:2,4:6:62.75:142,0,63 0/0:3,0:3:9.03:0,9,118 0/0:9,0:9:24.08:0,24,321 0/0:3,0:3:9.03:0,9,118 0/0:9,0:9:18.06:0,18,248 0/0:9,0:9:21.07:0,21,283 0/0:9,0:9:21.07:0,21,270 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.02:0,6,74 0/0:8,0:8:21.06:0,21,260 0/0:4,0:4:9.03:0,9,120 0/0:11,0:11:33.11:0,33,436 0/0:10,0:10:27.06:0,27,345 0/0:3,0:3:9.03:0,9,115 0/0:7,0:7:21.07:0,21,271 0/0:8,0:8:24.08:0,24,322 0/0:1,0:1:3.01:0,3,40 0/0:3,0:3:9.03:0,9,114 0/0:4,0:4:9.03:0,9,115 0/0:15,0:15:42.13:0,42,545 0/0:29,0:29:69.22:0,69,872 0/0:24,0:24:57.18:0,57,751 0/0:15,0:15:39.11:0,39,491 0/0:13,0:14:36.11:0,36,457 0/0:18,0:18:45.14:0,45,587 0/0:10,0:11:30.08:0,30,375 0/0:7,0:7:15.03:0,15,168 0/0:33,0:33:87.24:0,87,1100 0/0:9,0:9:27.09:0,27,348 0/0:15,0:15:42.13:0,42,536 0/0:28,0:28:75.24:0,75,953 0/0:27,0:27:72.23:0,72,939 0/0:27,0:27:75.24:0,75,967 0/0:20,0:20:57.15:0,57,728 0/0:16,0:16:42.11:0,42,511 0/0:17,0:17:48.15:0,48,606 0/0:22,0:22:60.19:0,60,792 0/0:5,0:5:15.05:0,15,184 0/0:13,0:13:33.10:0,33,422 0/0:16,0:16:42.13:0,42,549 0/0:9,0:9:24.07:0,24,303 -chr1 1118157 . C T 629.37 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.602;DP=775;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.4619;InbreedingCoeff=-0.0286;MQ=57.49;MQ0=0;MQRankSum=1.353;QD=15.73;ReadPosRankSum=-1.120;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|6),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|10),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|10),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|3),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:3:0,3,25 0/0:5,0:5:15.03:0,15,176 0/0:1,0:1:3:0,3,25 0/0:3,0:3:3.01:0,3,40 0/0:9,0:9:27.09:0,27,355 0/0:6,0:6:15.05:0,15,199 0/0:8,0:8:24.08:0,24,321 0/0:3,0:3:9.03:0,9,111 0/0:11,0:11:33.11:0,33,437 0/0:14,0:14:39.13:0,39,517 0/0:3,0:3:9.03:0,9,116 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:6.02:0,6,82 0/0:3,0:3:9.03:0,9,120 0/0:7,0:7:18.06:0,18,238 0/0:4,0:4:12.04:0,12,163 0/0:6,0:6:18.06:0,18,233 0/0:8,0:8:24.06:0,24,310 0/0:9,0:9:21.06:0,21,261 0/0:8,0:8:21.06:0,21,263 0/0:4,0:4:12.04:0,12,158 0/0:13,0:13:36.11:0,36,461 0/0:4,0:4:12.04:0,12,156 0/0:8,0:8:21.06:0,21,259 0/0:9,0:9:24.07:0,24,313 0/0:8,0:8:18.06:0,18,238 0/0:6,0:6:15.03:0,15,179 0/0:3,0:3:9.03:0,9,110 0/0:10,0:10:21.07:0,21,295 0/0:4,0:4:12.03:0,12,154 0/0:7,0:7:21.07:0,21,267 0/0:10,0:10:24.05:0,24,291 0/0:3,0:3:6.02:0,6,81 0/0:5,0:5:12.04:0,12,163 0/0:7,0:7:21.07:0,21,267 0/0:7,0:7:21.07:0,21,276 0/0:4,0:4:12.04:0,12,161 0/0:6,0:6:18.06:0,18,233 0/0:18,0:18:45.14:0,45,584 0/0:33,0:34:84.25:0,84,1052 0/0:27,0:27:72.21:0,72,916 0/0:25,0:25:63.19:0,63,785 0/0:16,0:16:48.15:0,48,623 0/0:16,0:16:39.12:0,39,505 0/0:18,0:18:51.16:0,51,666 0/0:18,0:18:48.15:0,48,622 0/0:42,0:43:99:0,114,1463 0/0:12,0:13:33.11:0,33,429 0/0:27,0:27:69.22:0,69,899 0/1:14,26:40:99:677,0,357 0/0:40,0:40:99:0,105,1322 0/0:28,0:29:72.22:0,72,904 0/0:30,0:31:84.25:0,84,1067 0/0:23,0:23:54.17:0,54,704 0/0:23,0:23:63.20:0,63,813 0/0:25,0:25:66.20:0,66,846 0/0:12,0:12:33.10:0,33,427 0/0:18,0:19:48.15:0,48,628 0/0:27,0:27:75.22:0,75,944 0/0:18,0:18:39.12:0,39,501 -chr1 1118212 . T C 16130.03 . AC=48;AF=0.4068;AN=118;BaseQRankSum=1.657;DP=1395;Dels=0.00;FS=12.889;HRun=1;HaplotypeScore=1.7343;InbreedingCoeff=0.1338;MQ=57.23;MQ0=0;MQRankSum=3.897;QD=20.34;ReadPosRankSum=-0.066;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|6),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|10),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|10),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|3),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:4,0:4:6.02:0,6,74 0/0:2,0:2:3.01:0,3,34 0/0:5,0:5:9.02:0,9,95 0/1:6,4:10:99:131,0,210 0/1:2,6:8:52.38:164,0,52 0/1:4,5:9:99:172,0,132 1/1:0,6:6:15.05:203,15,0 0/0:22,0:22:63.20:0,63,812 0/0:13,0:13:33.09:0,33,417 1/1:0,7:7:21.07:277,21,0 1/1:0,6:6:18.04:219,18,0 0/1:3,3:6:56.96:100,0,57 1/1:0,8:8:21.06:251,21,0 0/1:10,9:19:99:232,0,192 0/1:4,3:7:91.34:91,0,135 0/0:7,0:7:21.05:0,21,248 0/1:6,8:14:99:226,0,157 0/0:8,0:8:21.07:0,21,278 1/1:0,8:8:21.06:265,21,0 0/0:15,0:15:36.12:0,36,471 0/1:5,10:15:99:303,0,145 0/0:15,0:15:33.10:0,33,425 0/1:5,3:8:86.63:87,0,144 0/0:9,0:9:21.06:0,21,264 0/0:11,0:11:33.10:0,33,423 1/1:0,13:13:30.09:388,30,0 0/1:4,4:9:91.49:142,0,91 0/1:10,10:20:99:212,0,250 0/0:6,0:6:15.05:0,15,193 0/1:5,6:11:99:157,0,160 0/1:4,3:7:81.38:81,0,131 0/1:4,3:7:94.12:94,0,131 0/1:5,4:9:99:119,0,133 0/1:4,2:6:21.08:21,0,135 0/1:8,6:14:99:195,0,250 0/1:3,9:12:84.68:270,0,85 0/0:12,0:12:33.11:0,33,427 0/0:35,1:37:87.28:0,87,1131 0/0:58,0:59:99:0,153,1939 0/1:29,21:50:99:529,0,780 0/1:26,23:49:99:559,0,627 0/1:17,14:32:99:348,0,443 0/0:33,0:34:84.25:0,84,1055 1/1:0,31:31:81.22:990,81,0 0/0:43,1:45:89.62:0,90,1315 0/0:79,0:82:99:0,205,2481 1/1:0,27:27:72.22:893,72,0 0/0:55,0:55:99:0,123,1579 1/1:0,63:66:99:2012,162,0 1/1:0,56:57:99:1625,132,0 0/0:46,1:49:99:0,105,1304 1/1:1,51:53:98:1544,98,0 0/0:44,2:47:73.67:0,74,1345 1/1:2,49:51:72.61:1420,73,0 0/1:20,24:44:99:718,0,466 0/0:29,0:30:72.23:0,72,924 0/1:27,18:45:99:442,0,727 0/1:22,24:49:99:651,0,573 0/0:33,0:35:90.27:0,90,1125 -chr1 1118244 . C T 1034.91 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.695;DP=2048;Dels=0.00;FS=2.342;HRun=0;HaplotypeScore=1.2560;InbreedingCoeff=-0.0165;MQ=57.74;MQ0=0;MQRankSum=0.426;QD=10.78;ReadPosRankSum=-0.861;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|6),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|10),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|10),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|3),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:6.02:0,6,71 0/0:3,0:3:3.01:0,3,39 0/0:3,0:4:9.03:0,9,105 0/0:5,0:5:6.02:0,6,78 0/0:9,0:9:21.06:0,21,270 0/0:15,0:15:39.12:0,39,502 0/0:20,0:20:57.19:0,57,760 0/0:10,0:10:30.10:0,30,391 0/0:28,0:28:66.17:0,66,839 0/0:22,0:22:60.19:0,60,780 0/0:10,0:10:30.10:0,30,398 0/0:5,0:5:12.04:0,12,162 0/0:8,0:8:24.07:0,24,297 0/0:17,0:17:36.11:0,36,462 0/0:25,0:25:51.15:0,51,677 0/0:8,0:8:18.04:0,18,211 0/0:10,0:10:30.08:0,30,367 0/0:18,0:18:45.14:0,45,591 0/0:13,0:13:39.12:0,39,497 0/0:17,0:17:42.14:0,42,561 0/0:18,0:18:42.13:0,42,529 0/0:16,0:16:39.12:0,39,504 0/0:21,0:21:48.12:0,48,604 0/0:11,0:11:27.09:0,27,351 0/0:13,0:13:30.09:0,30,378 0/0:19,0:19:39.08:0,39,456 0/0:11,0:11:30.08:0,30,358 0/0:11,0:12:27.09:0,27,354 0/0:23,0:23:51.13:0,51,637 0/0:10,0:10:24.08:0,24,314 0/0:17,0:17:42.12:0,42,532 0/0:16,0:16:39.12:0,39,505 0/0:12,0:12:21.06:0,21,259 0/0:20,0:20:51.16:0,51,672 0/0:14,0:14:33.11:0,33,435 0/0:22,0:22:48.14:0,48,620 0/0:13,0:13:33.08:0,33,392 0/0:19,0:19:39.11:0,39,484 0/0:56,0:56:99:0,138,1788 0/0:84,0:85:99:0,217,2736 0/0:63,0:63:99:0,150,1906 0/0:72,0:72:99:0,168,2114 0/0:48,0:48:99:0,114,1484 0/0:49,0:49:99:0,114,1464 0/0:50,0:50:99:0,114,1469 0/0:65,0:66:99:0,153,1967 0/0:108,0:110:99:0,265,3263 0/0:41,0:41:99:0,105,1362 0/0:83,0:84:99:0,196,2490 0/0:100,0:101:99:0,235,2908 0/1:52,44:96:99:1083,0,1333 0/0:75,0:76:99:0,159,1986 0/0:83,0:83:99:0,190,2400 0/0:70,0:70:99:0,165,2023 0/0:67,0:67:99:0,165,2094 0/0:53,0:53:99:0,117,1527 0/0:42,0:42:93.29:0,93,1215 0/0:72,0:72:99:0,168,2168 0/0:66,0:66:99:0,160,2125 0/0:61,0:61:99:0,132,1747 -chr1 1118275 . C T 6047.77 . AC=9;AF=0.0750;AN=120;BaseQRankSum=-1.144;DP=2721;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.3228;InbreedingCoeff=-0.0826;MQ=57.77;MQ0=0;MQRankSum=4.599;QD=12.68;ReadPosRankSum=1.658;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),EXON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|4),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C239|404|TTLL10|protein_coding|CODING|ENST00000379288|),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C312|673|TTLL10|protein_coding|CODING|ENST00000379289|),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C312|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,synonymous_variant|tgC/tgT|C|ENSG00000162571|TTLL10|ENST00000379289|11/16|||312/673|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|4/5||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,synonymous_variant|tgC/tgT|C|ENSG00000162571|TTLL10|ENST00000379290|11/16|||312/673|protein_coding|1,synonymous_variant|tgC/tgT|C|ENSG00000162571|TTLL10|ENST00000379288|7/9|||239/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.03:0,12,140 0/0:7,0:7:18.05:0,18,220 0/0:10,0:10:30.09:0,30,376 0/0:5,0:5:12.03:0,12,141 0/0:16,0:16:45.13:0,45,581 0/0:11,0:11:33.11:0,33,435 0/0:26,0:26:78.25:0,78,1038 0/0:18,0:18:48.16:0,48,638 0/0:26,0:26:78.26:0,78,1058 0/0:26,0:26:78.23:0,78,987 0/0:9,0:9:27.09:0,27,364 0/0:15,0:15:45.15:0,45,598 0/0:14,0:14:42.14:0,42,555 0/0:17,0:17:36.12:0,36,503 0/1:20,11:31:99:255,0,619 0/0:7,0:7:18.06:0,18,238 0/0:14,0:14:42.13:0,42,549 0/0:29,0:29:66.22:0,66,904 0/0:22,0:22:60.18:0,60,806 0/1:13,8:21:99:199,0,386 0/0:21,0:21:51.16:0,51,679 0/0:20,0:20:51.17:0,51,703 0/0:34,0:34:84.27:0,84,1113 0/1:12,7:19:99:159,0,388 0/0:15,0:15:36.12:0,36,492 0/0:33,0:33:81.25:0,81,1073 0/1:3,12:15:83.56:395,0,84 0/0:21,0:21:54.16:0,54,691 0/0:24,0:24:60.19:0,60,800 0/0:18,0:18:45.15:0,45,604 0/0:35,0:35:87.28:0,87,1169 0/0:19,0:19:51.17:0,51,680 0/0:12,0:12:24.08:0,24,324 0/0:28,0:28:66.22:0,66,915 0/0:26,0:26:60.20:0,60,829 0/1:16,15:31:99:473,0,387 0/0:19,0:19:45.15:0,45,613 0/0:29,0:29:75.24:0,75,985 0/0:70,0:70:99:0,178,2320 0/0:134,0:134:99:0,343,4428 0/0:87,0:87:99:0,229,2955 0/0:92,0:92:99:0,235,3075 0/0:72,0:72:99:0,181,2380 0/0:68,0:68:99:0,184,2412 0/1:30,25:56:99:694,0,982 0/0:83,0:83:99:0,214,2776 0/0:147,0:148:99:0,385,4951 0/1:27,29:56:99:858,0,838 0/0:96,0:97:99:0,244,3203 0/1:74,51:127:99:1349,0,2263 0/1:67,54:121:99:1667,0,1975 0/0:88,0:89:99:0,238,3077 0/0:103,0:103:99:0,277,3550 0/0:94,1:95:99:0,229,2986 0/0:89,0:89:99:0,226,2918 0/0:71,0:71:99:0,187,2467 0/0:61,0:61:99:0,150,2000 0/0:91,0:91:99:0,226,2958 0/0:96,0:96:99:0,241,3195 0/0:68,0:68:99:0,172,2286 -chr1 1118491 . A G 315.28 . AC=4;AF=0.0339;AN=118;BaseQRankSum=-1.758;DP=1080;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=1.0651;InbreedingCoeff=-0.0464;MQ=56.58;MQ0=0;MQRankSum=0.706;QD=10.87;ReadPosRankSum=0.829;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|11),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|11),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|4),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:6.02:0,6,73 0/0:4,0:4:12.03:0,12,132 0/0:3,0:3:3.01:0,3,36 0/1:1,3:4:30.11:30,0,31 0/0:7,0:7:9.03:0,9,103 0/0:14,0:14:15.05:0,15,201 0/1:4,2:6:61.75:62,0,144 0/0:13,0:13:30.09:0,30,377 0/0:7,1:8:18.06:0,18,238 0/0:6,0:6:18.05:0,18,225 0/0:3,0:3:9.02:0,9,104 0/0:8,0:8:21.06:0,21,250 0/0:7,0:7:15.02:0,15,177 0/0:10,0:10:27.09:0,27,355 0/0:9,0:9:21.07:0,21,265 0/0:7,0:7:18.06:0,18,231 0/0:7,0:7:15.05:0,15,194 0/0:7,0:7:21.04:0,21,251 0/1:2,5:7:58.32:118,0,58 0/0:4,0:4:9.02:0,9,105 0/0:10,0:10:27.09:0,27,353 0/0:14,0:14:36.12:0,36,474 0/0:6,0:6:15.02:0,15,167 0/0:8,0:8:21.06:0,21,263 0/0:14,1:15:33.10:0,33,428 0/0:11,0:11:27.08:0,27,355 0/0:8,0:8:21.06:0,21,269 0/1:6,6:12:99:198,0,169 0/0:8,1:9:24.06:0,24,289 0/0:13,0:13:39.12:0,39,497 0/0:4,0:4:12.04:0,12,159 0/0:8,0:8:21.07:0,21,274 0/0:12,1:14:33.09:0,33,400 0/0:7,0:7:15.05:0,15,199 0/0:7,0:7:18.06:0,18,235 0/0:9,0:9:18.06:0,18,234 0/0:9,0:9:27.09:0,27,360 0/0:18,0:18:51.16:0,51,646 0/0:54,0:56:99:0,141,1754 0/0:32,0:32:81.25:0,81,1019 0/0:29,1:30:78.24:0,78,980 0/0:24,0:24:66.18:0,66,806 0/0:29,1:30:75.21:0,75,918 0/0:30,0:31:75.22:0,75,925 0/0:33,0:33:90.28:0,90,1150 0/0:58,0:58:99:0,156,1938 0/0:17,1:18:36.11:0,36,468 0/0:26,0:26:63.19:0,63,790 0/0:52,0:52:99:0,141,1796 0/0:52,1:54:99:0,135,1712 0/0:30,0:32:78.21:0,78,936 0/0:44,1:46:99:0,117,1384 0/0:52,0:52:99:0,132,1681 0/0:44,1:45:99:0,108,1332 0/0:35,0:35:93.27:0,93,1189 0/0:21,0:21:48.15:0,48,625 0/0:27,0:27:69.21:0,69,842 0/0:29,0:30:81.20:0,81,969 0/0:25,1:26:69.17:0,69,881 -chr1 1118522 . G A 231.29 . AC=2;AF=0.0169;AN=118;BaseQRankSum=0.115;DP=734;Dels=0.00;FS=22.046;HRun=0;HaplotypeScore=0.5763;InbreedingCoeff=-0.0479;MQ=55.98;MQ0=0;MQRankSum=0.916;QD=10.51;ReadPosRankSum=-2.177;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|11),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|11),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|4),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3:0,3,27 ./. 0/0:3,0:3:9.03:0,9,122 0/0:2,0:2:6.02:0,6,80 0/0:4,0:4:6.02:0,6,79 0/0:4,0:4:9.03:0,9,112 0/0:9,0:9:21.06:0,21,268 0/0:7,0:7:6.02:0,6,75 0/0:6,0:6:9.03:0,9,111 0/0:9,0:9:12.04:0,12,155 0/0:5,0:5:9.03:0,9,122 0/0:4,0:4:6.02:0,6,82 0/0:3,0:3:6.02:0,6,81 0/0:6,0:6:18.06:0,18,227 0/0:7,0:7:18.06:0,18,239 0/0:3,0:3:9.03:0,9,115 0/0:7,0:7:21.07:0,21,275 0/0:2,0:2:3.01:0,3,40 0/0:6,0:6:18.04:0,18,221 0/0:6,0:6:18.06:0,18,227 0/0:2,0:2:6.02:0,6,72 0/0:4,0:4:12.03:0,12,142 0/0:6,0:6:15.05:0,15,198 0/1:2,3:5:29.55:73,0,30 0/0:5,0:5:15.05:0,15,185 0/0:12,0:12:27.08:0,27,339 0/0:8,0:8:24.08:0,24,313 0/0:9,0:9:21.07:0,21,275 0/0:7,0:7:21.07:0,21,282 0/0:6,0:6:15.05:0,15,200 0/0:7,0:7:21.05:0,21,254 0/0:3,0:3:9.03:0,9,120 0/0:4,0:4:9.03:0,9,117 0/0:14,0:14:36.10:0,36,441 0/0:3,0:3:6.02:0,6,73 0/0:3,0:3:6.02:0,6,79 0/0:5,0:5:9.03:0,9,118 0/0:6,0:6:18.06:0,18,249 0/0:10,0:10:24.08:0,24,313 0/0:42,0:42:99:0,99,1273 0/0:22,0:22:60.17:0,60,742 0/0:19,0:19:45.14:0,45,563 0/0:17,0:17:48.15:0,48,620 0/0:31,0:31:84.25:0,84,1066 0/0:19,0:19:51.14:0,51,650 0/0:25,0:25:60.20:0,60,809 0/0:33,0:33:87.28:0,87,1135 0/0:16,1:17:39.12:0,39,498 0/0:18,0:18:48.15:0,48,617 0/0:37,0:37:99:0,99,1297 0/0:37,0:37:99:0,105,1327 0/0:24,0:24:69.21:0,69,862 0/0:26,0:26:66.20:0,66,830 0/0:35,0:35:99:0,102,1318 0/0:26,0:27:72.23:0,72,932 0/1:10,7:17:99:223,0,270 0/0:16,0:16:39.10:0,39,480 0/0:21,0:21:51.15:0,51,636 0/0:19,0:19:57.18:0,57,728 0/0:17,0:17:39.10:0,39,481 -chr1 1118529 . G C 35.12 . AC=5;AF=0.0431;AN=116;BaseQRankSum=-3.621;DP=699;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.6631;InbreedingCoeff=0.1223;MQ=55.74;MQ0=0;MQRankSum=-0.031;QD=1.60;ReadPosRankSum=-2.064;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|11),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|11),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|4),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:2,0:2:6.02:0,6,81 0/0:2,0:2:6.02:0,6,81 0/0:3,1:4:9.02:0,9,104 0/0:5,1:6:9.03:0,9,106 0/0:7,1:8:18.06:0,18,226 1/1:2,5:7:3.01:33,3,0 0/1:3,5:8:24.09:24,0,99 0/0:4,3:7:6.02:0,6,71 0/0:4,1:5:12.04:0,12,151 0/1:1,3:4:18.65:54,0,19 0/1:2,1:3:15.67:16,0,72 0/0:5,0:5:15.04:0,15,185 0/0:6,0:6:15.05:0,15,193 0/0:3,0:3:9.03:0,9,107 0/0:6,0:6:15.05:0,15,192 0/0:2,0:2:6.02:0,6,73 0/0:4,0:4:9.03:0,9,119 0/0:7,0:7:15.05:0,15,197 0/0:3,0:3:6.02:0,6,76 0/0:4,0:4:12.03:0,12,144 0/0:5,0:5:12.04:0,12,157 0/0:5,0:5:9.03:0,9,112 0/0:4,0:4:12.04:0,12,153 0/0:11,0:11:24.06:0,24,282 0/0:9,0:9:24.07:0,24,298 0/0:8,0:8:18.05:0,18,224 0/0:6,0:6:15.05:0,15,202 0/0:7,0:7:18.06:0,18,231 0/0:5,0:5:12.04:0,12,156 0/0:3,0:3:6.01:0,6,63 0/0:4,0:4:9.02:0,9,109 0/0:14,1:15:36.10:0,36,422 0/0:3,0:3:6.01:0,6,64 0/0:4,0:4:9.03:0,9,106 0/0:3,0:3:6.02:0,6,82 0/0:5,0:5:15.05:0,15,200 0/0:10,0:10:21.07:0,21,269 0/0:40,1:41:90.25:0,90,1120 0/0:22,0:22:60.16:0,60,719 0/0:17,0:17:39.06:0,39,443 0/0:14,0:14:39.11:0,39,479 0/0:29,1:30:78.22:0,78,958 0/0:18,0:18:51.15:0,51,636 0/0:24,1:25:60.17:0,60,740 0/0:32,1:34:84.23:0,84,1041 0/0:13,2:15:33.09:0,33,401 0/0:17,1:18:45.12:0,45,545 0/0:36,0:37:99:0,99,1206 0/0:36,0:36:96.29:0,96,1195 0/0:21,3:24:60.18:0,60,746 0/0:25,0:25:66.19:0,66,801 0/0:31,0:31:87.24:0,87,1063 0/0:24,0:24:63.19:0,63,783 0/0:13,0:14:27.08:0,27,340 0/0:16,0:16:39.11:0,39,490 0/0:17,1:18:39.12:0,39,488 0/0:18,0:18:48.15:0,48,593 0/0:15,1:16:36.10:0,36,439 -chr1 1118560 . C T 120.5 . AC=4;AF=0.0339;AN=118;BaseQRankSum=0.441;DP=502;Dels=0.00;FS=2.806;HRun=0;HaplotypeScore=0.5435;InbreedingCoeff=0.0953;MQ=53.92;MQ0=0;MQRankSum=2.564;QD=9.27;ReadPosRankSum=-0.278;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|11),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|11),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|4),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:9.02:0,9,103 0/0:3,0:3:3.01:0,3,39 ./. 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,31 0/0:3,0:3:9.03:0,9,114 0/0:3,0:4:6.02:0,6,75 0/1:3,1:5:24.42:24,0,56 0/0:9,0:9:18.06:0,18,235 0/0:15,0:15:27.06:0,27,302 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,41 0/0:5,0:5:12.03:0,12,138 0/0:7,0:7:18.05:0,18,222 0/0:4,0:4:9.03:0,9,127 0/0:2,0:2:6.02:0,6,71 0/0:3,0:3:9.03:0,9,111 0/0:2,0:2:6.02:0,6,80 0/0:2,0:2:3.01:0,3,33 0/1:3,3:6:97.22:99,0,97 0/0:1,0:2:3.01:0,3,33 0/0:5,0:5:12.03:0,12,144 0/0:2,0:2:6.02:0,6,74 0/0:4,0:4:12.04:0,12,153 0/0:4,0:4:9.03:0,9,125 0/0:7,0:7:21.07:0,21,272 0/0:9,0:9:21.07:0,21,277 0/0:5,0:5:12.03:0,12,142 1/1:0,2:2:6.02:80,6,0 0/0:3,0:3:6.02:0,6,76 0/0:6,0:6:12.04:0,12,152 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:6.02:0,6,71 0/0:12,0:12:36.11:0,36,444 0/0:4,0:4:6.02:0,6,70 0/0:2,0:2:6.02:0,6,76 0/0:1,0:1:3.01:0,3,36 0/0:2,0:2:3.01:0,3,45 0/0:10,0:10:24.06:0,24,286 0/0:32,0:32:78.22:0,78,964 0/0:16,0:16:39.13:0,39,517 0/0:19,0:19:45.13:0,45,562 0/0:12,0:12:27.09:0,27,343 0/0:16,0:16:42.12:0,42,509 0/0:9,0:9:24.06:0,24,294 0/0:16,0:16:36.10:0,36,429 0/0:18,0:18:51.16:0,51,646 0/0:12,0:13:33.09:0,33,392 0/0:9,0:9:27.09:0,27,347 0/0:24,0:24:63.19:0,63,759 0/0:23,0:23:60.18:0,60,752 0/0:16,0:16:45.14:0,45,562 0/0:19,0:19:45.09:0,45,516 0/0:19,0:19:51.16:0,51,645 0/0:22,0:22:63.17:0,63,758 0/0:8,0:8:21.06:0,21,260 0/0:14,0:14:36.11:0,36,476 0/0:14,0:16:36.11:0,36,436 0/0:9,0:9:27.08:0,27,321 0/0:9,0:9:24.07:0,24,305 -chr1 1118578 . G A 921.34 . AC=9;AF=0.0804;AN=112;BaseQRankSum=-0.517;DP=400;Dels=0.00;FS=2.546;HRun=1;HaplotypeScore=0.3066;InbreedingCoeff=-0.0266;MQ=53.56;MQ0=0;MQRankSum=0.375;QD=14.86;ReadPosRankSum=2.525;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|11),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|11),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|4),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.01:0,9,97 0/0:4,0:4:12.03:0,12,140 0/0:2,0:2:6.02:0,6,80 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:6.02:0,6,73 0/0:3,0:3:6.02:0,6,82 0/0:7,0:7:21.07:0,21,278 0/0:12,0:12:36.11:0,36,442 ./. ./. 0/0:4,0:4:12.03:0,12,135 0/0:5,0:5:15.05:0,15,185 1/1:0,1:1:3.01:40,3,0 ./. 0/0:2,0:2:6.02:0,6,75 0/0:2,0:2:6.02:0,6,79 ./. 0/1:3,2:5:64.17:64,0,102 0/0:2,0:2:3.01:0,3,39 0/0:3,0:3:9.03:0,9,114 0/0:2,0:2:6.02:0,6,81 0/1:1,1:2:32.56:35,0,33 0/0:3,0:3:6.02:0,6,87 0/0:5,0:5:15.04:0,15,191 0/1:4,3:7:74.46:103,0,74 0/0:3,0:3:6.02:0,6,75 0/0:2,0:2:6.02:0,6,82 0/0:3,0:3:9.03:0,9,120 0/0:6,0:6:12.04:0,12,160 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.01:0,6,64 0/0:10,0:10:30.09:0,30,376 0/0:4,0:4:12.04:0,12,139 0/1:1,1:2:33.99:36,0,34 0/0:1,0:1:3.01:0,3,34 0/0:2,0:2:3.01:0,3,45 0/0:8,0:8:21.06:0,21,258 0/0:26,0:26:69.21:0,69,851 0/0:15,0:15:42.14:0,42,561 0/0:14,0:14:36.11:0,36,468 0/0:9,0:9:24.07:0,24,298 0/0:13,0:13:33.10:0,33,417 0/0:5,0:5:12.04:0,12,149 0/0:16,0:16:42.13:0,42,526 0/0:12,0:12:36.11:0,36,469 0/1:5,5:12:99:158,0,155 0/0:8,0:8:24.08:0,24,306 0/1:4,11:15:99:301,0,109 0/1:8,10:18:99:315,0,199 0/0:18,0:18:48.15:0,48,595 0/0:14,0:15:39.11:0,39,472 0/0:13,0:13:36.12:0,36,476 0/0:15,0:15:42.13:0,42,535 0/0:10,0:10:24.07:0,24,301 0/0:11,0:11:27.08:0,27,356 0/0:13,0:13:33.10:0,33,427 0/0:6,0:6:18.06:0,18,225 0/0:8,0:8:21.07:0,21,273 -chr1 1119080 . T C 90.74 . AC=1;AF=0.0086;AN=116;BaseQRankSum=0.742;DP=369;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.3252;InbreedingCoeff=-0.0596;MQ=58.29;MQ0=0;MQRankSum=0.380;QD=12.96;ReadPosRankSum=-0.100;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|7),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|11),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|11),INTRON(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|4),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:3.01:0,3,37 0/0:3,0:3:9.02:0,9,109 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:6.02:0,6,78 0/0:5,0:5:15.05:0,15,195 ./. 0/0:3,0:3:9.03:0,9,124 0/0:4,0:4:12.04:0,12,164 0/0:4,0:4:12.04:0,12,165 0/0:7,0:7:21.07:0,21,270 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:12.04:0,12,150 0/0:2,0:2:6.02:0,6,81 0/0:9,0:9:24.08:0,24,330 0/0:10,0:10:27.09:0,27,355 0/0:7,0:7:21.06:0,21,261 0/1:3,4:7:94.28:138,0,94 0/0:10,0:10:27.09:0,27,367 0/0:11,0:11:30.09:0,30,390 0/0:11,0:11:30.10:0,30,397 0/0:9,0:9:27.09:0,27,355 0/0:15,0:15:42.13:0,42,551 0/0:12,0:12:33.11:0,33,438 0/0:6,0:6:15.05:0,15,204 0/0:13,0:13:39.11:0,39,493 0/0:16,0:16:42.14:0,42,581 0/0:7,0:7:18.03:0,18,215 0/0:8,0:8:24.08:0,24,314 0/0:13,0:13:36.12:0,36,472 0/0:6,0:6:15.05:0,15,194 0/0:14,0:14:39.10:0,39,503 0/0:11,0:11:24.08:0,24,313 0/0:9,0:9:27.09:0,27,368 0/0:14,0:14:42.13:0,42,537 0/0:9,0:9:21.06:0,21,267 0/0:12,0:12:36.12:0,36,481 0/0:10,0:10:30.10:0,30,396 0/0:16,0:16:48.16:0,48,635 0/0:1,0:1:3.01:0,3,42 0/0:3,0:3:3.01:0,3,42 0/0:7,0:7:21.07:0,21,280 0/0:2,0:2:6.02:0,6,81 0/0:5,0:5:15.05:0,15,196 0/0:2,0:2:6.02:0,6,82 0/0:3,0:3:9.03:0,9,127 0/0:3,0:3:9.03:0,9,113 0/0:5,0:5:6.02:0,6,76 0/0:2,0:2:6.02:0,6,76 0/0:3,0:3:9.02:0,9,100 0/0:5,0:5:15.05:0,15,193 0/0:3,0:3:6.02:0,6,85 0/0:2,0:2:6.02:0,6,78 0/0:5,0:5:15.05:0,15,199 0/0:6,0:6:15.04:0,15,180 0/0:2,0:2:6.02:0,6,78 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.02:0,6,81 ./. 0/0:1,0:1:3.01:0,3,35 -chr1 1119399 . C T 1267.07 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.885;DP=8859;DS;Dels=0.00;FS=6.806;HRun=0;HaplotypeScore=4.5609;InbreedingCoeff=-0.0084;MQ=59.04;MQ0=0;MQRankSum=-1.312;QD=11.73;ReadPosRankSum=1.342;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H323|404|TTLL10|protein_coding|CODING|ENST00000379288|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H396|673|TTLL10|protein_coding|CODING|ENST00000379289|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H396|673|TTLL10|protein_coding|CODING|ENST00000379290|),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,synonymous_variant|caC/caT|H|ENSG00000162571|TTLL10|ENST00000379289|12/16|||396/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,synonymous_variant|caC/caT|H|ENSG00000162571|TTLL10|ENST00000379290|12/16|||396/673|protein_coding|1,synonymous_variant|caC/caT|H|ENSG00000162571|TTLL10|ENST00000379288|8/9|||323/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:19,0:20:54.16:0,54,661 0/0:14,0:14:33.11:0,33,426 0/0:23,0:23:66.19:0,66,828 0/0:17,0:17:48.13:0,48,586 0/0:41,0:41:99:0,120,1614 0/0:28,0:28:84.27:0,84,1117 0/0:38,0:38:99:0,114,1521 0/0:26,0:26:78.25:0,78,1043 0/0:75,0:75:99:0,223,2975 0/0:76,0:76:99:0,229,3015 0/0:34,0:34:99:0,99,1323 0/0:33,0:34:99:0,99,1297 0/0:39,0:39:99:0,114,1515 0/0:225,0:225:99:0,587,7644 0/0:228,0:228:99:0,593,7643 0/0:223,0:223:99:0,539,7054 0/0:226,0:227:99:0,569,7392 0/0:215,1:216:99:0,545,7005 0/0:227,0:227:99:0,572,7484 0/0:221,0:221:99:0,572,7366 0/0:221,0:221:99:0,551,7179 0/0:229,1:230:99:0,571,7764 0/0:213,0:215:99:0,521,6772 0/0:185,2:187:99:0,455,6461 0/0:223,0:223:99:0,557,7267 0/0:203,0:203:99:0,515,6728 0/0:208,0:208:99:0,536,6929 0/0:234,0:234:99:0,581,7675 0/0:206,0:206:99:0,542,6965 0/0:237,0:238:99:0,563,7302 0/0:244,0:245:99:0,647,8292 0/0:219,0:219:99:0,545,7171 0/0:197,0:197:99:0,509,6570 0/0:196,0:196:99:0,533,6850 0/0:212,0:213:99:0,530,6931 0/0:216,0:216:99:0,533,6955 0/0:221,0:221:99:0,539,7024 0/0:250,0:250:99:0,635,8412 0/0:89,0:89:99:0,205,2671 0/0:202,0:202:99:0,488,6461 0/0:145,0:145:99:0,325,4275 0/0:127,0:127:99:0,304,4011 0/0:122,0:122:99:0,268,3532 0/0:96,0:96:99:0,223,2946 0/1:59,49:108:99:1315,0,1742 0/0:118,0:118:99:0,289,3799 0/0:218,0:218:99:0,500,6527 0/0:60,0:60:99:0,141,1825 0/0:150,0:151:99:0,337,4509 0/0:205,1:206:99:0,450,6341 0/0:173,1:174:99:0,398,5557 0/0:153,0:153:99:0,367,4778 0/0:176,0:176:99:0,391,5208 0/0:134,0:134:99:0,328,4289 0/0:113,0:113:99:0,259,3435 0/0:110,0:110:99:0,259,3400 0/0:77,0:77:99:0,178,2336 0/0:116,0:116:99:0,262,3500 0/0:114,1:115:99:0,232,3529 0/0:94,0:94:99:0,217,2818 -chr1 1119543 . G C 392.87 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.504;DP=2292;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.8936;InbreedingCoeff=-0.0096;MQ=59.06;MQ0=0;MQRankSum=0.601;QD=13.55;ReadPosRankSum=-1.427;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12.04:0,12,159 0/0:5,0:5:12.04:0,12,151 0/0:6,0:6:18.06:0,18,240 0/0:18,0:18:51.15:0,51,645 0/0:21,0:21:60.20:0,60,812 0/0:12,0:12:36.12:0,36,487 0/1:15,14:29:99:441,0,511 0/0:17,0:17:51.17:0,51,692 0/0:33,0:33:99:0,99,1352 0/0:37,0:37:99:0,111,1466 0/0:18,0:18:51.16:0,51,668 0/0:21,0:21:63.20:0,63,835 0/0:23,0:23:66.21:0,66,873 0/0:65,0:65:99:0,178,2342 0/0:74,1:75:99:0,220,2827 0/0:37,0:37:99:0,102,1347 0/0:71,1:72:99:0,199,2570 0/0:51,0:51:99:0,153,2029 0/0:64,0:65:99:0,181,2375 0/0:61,0:61:99:0,175,2285 0/0:67,0:67:99:0,199,2608 0/0:91,0:91:99:0,262,3430 0/0:55,0:56:99:0,153,2028 0/0:71,0:71:99:0,205,2650 0/0:55,0:55:99:0,160,2125 0/0:61,0:61:99:0,169,2215 0/0:49,0:49:99:0,141,1837 0/0:42,0:42:99:0,123,1632 0/0:63,0:63:99:0,190,2408 0/0:70,0:70:99:0,202,2636 0/0:73,0:74:99:0,211,2733 0/0:62,0:62:99:0,184,2388 0/0:72,0:72:99:0,199,2593 0/0:80,0:80:99:0,217,2836 0/0:41,0:41:99:0,120,1538 0/0:51,0:51:99:0,144,1906 0/0:65,0:65:99:0,184,2376 0/0:73,0:73:99:0,211,2810 0/0:20,0:20:57.17:0,57,733 0/0:37,0:38:99:0,102,1357 0/0:30,0:30:84.25:0,84,1107 0/0:19,0:19:54.17:0,54,696 0/0:18,0:18:48.16:0,48,638 0/0:15,0:15:39.13:0,39,529 0/0:15,0:15:45.13:0,45,549 0/0:20,0:20:60.19:0,60,757 0/0:42,0:42:99:0,117,1533 0/0:9,0:9:21.06:0,21,255 0/0:18,0:18:54.18:0,54,721 0/0:31,0:31:84.25:0,84,1087 0/0:24,0:24:69.22:0,69,901 0/0:20,0:20:54.17:0,54,703 0/0:30,0:30:75.23:0,75,977 0/0:27,0:27:72.23:0,72,961 0/0:22,0:22:57.18:0,57,750 0/0:17,0:17:48.14:0,48,628 0/0:21,0:21:60.19:0,60,800 0/0:12,0:12:33.11:0,33,446 0/0:19,0:19:48.14:0,48,616 0/0:11,0:11:30.10:0,30,402 -chr1 1119546 . G T 1327.72 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.808;DP=2166;Dels=0.00;FS=1.426;HRun=1;HaplotypeScore=1.8266;InbreedingCoeff=-0.0272;MQ=59.08;MQ0=0;MQRankSum=-0.008;QD=14.59;ReadPosRankSum=-1.147;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12.04:0,12,158 0/0:5,1:6:12.04:0,12,154 0/0:6,0:6:18.06:0,18,238 0/0:17,0:17:48.15:0,48,612 0/1:7,13:20:99:409,0,230 0/0:13,0:13:39.13:0,39,524 0/0:26,0:26:75.24:0,75,997 0/1:6,7:13:99:241,0,206 0/0:31,0:31:93.30:0,93,1256 0/0:34,0:34:99:0,99,1319 0/0:16,0:16:45.14:0,45,585 0/0:21,0:21:57.19:0,57,764 0/0:23,0:23:66.22:0,66,880 0/0:60,0:60:99:0,163,2152 0/0:67,0:67:99:0,196,2534 0/0:33,0:33:87.28:0,87,1153 0/0:68,1:69:99:0,193,2480 0/0:48,0:48:99:0,144,1906 0/0:66,0:66:99:0,190,2487 0/0:57,0:57:99:0,163,2154 0/0:65,0:65:99:0,187,2465 0/0:88,0:88:99:0,253,3320 0/0:56,0:56:99:0,157,2058 0/0:63,0:63:99:0,184,2331 0/0:50,2:52:70.66:0,71,1829 0/0:56,0:56:99:0,156,2043 0/0:42,1:43:85.60:0,86,1550 0/0:40,0:40:99:0,117,1566 0/1:34,24:58:99:758,0,1140 0/0:66,0:66:99:0,190,2452 0/0:71,0:71:99:0,202,2648 0/0:57,0:57:99:0,169,2192 0/0:70,0:70:99:0,190,2485 0/0:79,0:79:99:0,214,2809 0/0:37,0:37:99:0,108,1401 0/0:49,0:49:99:0,138,1836 0/0:59,0:59:99:0,168,2176 0/0:67,0:67:99:0,199,2643 0/0:19,0:19:54.17:0,54,704 0/0:37,0:37:99:0,105,1377 0/0:29,0:29:78.24:0,78,1034 0/0:18,0:18:54.17:0,54,693 0/0:17,0:17:48.14:0,48,627 0/0:15,0:15:36.12:0,36,487 0/0:15,0:15:45.14:0,45,570 0/0:17,1:18:29.47:0,29,607 0/0:41,0:41:99:0,114,1522 0/0:9,0:9:21.06:0,21,264 0/0:17,0:17:51.16:0,51,678 0/0:31,0:31:81.26:0,81,1064 0/0:24,0:24:69.21:0,69,887 0/0:19,0:19:54.17:0,54,702 0/0:30,0:30:75.23:0,75,966 0/0:24,0:24:63.21:0,63,848 0/0:20,0:20:48.16:0,48,637 0/0:16,0:16:48.13:0,48,605 0/0:19,1:20:14.96:0,15,684 0/0:11,0:12:33.11:0,33,437 0/0:17,0:17:42.14:0,42,556 0/0:11,0:11:33.10:0,33,425 -chr1 1119657 . G C 5454.82 . AC=49;AF=0.4375;AN=112;BaseQRankSum=3.181;DP=432;Dels=0.00;FS=3.269;HRun=3;HaplotypeScore=0.4863;InbreedingCoeff=0.1117;MQ=58.71;MQ0=0;MQRankSum=1.349;QD=20.58;ReadPosRankSum=-0.252;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:6.02:0,6,78 0/0:2,0:2:6.02:0,6,79 0/1:1,2:3:29.55:60,0,30 0/1:4,3:7:99:103,0,133 0/1:2,1:3:31.62:32,0,72 0/1:3,2:5:65.50:65,0,108 1/1:0,6:6:18.06:247,18,0 0/0:11,0:11:33.09:0,33,420 0/0:13,0:14:36.10:0,36,441 ./. 1/1:0,1:1:3.01:40,3,0 0/1:1,2:3:18.64:69,0,19 1/1:0,10:10:30.10:397,30,0 0/0:10,0:10:30.10:0,30,388 0/1:1,5:6:21.95:173,0,22 0/0:17,0:18:42.12:0,42,510 0/1:5,8:13:99:278,0,149 0/0:12,0:12:30.09:0,30,390 0/1:2,10:12:48.13:315,0,48 0/0:15,0:15:45.12:0,45,564 0/0:17,0:17:48.16:0,48,638 0/1:9,5:14:99:121,0,305 0/1:6,4:10:99:136,0,195 0/0:9,0:9:27.09:0,27,358 0/0:12,0:12:33.11:0,33,438 0/1:1,7:8:14.50:238,0,15 0/1:7,1:8:18.16:18,0,225 0/1:4,4:8:99:143,0,140 0/1:14,5:19:99:110,0,401 0/1:9,6:15:99:191,0,206 0/1:7,4:11:99:125,0,214 0/1:13,4:17:99:108,0,410 1/1:0,10:10:30.10:408,30,0 1/1:0,13:13:30.10:395,30,0 1/1:0,8:8:21.05:270,21,0 0/1:4,5:9:99:163,0,113 0/0:15,0:15:42.13:0,42,544 ./. 0/1:3,4:7:88.57:141,0,89 0/1:6,1:7:21.16:21,0,214 0/0:3,0:3:9.02:0,9,105 0/0:3,0:3:6.02:0,6,74 ./. 1/1:0,1:1:3.01:40,3,0 0/0:3,0:3:9.03:0,9,117 0/0:10,0:10:30.10:0,30,393 1/1:0,2:2:6.02:77,6,0 1/1:0,1:1:3.01:41,3,0 1/1:0,7:7:15.05:204,15,0 1/1:0,6:6:18.06:237,18,0 0/0:2,1:3:6.02:0,6,81 1/1:0,4:4:12.04:152,12,0 0/0:2,0:2:6.02:0,6,78 1/1:0,3:3:9.03:113,9,0 0/1:1,4:5:23.53:141,0,24 0/0:2,0:2:6.02:0,6,80 0/0:1,0:1:3.01:0,3,42 1/1:0,2:2:6.02:84,6,0 0/0:2,0:2:6.02:0,6,76 -chr1 1119796 . C T 91.64 . AC=5;AF=0.078;AN=64;BaseQRankSum=-0.197;DP=63;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.1159;InbreedingCoeff=-0.0863;MQ=58.22;MQ0=0;MQRankSum=0.250;QD=9.16;ReadPosRankSum=-0.408;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:6.01:0,6,61 0/0:4,0:4:12.03:0,12,147 0/0:2,0:2:6.02:0,6,79 ./. 0/1:1,2:3:32.20:72,0,32 ./. ./. 0/1:3,1:4:26.54:27,0,109 0/0:1,0:1:3.01:0,3,41 0/0:6,0:6:15.05:0,15,204 ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:3,0:3:6.02:0,6,84 0/0:3,0:3:9.03:0,9,113 ./. ./. ./. 0/1:1,1:2:32.56:33,0,33 0/0:2,0:2:6.02:0,6,71 ./. 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,70 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,79 1/1:0,1:1:3.01:39,3,0 0/0:4,0:4:9.03:0,9,120 0/0:1,0:1:3.01:0,3,38 0/0:2,0:2:6.02:0,6,70 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,74 0/0:1,0:1:3.01:0,3,37 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,31 ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,75 ./. ./. 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. -chr1 1119858 . C T 125.02 . AC=7;AF=0.130;AN=54;BaseQRankSum=-0.015;DP=50;Dels=0.00;FS=4.112;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=0.0152;MQ=56.27;MQ0=0;MQRankSum=0.412;QD=13.89;ReadPosRankSum=1.205;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12),UPSTREAM(MODIFIER|||||TTLL10-AS1|antisense|NON_CODING|ENST00000379317|);CSQ=upstream_gene_variant|||ENSG00000205231|TTLL10-AS1|ENST00000379317|||||antisense|1,upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.05:0,15,185 0/0:7,0:7:18.04:0,18,213 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,37 0/0:2,0:2:6.02:0,6,79 ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,82 1/1:0,2:2:6.02:82,6,0 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:1,0:1:3.01:0,3,41 0/1:1,1:2:18.68:19,0,36 ./. ./. 0/0:2,0:2:3.01:0,3,45 0/1:1,1:2:35.74:36,0,36 0/0:2,0:2:6.02:0,6,83 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,40 ./. 0/0:3,0:3:9.03:0,9,124 ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.01:0,6,63 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,40 ./. ./. 0/1:1,1:2:33.99:34,0,34 ./. 0/0:2,0:2:6.02:0,6,72 ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. ./. -chr1 1120091 . G A 172.79 . AC=11;AF=0.145;AN=76;BaseQRankSum=0.184;DP=127;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1032;InbreedingCoeff=0.0586;MQ=42.08;MQ0=0;MQRankSum=-1.381;QD=4.80;ReadPosRankSum=1.301;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12);CSQ=upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:2.98:0,3,22 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/0:2,0:2:3.01:0,3,42 1/1:0,1:1:3:25,3,0 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/1:2,1:3:29.55:30,0,60 0/0:2,0:2:6.02:0,6,70 0/0:3,0:3:9.01:0,9,94 0/0:3,0:3:6.02:0,6,67 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. 0/0:3,0:3:9.03:0,9,111 0/0:1,0:1:3.01:0,3,33 0/0:2,1:3:3.01:0,3,39 0/0:2,0:2:6.02:0,6,72 1/1:0,1:1:3.01:39,3,0 0/0:3,0:3:9.01:0,9,99 0/0:2,0:2:6.02:0,6,72 0/0:4,0:4:12.03:0,12,144 0/1:11,1:12:3.36:3,0,284 0/0:9,0:9:24.07:0,24,302 0/0:4,0:4:6.02:0,6,70 0/0:6,0:6:15.05:0,15,187 ./. 1/1:1,1:2:3.01:42,3,0 0/0:3,0:3:6.02:0,6,72 0/0:4,0:4:12.02:0,12,123 0/0:2,0:2:3.01:0,3,45 ./. 0/1:3,3:7:21.41:21,0,87 0/1:4,2:6:56.97:57,0,89 0/0:5,0:5:12.01:0,12,131 0/0:1,0:1:3.01:0,3,32 0/0:4,0:4:12.04:0,12,150 0/0:1,0:1:3.01:0,3,33 0/1:1,2:4:15.67:67,0,16 0/0:2,0:2:6.02:0,6,84 0/0:4,0:4:9.03:0,9,115 0/0:2,0:3:6:0,6,60 0/0:3,0:3:6.02:0,6,79 -chr1 1120307 . G A 5288.32 . AC=23;AF=0.235;AN=98;BaseQRankSum=-0.512;DP=784;Dels=0.00;FS=3.693;HRun=0;HaplotypeScore=0.5879;InbreedingCoeff=0.2421;MQ=53.35;MQ0=0;MQRankSum=3.646;QD=18.62;ReadPosRankSum=1.917;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12);CSQ=upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,34 ./. 0/0:2,0:2:6.01:0,6,64 1/1:0,14:14:42.14:566,42,0 1/1:0,19:19:51.14:647,51,0 0/0:11,0:11:33.09:0,33,426 0/0:23,0:23:66.20:0,66,839 0/0:24,0:24:63.21:0,63,847 0/0:15,0:15:42.13:0,42,544 0/0:14,0:14:42.14:0,42,564 0/0:15,0:15:42.13:0,42,560 0/0:21,0:21:60.19:0,60,788 0/1:8,3:11:90.70:91,0,223 0/0:18,0:18:48.14:0,48,631 0/0:14,0:14:36.11:0,36,455 0/0:17,0:17:48.15:0,48,609 0/1:11,14:25:99:423,0,355 0/1:8,6:14:99:170,0,271 0/0:29,0:29:84.25:0,84,1086 0/1:5,8:13:99:248,0,172 0/1:26,10:36:99:252,0,850 0/1:3,7:10:87.16:211,0,87 0/0:17,0:17:51.13:0,51,636 0/0:17,0:17:48.15:0,48,626 1/1:0,17:17:48.13:611,48,0 0/1:7,6:13:99:157,0,239 0/1:6,12:18:99:425,0,142 0/0:18,0:18:54.18:0,54,727 0/0:8,0:8:24.05:0,24,277 0/1:12,9:21:99:265,0,330 0/1:12,6:18:99:141,0,358 0/0:8,0:8:24.08:0,24,311 0/0:16,0:16:48.15:0,48,614 0/1:4,4:8:99:117,0,126 0/1:11,3:14:72.99:73,0,315 0/0:27,0:28:78.24:0,78,993 0/0:28,0:28:75.24:0,75,983 0/0:11,0:11:30.10:0,30,400 0/0:18,0:18:48.15:0,48,630 0/0:19,0:19:45.14:0,45,590 0/0:19,0:19:45.14:0,45,582 0/0:23,2:25:21.60:0,22,691 1/1:0,12:12:36.09:433,36,0 0/0:16,0:16:42.13:0,42,565 0/0:11,0:12:30.09:0,30,383 0/0:16,0:16:42.13:0,42,538 0/0:8,0:8:21.07:0,21,274 0/1:6,5:11:99:115,0,143 1/1:0,10:10:27.09:345,27,0 0/0:12,0:12:36.11:0,36,463 -chr1 1120337 . G A 33.77 . AC=2;AF=0.0167;AN=120;BaseQRankSum=0.146;DP=1640;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.8805;InbreedingCoeff=-0.0159;MQ=54.17;MQ0=0;MQRankSum=2.540;QD=0.70;ReadPosRankSum=2.633;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12);CSQ=upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.05:0,15,195 0/0:10,0:10:27.08:0,27,335 0/0:5,0:5:15.05:0,15,200 0/0:5,0:5:15.05:0,15,195 0/0:16,0:16:48.16:0,48,637 0/0:19,0:19:54.16:0,54,687 0/0:27,0:27:81.27:0,81,1093 0/0:12,0:12:33.11:0,33,442 0/0:44,0:44:99:0,132,1753 0/0:28,0:28:84.27:0,84,1109 0/0:22,0:22:66.22:0,66,890 0/0:11,0:11:33.11:0,33,447 0/0:20,0:20:57.17:0,57,729 0/0:25,0:25:69.22:0,69,880 0/0:35,0:35:93.27:0,93,1210 0/0:19,0:19:48.15:0,48,624 0/0:34,0:34:96.31:0,96,1264 0/0:37,0:37:99:0,105,1364 0/1:25,5:30:81.26:81,0,795 0/0:33,0:33:93.30:0,93,1229 0/0:35,0:35:87.28:0,87,1129 0/0:37,1:38:64.10:0,64,1286 0/0:22,0:23:63.20:0,63,824 0/0:30,0:30:75.24:0,75,991 0/0:26,0:26:69.21:0,69,886 0/0:30,0:30:78.25:0,78,1037 0/0:44,0:44:99:0,120,1586 0/0:20,0:20:51.17:0,51,688 0/0:39,0:39:99:0,99,1280 0/0:21,0:21:60.19:0,60,771 0/0:45,0:45:99:0,129,1699 0/0:25,0:25:72.22:0,72,930 0/0:33,0:33:87.27:0,87,1124 0/0:25,1:26:29.98:0,30,848 0/0:36,0:36:99:0,99,1244 0/0:26,0:26:66.21:0,66,870 0/0:35,0:35:93.31:0,93,1259 0/0:33,0:33:96.30:0,96,1269 0/0:18,0:18:54.15:0,54,684 0/0:41,0:41:99:0,108,1386 0/0:39,0:39:96.31:0,96,1264 0/0:27,0:27:81.25:0,81,1025 0/0:25,0:25:69.22:0,69,894 0/0:18,0:18:54.17:0,54,693 0/0:20,0:20:51.16:0,51,644 0/0:45,0:45:99:0,108,1418 0/0:52,0:53:99:0,138,1822 0/0:24,0:24:66.21:0,66,843 0/0:36,0:36:99:0,99,1280 0/0:36,0:36:99:0,102,1316 0/0:34,0:34:90.26:0,90,1147 0/0:35,0:35:87.26:0,87,1128 0/0:18,0:18:51.16:0,51,666 0/0:28,0:28:66.21:0,66,857 0/0:25,0:26:63.18:0,63,805 0/0:31,0:31:84.26:0,84,1081 0/0:19,0:19:54.18:0,54,721 0/1:16,2:18:5.64:6,0,440 0/0:21,0:21:60.18:0,60,767 0/0:25,0:25:72.23:0,72,956 -chr1 1120343 . C T 699.62 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.743;DP=1871;Dels=0.00;FS=5.662;HRun=0;HaplotypeScore=1.0425;InbreedingCoeff=-0.0085;MQ=54.11;MQ0=0;MQRankSum=0.033;QD=16.66;ReadPosRankSum=2.495;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|8),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|12),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|12);CSQ=upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,splice_region_variant&intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162571|TTLL10|ENST00000379288||||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:8,0:8:24.07:0,24,289 0/0:12,0:12:36.10:0,36,448 0/0:8,0:8:24.07:0,24,298 0/0:9,0:9:27.07:0,27,330 0/0:24,0:24:72.23:0,72,942 0/0:23,1:24:34.43:0,34,856 0/0:35,0:35:99:0,105,1398 0/0:16,0:16:48.15:0,48,621 0/0:53,0:53:99:0,160,2113 0/0:41,0:41:99:0,123,1589 0/0:31,0:31:93.28:0,93,1238 0/0:15,0:15:45.15:0,45,610 0/0:26,0:26:78.24:0,78,1012 0/0:27,0:27:72.23:0,72,939 0/0:37,0:37:96.26:0,96,1231 0/0:21,0:21:60.16:0,60,762 0/0:36,1:37:90.29:0,90,1208 0/0:41,0:41:99:0,111,1473 0/0:34,0:34:87.27:0,87,1139 0/0:35,0:35:96.31:0,96,1265 0/0:42,0:42:99:0,108,1407 0/0:43,0:43:99:0,117,1522 0/0:25,0:25:69.22:0,69,894 0/0:32,0:32:81.26:0,81,1074 0/0:30,1:31:56.56:0,57,981 0/0:33,1:34:87.28:0,87,1158 0/0:49,0:49:99:0,135,1768 0/0:24,0:24:60.20:0,60,810 0/0:42,0:42:99:0,111,1404 0/0:22,0:22:63.21:0,63,852 0/0:51,0:51:99:0,141,1868 0/0:28,0:29:75.24:0,75,983 0/0:34,0:34:90.26:0,90,1173 0/0:30,0:30:81.26:0,81,1064 0/0:36,0:36:99:0,99,1264 0/0:30,0:30:75.24:0,75,1001 0/0:40,0:40:99:0,105,1411 0/0:42,0:42:99:0,123,1651 0/0:21,0:21:63.18:0,63,811 0/0:46,0:46:99:0,120,1570 0/0:43,0:43:99:0,102,1298 0/0:27,0:27:78.21:0,78,994 0/0:28,0:28:75.23:0,75,973 0/0:21,0:21:60.19:0,60,780 0/0:21,0:21:57.15:0,57,708 0/0:49,0:49:99:0,117,1536 0/0:60,0:60:99:0,156,2063 0/0:24,0:25:63.20:0,63,827 0/0:41,0:41:99:0,111,1458 0/1:20,22:42:99:747,0,547 0/0:39,0:39:99:0,102,1342 0/0:36,0:36:90.28:0,90,1183 0/0:18,0:18:51.16:0,51,668 0/0:29,0:29:69.16:0,69,865 0/0:29,0:29:72.23:0,72,937 0/0:32,0:33:87.28:0,87,1130 0/0:21,0:21:60.19:0,60,795 0/0:21,0:21:51.17:0,51,681 0/0:23,0:23:63.19:0,63,824 0/0:28,0:28:78.25:0,78,1039 -chr1 1120370 . C G 708.51 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.070;DP=2729;Dels=0.00;FS=2.564;HRun=0;HaplotypeScore=1.4361;InbreedingCoeff=-0.0084;MQ=54.85;MQ0=0;MQRankSum=2.839;QD=10.12;ReadPosRankSum=1.250;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L355V|404|TTLL10|protein_coding|CODING|ENST00000379288|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L428V|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L428V|673|TTLL10|protein_coding|CODING|ENST00000379290|);CSQ=upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,missense_variant|Ctg/Gtg|L/V|ENSG00000162571|TTLL10|ENST00000379289|13/16|probably_damaging(0.951)|tolerated(0.12)|428/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,missense_variant|Ctg/Gtg|L/V|ENSG00000162571|TTLL10|ENST00000379290|13/16|probably_damaging(0.951)|tolerated(0.12)|428/673|protein_coding|1,missense_variant|Ctg/Gtg|L/V|ENSG00000162571|TTLL10|ENST00000379288|9/9|probably_damaging(0.999)|tolerated(0.12)|355/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:14,0:14:36.11:0,36,456 0/0:20,0:20:57.18:0,57,740 0/0:16,0:16:45.15:0,45,598 0/0:20,0:20:60.19:0,60,759 0/0:36,0:36:99:0,108,1461 0/0:43,0:43:99:0,126,1680 0/0:51,0:51:99:0,154,2046 0/0:42,0:42:99:0,126,1686 0/0:71,0:71:99:0,214,2850 0/0:76,0:76:99:0,226,2973 0/0:46,0:46:99:0,138,1858 0/0:31,0:31:93.29:0,93,1237 0/0:54,0:54:99:0,163,2167 0/0:40,0:40:96.31:0,96,1282 0/0:52,1:53:99:0,138,1857 0/0:33,0:33:78.25:0,78,1040 0/0:51,0:51:99:0,129,1743 0/0:64,0:64:99:0,150,2030 0/0:54,0:54:99:0,129,1743 0/0:52,0:52:99:0,135,1819 0/0:55,0:55:99:0,135,1814 0/0:65,0:65:99:0,172,2257 0/0:42,0:42:99:0,108,1438 0/0:49,0:49:99:0,117,1540 0/0:44,0:44:99:0,108,1452 0/0:62,0:62:99:0,153,2042 0/1:42,28:70:99:756,0,1257 0/0:28,0:28:69.23:0,69,945 0/0:53,0:53:99:0,132,1745 0/0:40,0:40:99:0,102,1356 0/0:62,0:62:99:0,166,2202 0/0:48,0:48:99:0,129,1716 0/0:53,0:53:99:0,138,1811 0/0:42,0:42:99:0,99,1346 0/0:53,0:53:99:0,135,1844 0/0:45,0:45:99:0,114,1528 0/0:65,0:65:99:0,172,2295 0/0:63,0:63:99:0,166,2231 0/0:26,0:26:75.24:0,75,991 0/0:57,0:57:99:0,147,1934 0/0:50,0:50:99:0,123,1654 0/0:36,0:36:93.30:0,93,1231 0/0:34,0:34:93.30:0,93,1232 0/0:26,0:26:66.19:0,66,853 0/0:27,0:27:72.20:0,72,921 0/0:65,0:65:99:0,163,2133 0/0:76,0:76:99:0,190,2568 0/0:30,0:30:81.26:0,81,1084 0/0:50,0:50:99:0,120,1591 0/0:60,0:60:99:0,175,2206 0/0:47,0:47:99:0,129,1666 0/0:47,0:47:99:0,123,1617 0/0:29,0:29:87.23:0,87,1097 0/0:39,0:39:90.29:0,90,1196 0/0:40,0:40:99:0,102,1352 0/0:42,0:42:99:0,105,1378 0/0:32,0:32:81.27:0,81,1096 0/0:33,0:33:81.26:0,81,1077 0/0:28,0:28:75.24:0,75,988 0/0:49,0:49:99:0,129,1706 -chr1 1120377 . T A 4655.8 . AC=5;AF=0.0417;AN=120;BaseQRankSum=1.090;DP=2884;Dels=0.00;FS=2.193;HRun=1;HaplotypeScore=1.7603;InbreedingCoeff=-0.0435;MQ=55.01;MQ0=0;MQRankSum=6.538;QD=16.22;ReadPosRankSum=-0.513;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aAg|M357K|404|TTLL10|protein_coding|CODING|ENST00000379288|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aAg|M430K|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aAg|M430K|673|TTLL10|protein_coding|CODING|ENST00000379290|);CSQ=upstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,missense_variant|aTg/aAg|M/K|ENSG00000162571|TTLL10|ENST00000379289|13/16|benign(0.181)|tolerated(0.99)|430/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,missense_variant|aTg/aAg|M/K|ENSG00000162571|TTLL10|ENST00000379290|13/16|benign(0.181)|tolerated(0.99)|430/673|protein_coding|1,missense_variant|aTg/aAg|M/K|ENSG00000162571|TTLL10|ENST00000379288|9/9|benign(0.088)|tolerated(0.91)|357/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:17,0:17:45.11:0,45,547 0/0:20,0:20:54.17:0,54,678 0/0:16,0:17:48.16:0,48,632 0/0:21,0:21:63.19:0,63,787 0/0:39,0:39:99:0,114,1525 0/0:43,0:43:99:0,126,1655 0/0:59,0:59:99:0,178,2366 0/0:46,0:46:99:0,138,1849 0/1:34,38:72:99:1308,0,1142 0/0:83,0:83:99:0,247,3220 0/0:40,0:40:99:0,120,1601 0/0:35,0:35:99:0,102,1342 0/0:55,0:55:99:0,163,2132 0/0:41,0:41:99:0,99,1320 0/0:55,0:55:99:0,147,1956 0/0:37,0:37:84.26:0,84,1118 0/0:55,0:55:99:0,147,1956 0/0:67,0:67:99:0,166,2212 0/0:57,0:57:99:0,132,1799 0/0:47,0:47:99:0,123,1669 0/0:61,0:61:99:0,150,2026 0/1:31,37:68:99:1073,0,898 0/0:47,1:48:83.95:0,84,1520 0/0:53,1:54:99:0,102,1713 0/0:52,0:52:99:0,126,1683 0/0:64,0:65:99:0,160,2109 0/0:72,0:72:99:0,175,2343 0/0:32,0:32:78.26:0,78,1060 0/0:56,0:56:99:0,138,1790 0/1:21,23:44:99:725,0,558 0/0:67,0:67:99:0,169,2278 0/0:52,0:53:99:0,135,1830 0/0:56,0:56:99:0,138,1837 0/0:45,0:45:99:0,102,1389 0/0:56,0:56:99:0,141,1933 0/0:51,0:51:99:0,132,1799 0/0:73,0:73:99:0,181,2410 0/0:64,0:64:99:0,163,2207 0/0:30,0:30:87.28:0,87,1136 0/1:36,26:63:99:706,0,971 0/0:48,0:49:99:0,123,1664 0/0:35,0:35:96.30:0,96,1252 0/0:33,0:33:90.29:0,90,1205 0/0:28,0:28:72.22:0,72,921 0/0:27,0:27:75.24:0,75,967 0/0:66,0:66:99:0,160,2110 0/0:78,0:78:99:0,193,2612 0/0:30,0:30:78.23:0,78,1032 0/0:51,0:51:99:0,117,1578 0/0:64,0:64:99:0,178,2299 0/0:52,0:52:99:0,141,1787 0/0:49,0:49:99:0,126,1670 0/0:33,0:33:90.29:0,90,1180 0/0:41,0:41:93.30:0,93,1226 0/0:42,0:42:99:0,105,1392 0/1:12,28:40:99:844,0,333 0/0:35,0:35:90.29:0,90,1209 0/0:35,0:35:90.28:0,90,1197 0/0:28,0:28:78.25:0,78,1030 0/0:52,0:52:99:0,129,1738 -chr1 1120431 . G A 10163.92 . AC=16;AF=0.1333;AN=120;BaseQRankSum=-1.606;DP=3363;Dels=0.00;FS=20.818;HRun=1;HaplotypeScore=1.5931;InbreedingCoeff=0.1346;MQ=56.00;MQ0=0;MQRankSum=8.100;QD=14.38;ReadPosRankSum=1.101;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S375N|404|TTLL10|protein_coding|CODING|ENST00000379288|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S448N|673|TTLL10|protein_coding|CODING|ENST00000379289|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S448N|673|TTLL10|protein_coding|CODING|ENST00000379290|);CSQ=missense_variant&NMD_transcript_variant|aGt/aAt|S/N|ENSG00000162571|TTLL10|ENST00000486379|1/5|unknown(0)||6/45|nonsense_mediated_decay|1,missense_variant|aGt/aAt|S/N|ENSG00000162571|TTLL10|ENST00000379289|13/16|benign(0)|tolerated(1)|448/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,missense_variant|aGt/aAt|S/N|ENSG00000162571|TTLL10|ENST00000379290|13/16|benign(0)|tolerated(1)|448/673|protein_coding|1,missense_variant|aGt/aAt|S/N|ENSG00000162571|TTLL10|ENST00000379288|9/9|benign(0)|tolerated(1)|375/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:12,0:12:36.11:0,36,462 0/0:12,0:12:36.10:0,36,451 0/0:16,0:16:48.15:0,48,614 0/0:20,0:20:57.17:0,57,700 0/0:49,0:49:99:0,144,1938 0/0:37,0:37:99:0,105,1344 0/0:58,0:58:99:0,172,2265 0/1:10,12:22:99:410,0,332 0/0:72,0:72:99:0,214,2854 0/0:74,0:74:99:0,223,2962 0/0:42,0:42:99:0,126,1678 0/0:36,0:36:99:0,108,1404 0/0:67,0:67:99:0,202,2645 0/0:47,0:47:99:0,114,1547 0/0:77,0:77:99:0,190,2511 0/0:45,0:46:99:0,105,1428 0/0:55,0:55:99:0,135,1838 0/0:83,0:83:99:0,193,2609 0/0:64,0:64:99:0,150,2051 0/1:30,33:63:99:887,0,947 0/0:74,0:74:99:0,163,2180 0/0:84,0:85:99:0,199,2683 0/0:70,0:71:99:0,147,1983 0/1:27,31:58:99:811,0,798 0/1:46,23:69:99:603,0,1402 0/0:74,0:74:99:0,178,2413 0/0:75,0:76:99:0,178,2377 0/0:48,0:48:99:0,123,1663 0/0:59,0:60:99:0,150,1983 0/0:63,0:63:99:0,169,2195 0/0:73,0:73:99:0,184,2423 0/1:33,33:66:99:864,0,858 0/0:65,0:66:99:0,162,2137 0/1:27,34:61:99:986,0,760 0/0:80,0:80:99:0,190,2507 0/0:67,0:67:99:0,156,2087 0/0:76,0:76:99:0,199,2591 0/0:75,0:75:99:0,199,2624 0/0:39,0:39:81.27:0,81,1106 0/0:70,0:70:99:0,163,2157 0/0:56,0:56:99:0,135,1777 0/0:42,0:42:99:0,102,1324 0/0:38,0:38:96.31:0,96,1295 0/1:20,16:36:99:421,0,505 1/1:0,28:28:60.18:780,60,0 0/0:57,0:57:99:0,129,1738 0/0:88,0:89:99:0,211,2816 0/1:25,12:37:99:287,0,648 0/0:64,0:65:99:0,156,2059 0/0:83,0:83:99:0,202,2651 0/1:48,21:69:99:590,0,1403 0/1:32,33:65:99:862,0,995 0/1:20,25:45:99:673,0,516 0/0:50,0:50:99:0,126,1670 1/1:0,51:51:99:1601,120,0 0/1:25,12:37:99:386,0,648 0/0:43,0:43:99:0,99,1337 0/0:60,0:60:99:0,123,1670 0/0:35,0:35:84.27:0,84,1104 0/0:74,0:74:99:0,163,2187 -chr1 1120536 . G A 3644.72 . AC=9;AF=0.0750;AN=120;BaseQRankSum=-1.719;DP=1842;Dels=0.00;FS=0.462;HRun=0;HaplotypeScore=1.6538;InbreedingCoeff=0.1586;MQ=56.93;MQ0=0;MQRankSum=7.086;QD=15.99;ReadPosRankSum=-0.320;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|13),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|13),UTR_3_PRIME(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|9);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,3_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|9/9|||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:10,0:10:30.10:0,30,385 0/0:8,0:8:24.08:0,24,314 0/0:17,0:17:51.16:0,51,662 0/0:14,0:14:27.08:0,27,340 0/0:29,0:29:84.28:0,84,1137 0/0:23,0:23:63.21:0,63,857 0/0:46,0:46:99:0,135,1801 0/0:31,0:31:93.30:0,93,1225 0/0:62,0:62:99:0,187,2496 0/0:67,0:67:99:0,202,2637 0/0:34,0:34:99:0,99,1299 0/0:35,0:35:99:0,102,1321 0/1:17,17:34:99:554,0,511 0/0:28,0:28:69.22:0,69,922 0/0:48,0:48:99:0,129,1688 0/1:14,11:25:99:314,0,388 0/0:27,0:27:75.22:0,75,970 0/1:16,17:33:99:503,0,505 0/0:22,0:22:57.19:0,57,767 0/0:41,0:41:99:0,111,1442 0/0:27,0:27:63.19:0,63,825 0/0:49,0:50:99:0,117,1542 0/0:20,0:20:51.16:0,51,670 0/0:46,0:46:99:0,117,1565 0/0:46,0:46:99:0,117,1546 0/0:35,0:35:90.29:0,90,1199 0/0:32,0:32:81.27:0,81,1105 0/0:25,0:25:63.20:0,63,829 0/0:38,0:38:93.28:0,93,1229 0/0:38,0:38:99:0,108,1359 0/0:29,0:29:81.25:0,81,1045 0/1:17,15:32:99:457,0,507 0/0:42,0:43:99:0,105,1382 0/0:31,0:31:81.26:0,81,1088 0/0:34,0:34:84.23:0,84,1090 0/0:30,0:31:75.23:0,75,993 0/0:47,0:47:99:0,105,1386 0/0:54,0:54:99:0,132,1784 0/0:11,0:11:33.11:0,33,434 0/0:32,0:32:72.23:0,72,939 0/0:28,0:28:75.23:0,75,944 0/0:28,0:28:75.24:0,75,989 0/1:10,10:20:99:320,0,262 0/0:21,0:21:51.15:0,51,624 0/1:8,10:18:99:316,0,183 0/0:22,0:22:66.21:0,66,841 0/0:39,1:41:70.07:0,70,1283 0/0:7,0:8:21.07:0,21,270 0/0:26,0:26:66.19:0,66,847 0/0:39,0:39:90.28:0,90,1165 0/1:27,16:43:99:464,0,779 0/0:23,0:23:57.17:0,57,714 0/0:23,0:23:60.19:0,60,759 0/0:27,0:27:66.20:0,66,827 1/1:0,22:22:57.15:716,57,0 0/0:24,0:24:63.20:0,63,796 0/0:14,0:14:42.13:0,42,543 0/0:32,0:32:78.25:0,78,1018 0/0:20,0:20:45.15:0,45,609 0/0:26,0:26:75.24:0,75,982 -chr1 1120587 . G A 207.5 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.370;DP=1099;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7829;InbreedingCoeff=-0.0101;MQ=57.36;MQ0=0;MQRankSum=0.481;QD=11.53;ReadPosRankSum=0.161;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|13),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|13),UTR_3_PRIME(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|9);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,3_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|9/9|||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:9.02:0,9,103 0/0:7,0:7:21.07:0,21,264 0/0:10,0:10:27.08:0,27,343 0/0:6,0:6:15.01:0,15,164 0/0:26,0:26:72.22:0,72,958 0/0:19,0:19:57.17:0,57,733 0/0:35,0:35:99:0,102,1358 0/0:25,0:25:75.25:0,75,1011 0/0:35,0:35:99:0,102,1353 0/0:46,0:46:99:0,132,1758 0/0:11,0:11:33.11:0,33,442 0/0:19,0:19:57.17:0,57,739 0/0:48,0:48:99:0,144,1876 0/0:21,0:21:57.19:0,57,752 0/0:28,0:28:72.23:0,72,942 0/0:12,0:12:36.12:0,36,477 0/0:14,0:14:39.13:0,39,511 0/0:18,0:18:48.15:0,48,634 0/0:11,0:11:30.10:0,30,393 0/0:26,0:26:63.20:0,63,822 0/0:23,0:23:51.16:0,51,657 0/0:25,0:25:69.22:0,69,906 0/0:12,0:12:33.10:0,33,423 0/0:17,0:17:51.17:0,51,687 0/0:21,0:21:60.19:0,60,780 0/0:15,0:15:42.14:0,42,552 0/0:13,0:14:33.10:0,33,423 0/0:14,0:14:39.12:0,39,507 0/0:17,0:17:45.13:0,45,562 0/0:21,0:21:57.19:0,57,776 0/0:23,0:23:66.21:0,66,856 0/0:18,0:18:54.17:0,54,719 0/0:29,0:29:78.26:0,78,1050 0/0:13,0:13:36.12:0,36,477 0/0:20,1:21:20.19:0,20,726 0/0:16,0:16:45.14:0,45,577 0/0:31,1:32:48.51:0,49,1073 0/0:25,0:25:66.22:0,66,901 0/0:7,0:7:21.06:0,21,272 0/0:20,0:20:54.17:0,54,724 0/0:16,0:16:39.12:0,39,503 0/0:14,0:14:42.13:0,42,538 0/0:13,0:13:39.12:0,39,506 0/0:13,0:13:33.11:0,33,438 0/0:9,0:9:27.09:0,27,356 0/0:14,0:14:42.13:0,42,542 0/0:22,0:22:63.20:0,63,817 0/0:7,0:7:21.07:0,21,269 0/0:12,0:12:33.11:0,33,442 0/0:24,0:24:60.19:0,60,781 0/0:28,0:28:84.27:0,84,1120 0/0:16,0:16:45.13:0,45,563 0/1:10,8:18:99:255,0,298 0/0:17,0:17:48.15:0,48,621 0/0:13,0:13:33.09:0,33,412 0/0:18,0:18:54.17:0,54,703 0/0:9,0:9:24.08:0,24,316 0/0:12,0:12:30.10:0,30,389 0/0:7,0:7:21.07:0,21,267 0/0:13,0:13:39.12:0,39,505 -chr1 1120621 . T C 922.19 . AC=6;AF=0.0500;AN=120;BaseQRankSum=-0.439;DP=752;Dels=0.00;FS=2.007;HRun=0;HaplotypeScore=0.6123;InbreedingCoeff=-0.0575;MQ=57.87;MQ0=0;MQRankSum=1.573;QD=10.72;ReadPosRankSum=-1.626;EFF=DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000460998|),DOWNSTREAM(MODIFIER|||||TTLL10|retained_intron|CODING|ENST00000514695|),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379289|13),INTRON(MODIFIER||||673|TTLL10|protein_coding|CODING|ENST00000379290|13),UTR_3_PRIME(MODIFIER||||404|TTLL10|protein_coding|CODING|ENST00000379288|9);CSQ=intron_variant&NMD_transcript_variant|||ENSG00000162571|TTLL10|ENST00000486379||||-/45|nonsense_mediated_decay|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379289||||-/673|protein_coding|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000460998|||||retained_intron|1,downstream_gene_variant|||ENSG00000162571|TTLL10|ENST00000514695|||||retained_intron|1,intron_variant|||ENSG00000162571|TTLL10|ENST00000379290||||-/673|protein_coding|1,3_prime_UTR_variant|||ENSG00000162571|TTLL10|ENST00000379288|9/9|||-/404|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:18.05:0,18,214 0/0:5,0:5:15.04:0,15,167 0/0:11,0:11:30.06:0,30,338 0/0:4,0:5:12.03:0,12,138 0/1:12,3:15:73.45:73,0,428 0/0:18,0:18:51.16:0,51,659 0/0:30,0:30:81.25:0,81,1046 0/1:15,8:23:99:249,0,515 0/0:28,0:28:84.27:0,84,1105 0/0:42,0:42:99:0,114,1459 0/0:13,0:13:36.12:0,36,471 0/0:15,0:15:45.15:0,45,584 0/0:30,0:30:87.26:0,87,1121 0/0:18,0:18:51.17:0,51,690 0/0:23,0:23:60.19:0,60,773 0/0:6,0:6:18.06:0,18,236 0/0:6,0:6:15.05:0,15,204 0/0:12,0:13:33.08:0,33,416 0/0:7,0:7:18.06:0,18,236 0/1:10,8:18:99:262,0,310 0/0:16,0:16:48.15:0,48,607 0/0:13,0:13:39.13:0,39,526 0/0:6,0:6:15.05:0,15,203 0/1:3,5:8:93.40:141,0,93 0/0:15,0:15:45.14:0,45,584 0/0:9,0:9:24.08:0,24,326 0/0:9,0:9:27.09:0,27,371 0/0:8,0:8:21.07:0,21,274 0/1:8,6:14:99:153,0,229 0/0:13,0:13:39.13:0,39,514 0/0:20,0:20:60.19:0,60,780 0/0:8,0:8:21.07:0,21,275 0/0:14,1:15:42.13:0,42,545 0/0:12,0:12:33.11:0,33,425 0/0:10,0:10:27.09:0,27,353 0/0:14,0:14:42.14:0,42,554 0/0:18,0:18:54.17:0,54,700 0/0:17,0:17:48.15:0,48,644 0/0:6,0:6:18.06:0,18,232 0/0:12,0:12:30.10:0,30,404 0/0:13,0:13:39.12:0,39,489 0/0:5,0:5:15.05:0,15,203 0/0:8,0:8:24.08:0,24,311 0/0:6,0:6:15.04:0,15,191 0/0:4,0:4:12.04:0,12,164 0/0:6,0:6:18.06:0,18,241 0/0:16,0:16:48.15:0,48,615 0/0:6,0:6:18.06:0,18,247 0/0:6,0:6:15.05:0,15,205 0/0:12,0:12:36.11:0,36,452 0/0:16,0:16:48.15:0,48,626 0/0:10,0:10:30.06:0,30,354 0/0:11,0:11:27.09:0,27,363 0/0:12,0:12:36.11:0,36,455 0/0:8,0:8:24.08:0,24,327 0/1:3,5:8:86.63:158,0,87 0/0:4,0:4:12.01:0,12,132 0/0:8,0:8:24.08:0,24,316 0/0:5,0:5:15.05:0,15,193 0/0:10,0:10:24.05:0,24,297 -chr1 1138735 . C G 141.37 . AC=8;AF=0.118;AN=68;BaseQRankSum=-0.596;DP=90;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3854;InbreedingCoeff=0.1736;MQ=56.04;MQ0=0;MQRankSum=-0.664;QD=11.78;ReadPosRankSum=0.289;EFF=DOWNSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|),DOWNSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),DOWNSTREAM(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|),DOWNSTREAM(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|),INTERGENIC(MODIFIER|||||||||);CSQ=downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,77 0/0:5,0:5:9.03:0,9,115 0/0:2,0:2:6.02:0,6,74 0/0:2,0:2:5.99:0,6,58 0/0:2,0:2:6.02:0,6,82 0/0:2,0:2:6.02:0,6,78 ./. 0/0:4,0:4:12.04:0,12,155 0/0:2,0:2:6.01:0,6,68 0/0:4,0:4:12.04:0,12,159 1/1:0,2:2:6.02:73,6,0 ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,83 ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:3.01:0,3,42 ./. 0/0:6,0:6:18.06:0,18,223 1/1:0,1:1:3.01:42,3,0 0/0:3,0:3:9.03:0,9,116 ./. 0/1:2,1:3:24.41:24,0,65 ./. 0/0:5,0:5:12.04:0,12,156 0/0:2,0:2:6.02:0,6,72 ./. 0/0:5,0:5:15.05:0,15,184 0/1:3,2:5:59.97:60,0,64 ./. 0/0:4,0:4:9.02:0,9,98 0/0:3,0:3:9.03:0,9,123 0/0:3,0:3:9.03:0,9,124 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,37 0/0:4,0:4:6.01:0,6,58 ./. 0/0:1,0:1:3.01:0,3,33 -chr1 1138913 . T C 4314.24 . AC=14;AF=0.1167;AN=120;BaseQRankSum=2.277;DP=804;Dels=0.00;FS=7.205;HRun=4;HaplotypeScore=0.3748;InbreedingCoeff=0.2363;MQ=56.65;MQ0=0;MQRankSum=1.461;QD=20.64;ReadPosRankSum=0.717;EFF=DOWNSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|),DOWNSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),UTR_3_PRIME(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|5),UTR_3_PRIME(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|4);CSQ=downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,3_prime_UTR_variant|||ENSG00000186891|TNFRSF18|ENST00000379268|5/5|||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,3_prime_UTR_variant|||ENSG00000186891|TNFRSF18|ENST00000328596|4/4|||-/255|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,74 0/0:6,0:6:18.04:0,18,194 0/0:4,0:4:12.04:0,12,150 0/0:2,0:2:6.02:0,6,72 0/0:6,0:6:18.06:0,18,228 0/0:6,0:6:18.06:0,18,240 0/0:20,0:20:60.19:0,60,760 0/0:5,0:5:12.04:0,12,144 0/0:25,0:26:75.25:0,75,998 0/0:13,0:13:39.12:0,39,490 1/1:0,3:3:9.03:121,9,0 0/0:4,0:4:12.02:0,12,142 0/1:4,6:10:99:149,0,116 0/0:7,0:7:21.07:0,21,271 0/0:4,0:4:9.03:0,9,120 0/1:1,3:4:32.73:78,0,33 0/0:5,0:5:15.05:0,15,193 0/1:7,2:9:54.67:55,0,195 0/0:3,0:3:9.03:0,9,121 0/0:8,0:8:24.07:0,24,299 0/0:5,0:5:9.03:0,9,127 0/0:7,0:7:18.06:0,18,234 0/0:6,0:6:18.06:0,18,228 0/0:4,0:4:9.01:0,9,98 0/0:3,0:3:9.03:0,9,122 0/0:2,0:2:6.02:0,6,74 0/0:3,0:3:9.03:0,9,105 0/0:2,0:2:6.02:0,6,79 0/0:5,0:5:12.04:0,12,161 0/0:9,0:9:24.07:0,24,303 0/0:2,0:2:6.02:0,6,81 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.02:0,6,78 0/1:1,3:4:27.98:97,0,28 0/0:3,0:3:9.03:0,9,116 0/0:2,0:3:6.02:0,6,76 0/0:4,0:4:9.03:0,9,125 0/0:4,0:4:12.04:0,12,160 0/0:20,0:20:45.14:0,45,568 0/0:37,0:37:93.25:0,93,1120 0/0:23,0:23:63.19:0,63,796 0/1:12,10:22:99:333,0,269 0/1:14,14:28:99:329,0,450 0/0:19,0:20:48.15:0,48,601 1/1:1,22:23:57.18:755,57,0 0/0:22,0:23:60.19:0,60,770 0/0:44,0:44:99:0,108,1353 0/1:5,12:17:99:313,0,135 0/0:25,0:25:57.16:0,57,722 1/1:0,44:45:99:1482,117,0 0/1:21,23:44:99:602,0,584 0/0:32,0:33:84.23:0,84,1057 0/0:27,0:28:81.21:0,81,967 0/0:31,2:34:14.06:0,14,1025 0/0:24,0:24:69.19:0,69,867 0/0:15,0:15:42.13:0,42,547 0/0:12,0:12:36.12:0,36,471 0/0:17,0:17:42.14:0,42,552 0/0:34,0:35:90.26:0,90,1138 0/0:17,1:18:45.14:0,45,588 -chr1 1138963 . C T 602.78 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.829;DP=1466;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.7567;InbreedingCoeff=-0.0248;MQ=57.17;MQ0=0;MQRankSum=0.908;QD=8.74;ReadPosRankSum=0.934;EFF=DOWNSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|),DOWNSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),UTR_3_PRIME(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|5),UTR_3_PRIME(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|4);CSQ=downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,3_prime_UTR_variant|||ENSG00000186891|TNFRSF18|ENST00000379268|5/5|||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,3_prime_UTR_variant|||ENSG00000186891|TNFRSF18|ENST00000328596|4/4|||-/255|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,75 0/0:6,0:6:15.05:0,15,191 0/0:9,0:9:21.05:0,21,252 0/0:5,0:5:6.01:0,6,58 0/1:7,4:11:99:132,0,247 0/0:16,0:16:45.15:0,45,603 0/0:26,0:26:78.26:0,78,1040 0/0:13,0:13:39.12:0,39,503 0/0:30,0:30:87.28:0,87,1152 0/0:26,0:26:78.25:0,78,1032 0/0:8,0:8:24.07:0,24,314 0/0:8,0:8:24.08:0,24,308 0/0:14,0:14:42.13:0,42,543 0/0:16,0:16:42.13:0,42,550 0/0:10,0:10:27.09:0,27,354 0/0:6,0:6:15.05:0,15,203 0/0:9,0:9:27.08:0,27,343 0/0:7,0:7:15.04:0,15,188 0/0:11,0:11:30.10:0,30,386 0/0:7,0:7:15.05:0,15,202 0/0:11,0:11:24.08:0,24,323 0/0:11,0:11:18.06:0,18,244 0/0:9,0:9:27.06:0,27,327 0/0:7,0:7:21.07:0,21,276 0/0:5,0:5:12.04:0,12,161 0/0:5,0:5:12.02:0,12,142 0/0:6,0:6:15.05:0,15,201 0/0:3,0:3:9.03:0,9,116 0/0:12,0:12:33.11:0,33,436 0/0:14,0:14:30.09:0,30,377 0/0:5,0:5:15.05:0,15,192 0/0:11,0:11:27.09:0,27,352 0/0:9,0:9:24.08:0,24,323 0/0:5,0:5:15.05:0,15,186 0/0:9,0:9:24.07:0,24,310 0/0:10,0:10:27.09:0,27,367 0/0:13,0:13:36.12:0,36,485 0/0:15,0:15:45.15:0,45,600 0/0:32,0:32:81.25:0,81,1050 0/0:63,0:63:99:0,153,1923 0/0:38,0:38:93.29:0,93,1207 0/0:45,0:45:99:0,111,1428 0/0:43,1:44:96.28:0,96,1230 0/0:29,0:29:84.26:0,84,1050 0/0:37,0:37:99:0,99,1276 0/0:45,0:45:99:0,102,1299 0/0:76,1:77:99:0,175,2237 0/0:29,0:29:69.19:0,69,864 0/0:56,0:56:99:0,120,1568 0/0:84,0:84:99:0,181,2284 0/0:71,0:71:99:0,187,2307 0/0:48,0:48:99:0,114,1482 0/0:60,0:61:99:0,129,1651 0/1:36,22:58:99:536,0,906 0/0:49,0:49:99:0,108,1393 0/0:39,0:39:96.30:0,96,1263 0/0:30,0:30:69.19:0,69,885 0/0:38,0:38:81.26:0,81,1070 0/0:53,0:53:99:0,120,1494 0/0:40,0:40:93.30:0,93,1241 -chr1 1139202 . T C 2450.32 . AC=16;AF=0.1333;AN=120;BaseQRankSum=2.131;DP=874;Dels=0.00;FS=3.615;HRun=0;HaplotypeScore=0.9934;InbreedingCoeff=0.3376;MQ=57.90;MQ0=0;MQRankSum=0.238;QD=14.94;ReadPosRankSum=0.958;EFF=DOWNSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|),DOWNSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P179|255|TNFRSF18|protein_coding|CODING|ENST00000328596|),UTR_3_PRIME(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|5);CSQ=downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,3_prime_UTR_variant|||ENSG00000186891|TNFRSF18|ENST00000379268|5/5|||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,synonymous_variant|ccA/ccG|P|ENSG00000186891|TNFRSF18|ENST00000328596|4/4|||179/255|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,25 0/0:2,0:2:6.02:0,6,73 0/0:2,0:2:6.01:0,6,65 0/0:4,0:5:9.03:0,9,111 0/0:12,0:12:30.08:0,30,384 0/0:6,0:7:9.03:0,9,109 0/0:13,0:14:30.10:0,30,388 0/0:7,0:10:18.05:0,18,221 0/0:20,0:21:36.12:0,36,470 0/0:21,0:25:54.13:0,54,645 1/1:0,5:5:6.02:78,6,0 0/0:3,0:4:9.03:0,9,121 1/1:1,5:7:6.02:78,6,0 0/0:16,0:16:36.10:0,36,447 0/0:8,0:8:21.06:0,21,253 0/1:7,5:12:99:127,0,222 0/0:19,1:21:48.12:0,48,586 0/1:5,1:6:32.73:33,0,66 0/0:19,0:19:39.09:0,39,458 0/0:11,0:13:30.09:0,30,371 0/0:19,0:20:51.14:0,51,618 0/0:13,0:13:27.08:0,27,339 0/0:14,0:16:36.08:0,36,422 0/0:12,0:13:36.11:0,36,468 0/0:15,0:15:39.10:0,39,456 0/0:11,0:11:24.08:0,24,322 0/0:7,0:7:21.06:0,21,254 0/0:8,0:8:21.06:0,21,255 0/0:18,0:18:39.10:0,39,477 0/0:12,0:12:33.09:0,33,386 0/0:26,0:28:72.19:0,72,888 0/1:5,5:11:99:113,0,140 0/0:17,0:19:39.08:0,39,452 0/1:10,3:14:87.72:88,0,256 0/0:10,0:10:24.06:0,24,289 0/0:14,0:14:39.11:0,39,468 0/0:17,0:17:39.07:0,39,450 0/0:26,0:27:69.20:0,69,858 0/0:10,0:10:30.10:0,30,385 0/0:32,0:32:84.25:0,84,1054 0/0:21,0:21:54.13:0,54,659 0/1:5,4:9:99:116,0,129 0/1:11,8:19:99:222,0,321 0/0:7,0:7:18.06:0,18,228 1/1:0,16:16:36.11:463,36,0 0/0:18,0:18:45.13:0,45,565 0/0:29,0:29:69.19:0,69,850 0/1:6,9:17:99:274,0,179 0/0:16,0:16:45.11:0,45,553 1/1:0,27:27:60.18:749,60,0 0/1:9,12:21:99:307,0,277 0/0:22,0:23:54.17:0,54,680 0/0:22,0:22:48.15:0,48,619 0/0:19,0:20:42.13:0,42,531 0/0:18,0:18:51.14:0,51,610 0/0:14,0:14:36.12:0,36,466 0/0:11,0:11:27.09:0,27,357 0/0:12,0:12:27.08:0,27,322 0/0:14,2:18:33.09:0,33,396 0/0:11,0:11:24.07:0,24,292 -chr1 1139216 . G A 192.87 . AC=3;AF=0.0250;AN=120;BaseQRankSum=1.202;DP=865;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6000;InbreedingCoeff=0.3637;MQ=58.10;MQ0=0;MQRankSum=0.774;QD=11.35;ReadPosRankSum=-0.636;EFF=DOWNSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|),DOWNSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R175C|255|TNFRSF18|protein_coding|CODING|ENST00000328596|),UTR_3_PRIME(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|5);CSQ=downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,3_prime_UTR_variant|||ENSG00000186891|TNFRSF18|ENST00000379268|5/5|||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,missense_variant|Cgt/Tgt|R/C|ENSG00000186891|TNFRSF18|ENST00000328596|4/4|benign(0)|tolerated(0.09)|175/255|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,2:2:3.01:39,3,0 0/0:6,0:6:12.04:0,12,148 0/0:1,0:1:3.01:0,3,39 0/0:4,1:5:12.04:0,12,153 0/0:13,0:13:39.13:0,39,511 0/0:10,0:10:18.03:0,18,217 0/0:18,0:18:48.15:0,48,615 0/0:11,0:11:27.07:0,27,340 0/0:20,0:20:48.14:0,48,605 0/0:20,0:20:48.16:0,48,648 0/0:5,0:5:9.03:0,9,123 0/0:5,0:5:15.05:0,15,195 0/0:8,0:8:18.06:0,18,242 0/0:16,0:16:36.11:0,36,461 0/0:7,0:7:21.06:0,21,259 0/0:13,0:13:36.11:0,36,460 0/0:21,0:21:57.14:0,57,688 0/0:4,2:7:12.04:0,12,153 0/0:23,0:23:48.15:0,48,623 0/0:13,0:13:33.10:0,33,411 0/0:18,0:19:48.15:0,48,619 0/0:16,0:16:36.11:0,36,467 0/0:15,0:15:42.10:0,42,507 0/0:15,0:15:39.13:0,39,518 0/0:13,0:13:36.11:0,36,460 0/0:11,0:11:21.07:0,21,276 0/0:6,0:6:18.05:0,18,213 0/0:9,0:9:24.07:0,24,303 0/0:20,0:21:45.13:0,45,578 0/0:11,0:11:30.09:0,30,380 0/0:30,0:30:78.25:0,78,1023 0/0:13,0:13:30.09:0,30,372 0/0:17,0:18:39.11:0,39,490 0/0:15,0:15:36.12:0,36,469 0/0:8,0:8:18.06:0,18,241 0/0:15,0:15:39.12:0,39,492 0/0:16,0:16:42.09:0,42,505 0/0:23,0:23:63.19:0,63,805 0/0:12,0:12:36.11:0,36,456 0/0:27,0:27:72.23:0,72,922 0/0:19,0:19:51.15:0,51,636 0/0:6,0:6:12.04:0,12,145 0/0:16,0:16:39.12:0,39,496 0/0:6,0:6:18.05:0,18,222 0/0:16,0:16:42.12:0,42,517 0/0:20,0:20:45.13:0,45,565 0/0:28,0:29:69.21:0,69,867 0/0:11,0:11:27.08:0,27,347 0/0:16,0:16:45.13:0,45,561 0/0:27,0:27:69.20:0,69,828 0/0:18,0:18:48.15:0,48,634 0/0:25,0:26:63.18:0,63,790 0/0:21,0:21:51.16:0,51,657 0/0:18,0:18:39.13:0,39,507 0/0:14,0:14:39.12:0,39,493 0/0:14,0:14:39.10:0,39,475 0/0:11,0:11:24.08:0,24,316 0/0:14,0:14:30.09:0,30,387 0/1:7,8:15:99:222,0,167 0/0:11,0:11:30.09:0,30,365 -chr1 1139498 . C T 443.47 . AC=4;AF=0.0333;AN=120;BaseQRankSum=-0.002;DP=812;Dels=0.00;FS=10.375;HRun=0;HaplotypeScore=0.5381;InbreedingCoeff=-0.0387;MQ=58.91;MQ0=0;MQRankSum=0.153;QD=7.92;ReadPosRankSum=-1.689;EFF=INTRON(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V101M|169|TNFRSF18|protein_coding|CODING|ENST00000486728|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V173M|234|TNFRSF18|protein_coding|CODING|ENST00000379265|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V173M|241|TNFRSF18|protein_coding|CODING|ENST00000379268|);CSQ=missense_variant|Gtg/Atg|V/M|ENSG00000186891|TNFRSF18|ENST00000379265|4/5|benign(0.2)|tolerated(0.25)|173/234|protein_coding|1,missense_variant|Gtg/Atg|V/M|ENSG00000186891|TNFRSF18|ENST00000379268|4/5|benign(0.2)|tolerated(0.26)|173/241|protein_coding|1,missense_variant|Gtg/Atg|V/M|ENSG00000186891|TNFRSF18|ENST00000486728|3/4|benign(0.2)|tolerated(0.14)|101/169|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,26 0/0:9,0:10:18.05:0,18,217 0/0:8,0:8:21.07:0,21,269 0/0:8,0:8:24.08:0,24,309 0/0:8,0:8:24.08:0,24,320 0/0:14,0:14:39.12:0,39,506 0/0:26,0:26:75.23:0,75,957 0/0:9,0:9:27.08:0,27,346 0/0:28,0:28:81.26:0,81,1058 0/0:28,0:29:84.27:0,84,1085 0/0:10,0:10:30.10:0,30,395 0/0:8,0:8:24.08:0,24,313 0/1:4,11:15:99:346,0,115 0/0:15,0:15:30.10:0,30,395 0/0:23,0:23:60.18:0,60,753 0/0:11,0:11:27.08:0,27,354 0/0:15,0:15:39.12:0,39,509 0/1:11,6:17:99:162,0,285 0/0:24,0:24:51.13:0,51,658 0/0:11,0:11:30.09:0,30,378 0/0:27,0:27:63.20:0,63,832 0/0:22,0:22:48.13:0,48,607 0/0:20,0:20:48.14:0,48,626 0/0:20,0:20:51.15:0,51,648 0/0:20,0:20:48.12:0,48,613 0/0:12,0:12:33.11:0,33,431 0/1:13,1:14:1.69:2,0,393 0/0:10,0:10:15.05:0,15,202 0/0:11,0:11:30.10:0,30,406 0/0:16,0:16:45.14:0,45,588 0/0:24,0:24:57.17:0,57,738 0/0:31,0:31:66.18:0,66,841 0/0:24,0:24:54.16:0,54,652 0/0:8,0:8:18.06:0,18,241 0/0:14,0:14:36.12:0,36,477 0/0:13,0:13:33.10:0,33,410 0/0:11,0:11:24.08:0,24,326 0/0:23,0:23:54.14:0,54,690 0/0:6,0:6:15.04:0,15,175 0/0:12,0:12:27.09:0,27,351 0/1:9,1:10:3.34:3,0,326 0/0:12,0:12:33.10:0,33,418 0/0:11,0:11:27.09:0,27,347 0/0:5,0:5:15.05:0,15,193 0/0:5,0:5:12.04:0,12,154 0/0:13,0:14:39.12:0,39,493 0/0:18,0:18:42.13:0,42,510 0/0:3,0:3:9.03:0,9,118 0/0:5,0:5:9.03:0,9,121 0/0:22,0:22:54.16:0,54,680 0/0:18,0:18:48.15:0,48,618 0/0:7,0:7:21.07:0,21,277 0/0:12,0:12:33.11:0,33,422 0/0:12,0:12:27.09:0,27,355 0/0:6,0:6:15.04:0,15,171 0/0:3,0:3:9.02:0,9,106 0/0:7,0:7:18.06:0,18,239 0/0:5,0:5:15.05:0,15,193 0/0:4,0:4:6.02:0,6,83 0/0:5,0:5:9.03:0,9,112 -chr1 1139862 . T C 4003.11 . AC=5;AF=0.0417;AN=120;BaseQRankSum=2.163;DP=3444;Dels=0.00;FS=24.530;HRun=0;HaplotypeScore=1.7331;InbreedingCoeff=0.3739;MQ=58.49;MQ0=0;MQRankSum=0.567;QD=18.88;ReadPosRankSum=-5.116;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K105|234|TNFRSF18|protein_coding|CODING|ENST00000379265|),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K105|241|TNFRSF18|protein_coding|CODING|ENST00000379268|),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K105|255|TNFRSF18|protein_coding|CODING|ENST00000328596|),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K33|169|TNFRSF18|protein_coding|CODING|ENST00000486728|);CSQ=synonymous_variant|aaA/aaG|K|ENSG00000186891|TNFRSF18|ENST00000379265|3/5|||105/234|protein_coding|1,synonymous_variant|aaA/aaG|K|ENSG00000186891|TNFRSF18|ENST00000379268|3/5|||105/241|protein_coding|1,synonymous_variant|aaA/aaG|K|ENSG00000186891|TNFRSF18|ENST00000486728|2/4|||33/169|protein_coding|1,synonymous_variant|aaA/aaG|K|ENSG00000186891|TNFRSF18|ENST00000328596|3/4|||105/255|protein_coding|1 GT:AD:DP:GQ:PL 0/0:18,0:19:39.09:0,39,468 0/0:21,0:21:54.12:0,54,641 0/0:27,0:27:78.24:0,78,983 0/0:25,0:25:69.20:0,69,869 0/0:34,0:35:99:0,99,1269 0/0:50,1:51:99:0,138,1802 0/0:89,0:89:99:0,265,3456 0/0:44,0:44:99:0,126,1571 0/0:110,0:110:99:0,322,4160 0/0:128,0:128:99:0,364,4678 1/1:0,51:51:99:1952,147,0 0/0:48,1:50:99:0,135,1729 0/1:38,32:70:99:1032,0,1217 0/0:69,0:69:99:0,162,2128 0/0:91,0:91:99:0,226,2973 0/0:45,0:45:99:0,108,1397 0/0:62,0:63:99:0,147,1960 0/1:26,26:52:99:714,0,698 0/0:52,1:53:99:0,126,1640 0/0:82,0:82:99:0,184,2419 0/0:59,0:60:99:0,156,1978 0/0:76,0:76:99:0,187,2439 0/0:63,0:64:99:0,150,1977 0/0:77,0:77:99:0,187,2493 0/0:72,0:73:99:0,178,2306 0/0:65,1:66:99:0,141,1899 0/0:69,0:69:99:0,153,2047 0/0:29,0:29:66.21:0,66,873 0/0:74,0:74:99:0,187,2426 0/0:83,1:84:99:0,196,2627 0/0:70,1:71:99:0,175,2336 0/0:55,0:56:99:0,129,1749 0/0:75,0:75:99:0,169,2267 0/0:61,0:61:99:0,153,1963 0/0:56,0:56:99:0,141,1840 0/0:63,0:63:99:0,147,1964 0/0:80,0:80:99:0,184,2468 0/0:108,0:108:99:0,253,3324 0/0:44,0:44:99:0,114,1484 0/0:76,0:76:99:0,171,2093 0/0:63,0:64:99:0,144,1819 0/1:26,13:39:99:304,0,737 0/0:51,0:51:99:0,123,1587 0/0:36,0:36:90.28:0,90,1158 0/0:53,0:54:99:0,123,1632 0/0:49,0:49:99:0,108,1386 0/0:73,1:74:99:0,184,2346 0/0:27,0:27:75.24:0,75,967 0/0:40,0:40:90.24:0,90,1153 0/0:63,0:63:99:0,156,1993 0/0:70,1:71:99:0,181,2241 0/0:44,0:44:99:0,111,1410 0/0:36,0:36:87.28:0,87,1123 0/0:56,0:56:99:0,123,1576 0/0:38,0:38:87.27:0,87,1106 0/0:34,1:35:75.23:0,75,978 0/0:23,0:23:54.17:0,54,674 0/0:36,0:36:93.28:0,93,1188 0/0:25,0:25:51.17:0,51,681 0/0:46,0:46:99:0,105,1371 -chr1 1140290 . T C 112.5 . AC=7;AF=0.146;AN=48;BaseQRankSum=1.165;DP=43;Dels=0.00;FS=8.424;HRun=1;HaplotypeScore=0.0347;InbreedingCoeff=0.1666;MQ=58.92;MQ0=0;MQRankSum=-0.621;QD=16.07;ReadPosRankSum=1.709;EFF=INTRON(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|1),INTRON(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|2),INTRON(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|2),INTRON(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|2);CSQ=intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,28 0/0:4,0:4:12.04:0,12,150 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,40 ./. 0/0:1,0:1:3.01:0,3,41 0/0:5,0:5:15.05:0,15,205 0/0:5,0:5:9.03:0,9,117 1/1:0,1:1:3.01:41,3,0 ./. 0/1:2,1:3:32.20:32,0,73 0/0:2,0:2:6.01:0,6,61 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,32 ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,35 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:3.01:0,3,39 ./. 1/1:0,2:2:6.02:77,6,0 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,42 ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. -chr1 1140336 . C A 41.02 . AC=7;AF=0.175;AN=40;BaseQRankSum=-2.498;DP=35;Dels=0.00;FS=16.166;HRun=3;HaplotypeScore=0.0909;InbreedingCoeff=0.1580;MQ=57.31;MQ0=0;MQRankSum=-0.221;QD=6.84;ReadPosRankSum=-1.676;EFF=INTRON(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|1),INTRON(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|2),INTRON(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|2),INTRON(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|2);CSQ=intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3.01:30,3,0 0/1:1,1:2:30.96:31,0,35 0/0:3,0:3:6.02:0,6,71 0/0:1,0:1:3.01:0,3,40 1/1:0,1:1:3:26,3,0 0/0:2,1:3:6.02:0,6,81 1/1:1,1:2:3:28,3,0 0/0:2,0:2:6.02:0,6,81 0/0:2,0:2:6.02:0,6,81 ./. ./. ./. 0/0:2,0:2:6.02:0,6,73 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3:0,3,26 ./. 0/0:2,0:2:6.02:0,6,73 ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. -chr1 1140435 . G T 467.03 . AC=25;AF=0.463;AN=54;BaseQRankSum=-0.385;DP=39;Dels=0.00;FS=1.380;HRun=1;HaplotypeScore=0.0000;InbreedingCoeff=0.2592;MQ=60.00;MQ0=0;MQRankSum=0.014;QD=24.58;ReadPosRankSum=-1.128;EFF=INTRON(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|1),INTRON(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|2),INTRON(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|2),INTRON(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|2);CSQ=intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3.01:34,3,0 0/0:2,0:2:6.01:0,6,64 0/0:1,0:1:3.01:0,3,32 0/0:3,0:3:9.01:0,9,94 0/0:1,0:1:3.01:0,3,40 ./. 0/1:1,1:2:28.33:28,0,35 1/1:0,2:2:6.02:82,6,0 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,41 ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:39,3,0 1/1:0,1:1:3.01:41,3,0 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. 0/1:1,1:2:16.68:17,0,32 0/0:2,0:2:6.02:0,6,80 ./. ./. 0/0:1,0:1:3.01:0,3,42 0/1:1,1:2:31.78:32,0,35 ./. ./. ./. ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:37,3,0 ./. 0/0:2,0:2:3.01:0,3,45 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. 0/0:2,0:2:6.02:0,6,78 ./. ./. 1/1:0,2:2:6.02:77,6,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 ./. 0/0:1,0:1:3.01:0,3,42 ./. 1/1:0,1:1:3.01:40,3,0 ./. -chr1 1140504 . T C 76.53 . AC=7;AF=0.090;AN=78;BaseQRankSum=-0.513;DP=85;Dels=0.00;FS=7.579;HRun=4;HaplotypeScore=0.1294;InbreedingCoeff=0.1345;MQ=58.35;MQ0=0;MQRankSum=0.232;QD=9.57;ReadPosRankSum=0.795;EFF=INTRON(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|1),INTRON(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|2),INTRON(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|2),INTRON(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|2);CSQ=intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:2.98:0,3,22 0/0:3,0:3:9.03:0,9,106 0/0:1,0:1:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,39 ./. 0/0:4,0:4:12.04:0,12,155 0/0:2,0:2:6.02:0,6,74 0/0:2,0:2:6.02:0,6,81 0/0:2,0:2:6.02:0,6,81 ./. ./. 0/1:2,2:4:55.64:56,0,70 0/0:2,0:2:3.01:0,3,45 0/0:1,0:1:3.01:0,3,34 ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:3,0:3:9.03:0,9,118 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. 0/0:2,1:3:6.02:0,6,74 0/0:2,0:2:3.01:0,3,41 ./. ./. 0/0:3,0:3:9.03:0,9,116 0/0:2,0:2:6.02:0,6,73 0/0:2,0:2:6.02:0,6,83 1/1:0,1:1:3.01:42,3,0 ./. ./. 0/0:2,0:2:3.01:0,3,39 ./. ./. 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:6.02:0,6,83 0/0:3,0:3:9.03:0,9,111 1/1:1,1:2:3:28,3,0 ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:2,0:2:6.02:0,6,79 ./. ./. 0/0:5,0:5:12.04:0,12,149 1/1:0,1:1:3.01:39,3,0 0/0:3,0:3:9.03:0,9,116 0/0:2,0:2:6.02:0,6,79 ./. 0/0:4,0:4:9.03:0,9,118 0/0:5,0:5:15.05:0,15,187 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.02:0,6,81 0/0:3,0:3:6.02:0,6,72 ./. -chr1 1140812 . TC T 426.77 . AC=1;AF=0.0083;AN=120;BaseQRankSum=3.763;DP=2438;FS=2.359;HRun=1;HaplotypeScore=140.7554;InbreedingCoeff=-0.0094;MQ=58.75;MQ0=0;MQRankSum=1.559;QD=21.34;ReadPosRankSum=0.995;EFF=FRAME_SHIFT(HIGH||-|-11|169|TNFRSF18|protein_coding|CODING|ENST00000486728|1),FRAME_SHIFT(HIGH||-|-83|234|TNFRSF18|protein_coding|CODING|ENST00000379265|2),FRAME_SHIFT(HIGH||-|-83|241|TNFRSF18|protein_coding|CODING|ENST00000379268|2),FRAME_SHIFT(HIGH||-|-83|255|TNFRSF18|protein_coding|CODING|ENST00000328596|2);CSQ=frameshift_variant&feature_truncation|||ENSG00000186891|TNFRSF18|ENST00000379265|2/5|||83/234|protein_coding|1,frameshift_variant&feature_truncation|||ENSG00000186891|TNFRSF18|ENST00000379268|2/5|||83/241|protein_coding|1,frameshift_variant&feature_truncation|||ENSG00000186891|TNFRSF18|ENST00000486728|1/4|||11/169|protein_coding|1,frameshift_variant&feature_truncation|||ENSG00000186891|TNFRSF18|ENST00000328596|2/4|||83/255|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.05:0,15,240 0/0:5,0:5:12.04:0,12,192 0/0:7,0:7:21.07:0,21,336 0/0:7,0:7:18.06:0,18,274 0/0:18,0:18:54.18:0,54,849 0/0:16,0:16:42.14:0,42,636 0/0:20,0:20:57.19:0,57,896 0/0:13,0:13:33.11:0,33,502 0/0:28,0:28:84.29:0,84,1333 0/0:19,0:19:54.18:0,54,864 0/0:17,0:17:51.17:0,51,797 0/0:13,0:13:36.12:0,36,559 0/0:23,0:23:63.21:0,63,994 0/0:35,0:35:99:0,99,1583 0/0:26,0:26:75.25:0,75,1183 0/0:22,0:22:63.21:0,63,1006 0/0:22,0:22:63.21:0,63,985 0/0:28,0:28:81.28:0,81,1293 0/0:23,0:23:69.24:0,69,1100 0/0:32,0:32:96.33:0,96,1535 0/0:30,0:30:84.29:0,84,1344 0/0:39,0:39:99:0,117,1871 0/0:18,0:18:48.16:0,48,766 0/1:7,13:20:99:484,0,276 0/0:26,0:26:78.27:0,78,1239 0/0:20,0:20:54.18:0,54,861 0/0:33,0:33:96.32:0,96,1475 0/0:35,0:35:96.33:0,96,1535 0/0:36,0:36:99:0,108,1718 0/0:37,0:37:99:0,111,1774 0/0:23,0:23:66.23:0,66,1054 0/0:12,0:12:36.12:0,36,576 0/0:29,0:29:84.29:0,84,1341 0/0:43,0:43:99:0,129,2027 0/0:21,0:21:60.20:0,60,960 0/0:23,0:23:66.23:0,66,1054 0/0:33,0:33:99:0,99,1578 0/0:40,0:40:99:0,111,1761 0/0:63,0:63:99:0,184,2906 0/0:108,0:108:99:0,298,4678 0/0:70,0:70:99:0,202,3182 0/0:68,0:68:99:0,181,2864 0/0:52,0:52:99:0,138,2175 0/0:42,0:42:99:0,114,1802 0/0:50,0:50:99:0,132,2106 0/0:75,0:75:99:0,220,3486 0/0:103,0:103:99:0,289,4591 0/0:43,0:43:99:0,117,1872 0/0:93,0:93:99:0,265,4160 0/0:93,0:93:99:0,274,4362 0/0:96,0:96:99:0,265,4157 0/0:68,0:68:99:0,190,3012 0/0:63,0:63:99:0,181,2859 0/0:81,0:81:99:0,229,3631 0/0:61,0:61:99:0,172,2734 0/0:72,0:72:99:0,208,3282 0/0:47,0:47:99:0,135,2149 0/0:57,0:57:99:0,169,2650 0/0:65,0:65:99:0,181,2871 0/0:71,0:71:99:0,193,3001 -chr1 1141556 . G C 130.07 . AC=7;AF=0.097;AN=72;BaseQRankSum=0.191;DP=66;Dels=0.00;FS=4.782;HRun=3;HaplotypeScore=0.1198;InbreedingCoeff=-0.0389;MQ=57.15;MQ0=0;MQRankSum=-0.406;QD=11.82;ReadPosRankSum=-0.358;EFF=INTRON(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|1),INTRON(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|1),INTRON(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|1),UPSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|);CSQ=intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,38 ./. 0/0:2,0:2:6.02:0,6,79 ./. ./. 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,36 0/0:2,0:2:3.01:0,3,41 1/1:0,1:1:3.01:36,3,0 0/0:1,0:1:3.01:0,3,37 ./. 0/0:3,0:3:6.02:0,6,76 0/0:1,0:1:3:0,3,29 1/1:0,1:1:3.01:40,3,0 0/0:1,0:1:3.01:0,3,41 0/1:2,1:3:29.23:36,0,29 0/0:1,0:1:3.01:0,3,34 0/0:2,0:2:6.02:0,6,72 ./. 0/0:2,0:2:6.02:0,6,77 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,42 ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:5,0:5:15.03:0,15,185 0/0:4,0:4:6.02:0,6,85 ./. ./. ./. 0/0:1,0:1:3.01:0,3,31 0/0:2,0:2:6.01:0,6,68 0/0:2,0:2:6.02:0,6,69 0/0:3,0:3:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,37 0/0:3,0:3:6.02:0,6,85 0/1:1,1:2:30.96:33,0,31 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/1:1,3:4:32.73:74,0,33 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 ./. 0/0:3,0:3:6.02:0,6,76 ./. ./. -chr1 1141723 . A G 877.55 . AC=13;AF=0.1204;AN=108;BaseQRankSum=0.547;DP=397;Dels=0.00;FS=2.262;HRun=3;HaplotypeScore=0.1820;InbreedingCoeff=0.0234;MQ=58.98;MQ0=0;MQRankSum=0.061;QD=11.40;ReadPosRankSum=-1.301;EFF=DOWNSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),DOWNSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),INTRON(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|1),INTRON(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|1),INTRON(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|1),UPSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|);CSQ=intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,intron_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,32 0/0:2,0:2:3.01:0,3,34 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,34 0/0:2,0:2:6.02:0,6,77 0/0:2,0:2:6.02:0,6,76 ./. 0/0:2,0:2:6.02:0,6,73 0/0:2,0:2:6.02:0,6,75 1/1:0,1:1:3.01:37,3,0 ./. ./. 0/1:10,1:11:11.50:11,0,260 0/0:12,0:12:18.05:0,18,240 0/1:3,2:5:32.51:33,0,99 0/0:17,1:18:39.11:0,39,475 0/1:2,9:12:39.18:223,0,39 0/0:16,0:16:36.11:0,36,478 0/0:6,0:6:15.05:0,15,198 0/0:8,0:8:18.06:0,18,250 0/0:15,0:15:42.13:0,42,540 0/0:12,0:12:33.10:0,33,429 0/0:9,0:9:18.04:0,18,205 0/0:12,0:12:30.08:0,30,376 0/0:3,0:3:6.01:0,6,59 0/0:12,0:12:27.07:0,27,349 0/0:9,0:9:18.05:0,18,225 0/0:6,0:6:15.04:0,15,192 0/0:18,0:18:33.08:0,33,395 0/0:10,0:10:27.09:0,27,356 0/1:5,5:10:74.46:116,0,74 0/0:13,0:13:30.07:0,30,361 0/1:8,5:13:99:118,0,139 0/0:12,0:12:21.07:0,21,278 0/0:11,0:11:27.06:0,27,327 0/0:17,0:17:39.10:0,39,495 0/0:16,0:16:39.13:0,39,505 0/0:3,0:3:6.02:0,6,82 0/0:13,1:14:30.09:0,30,377 0/0:4,1:5:12.04:0,12,144 0/1:3,2:5:52.23:60,0,52 0/1:1,2:3:19.63:57,0,20 ./. 1/1:0,2:2:6.02:72,6,0 0/0:4,0:4:12.04:0,12,150 0/0:8,0:8:21.06:0,21,249 0/0:3,0:3:6.02:0,6,74 0/0:3,0:3:5.98:0,6,47 0/1:2,8:10:43.33:234,0,43 0/1:2,3:5:35.73:69,0,36 0/0:3,0:3:6.02:0,6,81 0/0:5,0:5:12.04:0,12,153 ./. 0/0:7,0:7:12.03:0,12,143 0/0:6,0:6:12.03:0,12,146 ./. 0/0:4,0:4:9.02:0,9,102 0/0:2,0:2:6.02:0,6,79 0/0:3,0:3:6.01:0,6,69 -chr1 1142399 . A AC 117.53 . AC=8;AF=0.308;AN=26;BaseQRankSum=-2.601;DP=22;FS=0.000;HRun=4;HaplotypeScore=4.5003;InbreedingCoeff=0.4087;MQ=58.95;MQ0=0;MQRankSum=0.702;QD=23.51;ReadPosRankSum=0.537;EFF=DOWNSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),DOWNSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||169|TNFRSF18|protein_coding|CODING|ENST00000486728|),UPSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),UPSTREAM(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|),UPSTREAM(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|);CSQ=downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000486728||||-/169|protein_coding|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:5,0:5:15.04:0,15,170 ./. 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3.01:0,3,34 ./. ./. ./. 0/0:1,0:1:3.01:0,3,34 ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,34 1/1:0,2:2:6.02:73,6,0 0/0:2,0:2:6.02:0,6,68 ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,68 0/0:1,0:1:3.01:0,3,34 ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,68 ./. ./. -chr1 1146478 . T C 51.13 . AC=2;AF=0.050;AN=40;BaseQRankSum=-1.556;DP=39;Dels=0.00;FS=14.569;HRun=2;HaplotypeScore=0.1961;InbreedingCoeff=-0.2329;MQ=56.11;MQ0=0;MQRankSum=-1.373;QD=5.11;ReadPosRankSum=-1.373;EFF=DOWNSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),DOWNSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),INTERGENIC(MODIFIER|||||||||),UPSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),UPSTREAM(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|),UPSTREAM(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|);CSQ=downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/1:1,4:5:28.62:78,0,29 0/0:3,0:4:3.01:0,3,33 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.01:0,6,70 ./. 0/0:2,0:2:3.01:0,3,41 0/0:1,1:2:3.01:0,3,41 0/0:1,0:1:2.99:0,3,24 0/1:4,1:5:24.41:24,0,65 ./. ./. 0/0:2,0:2:6.01:0,6,65 0/0:1,0:1:3.01:0,3,32 ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,35 ./. ./. ./. 0/0:2,0:2:6.02:0,6,80 ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 ./. ./. 0/0:1,0:1:3.01:0,3,35 ./. ./. -chr1 1146785 . G C 472.67 . AC=4;AF=0.0333;AN=120;BaseQRankSum=0.520;DP=773;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3659;InbreedingCoeff=-0.0419;MQ=55.65;MQ0=0;MQRankSum=2.347;QD=10.28;ReadPosRankSum=0.755;EFF=DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|5),UPSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),UPSTREAM(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|),UPSTREAM(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|),UTR_3_PRIME(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|7);CSQ=downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|5/5||||retained_intron|1,3_prime_UTR_variant|||ENSG00000186827|TNFRSF4|ENST00000379236|7/7|||-/277|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,60 0/0:4,0:5:12.04:0,12,158 0/0:3,0:3:9.02:0,9,99 0/0:1,0:1:3.01:0,3,36 0/0:7,0:7:21.06:0,21,270 0/0:13,0:13:36.11:0,36,452 0/0:15,0:15:39.13:0,39,513 0/0:9,0:9:27.08:0,27,351 0/0:16,0:16:48.16:0,48,634 0/0:23,0:23:69.22:0,69,903 0/0:6,0:6:18.06:0,18,240 0/0:5,0:5:15.05:0,15,196 0/0:7,0:7:21.07:0,21,275 0/0:13,0:13:39.12:0,39,506 0/0:16,0:17:42.12:0,42,522 0/1:3,4:7:99:138,0,101 0/0:10,0:10:24.07:0,24,307 0/0:12,0:12:33.08:0,33,405 0/0:15,0:15:42.10:0,42,483 0/0:7,0:7:21.07:0,21,267 0/0:10,0:11:27.08:0,27,345 0/0:19,0:19:54.17:0,54,670 0/0:14,0:15:42.13:0,42,521 0/0:18,0:18:54.17:0,54,694 0/0:15,0:15:42.13:0,42,545 0/0:11,0:11:33.10:0,33,420 0/0:17,0:17:51.16:0,51,671 0/0:16,0:16:45.14:0,45,564 0/0:15,0:15:45.14:0,45,575 0/0:11,0:11:30.09:0,30,366 0/0:16,0:17:48.15:0,48,608 0/1:9,8:17:99:212,0,272 0/0:11,0:11:33.10:0,33,413 0/0:12,0:12:36.11:0,36,459 0/0:10,0:10:30.09:0,30,370 0/0:19,0:19:54.17:0,54,695 0/0:13,0:13:39.09:0,39,482 0/0:25,0:25:69.22:0,69,895 0/0:14,0:14:42.13:0,42,536 0/0:16,0:16:45.14:0,45,566 0/0:12,0:12:33.10:0,33,423 0/0:21,0:21:57.18:0,57,742 0/1:7,3:10:84.15:84,0,230 0/0:10,0:10:27.09:0,27,358 0/1:7,5:12:99:132,0,250 0/0:8,0:8:24.07:0,24,283 0/0:25,0:25:72.22:0,72,912 0/0:11,0:11:27.08:0,27,351 0/0:10,0:10:27.08:0,27,329 0/0:24,0:24:69.22:0,69,882 0/0:24,0:25:66.21:0,66,838 0/0:18,0:19:48.15:0,48,599 0/0:14,0:14:42.13:0,42,545 0/0:11,0:11:33.10:0,33,418 0/0:9,0:9:27.06:0,27,330 0/0:19,0:19:57.18:0,57,713 0/0:12,0:12:33.10:0,33,425 0/0:8,0:8:24.07:0,24,301 0/0:12,0:12:36.10:0,36,440 0/0:6,0:6:15.03:0,15,190 -chr1 1146853 . G A 316.99 . AC=4;AF=0.0339;AN=118;BaseQRankSum=-0.212;DP=1329;Dels=0.00;FS=8.508;HRun=0;HaplotypeScore=1.8407;InbreedingCoeff=-0.0495;MQ=50.41;MQ0=0;MQRankSum=0.063;QD=4.12;ReadPosRankSum=-1.639;EFF=DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|5),UPSTREAM(MODIFIER||||234|TNFRSF18|protein_coding|CODING|ENST00000379265|),UPSTREAM(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|),UPSTREAM(MODIFIER||||255|TNFRSF18|protein_coding|CODING|ENST00000328596|),UTR_3_PRIME(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|7);CSQ=downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379265||||-/234|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|5/5||||retained_intron|1,3_prime_UTR_variant|||ENSG00000186827|TNFRSF4|ENST00000379236|7/7|||-/277|protein_coding|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000328596||||-/255|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:6.02:0,6,78 0/0:4,0:4:3.01:0,3,39 ./. 0/0:4,0:5:6.02:0,6,69 0/0:9,0:9:18.04:0,18,223 0/0:8,1:9:9.03:0,9,115 0/0:18,0:19:27.08:0,27,346 0/0:7,0:7:6.02:0,6,65 0/0:33,0:34:33.09:0,33,413 0/0:30,0:30:36.12:0,36,479 0/0:11,0:12:9.03:0,9,113 0/0:9,0:9:12.04:0,12,163 0/0:9,0:9:6.02:0,6,75 0/0:24,0:24:36.08:0,36,421 0/0:26,0:26:27.06:0,27,308 0/1:11,11:23:99:117,0,110 0/0:19,0:19:18:0,18,178 0/0:31,0:31:30.03:0,30,308 0/0:22,0:22:21.07:0,21,266 0/0:21,0:21:24.03:0,24,263 0/0:23,0:23:39.11:0,39,450 0/0:29,0:29:39.09:0,39,442 0/0:19,0:19:18.03:0,18,213 0/0:24,0:24:21.02:0,21,230 0/0:19,0:19:27.07:0,27,317 0/0:29,0:29:30.07:0,30,370 0/0:37,0:37:45.09:0,45,492 0/0:24,0:25:33.06:0,33,372 0/0:32,0:32:42.11:0,42,515 0/0:17,0:18:18.05:0,18,217 0/0:33,0:33:33.08:0,33,380 0/1:11,6:17:29.36:106,0,29 0/0:21,0:22:27.06:0,27,308 0/0:25,0:25:39.11:0,39,472 0/0:20,0:20:15.04:0,15,173 0/0:30,0:30:24.07:0,24,300 0/0:23,0:24:24.06:0,24,299 0/0:28,0:29:36.11:0,36,463 0/0:20,0:20:21.02:0,21,214 0/0:32,0:32:45.11:0,45,517 0/0:26,0:26:30.09:0,30,372 0/0:26,0:26:27.05:0,27,301 0/1:14,9:23:99:102,0,150 0/0:22,0:22:30.08:0,30,359 0/1:8,6:14:84.54:85,0,112 0/0:20,0:21:30.08:0,30,356 0/0:39,0:39:45.07:0,45,489 0/0:13,0:13:18.04:0,18,220 0/0:18,0:18:21.06:0,21,253 0/0:35,0:35:42.11:0,42,497 0/0:51,0:51:51.12:0,51,574 0/0:35,0:35:48.11:0,48,554 0/0:37,0:37:42.10:0,42,468 0/0:28,0:28:39.09:0,39,444 0/0:25,0:25:36.10:0,36,428 0/0:19,0:19:27.08:0,27,330 0/0:17,1:18:21.06:0,21,256 0/0:26,0:26:27.06:0,27,307 0/0:13,0:13:21.01:0,21,219 0/0:15,0:15:18.03:0,18,187 -chr1 1146965 . G A 553.08 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.055;DP=3459;Dels=0.00;FS=2.776;HRun=0;HaplotypeScore=2.1270;InbreedingCoeff=-0.0086;MQ=56.15;MQ0=0;MQRankSum=0.024;QD=9.22;ReadPosRankSum=0.233;EFF=DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|5),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A268|277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|);CSQ=downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|5/5||||retained_intron|1,synonymous_variant|gcC/gcT|A|ENSG00000186827|TNFRSF4|ENST00000379236|7/7|||268/277|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:18.05:0,18,223 0/0:9,0:9:24.06:0,24,289 0/0:10,0:10:30.09:0,30,362 0/0:9,0:9:24.06:0,24,286 0/0:21,0:21:51.17:0,51,674 0/0:22,0:22:63.20:0,63,831 0/0:44,1:45:90.80:0,91,1562 0/0:27,0:27:75.24:0,75,988 0/0:57,0:57:99:0,169,2156 0/0:57,0:57:99:0,163,2078 0/0:24,0:24:72.23:0,72,944 0/0:22,0:22:60.19:0,60,770 0/0:24,0:24:69.22:0,69,888 0/0:62,0:63:99:0,147,1912 0/0:83,0:83:99:0,199,2556 0/0:57,0:57:99:0,135,1738 0/0:69,0:69:99:0,150,1907 0/0:75,0:75:99:0,172,2186 0/0:67,0:67:99:0,150,1940 0/0:66,0:67:99:0,147,1949 0/0:59,0:59:99:0,141,1787 0/0:76,0:76:99:0,172,2247 0/0:75,0:77:99:0,181,2303 0/0:72,0:72:99:0,175,2224 0/0:53,1:54:99:0,108,1601 0/0:76,0:76:99:0,196,2541 0/0:82,0:83:99:0,199,2565 0/0:62,0:62:99:0,138,1775 0/0:82,0:82:99:0,184,2312 0/0:83,0:84:99:0,193,2540 0/0:73,0:73:99:0,166,2155 0/0:84,0:84:99:0,193,2539 0/0:71,0:71:99:0,159,2021 0/0:88,0:88:99:0,205,2636 0/0:68,0:68:99:0,147,1924 0/0:63,0:63:99:0,138,1831 0/0:70,0:71:99:0,156,2051 0/0:107,0:109:99:0,244,3214 0/0:47,0:48:99:0,111,1409 0/0:102,0:102:99:0,238,2968 0/0:56,0:56:99:0,138,1743 0/0:59,0:60:99:0,138,1728 0/0:61,1:63:99:0,114,1826 0/0:56,0:56:99:0,135,1737 0/0:52,0:54:99:0,126,1602 0/0:46,0:46:99:0,105,1365 0/0:105,0:105:99:0,229,2912 0/0:39,0:39:90.26:0,90,1151 0/0:60,0:60:99:0,126,1608 0/1:36,24:60:99:601,0,931 0/0:87,0:87:99:0,223,2779 0/0:58,0:58:99:0,165,2022 0/0:59,0:59:99:0,135,1759 0/0:58,0:59:99:0,129,1592 0/0:41,0:41:99:0,102,1240 0/0:46,0:47:99:0,108,1429 0/0:39,0:39:84.26:0,84,1085 0/0:72,0:72:99:0,169,2157 0/0:48,0:48:99:0,108,1397 0/0:33,0:34:75.23:0,75,967 -chr1 1147024 . G A 429.09 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.041;DP=2325;Dels=0.00;FS=8.212;HRun=1;HaplotypeScore=2.0094;InbreedingCoeff=-0.0086;MQ=56.92;MQ0=0;MQRankSum=-0.049;QD=10.73;ReadPosRankSum=0.293;EFF=DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|5),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|6),UPSTREAM(MODIFIER||||241|TNFRSF18|protein_coding|CODING|ENST00000379268|);CSQ=downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,upstream_gene_variant|||ENSG00000186891|TNFRSF18|ENST00000379268||||-/241|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|5/5||||retained_intron|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1 GT:AD:DP:GQ:PL 0/0:8,0:8:18.04:0,18,205 0/0:13,0:13:39.11:0,39,471 0/0:10,0:10:30.09:0,30,372 0/0:10,0:10:30.09:0,30,375 0/0:14,0:14:39.13:0,39,514 0/0:24,0:24:69.18:0,69,846 0/0:40,1:41:99:0,117,1511 0/0:21,0:21:51.16:0,51,658 0/0:60,0:60:99:0,175,2248 0/0:51,0:51:99:0,150,1918 0/0:29,0:29:87.29:0,87,1176 0/0:23,0:23:66.20:0,66,851 0/0:30,0:30:90.29:0,90,1172 0/0:43,0:45:99:0,105,1353 0/0:69,0:69:99:0,178,2308 0/0:32,0:33:84.26:0,84,1084 0/0:51,0:51:99:0,126,1630 0/0:58,0:58:99:0,144,1835 0/0:52,0:52:99:0,141,1813 0/0:45,0:45:99:0,114,1503 0/0:50,0:50:99:0,117,1508 0/0:53,0:53:99:0,132,1729 0/0:44,0:44:99:0,105,1342 0/1:22,18:40:99:477,0,648 0/0:36,0:36:96.27:0,96,1219 0/0:42,0:42:99:0,108,1417 0/0:65,0:65:99:0,178,2276 0/0:41,0:41:99:0,105,1374 0/0:71,0:71:99:0,184,2360 0/0:64,0:64:99:0,150,1983 0/0:64,0:64:99:0,169,2197 0/0:46,0:46:99:0,120,1529 0/0:50,0:50:99:0,132,1726 0/0:48,0:48:99:0,120,1593 0/0:49,0:49:99:0,108,1430 0/0:38,0:38:99:0,99,1307 0/0:51,0:51:99:0,138,1753 0/0:72,0:72:99:0,178,2336 0/0:21,0:21:54.17:0,54,693 0/0:53,0:53:99:0,141,1746 0/0:32,0:32:87.27:0,87,1116 0/0:32,0:32:84.26:0,84,1074 0/0:32,0:32:81.24:0,81,1007 0/0:32,0:32:90.28:0,90,1168 0/0:28,0:28:69.22:0,69,908 0/0:28,0:28:72.22:0,72,913 0/0:63,0:64:99:0,153,1881 0/0:23,0:23:54.17:0,54,686 0/0:34,0:34:75.23:0,75,967 0/0:33,0:33:93.28:0,93,1155 0/0:43,0:43:99:0,114,1454 0/0:39,0:39:93.29:0,93,1194 0/0:29,0:29:72.23:0,72,935 0/0:26,0:26:63.16:0,63,760 0/0:33,0:33:72.20:0,72,905 0/0:22,0:22:54.17:0,54,710 0/0:24,0:24:69.22:0,69,900 0/0:30,0:30:78.22:0,78,985 0/0:29,0:29:72.23:0,72,958 0/0:24,0:24:57.18:0,57,718 -chr1 1147243 . A C 738.87 . AC=6;AF=0.0508;AN=118;BaseQRankSum=-0.595;DP=705;Dels=0.00;FS=3.973;HRun=2;HaplotypeScore=0.6191;InbreedingCoeff=-0.0615;MQ=56.78;MQ0=0;MQRankSum=-0.060;QD=13.94;ReadPosRankSum=-0.426;EFF=DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|5),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|4);CSQ=downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:9.02:0,9,97 0/0:5,0:5:12.02:0,12,135 0/0:1,0:1:3.01:0,3,41 0/0:9,0:9:27.09:0,27,349 0/0:7,0:7:21.07:0,21,277 0/0:7,0:7:21.07:0,21,277 0/0:9,0:9:27.07:0,27,331 0/0:15,0:15:45.14:0,45,584 0/0:21,0:21:63.20:0,63,810 0/0:8,0:8:24.08:0,24,310 0/0:8,0:8:24.07:0,24,299 0/0:7,0:7:21.06:0,21,253 0/0:6,0:6:18.06:0,18,232 0/1:6,3:9:79.16:79,0,202 0/0:9,0:9:27.07:0,27,320 0/0:7,0:7:21.04:0,21,254 0/0:6,0:6:15.05:0,15,191 0/0:15,0:15:39.10:0,39,471 0/0:5,0:5:15.03:0,15,170 0/0:5,0:5:12.03:0,12,152 0/0:8,0:8:24.07:0,24,303 0/0:8,0:8:21.07:0,21,271 0/0:5,0:5:15.05:0,15,188 0/0:18,0:18:51.16:0,51,661 0/0:7,1:8:18.06:0,18,237 0/0:7,0:7:21.07:0,21,265 0/0:8,0:8:18.06:0,18,240 0/0:15,0:15:36.11:0,36,458 0/1:1,1:2:27.42:31,0,27 0/0:8,0:8:24.05:0,24,283 0/0:10,0:10:27.09:0,27,358 0/0:9,0:9:27.07:0,27,332 0/0:10,0:10:30.09:0,30,374 0/1:4,7:11:73.98:204,0,74 0/1:2,9:11:48.49:286,0,48 0/0:6,0:6:18.06:0,18,240 0/0:18,0:18:51.11:0,51,630 0/0:9,0:9:27.08:0,27,339 0/0:25,0:25:66.21:0,66,843 0/0:19,0:19:51.16:0,51,624 0/0:14,0:14:36.12:0,36,475 0/0:17,0:17:48.15:0,48,616 0/0:14,0:14:42.13:0,42,538 0/0:16,0:16:45.15:0,45,591 0/0:16,0:16:48.15:0,48,601 0/0:38,0:38:99:0,99,1287 0/0:15,0:15:39.12:0,39,496 0/0:6,0:6:15.05:0,15,201 0/0:31,0:31:90.28:0,90,1128 0/0:32,1:33:90.25:0,90,1083 0/0:16,0:16:45.14:0,45,565 0/0:30,0:30:81.26:0,81,1049 0/0:20,0:20:45.13:0,45,545 0/0:18,0:18:54.15:0,54,691 0/1:6,5:11:99:162,0,178 0/0:6,0:6:12.04:0,12,157 0/0:10,1:11:30.09:0,30,386 0/1:6,3:9:90.95:91,0,139 0/0:7,0:7:18.05:0,18,215 -chr1 1147297 . G A 1091.92 . AC=6;AF=0.0508;AN=118;BaseQRankSum=-0.085;DP=1113;Dels=0.00;FS=5.569;HRun=0;HaplotypeScore=0.7306;InbreedingCoeff=-0.0597;MQ=55.37;MQ0=0;MQRankSum=0.517;QD=12.55;ReadPosRankSum=1.988;EFF=DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|5),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|4);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,40 0/0:4,0:4:6.02:0,6,68 ./. 0/0:6,0:6:18.05:0,18,219 0/0:8,0:8:24.08:0,24,321 0/0:8,0:8:24.08:0,24,319 0/0:16,0:16:48.14:0,48,596 0/0:9,0:9:27.08:0,27,342 0/0:29,0:29:87.28:0,87,1131 0/0:28,0:29:78.26:0,78,1045 0/0:9,0:9:24.08:0,24,323 0/0:6,0:6:18.04:0,18,218 0/0:13,0:13:39.13:0,39,514 0/0:11,0:11:33.10:0,33,427 0/1:12,6:18:99:147,0,325 0/0:11,0:11:27.08:0,27,336 0/0:6,0:6:18.05:0,18,221 0/0:6,0:6:15.02:0,15,169 0/0:11,0:12:30.10:0,30,387 0/0:8,0:8:24.08:0,24,316 0/0:12,0:12:36.12:0,36,479 0/0:9,0:9:27.09:0,27,346 0/0:12,0:12:36.11:0,36,462 0/0:7,0:7:18.06:0,18,234 0/0:20,0:20:54.17:0,54,702 0/0:6,0:6:15.03:0,15,190 0/0:4,0:4:12.02:0,12,142 0/0:7,0:7:18.06:0,18,242 0/0:15,0:15:36.12:0,36,482 0/1:4,4:8:95.04:96,0,95 0/0:11,0:12:33.11:0,33,435 0/0:7,0:7:21.06:0,21,258 0/0:11,0:11:27.09:0,27,352 0/0:14,0:14:39.13:0,39,523 0/1:2,4:6:61.75:126,0,62 0/1:1,5:6:24.18:165,0,24 0/0:10,0:10:24.07:0,24,305 0/0:17,0:17:51.14:0,51,629 0/0:27,0:27:66.21:0,66,866 0/0:43,0:44:99:0,102,1253 0/0:34,0:34:81.24:0,81,983 0/0:30,0:30:78.24:0,78,985 0/0:28,0:28:75.23:0,75,915 0/0:25,0:25:60.17:0,60,738 0/0:30,0:31:78.24:0,78,992 0/0:30,0:30:75.22:0,75,924 0/0:71,0:72:99:0,178,2201 0/0:26,0:26:63.17:0,63,774 0/0:22,0:22:60.18:0,60,754 0/0:54,0:55:99:0,138,1680 0/0:51,0:51:99:0,132,1553 0/0:38,0:38:90.28:0,90,1133 0/0:36,0:39:96.28:0,96,1178 0/0:28,0:29:63.19:0,63,781 0/0:24,0:24:69.19:0,69,863 0/1:10,11:21:99:325,0,210 0/0:20,0:20:48.15:0,48,613 0/0:22,0:23:57.18:0,57,729 0/1:15,12:28:99:347,0,423 0/0:20,0:22:48.14:0,48,582 -chr1 1147337 . C T 274.47 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.893;DP=1689;Dels=0.00;FS=5.279;HRun=0;HaplotypeScore=1.6439;InbreedingCoeff=-0.0134;MQ=55.97;MQ0=0;MQRankSum=3.240;QD=11.93;ReadPosRankSum=0.328;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),DOWNSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|4),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V207M|277|TNFRSF4|protein_coding|CODING|ENST00000379236|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,missense_variant|Gtg/Atg|V/M|ENSG00000186827|TNFRSF4|ENST00000379236|5/7|benign(0.024)|tolerated(0.21)|207/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|4/5||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:6,0:6:18.02:0,18,202 0/0:6,0:6:15.05:0,15,191 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:3.01:0,3,34 0/0:12,0:12:36.11:0,36,460 0/0:16,0:16:48.15:0,48,631 0/0:21,0:21:63.20:0,63,821 0/0:6,0:6:18.06:0,18,243 0/0:28,0:28:84.28:0,84,1121 0/0:30,0:30:90.29:0,90,1202 0/0:13,0:13:33.11:0,33,436 0/0:12,0:12:36.11:0,36,467 0/0:15,0:15:45.12:0,45,574 0/0:20,0:20:48.14:0,48,614 0/0:29,0:29:78.25:0,78,1012 0/0:18,0:18:42.14:0,42,580 0/0:15,0:15:39.09:0,39,474 0/0:12,0:12:33.11:0,33,433 0/0:18,0:18:45.13:0,45,581 0/0:13,0:13:30.10:0,30,402 0/0:19,0:19:45.15:0,45,608 0/0:13,0:13:36.11:0,36,458 0/0:20,0:20:54.16:0,54,683 0/0:12,0:12:30.09:0,30,381 0/0:22,0:22:54.18:0,54,732 0/0:9,0:9:27.08:0,27,336 0/0:15,0:15:39.12:0,39,519 0/0:10,0:11:24.08:0,24,318 0/0:16,0:16:45.15:0,45,586 0/0:12,0:12:30.10:0,30,405 0/0:22,0:22:57.18:0,57,744 0/0:7,0:7:18.06:0,18,230 0/1:11,12:23:99:322,0,269 0/0:25,0:25:63.20:0,63,824 0/0:8,0:8:24.08:0,24,300 0/0:9,0:9:27.09:0,27,366 0/0:17,0:17:36.11:0,36,484 0/0:29,0:29:75.24:0,75,991 0/0:47,0:47:99:0,114,1475 0/0:74,0:75:99:0,184,2355 0/0:59,0:59:99:0,147,1836 0/0:47,0:47:99:0,117,1461 0/0:36,1:37:56.82:0,57,1060 0/0:37,0:37:87.27:0,87,1115 0/0:41,0:41:99:0,99,1249 0/0:54,0:55:99:0,144,1815 0/0:96,0:96:99:0,238,3018 0/0:30,0:30:78.24:0,78,995 0/0:39,0:39:96.31:0,96,1252 0/0:91,0:92:99:0,196,2483 0/0:73,0:75:99:0,178,2195 0/0:61,0:61:99:0,150,1883 0/0:38,0:40:87.28:0,87,1113 0/0:50,0:51:99:0,108,1388 0/0:38,0:38:99:0,102,1290 0/0:34,0:34:87.25:0,87,1102 0/0:38,1:39:63.74:0,64,1228 0/0:40,0:40:99:0,105,1337 0/0:30,0:31:84.26:0,84,1053 0/0:41,0:41:99:0,105,1313 -chr1 1147422 . C T 34265.37 . AC=47;AF=0.3917;AN=120;BaseQRankSum=-3.610;DP=3511;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=2.1684;InbreedingCoeff=0.1904;MQ=57.58;MQ0=0;MQRankSum=0.337;QD=16.76;ReadPosRankSum=-0.698;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),EXON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|4),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|4),SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E178|277|TNFRSF4|protein_coding|CODING|ENST00000379236|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|4/4||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,synonymous_variant|gaG/gaA|E|ENSG00000186827|TNFRSF4|ENST00000379236|5/7|||178/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|4/5||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.03:0,15,169 0/0:6,0:7:18.06:0,18,232 0/0:7,0:7:18.05:0,18,223 0/0:3,0:3:9.03:0,9,109 0/1:13,11:24:99:375,0,370 0/0:18,0:18:54.17:0,54,710 0/1:24,26:50:99:829,0,715 1/1:0,18:18:54.16:689,54,0 0/0:45,0:45:99:0,135,1771 0/0:49,0:49:99:0,141,1759 1/1:0,16:16:48.16:638,48,0 1/1:1,23:24:24.98:783,25,0 0/1:14,10:24:99:312,0,418 1/1:0,19:19:45.10:552,45,0 0/0:37,0:37:84.26:0,84,1080 0/1:16,6:23:98.78:99,0,437 0/0:17,0:17:45.15:0,45,589 0/1:17,11:28:99:307,0,350 0/0:21,0:21:57.17:0,57,712 1/1:0,19:19:42.13:555,42,0 0/0:28,0:28:69.19:0,69,875 0/0:28,0:28:69.19:0,69,876 0/1:21,15:36:99:363,0,523 1/1:0,23:23:51.16:667,51,0 0/1:15,17:32:99:415,0,428 0/0:18,0:18:42.11:0,42,511 1/1:0,24:24:60.18:755,60,0 0/0:20,0:20:45.13:0,45,571 0/1:13,15:28:99:404,0,229 0/0:23,0:23:51.14:0,51,666 0/1:15,20:35:99:549,0,304 0/1:9,14:23:99:339,0,213 0/0:26,0:26:66.20:0,66,821 1/1:0,26:27:72.12:814,72,0 0/1:15,9:24:99:133,0,425 0/1:12,13:25:99:398,0,210 0/1:15,19:34:99:419,0,380 0/0:53,0:53:99:0,126,1636 0/1:47,41:89:99:1066,0,1307 0/0:184,1:185:99:0,399,5259 0/1:88,73:161:99:1825,0,2179 0/1:49,57:106:99:1426,0,1283 0/1:54,43:97:99:999,0,1378 1/1:1,96:98:99:2979,215,0 1/1:2,95:97:99:2706,152,0 0/0:113,1:116:99:0,280,3430 0/0:174,0:174:99:0,421,5219 0/1:34,32:67:99:724,0,732 0/0:110,2:112:99:0,262,3261 0/0:191,0:192:99:0,448,5526 0/1:85,70:156:99:1727,0,2201 0/1:59,51:110:99:1297,0,1407 1/1:2,101:103:99:2786,203,0 0/0:119,5:124:99:0,138,3136 1/1:0,86:87:99:2440,198,0 0/1:56,47:103:99:1026,0,1387 0/0:73,0:74:99:0,180,2194 0/1:57,58:115:99:1285,0,1322 0/1:43,57:100:99:1585,0,1027 0/0:83,0:83:99:0,202,2550 -chr1 1147655 . G A 774.9 . AC=2;AF=0.0172;AN=116;BaseQRankSum=-2.234;DP=863;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5174;InbreedingCoeff=-0.0388;MQ=57.75;MQ0=0;MQRankSum=2.030;QD=11.07;ReadPosRankSum=-0.644;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|4),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|3),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|3);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12.04:0,12,145 0/0:2,0:2:6.02:0,6,69 0/0:3,0:4:9.03:0,9,118 0/0:5,0:5:9.02:0,9,109 0/0:5,0:5:15.05:0,15,192 0/0:10,0:10:27.08:0,27,345 0/0:25,0:26:72.22:0,72,927 0/0:6,0:6:18.05:0,18,224 0/0:18,0:18:54.14:0,54,670 0/0:17,0:17:48.15:0,48,625 0/0:7,0:7:21.07:0,21,273 0/0:11,0:11:24.07:0,24,296 0/0:8,0:8:21.06:0,21,256 0/0:6,0:6:12.04:0,12,156 0/0:3,0:3:9.03:0,9,104 0/0:5,0:5:15.05:0,15,198 0/0:4,0:4:12.03:0,12,149 ./. 0/0:7,0:7:18.05:0,18,227 0/0:1,0:1:3.01:0,3,37 0/0:4,0:4:12.04:0,12,154 0/0:6,0:6:15.05:0,15,192 0/0:5,0:5:15.05:0,15,185 0/0:5,0:5:15.05:0,15,191 0/0:3,0:4:9.03:0,9,117 0/0:4,0:4:9.03:0,9,112 0/0:3,0:3:9.03:0,9,105 0/0:2,0:2:6.02:0,6,76 0/0:13,0:13:27.08:0,27,341 0/0:2,0:2:6.02:0,6,76 0/0:7,0:7:18.06:0,18,238 0/0:6,0:6:15.05:0,15,200 0/0:7,0:7:21.07:0,21,273 0/0:5,0:5:15.05:0,15,186 ./. 0/0:10,0:10:21.07:0,21,271 0/0:2,0:2:6.02:0,6,76 0/0:14,0:14:33.09:0,33,391 0/0:18,0:18:48.12:0,48,600 0/0:34,0:34:99:0,102,1273 0/0:24,0:24:63.20:0,63,789 0/0:22,0:22:60.18:0,60,756 0/0:21,0:23:45.14:0,45,573 0/0:22,0:22:63.19:0,63,795 0/0:22,0:22:63.19:0,63,767 0/0:22,0:23:57.15:0,57,695 0/0:47,0:48:99:0,114,1393 0/1:10,9:19:99:259,0,238 0/0:19,0:19:45.14:0,45,571 0/1:27,24:51:99:581,0,782 0/0:50,0:51:99:0,144,1766 0/0:41,0:41:99:0,114,1439 0/0:40,0:41:99:0,105,1299 0/0:28,0:28:66.20:0,66,816 0/0:29,0:29:75.22:0,75,929 0/0:20,0:20:54.16:0,54,678 0/0:23,0:23:63.19:0,63,783 0/0:22,1:23:57.17:0,57,718 0/0:14,1:15:39.12:0,39,488 0/0:18,0:18:39.10:0,39,491 -chr1 1147770 . G A 69.21 . AC=2;AF=0.0196;AN=102;BaseQRankSum=-0.351;DP=166;Dels=0.00;FS=2.592;HRun=0;HaplotypeScore=0.1050;InbreedingCoeff=-0.1133;MQ=58.60;MQ0=0;MQRankSum=0.830;QD=7.69;ReadPosRankSum=-1.788;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|4),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|3),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|3);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,113 0/0:4,0:4:12.04:0,12,156 0/0:2,0:2:3.01:0,3,38 0/0:2,0:2:3.01:0,3,32 0/0:3,0:3:9.02:0,9,110 0/0:5,0:5:15.05:0,15,192 0/0:4,0:4:12.04:0,12,156 ./. 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:9.03:0,9,123 ./. 0/0:2,0:2:6.02:0,6,82 0/0:3,0:3:6.02:0,6,81 0/0:2,0:2:6.02:0,6,84 ./. 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.02:0,6,65 0/0:2,0:2:6.01:0,6,67 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,37 ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. 0/0:3,0:3:6.02:0,6,78 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,83 0/0:2,0:2:6.02:0,6,83 0/1:2,2:4:60.11:60,0,64 0/0:2,0:2:6.02:0,6,76 0/0:2,0:2:6.02:0,6,76 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:9.03:0,9,114 0/0:6,0:6:18.06:0,18,247 0/0:4,0:4:12.04:0,12,156 0/0:4,0:4:12.03:0,12,153 0/0:4,0:4:12.04:0,12,151 0/0:4,0:4:9.03:0,9,122 0/0:6,0:6:18.06:0,18,247 0/0:3,0:3:9.03:0,9,121 0/0:9,0:9:24.08:0,24,310 0/0:4,0:4:9.03:0,9,121 0/0:1,0:1:3.01:0,3,41 0/0:10,0:10:27.09:0,27,361 0/0:8,0:8:24.08:0,24,306 0/0:4,0:4:12.04:0,12,162 0/0:9,0:9:18.05:0,18,229 0/0:3,0:3:9.03:0,9,112 0/0:3,0:3:9.03:0,9,119 0/0:1,0:1:3.01:0,3,40 ./. 0/0:6,0:6:15.05:0,15,196 0/1:3,2:5:70.95:71,0,73 0/0:1,0:1:3.01:0,3,37 -chr1 1147822 . C T 59.82 . AC=2;AF=0.023;AN=88;BaseQRankSum=-1.601;DP=102;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0561;InbreedingCoeff=0.0325;MQ=56.99;MQ0=0;MQRankSum=1.803;QD=11.96;ReadPosRankSum=-2.039;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|4),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|3),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|3);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:3:6.02:0,6,78 0/0:2,0:2:6.02:0,6,70 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,32 0/0:3,0:3:9.03:0,9,122 ./. ./. 0/0:2,0:2:6.02:0,6,73 ./. 0/0:2,0:2:6.02:0,6,75 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,35 ./. 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:6.02:0,6,72 ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:2,0:2:6.01:0,6,68 1/1:0,5:5:9.03:113,9,0 0/0:2,0:2:6.02:0,6,76 0/0:1,0:1:3.01:0,3,39 ./. 0/0:2,0:2:3.01:0,3,39 0/0:2,0:2:6.02:0,6,84 0/0:4,0:4:9.02:0,9,105 ./. 0/0:2,0:2:6.02:0,6,77 ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,80 0/0:2,0:2:3.01:0,3,42 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.02:0,6,75 0/0:4,0:4:12.03:0,12,144 0/0:2,0:2:6.02:0,6,80 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.02:0,6,71 0/0:1,0:1:3.01:0,3,41 0/0:8,0:8:18.06:0,18,237 0/0:2,0:2:6.02:0,6,76 ./. 0/0:4,0:4:12.03:0,12,149 0/0:4,0:4:12.04:0,12,158 0/0:3,0:3:9.03:0,9,122 0/0:5,0:5:12.04:0,12,147 0/0:2,0:2:6.02:0,6,81 0/0:2,0:2:6.02:0,6,82 0/0:2,0:2:6.02:0,6,77 0/0:1,0:1:3.01:0,3,38 0/0:4,0:4:12.04:0,12,164 0/0:1,0:1:3.01:0,3,35 ./. -chr1 1147976 . A AC 257.05 . AC=13;AF=0.1182;AN=110;BaseQRankSum=3.114;DP=421;FS=9.449;HRun=9;HaplotypeScore=46.1189;InbreedingCoeff=0.0619;MQ=53.84;MQ0=0;MQRankSum=-4.864;QD=2.79;ReadPosRankSum=-0.046;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|4),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|3),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|3);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. ./. 0/0:1,0:1:3:0,3,26 0/1:1,0:1:0:0,0,0 0/0:1,0:1:3:0,3,26 0/0:2,0:2:6:0,6,52 0/0:2,0:3:8.04:0,8,58 0/0:5,0:5:9:0,9,78 0/0:6,0:6:14.99:0,15,130 ./. 0/0:1,0:1:3:0,3,26 ./. 0/0:12,0:12:32.99:0,33,285 0/1:10,3:13:72.81:73,0,129 0/0:7,0:9:22.04:0,22,161 0/0:11,0:11:20.99:0,21,180 0/0:11,0:11:29.99:0,30,259 0/0:10,0:11:26.99:0,27,234 0/0:17,0:17:38.91:0,39,326 0/0:8,0:8:21:0,21,182 0/0:16,1:18:7.82:0,8,283 0/0:6,0:6:15:0,15,130 0/0:15,0:15:38.98:0,39,337 0/0:14,0:15:35.03:0,35,292 0/0:4,0:4:8.99:0,9,78 0/1:7,1:9:13.01:13,0,112 0/0:6,0:6:17.03:0,17,136 0/0:9,0:9:20.99:0,21,182 0/1:6,2:8:67.32:67,0,105 0/0:8,0:8:11.99:0,12,104 0/1:9,2:11:43.76:44,0,152 0/1:8,1:10:6.70:7,0,165 0/0:20,0:21:19.74:0,20,337 0/0:4,0:4:8.99:0,9,76 0/0:7,0:7:17.03:0,17,136 0/0:19,0:20:50.02:0,50,423 0/0:20,1:22:17.76:0,18,378 0/0:4,0:4:12:0,12,104 0/0:9,0:9:11.76:0,12,193 0/0:6,0:6:17.99:0,18,156 0/0:3,0:4:8.01:0,8,53 0/0:8,0:9:22.25:0,22,158 0/0:4,0:5:14.03:0,14,110 0/1:3,2:5:16.38:57,0,16 0/0:4,0:4:8.99:0,9,78 0/1:11,1:12:24.35:24,0,132 0/1:1,1:2:0:0,0,0 0/0:4,0:4:9:0,9,78 1/1:2,3:8:14.50:102,14,0 0/0:8,0:8:11.95:0,12,98 0/0:3,0:3:3:0,3,26 0/0:3,0:3:9:0,9,78 0/0:5,0:5:9:0,9,78 0/0:4,0:4:11.97:0,12,98 0/0:4,0:4:9:0,9,78 0/0:2,0:2:6:0,6,52 0/1:7,0:7:6.21:6,0,89 0/1:6,0:6:15.27:15,0,66 0/0:1,0:1:3:0,3,26 -chr1 1147983 . C T 450.24 . AC=6;AF=0.0545;AN=110;BaseQRankSum=-1.143;DP=492;Dels=0.01;FS=1.490;HRun=0;HaplotypeScore=2.2660;InbreedingCoeff=-0.0917;MQ=53.74;MQ0=0;MQRankSum=-5.572;QD=5.85;ReadPosRankSum=-5.673;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|4),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|3),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|3);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,121 0/0:5,0:5:15.05:0,15,204 0/0:3,0:3:9.03:0,9,123 0/0:6,0:6:18.06:0,18,224 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:9.03:0,9,124 ./. 0/0:12,0:12:30.10:0,30,399 0/1:14,9:23:99:240,0,308 0/0:9,0:9:27.09:0,27,354 0/0:12,0:12:24.08:0,24,309 0/0:12,0:12:33.09:0,33,423 0/0:11,0:11:30.08:0,30,385 0/0:21,0:21:51.16:0,51,661 0/0:10,0:10:24.07:0,24,307 0/0:19,0:19:48.15:0,48,619 0/0:7,0:7:18.06:0,18,230 0/0:18,0:18:45.13:0,45,586 0/0:17,0:17:45.13:0,45,566 0/0:6,0:6:15.04:0,15,182 0/0:9,0:9:18.06:0,18,233 0/0:8,0:8:24.08:0,24,313 0/0:9,0:9:24.08:0,24,309 0/1:7,4:11:75.35:75,0,240 0/0:10,0:10:21.05:0,21,255 0/1:10,5:15:99:112,0,328 0/0:11,0:11:33.09:0,33,403 0/0:22,0:22:54.17:0,54,702 0/1:4,1:5:18.39:18,0,137 0/1:7,3:10:75.04:75,0,200 0/0:25,0:25:66.21:0,66,879 0/0:26,0:26:69.22:0,69,877 0/0:4,0:4:12.04:0,12,160 0/0:9,0:9:27.08:0,27,349 0/0:7,0:7:21.07:0,21,275 0/0:4,0:4:6.02:0,6,86 0/0:10,0:10:27.08:0,27,347 0/0:5,0:5:15.05:0,15,184 0/0:5,0:5:12.02:0,12,139 0/0:5,0:5:15.05:0,15,183 0/0:12,0:12:24.07:0,24,294 0/0:3,0:3:6.02:0,6,76 0/0:4,0:4:9.03:0,9,109 0/1:7,3:10:39.79:40,0,207 0/0:8,0:8:21.06:0,21,253 0/0:3,0:3:3.01:0,3,39 0/0:3,0:3:9.03:0,9,124 0/0:7,0:7:15.05:0,15,189 0/0:5,0:5:12.04:0,12,160 0/0:5,0:5:12.04:0,12,148 0/0:3,0:3:9.03:0,9,107 0/0:7,0:7:15.03:0,15,181 0/0:7,0:7:18.05:0,18,225 0/0:1,0:1:3.01:0,3,37 -chr1 1147985 . C A 474.8 . AC=7;AF=0.0648;AN=108;BaseQRankSum=1.860;DP=505;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=2.2858;InbreedingCoeff=-0.0990;MQ=53.76;MQ0=0;MQRankSum=-5.601;QD=5.59;ReadPosRankSum=-5.790;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|4),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|3),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|3);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,122 0/0:5,0:5:15.05:0,15,197 0/0:3,0:3:9.03:0,9,121 0/0:5,0:5:15.05:0,15,189 ./. 0/0:3,0:3:9.03:0,9,124 ./. 0/0:12,0:12:33.11:0,33,432 0/1:13,10:23:99:245,0,334 0/0:9,0:9:27.08:0,27,337 0/0:11,0:11:24.08:0,24,302 0/0:12,0:12:33.09:0,33,423 0/0:12,0:12:30.10:0,30,399 0/0:21,0:21:48.16:0,48,636 0/0:10,0:10:24.08:0,24,311 0/0:19,0:19:42.13:0,42,552 0/0:7,0:7:15.05:0,15,190 0/0:19,0:19:48.16:0,48,645 0/0:18,0:18:39.11:0,39,483 0/0:6,0:6:15.05:0,15,189 0/0:9,0:9:18.05:0,18,229 0/0:8,0:8:24.08:0,24,321 0/0:9,0:9:21.07:0,21,271 0/1:8,3:11:67.20:67,0,275 0/0:10,0:10:21.06:0,21,259 0/1:10,5:15:99:125,0,323 0/0:11,0:11:30.07:0,30,359 0/0:23,0:23:57.18:0,57,723 0/1:4,1:5:18.39:18,0,131 0/1:7,3:10:79.79:80,0,206 0/0:25,0:25:63.20:0,63,823 0/0:29,0:29:75.23:0,75,938 0/0:4,0:4:12.04:0,12,163 0/0:9,0:9:27.08:0,27,339 0/0:7,0:7:21.07:0,21,280 0/0:7,0:7:15.05:0,15,197 0/0:10,0:10:24.08:0,24,313 0/0:6,0:6:18.05:0,18,210 0/0:4,0:5:12.04:0,12,142 0/0:5,0:5:12.04:0,12,148 0/0:13,0:13:24.07:0,24,288 0/0:3,0:3:6.02:0,6,72 0/0:4,0:4:9.03:0,9,109 0/1:8,2:10:42.80:43,0,177 0/0:8,0:8:18.05:0,18,208 0/0:3,0:3:3.01:0,3,39 0/0:4,0:4:9.03:0,9,125 0/0:8,0:8:18.06:0,18,228 0/0:5,0:5:12.04:0,12,163 0/0:5,0:5:12.04:0,12,150 0/0:3,0:3:9.03:0,9,102 0/0:7,0:7:15.03:0,15,179 0/1:7,1:8:14.19:14,0,201 0/0:1,0:1:3.01:0,3,39 -chr1 1148100 . G A 407.86 . AC=4;AF=0.0333;AN=120;BaseQRankSum=0.544;DP=1027;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7645;InbreedingCoeff=-0.0459;MQ=57.31;MQ0=0;MQRankSum=2.510;QD=7.16;ReadPosRankSum=-1.015;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|3),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|2),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|2);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,104 0/0:2,0:2:6.02:0,6,80 0/0:4,0:4:9.03:0,9,113 0/0:3,0:3:6.02:0,6,77 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:6.02:0,6,76 0/0:8,0:8:24.05:0,24,291 0/1:2,3:5:56.34:102,0,56 0/0:9,0:9:27.08:0,27,334 0/0:13,0:13:36.12:0,36,471 0/0:3,0:3:9.03:0,9,117 0/0:2,0:2:6.02:0,6,75 0/0:7,0:7:21.07:0,21,271 0/0:24,0:24:57.18:0,57,761 0/0:32,0:32:84.22:0,84,1052 0/1:11,9:20:99:244,0,273 0/0:19,0:19:54.18:0,54,707 0/0:20,0:20:54.17:0,54,702 0/0:15,0:16:39.13:0,39,527 0/0:24,0:24:63.20:0,63,843 0/0:14,0:14:39.05:0,39,475 0/0:22,0:22:51.17:0,51,697 0/0:15,0:15:39.12:0,39,510 0/0:18,0:18:48.16:0,48,638 0/0:29,0:29:69.21:0,69,892 0/0:17,0:17:39.09:0,39,491 0/0:18,0:18:42.10:0,42,531 0/0:16,0:16:39.12:0,39,509 0/0:18,0:18:51.16:0,51,650 0/0:19,0:19:48.14:0,48,614 0/0:22,0:22:51.16:0,51,680 0/0:8,0:21:21.06:0,21,270 0/0:25,0:25:63.17:0,63,793 0/0:26,0:27:69.21:0,69,875 0/0:18,0:18:42.13:0,42,546 0/0:26,0:26:57.18:0,57,744 0/0:28,0:28:75.24:0,75,973 0/0:38,0:38:93.29:0,93,1240 0/0:15,0:15:39.13:0,39,525 0/0:23,0:23:51.16:0,51,663 0/0:24,0:24:54.17:0,54,722 0/0:11,0:11:24.08:0,24,314 0/1:10,6:16:99:140,0,284 0/0:15,0:15:36.11:0,36,447 0/0:7,0:13:21.06:0,21,248 0/0:23,0:23:57.18:0,57,726 0/0:26,0:26:63.19:0,63,788 0/0:14,0:14:33.10:0,33,417 0/0:22,0:22:48.15:0,48,617 0/0:36,0:36:72.22:0,72,928 0/0:29,1:30:75.23:0,75,940 0/1:15,1:16:9.12:9,0,381 0/0:17,0:17:36.11:0,36,469 0/0:18,0:18:39.12:0,39,508 0/0:16,0:16:42.11:0,42,546 0/0:18,0:18:39.11:0,39,498 0/0:12,0:12:30.10:0,30,397 0/0:24,0:24:54.17:0,54,724 0/0:15,0:15:36.11:0,36,461 0/0:13,0:13:27.09:0,27,371 -chr1 1148354 . C G 126.37 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.471;DP=949;Dels=0.00;FS=7.261;HRun=1;HaplotypeScore=0.7234;InbreedingCoeff=-0.0178;MQ=58.63;MQ0=0;MQRankSum=0.297;QD=7.43;ReadPosRankSum=0.432;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|3),INTRON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|2),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|2);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.02:0,9,107 0/0:3,0:3:6.02:0,6,75 0/0:2,0:2:6.02:0,6,77 0/0:5,0:5:6.02:0,6,76 0/0:6,0:6:18.06:0,18,232 0/0:10,0:10:24.08:0,24,313 0/0:26,0:26:75.25:0,75,998 0/0:7,0:7:18.06:0,18,242 0/0:35,0:35:96.32:0,96,1300 0/0:22,0:22:66.20:0,66,839 0/0:10,0:10:30.06:0,30,374 0/0:9,0:9:24.08:0,24,314 0/0:11,0:11:33.10:0,33,424 0/1:9,8:17:99:174,0,240 0/0:21,1:22:57.16:0,57,723 0/0:20,0:20:51.16:0,51,666 0/0:25,0:25:63.18:0,63,795 0/0:22,0:22:54.17:0,54,714 0/0:27,0:28:63.20:0,63,854 0/0:16,0:16:39.13:0,39,523 0/0:10,0:10:24.07:0,24,298 0/0:27,0:27:66.21:0,66,852 0/0:25,1:26:57.16:0,57,709 0/0:25,0:26:57.17:0,57,737 0/0:14,0:14:33.09:0,33,420 0/0:16,0:16:42.12:0,42,539 0/0:18,0:18:45.14:0,45,587 0/0:21,0:21:48.14:0,48,618 0/0:23,0:24:48.13:0,48,630 0/0:19,0:19:45.14:0,45,595 0/0:34,0:34:75.23:0,75,973 0/0:25,0:25:48.14:0,48,607 0/0:21,0:21:42.13:0,42,572 0/0:22,0:22:51.15:0,51,667 0/0:17,0:17:45.13:0,45,568 0/0:20,0:20:45.12:0,45,554 0/0:23,0:23:57.18:0,57,738 0/0:31,0:31:87.27:0,87,1134 0/0:8,0:8:21.07:0,21,285 0/0:19,0:19:42.13:0,42,539 0/0:10,1:11:27.06:0,27,322 0/0:8,0:8:21.05:0,21,248 0/0:10,0:10:27.08:0,27,344 0/0:9,0:9:21.05:0,21,256 0/0:11,0:11:30.10:0,30,389 0/0:12,0:12:33.11:0,33,436 0/0:22,0:22:39.12:0,39,512 0/0:11,0:11:24.07:0,24,315 0/0:16,0:16:39.12:0,39,503 0/0:18,0:18:45.12:0,45,553 0/0:22,0:22:60.19:0,60,785 0/0:9,0:9:21.06:0,21,239 0/0:6,0:6:15.05:0,15,199 0/0:10,0:10:24.05:0,24,303 0/0:20,0:20:42.14:0,42,582 0/0:10,0:10:27.08:0,27,333 0/0:4,0:4:12.04:0,12,153 0/0:2,0:2:6.02:0,6,82 0/0:8,0:8:24.07:0,24,295 0/0:9,0:9:21.07:0,21,276 -chr1 1148445 . G A 646.52 . AC=4;AF=0.0333;AN=120;BaseQRankSum=-2.708;DP=1141;Dels=0.00;FS=9.672;HRun=0;HaplotypeScore=0.7418;InbreedingCoeff=-0.0474;MQ=58.91;MQ0=0;MQRankSum=1.939;QD=10.60;ReadPosRankSum=0.841;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),EXON(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|2),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|2),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C99|277|TNFRSF4|protein_coding|CODING|ENST00000379236|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|2/4||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,synonymous_variant|tgC/tgT|C|ENSG00000186827|TNFRSF4|ENST00000379236|3/7|||99/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|2/5||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:6,0:6:18.04:0,18,209 0/0:1,0:1:3.01:0,3,34 0/0:7,0:7:15.04:0,15,184 0/0:2,0:2:6.02:0,6,77 0/0:6,0:6:15.05:0,15,188 0/0:7,0:7:15.05:0,15,194 0/0:25,0:25:72.20:0,72,896 0/1:6,4:10:86.88:87,0,194 0/0:32,0:32:84.26:0,84,1072 0/0:24,0:24:60.19:0,60,776 0/0:12,0:12:33.09:0,33,404 0/0:7,0:7:15.04:0,15,180 0/0:13,0:13:39.12:0,39,504 0/0:32,0:32:78.22:0,78,985 0/0:21,0:21:51.16:0,51,665 0/0:23,0:23:54.15:0,54,703 0/0:30,0:30:75.23:0,75,973 0/0:29,0:29:63.20:0,63,823 0/0:24,0:24:54.18:0,54,732 0/0:34,0:34:75.21:0,75,976 0/0:16,0:16:33.11:0,33,439 0/0:36,0:36:75.24:0,75,1006 0/0:26,0:26:66.19:0,66,797 0/0:27,0:27:60.17:0,60,765 0/1:12,12:24:99:267,0,304 0/0:25,0:25:54.17:0,54,718 0/0:26,0:26:63.20:0,63,821 0/0:24,0:24:54.17:0,54,699 0/0:32,0:32:60.19:0,60,814 0/0:33,0:33:63.19:0,63,837 0/0:22,0:22:60.19:0,60,767 0/0:31,0:31:75.22:0,75,964 0/0:22,0:22:54.16:0,54,688 0/0:33,0:33:69.20:0,69,891 0/0:18,0:18:42.14:0,42,565 0/0:29,0:30:60.18:0,60,787 0/0:23,0:23:63.20:0,63,827 0/0:46,0:46:99:0,114,1524 0/0:3,0:3:9.02:0,9,106 0/0:33,0:33:72.23:0,72,949 0/0:21,0:21:54.12:0,54,639 0/0:10,0:10:24.05:0,24,293 0/0:10,0:10:24.08:0,24,302 0/1:8,3:11:62.99:63,0,240 0/0:12,0:12:30.08:0,30,360 0/0:7,0:7:15.05:0,15,195 0/0:25,0:25:54.15:0,54,658 0/0:9,0:9:15.05:0,15,194 0/0:15,0:15:36.12:0,36,489 0/0:28,0:29:63.16:0,63,747 0/0:25,0:25:60.16:0,60,740 0/1:5,11:16:99:322,0,125 0/0:10,0:10:27.09:0,27,350 0/0:8,0:8:21.07:0,21,281 0/0:17,2:19:0.40:0,0,499 0/0:11,0:11:33.10:0,33,406 0/0:4,0:4:12.04:0,12,145 0/0:6,0:6:18.05:0,18,226 0/0:6,0:6:15.03:0,15,169 0/0:12,0:12:30.09:0,30,393 -chr1 1149222 . C G 291.64 . AC=2;AF=0.0169;AN=118;BaseQRankSum=1.786;DP=868;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7514;InbreedingCoeff=-0.0246;MQ=55.49;MQ0=0;MQRankSum=1.770;QD=10.80;ReadPosRankSum=1.215;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|1),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|1),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:9.01:0,9,99 0/0:2,0:2:6.02:0,6,74 0/0:4,0:4:12.03:0,12,148 0/0:5,0:5:15.04:0,15,190 0/0:8,0:8:24.08:0,24,318 0/0:7,0:7:21.07:0,21,281 0/0:3,0:3:9.03:0,9,117 0/0:18,0:18:48.16:0,48,641 0/0:11,0:11:33.10:0,33,433 0/0:4,0:4:12.04:0,12,159 0/0:3,0:3:9.03:0,9,110 0/0:10,0:10:27.08:0,27,339 0/0:6,0:6:18.06:0,18,226 0/0:13,0:13:39.12:0,39,478 0/1:4,6:10:99:167,0,119 0/0:7,0:7:18.06:0,18,231 0/0:7,0:7:18.06:0,18,230 0/0:15,0:15:42.07:0,42,477 0/0:10,0:10:30.06:0,30,347 0/0:13,0:13:33.10:0,33,418 0/0:17,0:17:39.10:0,39,466 0/0:17,0:17:45.13:0,45,555 0/0:11,0:11:33.10:0,33,411 0/0:15,0:15:36.10:0,36,421 0/0:8,0:8:24.07:0,24,295 0/0:16,0:16:48.12:0,48,566 0/0:8,0:8:24.07:0,24,300 0/0:11,0:11:30.09:0,30,369 0/0:10,0:10:27.08:0,27,336 0/0:17,0:17:45.14:0,45,569 0/0:9,0:9:24.08:0,24,300 0/0:16,0:16:30.08:0,30,355 0/0:11,0:11:30.09:0,30,380 0/0:11,0:11:24.07:0,24,289 0/0:13,0:13:36.08:0,36,432 0/0:17,0:17:48.14:0,48,580 0/0:14,0:14:36.11:0,36,458 0/0:20,0:20:42.13:0,42,521 0/0:35,0:35:93.28:0,93,1142 0/0:30,0:30:78.21:0,78,926 0/0:13,0:13:33.10:0,33,415 0/1:10,7:17:99:190,0,308 0/0:18,0:18:48.13:0,48,592 0/0:15,0:15:36.10:0,36,437 0/0:37,0:37:84.26:0,84,1061 0/0:32,0:32:75.22:0,75,932 0/0:11,0:11:12.04:0,12,148 0/0:14,0:14:39.12:0,39,489 0/0:38,0:38:96.28:0,96,1177 0/0:41,2:43:99:0,108,1312 0/0:31,0:31:72.22:0,72,895 0/0:25,0:25:72.15:0,72,808 0/0:16,0:16:39.10:0,39,463 0/0:20,0:20:48.12:0,48,584 0/0:15,0:15:30.08:0,30,349 0/0:14,0:14:36.12:0,36,461 0/0:16,0:16:42.12:0,42,501 0/0:14,0:14:33.10:0,33,410 0/0:14,0:14:36.08:0,36,419 -chr1 1149272 . T C 57.68 . AC=9;AF=0.0750;AN=120;BaseQRankSum=-9.463;DP=854;Dels=0.00;FS=62.532;HRun=5;HaplotypeScore=2.2956;InbreedingCoeff=-0.0979;MQ=53.68;MQ0=0;MQRankSum=-8.286;QD=0.57;ReadPosRankSum=-1.613;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|1),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|1),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,37 0/0:4,0:4:6.02:0,6,81 0/0:7,0:7:21.06:0,21,264 0/0:7,1:8:18.06:0,18,238 0/0:12,0:12:36.08:0,36,442 0/0:7,0:7:18.05:0,18,213 0/0:18,0:18:51.13:0,51,619 0/0:21,0:21:63.14:0,63,730 0/0:8,0:8:24.07:0,24,308 0/0:8,0:8:15.04:0,15,176 0/0:12,1:13:27.06:0,27,331 0/0:8,1:9:15.04:0,15,175 0/1:9,3:12:6.66:7,0,143 0/0:14,1:16:14.39:0,14,396 0/0:10,0:10:24.07:0,24,301 0/1:5,1:6:12.66:13,0,95 0/0:16,5:21:23.44:0,23,515 0/0:10,6:16:0.37:0,0,233 0/0:16,4:20:33.09:0,33,413 0/0:15,5:20:33.09:0,33,399 0/1:11,4:15:4.60:5,0,212 0/0:8,3:11:21.05:0,21,239 0/0:13,3:16:30.02:0,30,314 0/0:14,4:18:24.05:0,24,268 0/0:16,3:19:14.42:0,14,422 0/1:7,1:8:10.50:11,0,174 0/0:12,1:13:30.06:0,30,360 0/0:13,2:15:24.08:0,24,314 0/0:14,4:18:32.69:0,33,393 0/0:12,2:14:24.05:0,24,278 0/0:12,5:17:1.55:0,2,342 0/0:10,3:13:3.38:0,3,275 0/0:14,2:16:30.07:0,30,337 0/1:7,2:9:32.28:32,0,167 0/0:11,7:19:15.61:0,16,228 0/0:12,4:16:18.06:0,18,230 0/1:7,7:14:57.75:58,0,189 0/0:21,3:24:33.46:0,33,627 0/0:17,3:20:51.12:0,51,578 0/0:13,2:15:6.47:0,6,348 0/0:14,2:16:33.10:0,33,403 0/0:9,0:9:18.05:0,18,216 0/0:18,1:19:42.10:0,42,499 0/0:20,4:24:25.61:0,26,627 0/0:28,2:30:60.18:0,60,752 0/1:9,2:12:6.39:6,0,245 0/0:8,2:10:18.06:0,18,226 0/0:22,7:29:63.19:0,63,765 0/0:21,5:27:20.82:0,21,751 0/0:18,7:25:48.14:0,48,598 0/0:14,3:17:39.10:0,39,457 0/0:13,0:13:36.10:0,36,445 0/0:11,1:12:30.08:0,30,350 0/1:11,4:15:0.33:0,0,353 0/0:12,0:13:33.09:0,33,391 0/0:14,0:14:33.10:0,33,413 0/1:7,4:11:37.33:37,0,99 0/0:6,1:7:12.04:0,12,162 -chr1 1149316 . C G 1809.62 . AC=6;AF=0.0500;AN=120;BaseQRankSum=-2.427;DP=1206;Dels=0.00;FS=7.512;HRun=0;HaplotypeScore=1.0567;InbreedingCoeff=0.2590;MQ=55.74;MQ0=0;MQRankSum=3.245;QD=14.14;ReadPosRankSum=1.300;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),INTRON(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|1),INTRON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|1),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:3:6.01:0,6,64 0/0:3,0:3:9.03:0,9,111 0/0:3,0:3:6.02:0,6,81 0/0:3,0:3:9.03:0,9,105 0/0:10,0:10:30.10:0,30,407 0/0:7,0:7:18.06:0,18,238 0/0:16,0:16:42.11:0,42,524 0/0:6,0:6:18.06:0,18,243 0/0:20,0:20:60.20:0,60,802 0/0:18,0:18:54.17:0,54,711 0/0:13,0:13:39.13:0,39,523 0/0:16,0:16:45.14:0,45,572 0/0:11,0:11:30.09:0,30,385 0/0:24,0:24:54.16:0,54,692 0/0:17,0:17:39.12:0,39,503 0/1:17,12:29:99:273,0,459 0/0:22,0:22:57.19:0,57,785 0/0:14,0:14:33.11:0,33,435 0/0:28,0:28:66.21:0,66,871 0/0:26,0:26:60.14:0,60,739 0/0:30,0:30:66.21:0,66,889 0/0:26,0:27:69.22:0,69,902 0/0:26,0:26:66.21:0,66,858 0/0:16,0:17:39.13:0,39,520 0/0:35,0:35:90.29:0,90,1186 0/0:25,0:25:54.17:0,54,695 0/0:27,0:27:57.18:0,57,757 0/0:14,0:14:39.13:0,39,515 0/0:24,0:24:45.14:0,45,601 0/0:20,0:20:57.17:0,57,709 0/0:35,0:35:90.29:0,90,1196 0/1:16,13:29:99:265,0,420 0/0:26,0:26:66.21:0,66,865 0/0:26,0:26:54.17:0,54,693 0/0:29,0:29:63.16:0,63,801 0/0:15,0:15:42.12:0,42,531 0/0:29,0:29:72.22:0,72,917 0/0:27,0:27:63.20:0,63,849 0/0:15,0:16:36.11:0,36,474 0/0:25,0:25:60.19:0,60,810 0/0:25,0:25:66.21:0,66,855 0/0:17,0:17:42.11:0,42,502 0/1:9,9:18:99:202,0,269 0/0:13,0:13:30.08:0,30,374 1/1:0,24:24:63.19:792,63,0 0/0:19,0:19:51.16:0,51,661 0/0:40,0:40:99:0,102,1298 0/0:16,0:16:45.12:0,45,561 0/0:9,0:9:24.07:0,24,297 0/1:13,15:28:99:398,0,327 0/0:32,0:32:78.23:0,78,995 0/0:29,0:29:72.23:0,72,932 0/0:18,0:18:54.16:0,54,682 0/0:21,0:21:60.19:0,60,789 0/0:21,0:21:54.14:0,54,677 0/0:15,0:15:42.13:0,42,540 0/0:17,1:18:48.15:0,48,609 0/0:20,0:20:51.15:0,51,660 0/0:21,0:21:51.16:0,51,653 0/0:10,0:10:27.08:0,27,336 -chr1 1149480 . G A 811.03 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.272;DP=1806;Dels=0.00;FS=0.697;HRun=0;HaplotypeScore=1.2218;InbreedingCoeff=-0.0227;MQ=56.24;MQ0=0;MQRankSum=1.175;QD=12.48;ReadPosRankSum=1.574;EFF=DOWNSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),DOWNSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),DOWNSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),DOWNSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|),EXON(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R10C|277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,missense_variant|Cgc/Tgc|R/C|ENSG00000186827|TNFRSF4|ENST00000379236|1/7|unknown(0)|deleterious(0)|10/277|protein_coding|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|1/5||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.01:0,6,64 0/0:5,0:5:12.04:0,12,154 0/0:5,0:5:15.05:0,15,189 0/0:9,0:9:21.04:0,21,234 0/0:15,0:15:30.10:0,30,404 0/0:8,0:8:21.07:0,21,274 0/0:23,0:23:51.17:0,51,667 0/0:10,0:10:24.08:0,24,310 0/0:19,0:19:48.15:0,48,613 0/0:17,0:17:36.12:0,36,478 0/0:12,0:12:24.08:0,24,317 0/0:7,0:7:6.02:0,6,78 0/0:7,0:7:18.06:0,18,235 0/0:23,0:23:54.14:0,54,665 0/0:18,0:18:39.13:0,39,532 0/0:4,0:4:9.03:0,9,114 0/0:22,0:23:54.16:0,54,671 0/0:21,0:21:51.16:0,51,667 0/0:13,0:13:27.09:0,27,353 0/0:18,0:18:48.15:0,48,618 0/0:37,0:37:78.21:0,78,987 0/0:30,0:30:72.21:0,72,909 0/0:19,0:19:42.12:0,42,508 0/1:12,11:23:99:234,0,271 0/0:30,0:30:63.17:0,63,796 0/0:21,0:21:51.16:0,51,658 0/0:22,0:22:48.12:0,48,571 0/0:7,0:7:18.05:0,18,220 0/0:13,0:14:33.08:0,33,375 0/0:19,0:19:42.12:0,42,517 0/0:31,0:31:69.22:0,69,875 0/0:19,0:19:48.16:0,48,642 0/0:13,0:13:33.10:0,33,418 0/0:13,0:13:30.09:0,30,388 0/0:16,0:16:33.10:0,33,418 0/0:24,0:24:45.13:0,45,580 0/0:30,0:30:72.23:0,72,934 0/0:39,0:39:93.29:0,93,1199 0/0:43,0:43:99:0,108,1350 0/0:54,0:56:99:0,129,1544 0/0:59,0:59:99:0,132,1612 0/0:55,0:55:99:0,132,1623 0/0:60,0:61:99:0,126,1565 0/0:47,0:47:99:0,102,1248 0/0:43,0:44:99:0,102,1254 0/0:50,0:50:99:0,114,1441 0/0:99,0:100:99:0,199,2444 0/0:27,0:27:63.19:0,63,770 0/0:51,1:52:99:0,123,1548 0/0:48,0:48:99:0,117,1412 0/0:74,0:75:99:0,165,2040 0/0:38,0:39:78.24:0,78,1002 0/0:50,0:51:99:0,111,1383 0/0:62,0:63:99:0,141,1744 0/0:66,0:67:99:0,147,1903 0/1:17,24:42:99:642,0,317 0/0:29,0:29:63.17:0,63,760 0/0:51,0:51:99:0,111,1423 0/0:36,0:36:84.24:0,84,1012 0/0:43,0:43:81.23:0,81,1009 -chr1 1152631 . C A 73.67 . AC=6;AF=0.333;AN=18;BaseQRankSum=1.036;DP=11;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=57.87;MQ0=0;MQRankSum=0.000;QD=18.42;ReadPosRankSum=0.365;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|2),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|3),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),UTR_3_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|7),UTR_3_PRIME(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|7),UTR_3_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|7);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|7/7|||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|3/3||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|2/2||||retained_intron|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000263741|7/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000360001|7/7|||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3.01:41,3,0 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. 1/1:0,2:2:3.01:45,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,37 ./. ./. ./. ./. ./. ./. ./. -chr1 1152794 . A G 38.74 . AC=6;AF=0.250;AN=24;BaseQRankSum=0.720;DP=37;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=0.4589;InbreedingCoeff=0.4010;MQ=52.01;MQ0=0;MQRankSum=-2.348;QD=12.91;ReadPosRankSum=-0.407;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|2),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|3),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),UTR_3_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|7),UTR_3_PRIME(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|7),UTR_3_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|7);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|7/7|||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|3/3||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|2/2||||retained_intron|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000263741|7/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000360001|7/7|||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. 1/1:0,1:1:3.01:33,3,0 ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. 0/0:3,0:3:3.01:0,3,45 ./. ./. 0/0:4,0:4:6.02:0,6,73 0/0:5,0:5:15.04:0,15,177 0/0:8,0:8:24.07:0,24,292 0/0:6,0:6:12.04:0,12,145 ./. 0/0:2,0:2:3.01:0,3,45 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. -chr1 1152798 . A C 38.42 . AC=6;AF=0.250;AN=24;BaseQRankSum=0.147;DP=40;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.4236;InbreedingCoeff=0.4263;MQ=52.65;MQ0=0;MQRankSum=-2.740;QD=12.81;ReadPosRankSum=-1.267;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|2),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|3),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),UTR_3_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|7),UTR_3_PRIME(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|7),UTR_3_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|7);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|7/7|||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|3/3||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|2/2||||retained_intron|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000263741|7/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000360001|7/7|||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. 1/1:0,1:1:3.01:33,3,0 ./. 0/0:1,0:2:3.01:0,3,39 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:3:3.01:0,3,45 ./. ./. 0/0:6,0:6:12.04:0,12,150 0/0:5,0:5:15.05:0,15,181 0/0:8,0:8:21.06:0,21,255 0/0:6,0:6:15.04:0,15,181 ./. 0/0:2,0:2:3.01:0,3,45 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,37 ./. ./. ./. -chr1 1152800 . G C 38.25 . AC=6;AF=0.250;AN=24;BaseQRankSum=-0.172;DP=40;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1945;InbreedingCoeff=0.4359;MQ=52.65;MQ0=0;MQRankSum=-2.690;QD=12.75;ReadPosRankSum=-2.003;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|2),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|3),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),UTR_3_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|7),UTR_3_PRIME(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|7),UTR_3_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|7);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|7/7|||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|3/3||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|2/2||||retained_intron|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000263741|7/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000360001|7/7|||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. 1/1:0,1:1:3.01:33,3,0 ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:3,0:3:3.01:0,3,45 ./. ./. 0/0:6,0:6:18.05:0,18,213 0/0:5,0:5:15.05:0,15,183 0/0:8,0:8:24.07:0,24,292 0/0:6,0:7:18.06:0,18,222 ./. 0/0:2,0:2:3.01:0,3,45 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. -chr1 1152904 . G A 446.25 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.116;DP=2117;Dels=0.00;FS=5.998;HRun=0;HaplotypeScore=1.1651;InbreedingCoeff=-0.0085;MQ=59.10;MQ0=0;MQRankSum=0.448;QD=16.53;ReadPosRankSum=0.722;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|2),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|3),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H359|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),UTR_3_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|7),UTR_3_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|7);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|7/7|||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|3/3||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|2/2||||retained_intron|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000263741|7/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,synonymous_variant|caC/caT|H|ENSG00000078808|SDF4|ENST00000360001|7/7|||359/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/0:16,0:16:42.13:0,42,528 0/0:17,0:17:48.15:0,48,601 0/0:17,0:17:45.14:0,45,585 0/0:10,0:11:24.08:0,24,307 0/0:33,0:33:99:0,99,1344 0/0:34,0:34:99:0,102,1335 0/0:63,0:63:99:0,184,2414 0/0:22,0:22:66.22:0,66,880 0/0:78,0:78:99:0,235,3107 0/0:98,0:98:99:0,289,3825 0/0:31,0:31:90.28:0,90,1172 0/0:22,0:22:63.21:0,63,840 0/0:49,0:49:99:0,147,1937 0/0:36,0:37:99:0,105,1377 0/0:36,0:36:99:0,102,1329 0/0:29,0:29:84.27:0,84,1084 0/0:42,1:43:72.78:0,73,1399 0/0:41,0:41:99:0,114,1501 0/0:39,0:39:99:0,108,1419 0/0:50,0:50:99:0,129,1734 0/0:39,0:39:99:0,99,1281 0/0:48,0:48:99:0,135,1776 0/0:36,0:36:99:0,102,1301 0/0:39,0:40:99:0,102,1341 0/0:40,0:40:99:0,114,1509 0/0:45,0:46:99:0,117,1525 0/0:30,0:30:90.26:0,90,1161 0/0:25,0:25:66.20:0,66,860 0/0:48,0:49:99:0,129,1662 0/0:45,0:45:99:0,126,1669 0/0:63,0:63:99:0,178,2290 0/0:41,0:41:99:0,114,1419 0/0:42,0:42:99:0,117,1511 0/0:33,0:33:96.24:0,96,1190 0/0:40,0:40:99:0,102,1362 0/0:38,0:38:99:0,99,1254 0/0:40,0:40:99:0,108,1413 0/0:67,0:67:99:0,184,2393 0/0:26,0:26:69.18:0,69,850 0/0:43,0:43:99:0,108,1415 0/1:9,18:27:99:494,0,279 0/0:14,0:15:33.09:0,33,423 0/0:16,0:16:45.13:0,45,570 0/0:26,0:26:69.20:0,69,861 0/0:25,0:25:60.19:0,60,789 0/0:34,0:34:81.24:0,81,1026 0/0:30,0:30:81.24:0,81,1028 0/0:9,0:9:27.08:0,27,347 0/0:24,0:24:60.17:0,60,761 0/0:36,0:38:87.26:0,87,1112 0/0:44,0:44:99:0,105,1345 0/0:35,0:35:90.26:0,90,1128 0/0:38,0:38:90.25:0,90,1136 0/0:25,0:25:54.15:0,54,667 0/0:25,0:25:69.22:0,69,911 0/0:17,0:17:48.15:0,48,607 0/0:14,0:14:36.11:0,36,471 0/0:30,0:30:69.21:0,69,886 0/0:26,0:27:66.17:0,66,825 0/0:20,0:20:45.13:0,45,567 -chr1 1153009 . G A 2720.69 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-1.647;DP=5548;Dels=0.00;FS=10.837;HRun=0;HaplotypeScore=3.0829;InbreedingCoeff=0.9964;MQ=59.14;MQ0=0;MQRankSum=-1.581;QD=29.57;ReadPosRankSum=-0.625;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|2),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|3),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A324|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),UTR_3_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|7),UTR_3_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|7);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|7/7|||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|3/3||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|2/2||||retained_intron|1,3_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000263741|7/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000078808|SDF4|ENST00000360001|7/7|||324/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/0:19,1:20:21.52:0,22,563 0/0:17,0:17:42.12:0,42,499 0/0:19,0:19:54.15:0,54,672 0/0:18,0:18:51.09:0,51,575 0/0:57,0:57:99:0,163,2102 0/0:45,0:45:99:0,132,1693 0/0:83,0:84:99:0,238,3075 0/0:29,0:29:87.27:0,87,1118 0/0:115,0:115:99:0,340,4437 0/0:105,0:106:99:0,304,3894 0/0:56,0:56:99:0,156,2000 0/0:34,0:36:96.30:0,96,1221 0/0:61,0:62:99:0,178,2282 0/0:148,0:148:99:0,334,4415 0/0:166,0:169:99:0,385,5002 0/0:124,0:124:99:0,277,3630 0/0:104,0:104:99:0,247,3261 0/0:119,0:119:99:0,283,3641 0/0:165,0:165:99:0,379,5030 0/0:158,0:158:99:0,337,4454 0/0:120,0:120:99:0,250,3319 0/0:162,0:163:99:0,367,4778 0/0:122,0:122:99:0,274,3618 0/0:111,0:111:99:0,271,3529 0/0:127,0:127:99:0,292,3856 0/0:114,0:114:99:0,268,3470 0/0:136,0:136:99:0,310,4070 0/0:84,0:85:99:0,196,2600 0/0:139,0:140:99:0,313,4146 0/0:141,0:141:99:0,328,4196 0/0:147,1:148:99:0,373,4809 0/0:120,0:121:99:0,268,3517 0/0:159,0:160:99:0,376,4920 0/0:145,0:145:99:0,301,3989 0/0:97,0:98:99:0,211,2782 0/0:149,0:150:99:0,313,4240 0/0:143,0:144:99:0,322,4168 0/0:205,0:207:99:0,463,6148 0/0:46,1:47:99:0,108,1430 0/0:95,0:96:99:0,208,2750 0/0:81,0:81:99:0,175,2249 0/0:47,0:47:99:0,99,1301 0/0:53,0:53:99:0,120,1536 0/0:55,0:55:99:0,126,1674 0/0:52,0:52:99:0,123,1576 0/0:64,0:65:99:0,153,1980 0/0:97,0:97:99:0,202,2590 0/0:33,0:33:81.26:0,81,1056 0/0:73,0:73:99:0,159,2122 1/1:0,92:92:99:2792,220,0 0/0:88,0:88:99:0,202,2536 0/0:67,0:69:99:0,175,2254 0/0:77,0:77:99:0,187,2363 0/0:62,0:63:99:0,144,1832 0/0:65,0:65:99:0,144,1877 0/0:69,0:70:99:0,150,1953 0/0:37,0:37:93.29:0,93,1189 0/0:86,0:87:99:0,184,2370 0/0:60,0:60:99:0,132,1761 0/0:56,0:56:99:0,114,1512 -chr1 1153113 . G A 16021.84 . AC=14;AF=0.1167;AN=120;BaseQRankSum=1.612;DP=4750;Dels=0.00;FS=29.208;HRun=1;HaplotypeScore=3.8427;InbreedingCoeff=0.1934;MQ=58.59;MQ0=0;MQRankSum=-0.299;QD=16.67;ReadPosRankSum=2.245;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|6),INTRON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|1),INTRON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|2),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L328|348|SDF4|protein_coding|CODING|ENST00000263741|),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|),UTR_3_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|7);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|7/7|||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,synonymous_variant|ctC/ctT|L|ENSG00000078808|SDF4|ENST00000263741|7/7|||328/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/1:3,6:9:17.59:96,0,18 0/0:15,0:17:27.07:0,27,323 0/0:19,0:20:42.12:0,42,504 0/0:10,0:10:24.06:0,24,283 0/0:50,0:50:99:0,108,1306 0/0:40,0:40:96.29:0,96,1228 0/0:84,0:84:99:0,211,2578 0/0:28,0:28:54.14:0,54,659 0/0:99,0:99:99:0,241,2955 0/0:101,1:102:99:0,232,2834 0/0:51,0:51:99:0,120,1475 0/0:36,0:37:78.22:0,78,963 0/0:63,0:63:99:0,159,1961 0/0:94,0:94:99:0,238,3163 0/1:65,67:132:99:1704,0,1714 0/1:60,42:102:99:1247,0,1481 0/0:106,0:106:99:0,259,3374 0/0:94,0:95:99:0,241,3100 0/0:131,0:132:99:0,331,4283 0/0:108,0:108:99:0,247,3195 0/0:81,0:81:99:0,199,2572 0/0:106,0:106:99:0,268,3519 0/0:92,0:95:99:0,229,2966 0/0:101,2:103:99:0,232,3043 0/0:111,0:111:99:0,271,3575 0/0:95,0:95:99:0,238,3071 0/0:112,1:113:99:0,222,3302 0/0:74,0:74:99:0,159,2106 0/0:113,0:113:99:0,283,3595 0/1:65,59:124:99:1554,0,1762 0/0:127,0:127:99:0,337,4379 0/1:47,40:89:99:1164,0,1259 0/0:100,0:100:99:0,253,3224 0/0:90,0:90:99:0,214,2811 0/1:46,48:94:99:1324,0,1215 0/1:47,55:102:99:1576,0,1294 0/0:128,0:128:99:0,304,3963 0/0:160,0:160:99:0,397,5211 0/0:61,0:61:99:0,156,2039 0/0:112,0:112:99:0,271,3471 0/0:84,0:85:99:0,202,2586 0/0:56,0:56:99:0,156,2007 0/1:17,18:35:99:508,0,411 0/0:49,0:49:99:0,105,1390 1/1:0,53:54:99:1741,138,0 0/0:65,1:66:99:0,125,1960 0/0:86,0:86:99:0,196,2529 0/0:42,0:42:99:0,102,1308 0/0:59,0:60:99:0,135,1766 1/1:0,106:106:99:3530,280,0 0/0:90,0:91:99:0,244,3017 0/0:66,0:67:99:0,156,1988 0/0:77,0:78:99:0,205,2625 0/0:67,0:69:99:0,150,1924 0/0:73,0:74:99:0,175,2211 0/1:25,34:59:99:897,0,769 0/0:39,0:39:93.29:0,93,1180 0/0:64,1:66:99:0,126,1996 0/1:27,27:55:99:680,0,804 0/0:56,0:56:99:0,129,1678 -chr1 1153658 . C T 180.9 . AC=3;AF=0.0254;AN=118;BaseQRankSum=-1.007;DP=436;Dels=0.00;FS=8.257;HRun=0;HaplotypeScore=0.1613;InbreedingCoeff=-0.0432;MQ=57.74;MQ0=0;MQRankSum=-0.296;QD=10.05;ReadPosRankSum=0.424;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|6),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|6),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|6),INTRON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|1),INTRON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|2),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:6.02:0,6,77 0/0:3,0:3:6.02:0,6,73 0/0:3,0:3:9.03:0,9,121 0/0:7,0:7:21.07:0,21,276 0/0:7,0:7:21.07:0,21,269 0/0:10,0:10:30.09:0,30,392 0/0:11,0:11:33.11:0,33,438 0/0:7,0:7:18.06:0,18,242 0/0:11,0:11:33.11:0,33,444 0/0:18,0:18:51.17:0,51,692 0/0:12,0:12:36.12:0,36,481 0/1:4,5:9:99:165,0,136 0/0:12,0:12:30.07:0,30,386 0/0:4,0:4:12.04:0,12,163 0/0:6,0:6:18.06:0,18,239 0/0:4,0:4:12.04:0,12,164 0/0:6,0:6:18.06:0,18,241 0/0:4,0:4:12.04:0,12,153 0/0:13,0:13:36.12:0,36,469 0/0:9,0:9:27.09:0,27,363 0/0:6,0:6:18.06:0,18,232 0/0:5,0:5:15.05:0,15,201 0/0:8,0:8:24.07:0,24,299 0/0:5,0:5:15.05:0,15,185 0/0:6,0:6:18.06:0,18,232 0/0:3,0:3:6.02:0,6,78 0/0:9,0:9:27.09:0,27,356 0/0:6,0:6:18.06:0,18,231 0/0:7,0:7:18.06:0,18,226 0/0:11,0:11:33.11:0,33,431 0/0:13,0:13:30.10:0,30,406 0/0:7,0:7:21.07:0,21,266 0/0:3,0:3:9.03:0,9,122 0/0:7,0:7:21.06:0,21,274 0/0:9,0:9:24.08:0,24,329 ./. 0/0:3,0:4:9.03:0,9,123 0/0:17,0:17:45.13:0,45,549 0/0:8,0:8:15.05:0,15,213 0/0:10,0:11:27.08:0,27,338 0/1:4,3:7:60.15:60,0,149 0/0:6,0:6:18.06:0,18,241 0/0:8,0:8:24.07:0,24,296 0/0:6,0:6:15.05:0,15,192 0/0:7,0:8:21.07:0,21,275 0/0:6,0:6:18.06:0,18,227 0/0:13,0:13:36.11:0,36,452 0/0:3,0:3:9.02:0,9,107 0/0:6,0:6:15.05:0,15,186 0/0:7,0:7:21.07:0,21,272 0/0:14,0:14:42.14:0,42,568 0/0:6,0:6:15.05:0,15,188 0/0:7,0:7:21.07:0,21,279 0/0:6,0:6:18.06:0,18,222 0/0:6,0:6:15.05:0,15,206 0/0:4,0:4:12.04:0,12,155 0/0:8,0:8:21.07:0,21,265 0/1:1,1:2:35.21:35,0,36 0/0:4,0:4:9.03:0,9,119 0/0:4,0:4:12.04:0,12,163 -chr1 1153671 . C T 201.6 . AC=1;AF=0.0083;AN=120;BaseQRankSum=1.401;DP=557;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3657;InbreedingCoeff=-0.0187;MQ=57.34;MQ0=0;MQRankSum=0.747;QD=20.16;ReadPosRankSum=1.045;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|6),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|6),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|6),INTRON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|1),INTRON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|2),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|processed_transcript|CODING|ENST00000453580|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|);CSQ=downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000453580|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:15.04:0,15,172 0/0:4,0:4:12.04:0,12,152 0/0:3,0:3:9.03:0,9,117 0/0:8,0:8:24.08:0,24,314 0/0:8,0:8:24.08:0,24,321 0/0:11,0:11:33.11:0,33,442 0/0:18,0:18:54.17:0,54,713 0/0:9,0:9:27.09:0,27,362 0/0:16,0:16:48.16:0,48,650 0/0:23,0:23:66.22:0,66,879 0/0:13,0:13:39.12:0,39,507 0/0:12,0:12:36.11:0,36,466 0/0:12,0:12:33.09:0,33,420 0/0:5,0:5:15.05:0,15,200 0/0:7,0:7:21.07:0,21,284 0/0:5,0:5:15.05:0,15,196 0/0:9,0:9:24.08:0,24,309 0/0:8,0:8:24.07:0,24,297 0/0:17,0:17:36.11:0,36,464 0/0:9,0:9:27.09:0,27,361 0/0:6,0:6:18.06:0,18,241 0/0:7,0:7:21.06:0,21,269 0/0:9,0:9:21.07:0,21,281 0/0:7,0:7:18.06:0,18,229 0/0:11,0:11:33.11:0,33,425 0/0:6,0:6:15.05:0,15,193 0/0:12,0:12:36.11:0,36,466 0/0:8,0:8:24.05:0,24,286 0/0:10,0:10:27.07:0,27,344 0/0:12,0:12:36.12:0,36,475 0/0:15,0:15:36.11:0,36,468 0/0:9,0:9:27.08:0,27,338 0/0:5,0:5:15.05:0,15,196 0/0:8,0:8:24.08:0,24,331 0/0:11,0:11:27.09:0,27,367 0/0:2,0:2:3.01:0,3,33 0/0:8,0:8:21.07:0,21,272 0/0:18,0:18:51.13:0,51,623 0/0:9,0:9:21.07:0,21,280 0/0:12,0:12:30.09:0,30,383 0/0:9,0:9:24.08:0,24,322 0/0:10,0:10:30.09:0,30,383 0/0:9,0:9:27.07:0,27,323 0/0:6,0:6:15.05:0,15,195 0/0:10,0:10:24.06:0,24,301 0/0:10,0:10:30.10:0,30,387 0/0:16,0:16:39.12:0,39,502 0/0:3,0:3:9.02:0,9,109 0/0:7,0:7:21.03:0,21,235 0/1:3,7:10:85.46:249,0,85 0/0:17,0:17:51.17:0,51,691 0/0:11,0:11:24.07:0,24,294 0/0:9,0:9:27.09:0,27,364 0/0:7,0:7:21.06:0,21,249 0/0:8,0:8:21.07:0,21,280 0/0:4,0:4:12.04:0,12,160 0/0:11,0:11:30.08:0,30,355 0/0:3,0:3:9.03:0,9,119 0/0:5,0:5:12.03:0,12,142 0/0:4,0:4:12.04:0,12,164 -chr1 1154121 . G A 626.94 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.070;DP=2668;Dels=0.00;FS=1.726;HRun=0;HaplotypeScore=1.8437;InbreedingCoeff=-0.0088;MQ=57.56;MQ0=0;MQRankSum=2.723;QD=11.61;ReadPosRankSum=-0.999;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|1),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|5),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|5),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|5),INTRON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|1),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|1/2||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1 GT:AD:DP:GQ:PL 0/0:8,0:8:18.04:0,18,199 0/0:9,0:9:24.07:0,24,292 0/0:9,0:9:27.08:0,27,342 0/0:5,0:5:15.04:0,15,178 0/0:23,0:23:66.22:0,66,876 0/0:26,0:26:72.23:0,72,943 0/0:40,0:40:99:0,114,1505 0/0:24,0:24:72.22:0,72,936 0/0:62,0:62:99:0,184,2375 0/0:57,0:57:99:0,166,2160 0/0:34,0:34:96.31:0,96,1251 0/0:21,0:21:54.16:0,54,683 0/0:36,0:36:99:0,102,1264 0/0:40,0:40:99:0,108,1384 0/0:39,0:39:99:0,105,1316 0/0:19,0:19:48.15:0,48,621 0/0:38,0:38:99:0,105,1328 0/0:33,0:33:69.22:0,69,905 0/0:39,0:39:99:0,99,1288 0/0:24,0:24:63.20:0,63,807 0/0:23,0:23:57.18:0,57,743 0/0:30,0:30:75.21:0,75,946 0/0:29,0:29:75.20:0,75,943 0/0:26,0:28:69.22:0,69,898 0/0:34,0:34:75.23:0,75,988 0/0:38,0:40:96.29:0,96,1241 0/0:32,0:32:81.26:0,81,1052 0/0:24,0:24:54.15:0,54,684 0/0:41,0:41:99:0,102,1308 0/0:37,0:38:90.29:0,90,1195 0/0:51,0:51:99:0,141,1799 0/0:29,0:29:69.22:0,69,928 0/0:37,0:37:96.29:0,96,1240 0/0:48,0:48:99:0,114,1510 0/0:23,0:23:66.22:0,66,886 0/0:43,0:43:99:0,105,1363 0/0:34,0:34:93.29:0,93,1183 0/0:56,0:56:99:0,147,1954 0/0:56,0:56:99:0,138,1791 0/0:118,0:118:99:0,277,3562 0/0:88,0:88:99:0,223,2814 0/0:53,0:53:99:0,141,1804 0/0:53,0:53:99:0,144,1819 0/0:54,0:54:99:0,135,1747 0/1:28,26:54:99:675,0,748 0/0:58,1:60:99:0,135,1716 0/0:99,0:100:99:0,250,3118 0/0:31,0:31:87.26:0,87,1075 0/0:65,0:65:99:0,172,2212 0/0:99,0:99:99:0,253,3197 0/0:94,0:94:99:0,235,3010 0/0:67,0:68:99:0,165,2095 0/0:59,0:59:99:0,153,1908 0/0:65,1:66:99:0,153,1951 0/0:56,0:56:99:0,132,1693 0/0:58,0:58:99:0,144,1837 0/0:35,0:35:93.27:0,93,1169 0/0:72,0:73:99:0,175,2191 0/0:44,0:45:99:0,117,1469 0/0:56,0:56:99:0,141,1842 -chr1 1154374 . G A 229.71 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.034;DP=1145;Dels=0.00;FS=3.775;HRun=1;HaplotypeScore=0.6454;InbreedingCoeff=-0.0116;MQ=58.50;MQ0=0;MQRankSum=0.802;QD=7.92;ReadPosRankSum=0.928;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|1),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|1),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER||||277|TNFRSF4|protein_coding|CODING|ENST00000379236|),UPSTREAM(MODIFIER|||||TNFRSF4|retained_intron|CODING|ENST00000497869|);CSQ=missense_variant|Cgg/Tgg|R/W|ENSG00000078808|SDF4|ENST00000403997|4/5|possibly_damaging(0.833)|deleterious(0.02)|132/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|1/3||||retained_intron|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000497869|||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|1/2||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000186827|TNFRSF4|ENST00000379236||||-/277|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:21.06:0,21,261 0/0:12,0:12:36.10:0,36,435 0/0:6,0:6:18.06:0,18,223 0/0:5,0:5:9.03:0,9,112 0/0:19,0:19:57.19:0,57,769 0/0:19,0:19:57.18:0,57,749 0/0:34,0:34:96.31:0,96,1273 0/0:13,0:13:36.11:0,36,444 0/0:46,0:46:99:0,135,1824 0/0:25,0:25:72.24:0,72,969 0/0:15,0:15:45.15:0,45,613 0/0:17,0:17:51.16:0,51,672 0/0:20,0:20:57.17:0,57,735 0/0:7,0:7:18.06:0,18,237 0/0:12,0:12:33.10:0,33,419 0/0:6,0:6:15.05:0,15,204 0/0:9,0:9:24.07:0,24,303 0/0:8,0:8:18.06:0,18,248 0/0:14,0:14:27.09:0,27,355 0/0:17,0:17:39.12:0,39,504 0/0:7,0:7:21.07:0,21,278 0/0:11,0:11:30.10:0,30,400 0/0:8,0:8:18.06:0,18,234 0/0:12,0:12:36.11:0,36,465 0/0:11,0:11:24.08:0,24,324 0/0:6,0:6:15.05:0,15,195 0/0:9,0:9:27.09:0,27,350 0/0:5,0:5:15.05:0,15,200 0/0:5,0:5:15.05:0,15,195 0/0:7,0:7:15.05:0,15,209 0/0:12,0:12:36.11:0,36,471 0/0:11,0:11:27.09:0,27,372 0/0:8,0:8:24.07:0,24,307 0/0:11,0:11:30.10:0,30,393 0/0:9,0:9:24.07:0,24,316 0/0:8,0:8:21.07:0,21,277 0/0:19,0:19:54.17:0,54,704 0/0:10,0:10:30.10:0,30,387 0/0:25,0:25:63.20:0,63,833 0/0:40,0:40:99:0,102,1316 0/0:41,0:41:96.31:0,96,1272 0/0:27,0:27:66.21:0,66,858 0/0:23,0:23:63.20:0,63,804 0/1:17,12:29:99:277,0,528 0/0:19,0:19:45.14:0,45,596 0/0:35,0:35:87.28:0,87,1139 0/0:42,1:43:99:0,99,1269 0/0:13,0:13:36.11:0,36,462 0/0:25,0:25:60.18:0,60,808 0/0:43,0:43:99:0,105,1372 0/0:35,0:35:90.29:0,90,1200 0/0:35,0:36:93.29:0,93,1202 0/0:35,0:35:84.24:0,84,1084 0/0:30,0:30:75.24:0,75,1009 0/0:26,0:26:66.18:0,66,832 0/0:27,0:27:66.21:0,66,887 0/0:33,0:33:75.22:0,75,985 0/0:24,0:24:66.17:0,66,837 0/0:34,0:34:87.28:0,87,1151 0/0:22,0:22:60.19:0,60,794 -chr1 1154539 . G A 108.45 . AC=6;AF=0.068;AN=88;BaseQRankSum=-1.095;DP=122;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0697;InbreedingCoeff=0.0875;MQ=56.71;MQ0=0;MQRankSum=-1.837;QD=10.84;ReadPosRankSum=1.197;EFF=DOWNSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|1),EXON(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|1),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000494748|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000478938|1/2||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:4,0:4:9.03:0,9,108 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,30 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:9.03:0,9,123 0/0:4,0:4:12.04:0,12,161 0/0:12,0:12:33.11:0,33,448 0/0:2,0:2:6.02:0,6,80 0/0:2,0:2:6.01:0,6,69 0/0:5,0:5:15.04:0,15,188 0/0:3,0:3:9.03:0,9,120 ./. ./. 0/0:1,0:1:3.01:0,3,32 ./. ./. 0/0:2,0:2:6.02:0,6,76 ./. 0/0:3,0:3:9.03:0,9,106 0/0:1,0:1:3.01:0,3,35 ./. 0/0:3,0:3:9.03:0,9,116 ./. ./. ./. 0/0:2,0:2:6.02:0,6,82 1/1:0,1:1:3.01:42,3,0 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,36 0/0:1,0:1:3.01:0,3,41 ./. ./. 1/1:0,2:2:6.02:73,6,0 ./. 0/0:2,0:2:3.01:0,3,39 0/0:1,0:1:3.01:0,3,34 0/0:7,0:7:15.05:0,15,186 0/0:3,0:3:6.02:0,6,81 ./. 0/0:3,0:3:6.02:0,6,83 0/0:3,0:3:9.03:0,9,114 0/0:2,0:2:6.02:0,6,83 0/0:5,0:5:12.03:0,12,155 0/0:3,0:3:9.03:0,9,118 0/0:2,0:2:3.01:0,3,39 0/0:4,0:4:9.03:0,9,122 0/0:4,0:4:12.03:0,12,141 0/0:2,0:2:6.02:0,6,69 0/0:5,0:5:15.05:0,15,188 0/0:2,0:2:6.01:0,6,68 0/0:2,0:2:6.02:0,6,75 ./. 0/1:1,2:3:30.29:59,0,30 ./. 0/0:3,0:3:9.03:0,9,123 0/1:3,1:4:25.76:26,0,109 0/0:1,0:1:3.01:0,3,36 -chr1 1158070 . C T 64.6 . AC=4;AF=0.154;AN=26;BaseQRankSum=-0.623;DP=14;Dels=0.00;FS=2.688;HRun=0;HaplotypeScore=0.1231;InbreedingCoeff=0.1888;MQ=58.33;MQ0=0;MQRankSum=-1.090;QD=21.53;ReadPosRankSum=-1.713;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. ./. 1/1:0,2:2:6.02:77,6,0 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 ./. 0/0:1,0:1:3.01:0,3,40 ./. 0/0:1,0:1:3.01:0,3,30 ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,36 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 -chr1 1158277 . G A 258.06 . AC=7;AF=0.0660;AN=106;BaseQRankSum=1.218;DP=155;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0943;InbreedingCoeff=0.0730;MQ=58.19;MQ0=0;MQRankSum=0.130;QD=14.34;ReadPosRankSum=0.779;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,40 ./. 0/0:2,0:2:6.02:0,6,75 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,31 0/0:7,0:7:21.06:0,21,271 0/0:4,0:4:12.04:0,12,165 ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/1:1,1:2:29.23:29,0,30 0/0:1,0:1:3.01:0,3,42 0/0:3,0:3:9.03:0,9,118 0/0:2,0:2:6.02:0,6,80 0/0:3,0:3:6.02:0,6,87 ./. 0/0:3,0:3:9.03:0,9,116 0/0:4,0:4:12.03:0,12,151 0/0:4,0:4:9.03:0,9,126 ./. 0/0:4,0:4:12.04:0,12,167 0/0:3,0:4:9.03:0,9,121 0/0:3,0:3:6.02:0,6,78 0/0:2,0:2:6.02:0,6,81 0/0:5,0:5:15.05:0,15,188 0/1:3,3:6:70.37:70,0,87 0/0:2,0:2:6.02:0,6,73 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,31 0/0:2,0:2:6.02:0,6,82 0/0:2,0:2:3.01:0,3,45 0/0:2,0:2:3.01:0,3,34 0/0:5,0:5:15.04:0,15,181 0/0:10,0:10:21.07:0,21,293 0/0:4,0:4:9.03:0,9,120 0/0:5,0:5:15.04:0,15,193 0/0:2,0:2:6.02:0,6,73 0/0:5,0:5:12.03:0,12,141 0/0:2,0:2:6.02:0,6,83 0/0:3,0:3:9.03:0,9,108 1/1:0,3:3:9.03:117,9,0 0/0:1,0:1:3.01:0,3,37 0/0:6,0:6:15.05:0,15,194 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,37 1/1:0,3:3:6.02:83,6,0 0/0:4,0:4:12.04:0,12,159 0/0:3,0:3:6.02:0,6,83 0/0:3,0:3:3.01:0,3,37 0/0:3,0:3:6.02:0,6,82 ./. 0/1:2,2:4:35.74:67,0,36 0/0:4,0:4:12.04:0,12,158 0/0:3,0:3:9.03:0,9,119 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:9.03:0,9,114 -chr1 1158326 . G A 805.01 . AC=13;AF=0.1102;AN=118;BaseQRankSum=1.271;DP=279;Dels=0.00;FS=5.053;HRun=0;HaplotypeScore=0.2930;InbreedingCoeff=0.1676;MQ=57.56;MQ0=0;MQRankSum=-0.687;QD=17.13;ReadPosRankSum=-0.913;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,2:2:6.02:75,6,0 0/0:7,0:7:21.05:0,21,263 0/0:3,0:3:6.02:0,6,81 0/0:8,0:8:24.07:0,24,298 0/0:3,0:3:9.03:0,9,124 0/0:3,0:3:9.03:0,9,119 0/1:2,1:3:32.20:32,0,73 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:6.02:0,6,82 0/0:4,0:4:12.03:0,12,142 0/0:5,0:5:15.05:0,15,190 0/0:1,0:2:3.01:0,3,40 0/0:2,0:2:6.02:0,6,82 0/0:2,0:2:6.02:0,6,76 0/1:2,2:4:62.04:69,0,62 ./. 0/0:6,0:6:15.05:0,15,196 0/0:3,0:3:3.01:0,3,41 0/0:6,0:6:18.06:0,18,230 0/0:1,0:1:3.01:0,3,42 0/0:8,0:8:18.05:0,18,231 0/0:6,0:6:9.03:0,9,116 0/0:4,0:4:12.04:0,12,150 0/0:1,0:1:3.01:0,3,42 0/0:5,0:5:15.05:0,15,187 0/0:3,0:3:6.02:0,6,78 0/0:2,0:2:6.02:0,6,75 0/0:5,0:5:12.04:0,12,160 0/0:9,0:9:18.06:0,18,230 0/1:1,3:5:20.46:98,0,20 0/0:5,0:5:15.04:0,15,180 0/0:4,0:4:9.03:0,9,113 0/0:4,0:4:12.04:0,12,145 0/0:6,0:6:12.04:0,12,167 0/1:2,1:3:24.41:24,0,73 0/1:4,5:9:99:105,0,136 0/0:8,0:8:21.07:0,21,275 0/0:12,0:12:36.12:0,36,478 0/0:5,0:5:9.03:0,9,117 0/0:9,0:9:21.07:0,21,280 0/0:5,0:5:6.02:0,6,75 0/0:5,0:5:12.03:0,12,136 0/0:4,0:4:12.04:0,12,156 0/0:5,0:5:6.02:0,6,76 1/1:0,3:3:9.03:105,9,0 0/0:3,0:3:9.03:0,9,124 0/0:9,0:9:27.09:0,27,349 0/0:1,0:1:3.01:0,3,39 0/0:6,0:6:18.06:0,18,243 1/1:0,9:9:27.09:343,27,0 0/0:5,0:5:15.04:0,15,187 0/0:6,0:6:12.04:0,12,168 0/0:10,0:10:24.08:0,24,324 0/0:4,0:4:12.04:0,12,160 0/0:1,0:1:3.01:0,3,41 0/1:3,2:5:67.52:68,0,73 0/0:2,0:2:6.02:0,6,71 0/0:6,0:6:18.06:0,18,235 0/1:2,2:4:54.83:55,0,70 0/0:5,0:5:12.03:0,12,150 -chr1 1158357 . A G 916.43 . AC=10;AF=0.0833;AN=120;BaseQRankSum=-1.540;DP=426;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.2650;InbreedingCoeff=0.0655;MQ=57.91;MQ0=0;MQRankSum=-0.479;QD=14.10;ReadPosRankSum=1.027;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,1:3:6.02:0,6,80 0/0:4,0:4:9.03:0,9,120 0/0:4,0:4:12.04:0,12,154 0/0:9,0:9:27.09:0,27,344 0/0:5,0:5:12.04:0,12,160 0/0:3,0:3:9.03:0,9,122 0/1:3,1:4:25.76:26,0,112 0/0:2,0:2:6.02:0,6,82 0/0:5,0:5:15.05:0,15,198 0/0:14,0:14:42.14:0,42,574 0/0:5,0:5:15.05:0,15,204 0/0:3,0:3:6.02:0,6,79 0/0:6,0:6:18.06:0,18,239 0/0:6,0:6:18.06:0,18,233 0/1:2,2:4:59.29:67,0,59 0/0:5,0:5:15.05:0,15,200 0/0:8,0:8:21.07:0,21,270 0/0:4,0:4:9.03:0,9,111 0/0:7,0:7:21.05:0,21,241 0/0:3,0:3:9.03:0,9,119 0/0:11,0:11:27.08:0,27,345 0/0:5,0:5:15.05:0,15,197 0/0:5,0:5:15.05:0,15,202 0/0:2,0:2:6.02:0,6,80 0/0:4,0:4:12.04:0,12,160 0/0:7,0:7:18.06:0,18,246 0/0:5,0:5:15.05:0,15,187 0/0:5,0:5:12.04:0,12,163 0/0:7,0:7:15.05:0,15,189 0/1:3,4:8:54.86:102,0,55 0/0:11,0:11:30.10:0,30,404 0/0:6,0:6:15.05:0,15,193 0/0:5,0:5:15.05:0,15,190 0/0:14,0:14:33.11:0,33,450 0/1:2,2:4:59.52:60,0,63 0/1:4,6:10:99:106,0,105 0/0:9,0:9:24.07:0,24,293 0/0:13,0:13:33.11:0,33,433 0/0:4,0:4:9.03:0,9,111 0/0:15,0:15:39.12:0,39,507 0/0:7,1:8:12.04:0,12,159 0/0:5,0:5:15.05:0,15,191 0/0:4,0:4:12.03:0,12,136 0/0:3,0:3:6.02:0,6,86 0/1:1,1:2:22.63:23,0,36 0/0:6,0:6:18.06:0,18,242 0/0:17,0:17:48.15:0,48,619 0/0:8,0:8:21.06:0,21,265 0/0:14,0:14:33.11:0,33,438 1/1:0,22:22:48.15:610,48,0 0/0:10,0:10:27.09:0,27,352 0/0:10,0:10:27.08:0,27,344 0/0:15,0:15:39.13:0,39,530 0/0:6,0:6:18.06:0,18,244 0/0:9,0:9:27.09:0,27,360 0/1:1,1:2:30.11:30,0,32 0/0:7,0:7:18.06:0,18,253 0/0:9,0:9:24.08:0,24,312 0/1:7,2:9:46.93:47,0,148 0/0:6,0:6:15.04:0,15,181 -chr1 1158427 . C CTCAT 100.01 . AC=7;AF=0.0583;AN=120;BaseQRankSum=4.538;DP=1071;FS=0.000;HRun=0;HaplotypeScore=95.9447;InbreedingCoeff=-0.0617;MQ=58.35;MQ0=0;MQRankSum=-4.421;QD=0.89;ReadPosRankSum=1.472;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/0:8,0:8:21.07:0,21,441 0/0:11,0:11:27.09:0,27,562 0/0:9,0:9:27.09:0,27,488 0/0:9,0:9:24.08:0,24,460 0/0:14,0:14:42.14:0,42,855 0/0:18,0:18:48.16:0,48,906 0/0:22,0:22:60.20:0,60,1163 0/0:10,0:10:30.10:0,30,578 0/0:33,0:33:93.32:0,93,1894 0/0:37,0:38:99:0,100,2056 0/0:15,0:15:36.12:0,36,703 0/0:13,0:13:39.13:0,39,769 0/0:13,0:13:39.13:0,39,793 0/0:17,0:17:45.15:0,45,944 0/1:14,1:15:39.25:39,0,656 0/0:15,0:15:45.15:0,45,912 0/0:24,0:24:69.19:0,69,1308 0/0:16,0:16:48.16:0,48,1007 0/0:13,0:13:33.11:0,33,688 0/0:18,0:18:51.17:0,51,1007 0/0:21,0:21:57.20:0,57,1193 0/0:18,0:18:48.16:0,48,1005 0/0:12,0:12:36.12:0,36,755 0/0:8,0:8:21.05:0,21,368 0/0:19,0:19:57.20:0,57,1196 0/0:24,0:24:72.23:0,72,1383 0/0:14,0:14:42.14:0,42,852 0/0:8,0:8:24.08:0,24,458 0/0:16,0:16:45.15:0,45,883 0/1:19,1:20:29.84:30,0,1015 0/0:23,0:23:63.21:0,63,1240 0/0:14,0:14:42.14:0,42,846 0/0:22,0:22:66.23:0,66,1384 0/0:18,0:18:48.12:0,48,923 0/1:13,1:14:47.73:48,0,684 0/1:10,1:11:46.27:46,0,541 0/0:25,0:25:63.21:0,63,1288 0/0:36,0:36:99:0,99,2036 0/0:8,0:8:24.08:0,24,437 0/0:29,0:29:81.21:0,81,1556 0/0:20,0:20:57.18:0,57,1130 0/0:23,0:23:63.21:0,63,1289 0/0:12,0:12:30.10:0,30,597 0/1:10,1:11:35.73:36,0,475 0/0:10,0:10:30.10:0,30,630 0/0:16,0:16:45.15:0,45,900 0/0:30,0:30:84.28:0,84,1696 0/0:19,0:19:39.12:0,39,750 0/1:20,1:21:11.72:12,0,984 0/0:39,0:39:96.33:0,96,2011 0/0:33,0:33:93.31:0,93,1889 0/0:26,0:26:75.25:0,75,1506 0/0:15,0:15:42.14:0,42,881 0/0:21,0:21:60.20:0,60,1227 0/0:21,0:21:60.20:0,60,1230 0/0:8,0:8:24.08:0,24,471 0/0:9,0:9:27.09:0,27,567 0/0:17,0:17:48.16:0,48,947 0/1:20,1:21:21.03:21,0,1105 0/0:8,0:7:21.07:0,21,413 -chr1 1158441 . GCA G 2419.37 . AC=7;AF=0.0583;AN=120;BaseQRankSum=8.159;DP=1188;FS=0.719;HRun=0;HaplotypeScore=80.9615;InbreedingCoeff=-0.0625;MQ=58.49;MQ0=0;MQRankSum=0.055;QD=13.82;ReadPosRankSum=-1.278;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/0:13,0:13:36.12:0,36,628 0/0:13,0:13:39.13:0,39,676 0/0:6,0:6:18.06:0,18,320 0/0:10,0:10:24.08:0,24,409 0/0:14,0:14:36.12:0,36,628 0/0:16,0:16:42.14:0,42,746 0/1:13,11:24:99:425,0,506 0/0:12,0:12:36.12:0,36,627 0/1:15,20:35:99:725,0,588 0/0:41,0:41:99:0,111,1963 0/0:13,0:13:27.09:0,27,480 0/0:14,0:14:36.12:0,36,612 0/0:17,0:17:51.17:0,51,906 0/0:23,0:23:66.23:0,66,1152 0/0:19,0:19:45.15:0,45,800 0/0:17,0:17:51.17:0,51,905 0/0:29,0:29:84.29:0,84,1485 0/0:18,0:18:51.17:0,51,887 0/1:11,3:14:84.60:85,0,494 0/0:22,0:22:66.23:0,66,1172 0/0:23,0:23:66.23:0,66,1172 0/1:14,9:23:99:269,0,579 0/0:15,0:15:42.14:0,42,746 0/0:10,0:10:30.10:0,30,531 0/0:20,0:20:60.21:0,60,1065 0/0:25,0:25:69.24:0,69,1225 0/0:18,0:18:54.18:0,54,950 0/0:11,0:11:30.10:0,30,521 0/0:25,0:25:72.25:0,72,1273 0/1:12,8:20:99:273,0,469 0/0:23,0:23:66.23:0,66,1166 0/0:15,0:15:45.15:0,45,772 0/0:24,0:24:69.24:0,69,1225 0/0:16,0:16:39.13:0,39,692 0/0:17,0:17:50.76:0,51,861 0/0:14,0:14:41.81:0,42,703 0/0:30,0:30:87.30:0,87,1533 0/0:44,0:44:99:0,123,2142 0/0:10,0:10:27.09:0,27,479 0/1:20,8:28:99:372,0,738 0/0:21,1:22:18.97:0,19,971 0/0:28,0:28:75.26:0,75,1326 0/0:14,0:14:39.13:0,39,692 0/0:13,0:13:35.99:0,36,605 0/0:9,0:9:27.09:0,27,480 0/0:15,0:15:39.13:0,39,693 0/1:21,10:31:99:404,0,812 0/0:17,0:17:39.13:0,39,691 0/0:21,0:21:51.13:0,51,900 0/0:43,0:43:99:0,105,1853 0/0:37,1:38:99:0,99,1727 0/0:30,0:30:90.31:0,90,1593 0/0:14,0:14:39.13:0,39,693 0/0:25,0:25:72.25:0,72,1278 0/0:20,0:20:57.19:0,57,983 0/0:8,0:8:24.08:0,24,426 0/0:6,0:6:18.06:0,18,300 0/0:20,0:20:60.21:0,60,1048 0/0:23,0:23:57.67:0,58,1013 0/0:10,0:9:30.10:0,30,526 -chr1 1158534 . G GAC 10837.11 . AC=11;AF=0.0917;AN=120;BaseQRankSum=10.503;DP=3575;FS=3.271;HRun=0;HaplotypeScore=253.2703;InbreedingCoeff=0.0992;MQ=58.17;MQ0=0;MQRankSum=-7.407;QD=20.14;ReadPosRankSum=-0.456;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/1:17,2:19:99:150,0,389 0/0:20,0:20:51.17:0,51,669 0/0:21,0:21:54.18:0,54,705 0/0:15,0:15:33.11:0,33,428 0/0:32,0:32:84.27:0,84,1101 0/0:45,0:45:99:0,129,1686 0/1:61,32:93:99:1660,0,1436 0/0:35,0:35:93.30:0,93,1218 0/0:94,0:94:99:0,232,3013 0/0:113,0:112:99:0,286,3726 0/0:51,0:51:99:0,129,1694 0/0:54,0:53:99:0,135,1762 0/0:61,0:61:99:0,175,2280 0/0:79,0:79:99:0,214,2791 0/1:43,28:71:99:1345,0,1203 0/0:46,0:46:99:0,117,1514 0/0:75,0:74:99:0,193,2493 0/0:77,0:77:99:0,223,2894 0/0:79,0:79:99:0,211,2706 0/0:73,0:73:99:0,205,2651 0/0:78,0:78:99:0,220,2829 0/0:83,0:81:99:0,229,2968 0/0:62,0:62:99:0,169,2202 0/0:62,0:62:99:0,163,2108 0/0:67,0:67:99:0,184,2384 0/0:61,0:61:99:0,166,2161 0/0:55,0:55:99:0,147,1910 0/0:56,0:55:99:0,160,2087 0/0:80,0:79:99:0,211,2718 0/1:38,24:62:99:1075,0,983 0/0:117,0:116:99:0,307,3983 0/0:49,0:49:99:0,129,1683 0/0:103,0:103:99:0,253,3301 0/0:85,0:85:99:0,235,3042 0/1:43,19:62:99:956,0,1190 0/1:34,22:56:99:1173,0,713 0/0:78,0:78:99:0,199,2586 0/0:110,0:110:99:0,310,4027 0/0:35,0:35:90.29:0,90,1183 0/0:79,0:79:99:0,216,2794 0/0:50,0:50:99:0,135,1741 0/0:42,0:42:99:0,105,1363 0/0:29,0:29:72.23:0,72,940 0/0:37,0:37:96.31:0,96,1261 0/1:19,11:30:99:620,0,368 0/0:47,0:47:99:0,126,1648 0/0:86,0:85:99:0,217,2823 0/0:29,0:29:69.22:0,69,907 0/0:49,0:49:99:0,129,1686 1/1:22,49:71:98.65:2769,99,0 0/0:82,0:82:99:0,202,2623 0/0:90,0:90:99:0,220,2866 0/0:50,0:50:99:0,123,1604 0/0:52,0:52:99:0,138,1807 0/0:41,0:41:99:0,114,1492 0/1:29,12:41:99:506,0,866 0/0:37,0:37:99:0,99,1301 0/0:47,0:47:99:0,126,1639 0/1:21,12:32:99:582,0,544 0/0:39,0:39:99:0,105,1380 -chr1 1158543 . G A 443.06 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.994;DP=3849;Dels=0.00;FS=6.053;HRun=0;HaplotypeScore=6.1083;InbreedingCoeff=-0.0084;MQ=58.27;MQ0=0;MQRankSum=0.950;QD=14.77;ReadPosRankSum=-2.545;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/0:24,0:24:69.20:0,69,823 0/0:20,0:20:57.18:0,57,727 0/0:21,0:21:63.20:0,63,827 0/0:19,0:19:51.16:0,51,651 0/0:35,0:35:99:0,105,1418 0/0:52,0:52:99:0,157,2086 0/0:101,2:103:99:0,230,3898 0/0:38,0:38:99:0,114,1494 0/0:102,0:102:99:0,298,3937 0/0:121,0:121:99:0,361,4805 0/0:52,0:52:99:0,154,2054 0/0:61,0:61:99:0,175,2279 0/0:64,0:64:99:0,193,2505 0/0:85,0:85:99:0,226,2900 0/0:81,0:81:99:0,211,2622 0/0:48,0:48:99:0,135,1723 0/0:78,0:78:99:0,205,2605 0/0:87,0:87:99:0,229,2987 0/0:83,0:83:99:0,217,2830 0/0:76,0:79:99:0,202,2595 0/0:89,2:91:99:0,196,2993 0/0:88,0:88:99:0,238,3046 0/0:66,0:66:99:0,175,2218 0/0:68,0:69:99:0,178,2223 0/0:70,0:70:99:0,199,2559 0/0:71,0:71:99:0,178,2335 0/0:61,0:61:99:0,166,2147 0/0:59,0:59:99:0,165,2133 0/0:84,0:85:99:0,226,2933 0/0:69,2:71:99:0,145,2179 0/0:123,0:124:99:0,325,4207 0/0:58,0:59:99:0,153,1946 0/0:106,0:107:99:0,268,3477 0/0:89,0:90:99:0,217,2845 0/0:69,1:71:99:0,187,2306 0/0:62,1:63:99:0,141,2095 0/0:76,0:76:99:0,199,2571 0/0:118,1:119:99:0,290,4054 0/0:36,0:36:87.25:0,87,1110 0/0:80,0:80:99:0,205,2635 0/0:53,0:54:99:0,135,1744 0/0:43,0:43:99:0,114,1481 0/0:30,0:30:78.22:0,78,962 0/0:38,0:38:93.28:0,93,1209 0/1:14,16:30:99:491,0,298 0/0:51,0:51:99:0,138,1761 0/0:91,0:91:99:0,214,2759 0/0:31,0:31:75.23:0,75,966 0/0:55,0:55:99:0,144,1825 0/0:72,4:76:99:0,116,2193 0/0:77,0:78:99:0,184,2397 0/0:85,0:86:99:0,217,2796 0/0:56,0:57:99:0,147,1904 0/0:57,0:57:99:0,150,1974 0/0:44,0:44:99:0,102,1317 0/0:50,1:51:87.81:0,88,1512 0/0:38,0:38:96.29:0,96,1215 0/0:48,0:49:99:0,126,1608 0/0:37,0:37:99:0,102,1275 0/0:43,0:43:99:0,108,1403 -chr1 1158562 . AAC A 12359.87 . AC=11;AF=0.0917;AN=120;BaseQRankSum=19.423;DP=4760;FS=4.102;HRun=0;HaplotypeScore=407.7083;InbreedingCoeff=0.0992;MQ=58.43;MQ0=0;MQRankSum=-2.532;QD=17.12;ReadPosRankSum=-0.503;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/1:17,10:27:99:345,0,621 0/0:31,0:31:81.28:0,81,1433 0/0:29,0:29:81.25:0,81,1389 0/0:33,0:33:96.32:0,96,1646 0/0:54,0:54:99:0,154,2678 0/0:62,0:62:99:0,172,3029 0/1:94,30:124:99:1732,0,2891 0/0:47,0:47:99:0,123,2115 0/0:156,0:156:99:0,436,7645 0/0:150,0:150:99:0,433,7433 0/0:71,0:71:99:0,202,3474 0/0:67,0:67:99:0,190,3131 0/0:72,0:72:99:0,187,2991 0/0:117,0:117:99:0,328,5676 0/1:69,33:102:99:1582,0,2223 0/0:66,0:66:99:0,181,3071 0/0:104,0:103:99:0,274,4792 0/0:105,0:105:99:0,301,5158 0/0:108,0:108:99:0,316,5461 0/0:98,0:98:99:0,274,4763 0/0:124,0:123:99:0,346,5871 0/0:108,0:106:99:0,304,5304 0/0:83,0:83:99:0,238,4071 0/0:83,0:83:99:0,223,3900 0/0:98,0:98:99:0,271,4768 0/0:96,0:96:99:0,247,4327 0/0:92,0:92:99:0,259,4464 0/0:82,0:81:99:0,227,3961 0/0:97,0:95:99:0,264,4587 0/1:50,32:82:99:1351,0,1642 0/0:143,0:142:99:0,394,6902 0/0:70,0:69:99:0,196,3234 0/0:130,0:130:99:0,358,6276 0/0:109,0:109:99:0,301,5267 0/1:55,32:87:99:1458,0,2047 0/1:62,31:93:99:1367,0,2324 0/0:103,0:103:99:0,289,4943 0/0:161,0:161:99:0,454,7930 0/0:44,0:44:99:0,120,2110 0/0:89,0:89:99:0,244,4266 0/0:53,0:53:99:0,138,2318 0/0:50,0:50:99:0,134,2331 0/0:32,0:32:78.26:0,78,1331 0/0:42,0:42:99:0,117,2026 0/1:19,10:29:99:386,0,485 0/0:57,0:57:99:0,159,2684 0/0:106,0:105:99:0,292,5039 0/0:33,0:33:93.31:0,93,1616 0/0:72,0:72:99:0,187,3235 1/1:22,57:79:99:2704,153,0 0/0:88,0:88:99:0,223,3861 0/0:94,0:94:99:0,262,4616 0/0:69,0:69:99:0,181,3103 0/0:61,0:61:99:0,175,2969 0/0:54,0:54:99:0,153,2535 0/1:41,17:58:99:677,0,1610 0/0:46,0:46:99:0,126,2184 0/0:50,0:50:99:0,141,2512 0/1:26,15:40:99:758,0,867 0/0:49,0:49:99:0,135,2324 -chr1 1158567 . A G 234.79 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-2.278;DP=5021;Dels=0.00;FS=38.170;HRun=0;HaplotypeScore=12.5431;InbreedingCoeff=-0.0170;MQ=58.49;MQ0=0;MQRankSum=-1.361;QD=1.06;ReadPosRankSum=-7.229;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|4),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|4),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|4),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/0:30,0:30:84.21:0,84,1006 0/0:31,0:31:87.27:0,87,1100 0/0:33,0:33:99:0,99,1303 0/0:38,0:38:99:0,108,1373 0/0:57,0:57:99:0,172,2278 0/0:62,0:62:99:0,187,2513 0/1:118,15:133:99:199,0,4221 0/0:46,0:46:99:0,135,1770 0/0:160,0:160:99:0,479,6432 0/0:164,0:164:99:0,491,6581 0/0:72,0:72:99:0,217,2923 0/0:68,0:68:99:0,202,2654 0/0:72,0:72:99:0,214,2808 0/0:124,0:125:99:0,310,4066 0/0:99,9:108:99:0,99,3086 0/0:70,0:71:99:0,184,2364 0/0:111,0:112:99:0,262,3383 0/0:104,0:104:99:0,268,3466 0/0:118,0:119:99:0,301,3936 0/0:102,1:104:99:0,256,3279 0/0:136,0:138:99:0,325,4223 0/0:117,0:118:99:0,313,3977 0/0:93,0:93:99:0,232,2989 0/0:93,0:93:99:0,238,3075 0/0:99,0:99:99:0,256,3385 0/0:92,3:98:99:0,229,2905 0/0:96,0:96:99:0,241,3182 0/0:85,0:85:99:0,223,2884 0/0:100,0:100:99:0,250,3252 0/0:80,5:86:74.51:0,75,2477 0/0:147,0:149:99:0,367,4766 0/0:76,0:77:99:0,190,2508 0/0:132,0:133:99:0,328,4211 0/0:118,0:119:99:0,274,3600 0/0:92,5:97:99:0,103,3007 0/0:93,3:97:99:0,192,3201 0/0:109,0:109:99:0,289,3729 0/0:169,1:171:99:0,427,5635 0/0:42,1:43:99:0,99,1287 0/0:87,0:87:99:0,220,2764 0/0:53,0:54:99:0,129,1666 0/0:51,0:53:99:0,129,1602 0/0:34,0:35:81.25:0,81,1030 0/0:42,0:42:99:0,102,1343 0/0:25,2:30:35.22:0,35,782 0/0:59,1:61:99:0,141,1812 0/0:108,0:108:99:0,235,3037 0/0:32,0:33:78.25:0,78,1022 0/0:72,1:73:99:0,168,2152 0/1:77,11:88:99:101,0,1907 0/0:93,0:95:99:0,214,2702 0/0:100,0:101:99:0,235,2995 0/0:75,0:76:99:0,175,2244 0/0:63,0:64:99:0,159,1992 0/0:55,0:55:99:0,120,1559 0/0:58,2:60:91.77:0,92,1774 0/0:48,0:49:99:0,123,1533 0/0:52,0:52:99:0,135,1729 0/0:42,1:43:99:0,114,1376 0/0:50,0:52:99:0,117,1511 -chr1 1158631 . A G 241536.85 . AC=114;AF=0.9500;AN=120;BaseQRankSum=1.928;DP=8050;DS;Dels=0.00;FS=8.602;HRun=0;HaplotypeScore=3.7991;InbreedingCoeff=-0.0526;MQ=58.98;MQ0=0;MQRankSum=-0.435;QD=30.00;ReadPosRankSum=-0.542;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),EXON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D190|202|SDF4|protein_coding|CODING|ENST00000545427|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D190|348|SDF4|protein_coding|CODING|ENST00000263741|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D190|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=synonymous_variant|gaT/gaC|D|ENSG00000078808|SDF4|ENST00000403997|3/5|||125/243|protein_coding|1,synonymous_variant&NMD_transcript_variant|gaT/gaC|D|ENSG00000078808|SDF4|ENST00000465727|4/7|||190/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,synonymous_variant|gaT/gaC|D|ENSG00000078808|SDF4|ENST00000263741|4/7|||190/348|protein_coding|1,synonymous_variant|gaT/gaC|D|ENSG00000078808|SDF4|ENST00000360001|4/7|||190/362|protein_coding|1,synonymous_variant|gaT/gaC|D|ENSG00000078808|SDF4|ENST00000545427|4/5|||190/202|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,43:43:99:1397,117,0 1/1:0,49:49:99:1639,132,0 1/1:0,47:47:99:1596,123,0 1/1:0,34:34:90.28:1144,90,0 1/1:0,77:77:99:2950,229,0 1/1:0,85:85:99:3236,247,0 1/1:0,158:158:99:6174,469,0 1/1:0,78:78:99:2879,223,0 1/1:1,189:190:99:7262,525,0 1/1:0,197:197:99:7349,566,0 1/1:0,86:87:99:3267,250,0 0/1:54,50:104:99:1631,0,1705 1/1:1,112:113:99:4294,308,0 1/1:0,215:215:99:6631,506,0 1/1:0,227:227:99:6610,506,0 0/1:85,58:145:99:1373,0,2242 1/1:0,200:202:99:6337,484,0 1/1:0,204:206:99:6468,497,0 1/1:0,203:207:99:6267,484,0 1/1:0,204:205:99:6436,485,0 1/1:1,233:236:99:7000,500,0 1/1:1,228:229:99:6859,482,0 0/1:89,89:178:99:2136,0,2370 1/1:0,218:219:99:6658,512,0 1/1:2,192:196:99:5816,407,0 1/1:0,175:176:99:5526,415,0 1/1:0,204:205:99:6051,457,0 1/1:0,157:157:99:4981,382,0 1/1:0,209:209:99:6672,506,0 1/1:0,185:185:99:5482,427,0 1/1:0,250:250:99:7592,578,0 1/1:0,142:143:99:4428,343,0 1/1:0,222:224:99:6936,530,0 1/1:0,191:191:99:6069,463,0 1/1:0,187:187:99:5389,415,0 1/1:0,197:198:99:5892,460,0 1/1:0,223:226:99:6711,509,0 1/1:1,249:250:99:7749,565,0 1/1:0,61:61:99:1870,141,0 1/1:0,112:112:99:3567,274,0 0/1:45,46:91:99:1205,0,1209 1/1:0,73:73:99:2157,165,0 1/1:0,54:54:99:1777,135,0 1/1:0,42:43:99:1290,99,0 1/1:0,48:49:99:1521,120,0 1/1:0,80:80:99:2550,196,0 1/1:0,109:109:99:3343,256,0 1/1:0,39:39:87.28:1159,87,0 0/1:46,44:90:99:1103,0,1182 1/1:1,111:114:99:3359,236,0 1/1:0,106:107:99:3353,262,0 1/1:0,112:112:99:3627,280,0 1/1:0,118:119:99:3462,265,0 1/1:1,75:77:99:2412,190,0 1/1:0,70:70:99:2109,159,0 1/1:0,64:65:99:2038,153,0 1/1:1,63:65:99:1923,120,0 0/1:29,33:62:99:934,0,730 1/1:0,61:61:99:1791,135,0 1/1:0,67:68:99:2099,162,0 -chr1 1158667 . G A 386.78 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.651;DP=8431;DS;Dels=0.00;FS=0.701;HRun=0;HaplotypeScore=4.5114;InbreedingCoeff=-0.0084;MQ=59.13;MQ0=0;MQRankSum=2.552;QD=11.72;ReadPosRankSum=-0.218;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),EXON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|4),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A178|202|SDF4|protein_coding|CODING|ENST00000545427|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A178|348|SDF4|protein_coding|CODING|ENST00000263741|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A178|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=synonymous_variant|gcC/gcT|A|ENSG00000078808|SDF4|ENST00000403997|3/5|||113/243|protein_coding|1,synonymous_variant&NMD_transcript_variant|gcC/gcT|A|ENSG00000078808|SDF4|ENST00000465727|4/7|||178/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,synonymous_variant|gcC/gcT|A|ENSG00000078808|SDF4|ENST00000263741|4/7|||178/348|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000078808|SDF4|ENST00000360001|4/7|||178/362|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000078808|SDF4|ENST00000545427|4/5|||178/202|protein_coding|1 GT:AD:DP:GQ:PL 0/0:62,0:63:99:0,169,2064 0/0:61,0:61:99:0,165,2063 0/0:43,0:43:99:0,123,1541 0/0:57,1:58:99:0,165,2048 0/0:116,0:116:99:0,340,4443 0/0:103,0:103:99:0,307,4027 0/0:198,0:198:99:0,581,7614 0/0:95,0:95:99:0,280,3716 0/0:238,1:239:99:0,669,9336 0/0:242,0:242:99:0,698,9153 0/0:118,0:118:99:0,343,4553 0/0:109,0:109:99:0,313,4075 0/0:149,0:151:99:0,442,5762 0/0:217,1:218:99:0,473,6747 0/0:232,0:234:99:0,518,6876 0/0:157,0:158:99:0,364,4830 0/0:210,1:211:99:0,472,6631 0/0:233,2:235:99:0,506,7261 0/0:206,0:206:99:0,479,6395 0/0:205,1:210:99:0,425,6187 0/0:231,2:236:99:0,455,6890 0/0:244,0:245:99:0,590,7896 0/0:185,0:186:99:0,412,5526 0/0:246,0:246:99:0,557,7401 0/0:224,0:225:99:0,539,7100 0/0:190,0:191:99:0,436,5804 0/0:228,2:231:99:0,449,6554 0/0:146,0:146:99:0,352,4652 0/0:236,0:237:99:0,548,7322 0/0:177,0:177:99:0,412,5388 0/0:236,1:239:99:0,566,7409 0/0:171,0:171:99:0,391,5213 0/0:218,0:218:99:0,524,6960 0/0:197,2:200:99:0,398,6048 0/0:204,0:206:99:0,457,6008 0/0:197,0:198:99:0,472,6174 0/0:240,0:244:99:0,578,7614 0/0:242,1:245:99:0,581,7727 0/0:56,0:56:99:0,120,1629 0/0:98,1:99:99:0,209,3212 0/0:88,0:90:99:0,196,2624 0/0:67,0:67:99:0,153,2000 0/0:60,0:60:99:0,132,1742 0/0:42,0:42:99:0,105,1400 0/0:49,0:49:99:0,114,1488 0/0:71,0:71:99:0,172,2294 0/0:88,0:88:99:0,214,2776 0/1:18,15:33:99:435,0,480 0/0:75,0:75:99:0,181,2366 0/0:99,0:100:99:0,271,3379 0/0:91,0:92:99:0,223,2900 0/0:91,0:91:99:0,229,3022 0/0:86,0:87:99:0,214,2808 0/0:76,0:76:99:0,172,2251 0/0:62,0:62:99:0,138,1841 0/0:54,0:55:99:0,132,1727 0/0:55,0:55:99:0,129,1699 0/0:56,0:57:99:0,141,1877 0/0:49,0:49:99:0,129,1649 0/0:68,0:68:99:0,132,1798 -chr1 1158948 . A G 660.52 . AC=12;AF=0.1034;AN=116;BaseQRankSum=1.771;DP=442;Dels=0.00;FS=0.846;HRun=1;HaplotypeScore=0.2202;InbreedingCoeff=0.0086;MQ=59.04;MQ0=0;MQRankSum=1.540;QD=9.57;ReadPosRankSum=1.061;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/1:2,3:5:40.09:91,0,40 0/0:6,0:6:18.05:0,18,217 0/0:7,0:7:21.06:0,21,250 0/0:9,0:9:24.08:0,24,310 0/0:18,0:18:54.15:0,54,687 0/0:6,0:6:18.06:0,18,238 0/1:8,5:13:99:161,0,268 0/0:8,0:8:21.06:0,21,262 0/0:27,0:27:75.24:0,75,957 0/0:30,0:30:87.27:0,87,1101 0/0:8,0:8:21.07:0,21,267 0/0:8,0:8:24.07:0,24,294 0/0:10,0:10:27.06:0,27,331 0/0:8,0:8:21.07:0,21,269 0/1:4,5:9:99:170,0,131 0/0:6,0:6:18.05:0,18,220 0/0:5,0:5:12.04:0,12,164 0/0:9,0:9:24.08:0,24,306 0/0:19,0:19:54.16:0,54,680 0/0:10,0:10:27.08:0,27,339 0/0:8,0:8:21.06:0,21,269 0/0:5,0:6:15.03:0,15,179 0/0:6,0:6:18.05:0,18,218 0/0:11,0:11:30.10:0,30,387 0/0:10,1:11:27.09:0,27,351 0/0:8,0:8:24.08:0,24,308 0/0:8,0:8:21.03:0,21,239 0/0:10,0:10:27.09:0,27,348 0/0:6,0:6:15.05:0,15,190 0/1:3,2:5:64.99:65,0,88 0/0:9,0:9:27.06:0,27,311 0/0:8,0:8:24.07:0,24,297 0/0:7,0:7:21.04:0,21,253 0/0:6,0:6:15.02:0,15,182 0/1:1,2:3:31.62:57,0,32 0/1:7,1:8:24.17:24,0,176 0/0:14,0:14:39.12:0,39,495 0/0:10,1:11:30.10:0,30,405 0/0:2,0:2:6.02:0,6,76 0/0:3,0:3:6.02:0,6,73 0/0:2,0:2:6.02:0,6,74 0/0:5,0:5:15.05:0,15,198 0/0:2,0:2:6.02:0,6,81 0/0:3,0:3:9.02:0,9,103 0/1:4,1:5:18.39:18,0,149 0/0:1,0:1:3.01:0,3,41 0/1:10,1:11:12.23:12,0,286 ./. 0/0:2,0:2:6.02:0,6,82 1/1:0,4:4:12.04:163,12,0 0/0:5,0:5:15.05:0,15,196 0/0:4,0:4:6.02:0,6,77 0/0:5,0:5:12.04:0,12,163 0/0:4,0:4:12.04:0,12,161 ./. 0/1:3,1:4:25.76:26,0,92 0/0:4,0:4:12.02:0,12,143 0/0:2,0:2:6.02:0,6,72 0/1:1,1:2:33.99:34,0,34 0/0:3,0:3:9.03:0,9,111 -chr1 1158973 . A T 563.68 . AC=11;AF=0.0932;AN=118;BaseQRankSum=-1.928;DP=394;Dels=0.00;FS=3.023;HRun=0;HaplotypeScore=0.2474;InbreedingCoeff=0.1727;MQ=58.52;MQ0=0;MQRankSum=0.128;QD=11.74;ReadPosRankSum=-0.053;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/1:2,1:3:28.33:35,0,28 0/0:3,0:3:9.03:0,9,108 0/0:8,0:8:24.06:0,24,278 0/0:5,0:5:15.05:0,15,200 0/0:10,0:10:30.10:0,30,400 0/0:4,0:4:12.04:0,12,162 0/1:6,5:11:99:168,0,193 0/0:3,0:3:9.03:0,9,115 0/0:16,0:16:45.14:0,45,589 0/0:18,0:18:54.17:0,54,696 0/0:4,0:5:12.04:0,12,155 0/0:5,0:5:15.05:0,15,198 0/0:6,0:6:18.06:0,18,231 0/0:7,0:7:18.06:0,18,226 0/1:3,4:7:98.17:117,0,98 0/0:9,0:9:27.09:0,27,352 0/0:6,0:6:15.05:0,15,189 0/0:9,0:9:27.09:0,27,358 0/0:17,0:17:48.15:0,48,630 0/0:12,0:12:30.08:0,30,373 0/0:6,0:6:18.06:0,18,232 0/0:10,0:10:30.09:0,30,380 0/0:5,0:5:15.05:0,15,195 0/0:10,0:10:24.08:0,24,319 0/0:9,0:9:24.05:0,24,282 0/0:7,0:7:21.07:0,21,281 0/0:12,0:12:33.10:0,33,413 0/0:9,0:9:27.07:0,27,341 0/0:6,0:6:18.06:0,18,242 0/1:4,3:7:91.41:91,0,118 0/0:7,0:7:21.05:0,21,246 0/0:3,0:3:9.03:0,9,106 0/0:7,0:8:21.07:0,21,277 0/0:7,0:7:18.06:0,18,249 0/1:2,1:3:26.48:26,0,30 0/1:4,1:5:6.64:7,0,141 0/0:11,0:11:30.10:0,30,398 0/0:13,0:13:33.07:0,33,403 0/0:3,0:3:9.03:0,9,117 0/0:4,0:4:12.04:0,12,162 0/0:4,0:4:12.04:0,12,153 0/0:5,0:5:15.05:0,15,197 0/0:4,0:4:12.04:0,12,161 0/0:3,0:3:9.03:0,9,118 0/1:4,1:5:6.64:7,0,146 0/0:4,0:4:12.04:0,12,153 0/0:11,0:11:30.08:0,30,382 ./. 0/0:4,0:4:12.04:0,12,163 1/1:0,6:6:18.05:221,18,0 0/0:6,0:6:18.06:0,18,228 0/0:4,0:4:6.02:0,6,72 0/0:9,0:9:24.07:0,24,308 0/0:6,0:6:15.05:0,15,196 0/0:1,0:1:3.01:0,3,32 0/0:3,0:3:9.02:0,9,102 0/0:4,0:4:9.03:0,9,121 0/0:2,0:2:6.02:0,6,70 1/1:0,1:1:3.01:39,3,0 0/0:3,0:3:9.03:0,9,122 -chr1 1158975 . A C 547.46 . AC=10;AF=0.0847;AN=118;BaseQRankSum=0.388;DP=392;Dels=0.00;FS=6.029;HRun=1;HaplotypeScore=0.2379;InbreedingCoeff=0.1826;MQ=58.58;MQ0=0;MQRankSum=-0.688;QD=12.73;ReadPosRankSum=0.857;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,36 0/0:3,0:3:9.03:0,9,112 0/0:8,0:8:24.08:0,24,303 0/0:4,0:4:12.04:0,12,158 0/0:10,0:10:30.10:0,30,405 0/0:4,0:4:12.04:0,12,164 0/1:5,5:10:99:169,0,160 0/0:3,0:3:9.03:0,9,119 0/0:16,0:16:45.14:0,45,593 0/0:19,0:19:57.19:0,57,765 0/0:6,0:6:15.05:0,15,203 0/0:5,0:5:15.05:0,15,202 0/0:6,0:6:18.06:0,18,239 0/0:6,0:6:15.05:0,15,196 0/1:3,3:6:92.83:99,0,93 0/0:9,0:9:27.09:0,27,360 0/0:6,0:6:15.03:0,15,175 0/0:10,0:10:27.09:0,27,366 0/0:16,0:16:48.16:0,48,642 0/0:15,0:15:42.13:0,42,534 0/0:6,0:6:15.05:0,15,197 0/0:10,0:10:30.10:0,30,397 0/0:5,0:5:15.05:0,15,194 0/0:11,0:11:30.09:0,30,389 0/0:9,0:9:27.08:0,27,339 0/0:7,0:7:21.07:0,21,281 0/0:12,0:12:36.11:0,36,459 0/0:8,0:8:24.08:0,24,325 0/0:6,0:6:18.06:0,18,240 0/1:4,3:7:95.26:95,0,118 0/0:8,0:8:24.08:0,24,307 0/0:4,0:4:9.03:0,9,116 0/0:7,0:7:21.07:0,21,269 0/0:7,0:7:18.06:0,18,243 0/1:2,1:3:22.63:35,0,23 0/1:4,1:5:13.60:14,0,144 0/0:11,0:11:30.10:0,30,406 0/0:12,0:12:30.09:0,30,386 0/0:3,0:3:9.03:0,9,118 0/0:4,0:4:12.04:0,12,161 0/0:4,0:4:12.04:0,12,153 0/0:4,0:4:12.04:0,12,157 0/0:4,0:4:12.04:0,12,163 0/0:3,0:3:9.03:0,9,123 0/1:4,1:5:8.65:9,0,142 0/0:4,0:4:12.04:0,12,161 0/0:11,0:11:30.08:0,30,386 ./. 0/0:4,0:4:12.04:0,12,161 1/1:0,6:6:18.06:227,18,0 0/0:6,0:6:18.06:0,18,240 0/0:4,0:4:6.02:0,6,83 0/0:9,0:9:24.07:0,24,306 0/0:6,0:6:18.06:0,18,229 0/0:1,0:1:3.01:0,3,37 0/0:3,0:3:9.03:0,9,116 0/0:4,0:4:9.03:0,9,122 0/0:2,0:2:3.01:0,3,41 1/1:0,1:1:3.01:42,3,0 0/0:3,0:3:9.03:0,9,125 -chr1 1159020 . A G 979.85 . AC=12;AF=0.1000;AN=120;BaseQRankSum=0.104;DP=496;Dels=0.00;FS=2.803;HRun=0;HaplotypeScore=0.5310;InbreedingCoeff=0.1557;MQ=58.21;MQ0=0;MQRankSum=1.781;QD=13.80;ReadPosRankSum=-2.245;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/1:1,1:2:19.67:33,0,20 0/0:4,0:4:12.03:0,12,142 0/0:4,0:4:9.03:0,9,114 0/0:5,0:5:15.04:0,15,183 0/0:3,0:3:9.01:0,9,99 0/0:2,0:2:6.01:0,6,68 1/1:0,4:4:12.04:159,12,0 0/0:4,0:4:9.03:0,9,108 0/0:7,1:8:18.04:0,18,207 0/0:14,1:15:36.11:0,36,457 0/0:3,0:3:9.01:0,9,101 0/0:2,0:3:3:0,3,25 0/0:1,0:1:3.01:0,3,37 0/0:10,0:10:27.09:0,27,358 0/1:3,2:5:69.84:70,0,74 0/0:10,0:10:27.08:0,27,335 0/0:7,0:7:18.06:0,18,228 0/0:14,0:14:39.12:0,39,498 0/0:17,0:18:42.13:0,42,542 0/0:12,0:12:30.09:0,30,390 0/0:12,0:12:33.08:0,33,390 0/0:20,0:20:51.17:0,51,691 0/0:3,0:3:6:0,6,61 0/0:14,0:14:39.11:0,39,500 0/0:10,0:11:27.08:0,27,337 0/0:15,0:15:42.13:0,42,549 0/0:14,0:14:39.10:0,39,495 0/0:8,0:8:21.07:0,21,271 0/0:14,0:14:36.11:0,36,479 0/1:8,6:15:99:187,0,274 0/0:13,0:13:39.09:0,39,476 0/0:3,1:4:6.02:0,6,83 0/0:12,0:12:30.07:0,30,374 0/0:4,0:4:9.03:0,9,120 0/1:4,4:8:95.87:138,0,96 0/1:5,4:9:65.93:66,0,179 0/0:12,1:13:36.12:0,36,465 0/0:14,0:14:33.08:0,33,412 0/0:5,0:5:15.05:0,15,199 0/0:15,0:15:45.14:0,45,575 0/0:9,0:9:27.08:0,27,344 0/0:8,0:8:15.05:0,15,202 0/0:6,0:6:18.06:0,18,243 0/0:2,0:2:6.02:0,6,84 0/1:4,2:6:18.39:18,0,141 0/0:5,0:5:15.05:0,15,190 0/0:12,0:12:30.10:0,30,385 0/0:3,0:4:9.02:0,9,103 0/0:7,0:7:21.07:0,21,271 1/1:0,11:11:30.09:383,30,0 0/0:16,0:16:45.15:0,45,599 0/0:4,0:5:9.03:0,9,123 0/0:12,0:12:33.10:0,33,415 0/0:7,0:7:18.06:0,18,223 0/0:5,0:5:12.04:0,12,150 0/1:3,1:4:30.20:30,0,91 0/0:8,0:8:21.05:0,21,255 0/0:1,0:1:3.01:0,3,39 0/1:4,3:7:65.29:65,0,130 0/0:3,0:4:9.03:0,9,117 -chr1 1159024 . C T 1054.21 . AC=12;AF=0.1000;AN=120;BaseQRankSum=1.335;DP=502;Dels=0.00;FS=1.571;HRun=1;HaplotypeScore=0.4565;InbreedingCoeff=0.1688;MQ=58.19;MQ0=0;MQRankSum=-0.153;QD=14.25;ReadPosRankSum=-1.099;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/1:1,1:2:20.66:33,0,21 0/0:4,0:4:12.04:0,12,154 0/0:3,0:3:6.02:0,6,74 0/0:5,0:5:15.05:0,15,200 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3:0,3,26 1/1:0,4:4:12.04:161,12,0 0/0:4,0:4:12.04:0,12,162 0/0:8,0:8:24.07:0,24,304 0/0:12,0:12:36.10:0,36,461 0/0:2,0:2:6.02:0,6,80 0/0:3,0:3:9.03:0,9,108 0/0:1,0:1:3.01:0,3,41 0/0:11,0:11:30.07:0,30,377 0/1:3,2:5:70.84:71,0,73 0/0:10,0:10:27.09:0,27,361 0/0:8,0:8:24.08:0,24,305 0/0:15,0:15:39.13:0,39,517 0/0:18,0:18:48.16:0,48,635 0/0:13,0:13:39.13:0,39,506 0/0:13,0:13:39.12:0,39,502 0/0:20,0:20:48.15:0,48,639 0/0:3,0:3:9.03:0,9,113 0/0:14,0:14:42.14:0,42,552 0/0:11,0:11:30.09:0,30,380 0/0:17,0:17:48.15:0,48,637 0/0:14,0:14:42.14:0,42,560 0/0:9,0:9:27.08:0,27,334 0/0:16,0:16:42.14:0,42,572 0/1:9,6:15:99:188,0,286 0/0:13,0:13:36.11:0,36,468 0/0:3,0:3:9.03:0,9,120 0/0:12,0:12:33.10:0,33,431 0/0:5,0:5:12.01:0,12,133 0/1:4,4:8:99:129,0,127 0/1:5,5:10:99:101,0,168 0/0:12,0:12:36.12:0,36,471 0/0:14,0:14:36.12:0,36,480 0/0:6,0:6:18.06:0,18,242 0/0:15,0:15:42.13:0,42,532 0/0:9,0:9:27.09:0,27,357 0/0:8,0:8:18.06:0,18,228 0/0:6,0:6:18.06:0,18,243 0/0:3,0:3:9.03:0,9,116 0/0:4,0:5:12.04:0,12,152 0/0:5,0:5:15.05:0,15,188 0/0:13,0:13:30.10:0,30,396 0/0:5,0:5:9.02:0,9,103 0/1:7,1:8:18.94:19,0,217 1/1:0,11:11:33.10:426,33,0 0/0:15,0:15:42.14:0,42,570 0/0:5,0:5:15.03:0,15,187 0/0:11,0:11:27.09:0,27,357 0/0:7,0:7:18.06:0,18,231 0/0:5,0:5:12.04:0,12,162 0/1:3,1:4:30.20:30,0,94 0/0:8,0:8:21.07:0,21,265 0/0:2,0:2:6.02:0,6,75 0/1:4,3:7:65.30:65,0,129 0/0:4,0:4:12.04:0,12,149 -chr1 1159062 . T C 2118.4 . AC=9;AF=0.0833;AN=108;BaseQRankSum=4.132;DP=759;Dels=0.00;FS=2.568;HRun=0;HaplotypeScore=0.5732;InbreedingCoeff=0.1030;MQ=58.19;MQ0=0;MQRankSum=0.274;QD=18.11;ReadPosRankSum=0.765;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:6.02:0,6,71 0/0:2,0:2:6.01:0,6,56 ./. ./. 0/0:2,0:2:6.02:0,6,78 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,39 0/0:5,0:5:12.04:0,12,158 0/0:6,0:6:18.05:0,18,220 ./. ./. ./. 0/0:16,0:16:48.13:0,48,604 0/1:10,9:19:99:299,0,331 0/0:13,0:13:36.09:0,36,441 0/0:14,0:14:42.13:0,42,545 0/0:21,0:21:51.16:0,51,671 0/0:28,0:28:84.26:0,84,1061 0/0:17,0:17:48.13:0,48,595 0/0:19,0:19:54.16:0,54,685 0/0:24,0:24:63.18:0,63,794 0/0:4,0:4:12.04:0,12,157 0/0:19,0:19:48.15:0,48,634 0/0:19,0:20:51.15:0,51,629 0/0:21,0:21:54.17:0,54,705 0/0:24,0:24:69.19:0,69,840 0/0:16,0:16:42.13:0,42,525 0/0:25,0:25:69.22:0,69,913 0/1:12,12:24:99:416,0,321 0/0:18,0:18:54.16:0,54,675 0/0:14,0:14:42.14:0,42,555 0/0:16,0:16:45.14:0,45,566 0/0:15,0:15:39.13:0,39,517 0/1:9,6:15:99:196,0,304 0/1:4,8:12:99:251,0,129 0/0:20,0:20:57.18:0,57,737 0/0:24,0:24:72.23:0,72,958 0/0:11,0:11:33.10:0,33,426 0/0:23,1:24:69.21:0,69,875 0/0:15,0:15:45.14:0,45,582 0/0:13,0:13:36.09:0,36,435 0/0:8,0:8:24.06:0,24,290 0/0:7,0:7:18.06:0,18,235 0/1:5,3:8:54.75:55,0,108 0/0:8,0:8:21.06:0,21,267 0/0:19,0:19:51.15:0,51,617 0/0:10,0:11:27.06:0,27,323 0/0:11,0:11:33.09:0,33,415 1/1:0,24:24:66.21:846,66,0 0/0:28,0:28:78.24:0,78,1005 0/0:18,0:18:48.15:0,48,620 0/0:19,0:19:48.12:0,48,603 0/0:9,0:9:24.08:0,24,317 0/0:14,0:14:36.11:0,36,465 0/1:3,4:7:90.04:140,0,90 0/0:8,0:8:18.06:0,18,231 0/0:6,0:6:15.05:0,15,210 0/1:6,2:8:57.80:58,0,215 0/0:5,0:5:15.05:0,15,189 -chr1 1159107 . G A 3662.49 . AC=10;AF=0.0926;AN=108;BaseQRankSum=1.981;DP=1308;Dels=0.00;FS=17.272;HRun=0;HaplotypeScore=1.1121;InbreedingCoeff=0.0871;MQ=52.60;MQ0=0;MQRankSum=2.390;QD=16.35;ReadPosRankSum=1.115;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. 0/0:3,0:3:6.01:0,6,62 0/0:2,0:2:6.02:0,6,81 0/0:4,0:4:9.02:0,9,107 0/1:2,1:3:32.20:32,0,69 ./. 0/0:3,0:3:9.03:0,9,122 0/0:3,0:4:9.03:0,9,122 ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:26,0:26:75.20:0,75,902 0/1:17,18:35:99:472,0,514 0/0:23,0:23:63.15:0,63,740 0/0:29,0:29:78.20:0,78,928 0/0:32,0:33:81.22:0,81,958 0/0:32,0:32:87.25:0,87,1089 0/0:26,0:28:75.17:0,75,830 0/0:36,0:36:93.21:0,93,1053 0/0:34,1:35:57.72:0,58,1142 0/0:15,0:15:42.13:0,42,525 0/0:28,0:28:69.19:0,69,864 0/0:29,0:31:75.17:0,75,929 0/0:17,0:18:48.13:0,48,571 0/0:28,0:30:69.20:0,69,836 0/0:24,0:25:60.19:0,60,771 0/0:37,0:37:99:0,108,1266 0/1:17,20:37:99:533,0,477 0/0:33,0:34:81.22:0,81,960 0/0:26,0:26:72.21:0,72,869 0/0:26,0:27:72.21:0,72,880 0/0:30,0:31:84.24:0,84,1010 0/1:13,11:24:99:355,0,357 0/1:16,14:31:99:425,0,483 0/0:37,0:37:99:0,108,1313 0/0:50,0:50:99:0,132,1575 0/0:20,0:21:57.15:0,57,682 0/0:42,0:43:99:0,102,1200 0/0:26,1:28:72.17:0,72,812 0/0:22,0:22:60.16:0,60,702 0/0:14,0:14:39.10:0,39,465 0/0:11,0:12:27.06:0,27,314 0/1:9,8:17:99:216,0,224 0/0:24,0:24:69.19:0,69,802 0/0:34,0:34:96.28:0,96,1163 0/0:12,0:12:27.08:0,27,322 0/0:22,0:22:60.16:0,60,716 1/1:0,41:41:99:1299,108,0 0/0:40,0:41:99:0,105,1282 0/0:38,0:40:99:0,99,1173 0/0:25,0:26:57.15:0,57,679 0/0:26,0:26:72.22:0,72,905 0/0:23,0:23:57.15:0,57,691 0/1:12,10:22:99:296,0,326 0/0:17,0:17:42.12:0,42,505 0/0:15,0:15:33.10:0,33,402 0/1:11,2:14:33.83:34,0,351 0/0:15,0:15:39.12:0,39,466 -chr1 1159165 . T TG 273.77 . AC=12;AF=0.1132;AN=106;BaseQRankSum=7.494;DP=2291;FS=100.981;HRun=1;HaplotypeScore=440.9019;InbreedingCoeff=-0.1415;MQ=41.07;MQ0=0;MQRankSum=-7.908;QD=0.51;ReadPosRankSum=7.023;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,39 ./. 0/0:2,0:2:6.02:0,6,78 ./. ./. ./. 0/0:4,0:4:12.04:0,12,156 ./. 0/0:2,0:2:3.01:0,3,39 0/0:2,0:2:3.01:0,3,39 0/0:48,0:48:56.54:0,57,941 0/0:61,1:62:99:0,116,1303 0/0:37,0:37:21.06:0,21,618 0/0:41,0:41:25.49:0,25,656 0/0:40,0:40:28.06:0,28,702 0/1:58,0:58:17.91:18,0,900 0/0:53,0:53:45.24:0,45,960 0/0:47,0:47:73.34:0,73,926 0/0:74,2:76:68.26:0,68,1317 0/0:47,0:47:12.40:0,12,822 0/0:54,0:54:32.60:0,33,783 0/0:49,1:50:37.46:0,37,842 0/0:55,1:56:85.39:0,85,1268 0/0:44,0:44:41.46:0,41,810 0/0:38,0:38:60.52:0,61,701 0/0:63,0:63:96.21:0,96,1293 0/0:52,0:52:80.39:0,80,893 0/0:58,0:58:98.33:0,98,1380 0/0:37,0:36:77.37:0,77,792 0/0:50,0:50:68.33:0,68,1053 0/0:57,1:58:77.75:0,78,1003 0/0:39,1:41:43.28:0,43,670 0/0:48,0:49:34.45:0,34,919 0/0:72,0:72:89.72:0,90,1188 0/0:93,0:93:58.19:0,58,1880 0/0:30,0:30:7.45:0,7,325 0/0:85,0:85:52.41:0,52,1131 0/1:56,1:57:89.08:89,0,635 0/0:30,0:31:2.92:0,3,388 0/1:30,0:31:1.60:2,0,312 0/1:45,0:45:12.25:12,0,918 0/0:43,1:44:29.65:0,30,969 0/1:42,1:43:75.20:75,0,454 0/0:58,0:59:18.06:0,18,750 0/0:19,1:21:11.81:0,12,280 0/1:38,1:39:11.03:11,0,632 0/1:63,1:64:1.83:2,0,882 0/1:60,1:64:2.99:3,0,881 0/0:48,1:49:11.18:0,11,633 0/0:37,0:37:7.09:0,7,395 0/0:47,0:47:7.46:0,7,625 0/0:43,0:43:66.42:0,66,843 0/1:31,0:31:8.75:9,0,368 0/0:24,0:24:28.01:0,28,385 0/1:33,0:33:11.31:11,0,427 0/1:39,1:39:99:157,0,287 0/1:37,0:37:24.13:24,0,598 -chr1 1159166 . G GC 3218.59 . AC=42;AF=0.3962;AN=106;BaseQRankSum=8.299;DP=2329;FS=244.281;HRun=3;HaplotypeScore=445.7226;InbreedingCoeff=-0.6799;MQ=40.93;MQ0=0;MQRankSum=-10.648;QD=1.55;ReadPosRankSum=6.277;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3.01:0,3,36 0/0:1,0:1:3.01:0,3,36 ./. 0/0:2,0:2:6.02:0,6,72 ./. ./. ./. 0/0:4,0:4:12.04:0,12,144 ./. 0/0:2,0:2:3.01:0,3,36 0/0:2,0:2:3.01:0,3,36 0/1:44,3:48:16.56:17,0,521 0/0:56,6:62:44.97:0,45,857 0/1:34,3:37:26.06:26,0,390 0/1:42,1:43:30.95:31,0,366 0/1:37,4:41:60.31:60,0,353 0/1:55,2:58:99:170,0,511 0/1:51,3:54:9.52:10,0,581 0/1:48,0:49:12.99:13,0,514 0/1:74,3:77:99:106,0,831 0/1:46,2:48:44.34:44,0,583 0/1:51,4:56:89.14:89,0,391 0/1:45,4:49:99:104,0,494 0/0:53,3:56:39.64:0,40,882 0/1:42,2:45:26.10:26,0,540 0/1:38,0:38:12.17:12,0,310 0/1:57,5:62:1.64:2,0,798 0/0:50,1:52:17.37:0,17,315 0/1:58,1:59:14.51:15,0,726 0/0:34,3:36:37.88:0,38,462 0/1:48,1:49:46.50:46,0,637 0/1:53,8:61:93.57:94,0,545 0/1:41,3:44:18.18:18,0,415 0/1:47,3:50:41.82:42,0,593 0/1:67,5:72:54.18:54,0,667 0/1:92,4:96:99:197,0,1065 0/1:29,1:30:90.79:91,0,116 0/1:75,7:87:91.55:92,0,706 0/1:59,1:60:99:238,0,345 0/1:31,0:32:12:12,0,222 0/1:28,3:31:36.62:37,0,185 0/1:43,1:45:73.78:74,0,538 0/1:44,1:45:30.65:31,0,614 0/1:39,3:42:99:184,0,193 0/1:55,3:60:99:124,0,362 0/1:20,0:22:25.54:26,0,131 0/1:38,3:41:80.53:81,0,475 0/1:63,2:65:99:134,0,574 0/1:61,3:65:93.88:94,0,592 0/1:46,4:50:99:109,0,311 0/1:30,3:37:95.92:96,0,228 0/1:44,3:48:87.92:88,0,385 0/1:35,7:44:61.48:61,0,336 0/1:27,3:31:99:117,0,149 0/0:26,0:26:13.49:0,13,306 0/1:32,2:34:99:138,0,186 0/1:38,2:39:99:282,0,150 0/1:36,2:38:99:149,0,407 -chr1 1159170 . G C 5417.07 . AC=46;AF=0.4182;AN=110;BaseQRankSum=-10.941;DP=2442;Dels=0.01;FS=490.296;HRun=4;HaplotypeScore=12.6085;InbreedingCoeff=-0.7658;MQ=41.38;MQ0=0;MQRankSum=-18.721;QD=2.30;ReadPosRankSum=6.341;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:6.02:0,6,79 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:6.02:0,6,80 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:4,0:4:12.04:0,12,154 ./. 0/0:1,0:2:3.01:0,3,40 0/0:4,0:4:9.03:0,9,122 0/1:25,18:46:86.28:86,0,188 0/1:46,16:62:99:119,0,403 0/1:22,15:37:60.77:61,0,121 0/1:25,16:41:50.96:51,0,199 0/1:25,17:42:77.16:77,0,288 0/1:36,28:64:99:114,0,392 0/1:35,21:56:33.90:34,0,371 0/1:31,19:50:71.55:72,0,245 0/1:56,26:82:43.28:43,0,602 0/1:36,14:50:26.70:27,0,502 0/1:33,22:55:99:100,0,348 0/1:26,22:48:99:206,0,281 0/1:41,15:57:13.87:14,0,526 0/1:28,18:46:21.73:22,0,491 0/1:20,19:39:25.24:25,0,231 0/0:45,22:67:19.88:0,20,694 0/1:19,32:51:99:108,0,221 0/1:41,21:64:51.46:51,0,481 0/1:23,15:38:49.70:50,0,282 0/1:33,19:52:99:102,0,392 0/1:39,24:64:99:139,0,416 0/1:26,22:49:57.51:58,0,373 0/1:31,21:52:57.57:58,0,344 0/1:46,27:74:60.95:61,0,520 0/1:48,50:98:99:356,0,796 0/1:12,19:32:99:127,0,112 0/1:48,36:85:99:172,0,652 0/1:34,28:62:99:260,0,497 0/1:21,12:34:85.14:85,0,207 0/1:18,15:33:83.31:83,0,212 0/1:22,25:47:99:132,0,284 0/1:26,17:44:99:124,0,406 0/1:20,23:43:99:175,0,238 0/1:30,37:67:99:190,0,434 0/1:13,10:24:7.64:8,0,152 0/1:24,19:43:99:117,0,324 0/1:33,35:68:99:128,0,453 0/1:38,33:71:99:245,0,466 0/1:29,25:54:99:238,0,390 0/1:17,21:38:98.79:145,0,99 0/1:23,28:51:99:117,0,293 0/1:22,23:46:99:188,0,209 0/1:15,16:32:99:170,0,178 0/1:20,10:30:20.31:20,0,235 0/1:19,18:38:99:175,0,203 0/1:17,21:40:99:282,0,104 0/1:21,22:43:99:207,0,402 -chr1 1159170 . G GC 3955.45 . AC=43;AF=0.3909;AN=110;BaseQRankSum=10.923;DP=2473;FS=560.241;HRun=4;HaplotypeScore=452.2142;InbreedingCoeff=-0.6871;MQ=41.56;MQ0=0;MQRankSum=-13.253;QD=1.73;ReadPosRankSum=9.759;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3.01:0,3,34 0/0:3,0:3:9.02:0,9,97 0/0:1,0:1:3.01:0,3,34 0/0:3,0:3:9.02:0,9,98 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:4,0:4:9.03:0,9,102 ./. 0/0:2,0:2:3.01:0,3,34 0/0:4,0:4:9.03:0,9,101 0/0:47,0:47:17.13:0,17,362 0/1:61,3:65:37.80:38,0,538 0/1:37,0:37:45.16:45,0,303 0/1:39,4:43:38.80:39,0,223 0/1:43,2:45:72.48:72,0,289 0/1:63,1:65:99:216,0,409 0/1:55,1:56:6.02:6,0,594 0/1:50,0:50:53.05:53,0,354 0/1:81,1:82:99:127,0,832 0/1:51,0:51:89.69:90,0,510 0/1:55,1:56:99:112,0,419 0/1:48,2:50:99:150,0,326 0/1:57,1:58:20.99:21,0,737 0/1:45,1:46:35.65:36,0,594 0/1:39,1:40:55.89:56,0,314 0/1:66,1:67:61.27:61,0,714 0/1:50,1:51:42.36:42,0,204 0/1:63,1:64:19.08:19,0,588 0/0:38,1:38:12.20:0,12,381 0/1:50,1:51:99:100,0,467 0/1:64,0:64:73.97:74,0,577 0/1:48,1:49:11.52:12,0,511 0/1:52,0:52:83.99:84,0,576 0/1:71,3:75:99:99,0,671 0/1:96,2:98:99:235,0,1003 0/1:30,2:32:91.14:91,0,146 0/1:85,2:87:88.32:88,0,717 0/1:62,1:63:99:223,0,643 0/1:36,0:36:32.70:33,0,247 0/1:33,0:33:5.77:6,0,258 0/1:47,0:47:99:102,0,446 0/1:46,1:47:40.32:40,0,491 0/1:45,0:45:99:172,0,259 0/1:67,1:68:99:119,0,425 0/1:24,0:24:45.14:45,0,172 0/1:45,1:46:41.68:42,0,456 0/1:69,1:70:99:136,0,608 0/1:71,2:73:99:139,0,557 0/1:51,3:54:77.31:77,0,497 0/1:38,0:38:89.12:89,0,190 0/1:50,2:52:99:138,0,348 0/0:44,2:45:2.27:0,2,351 0/1:33,0:33:77.42:77,0,169 0/0:32,0:32:11.20:0,11,330 0/1:36,1:38:99:151,0,321 0/1:39,2:41:99:287,0,149 0/1:46,0:46:99:113,0,474 -chr1 1159174 . CG C 53.97 . AC=7;AF=0.0614;AN=114;BaseQRankSum=10.925;DP=2603;FS=201.126;HRun=1;HaplotypeScore=455.1303;InbreedingCoeff=-0.0824;MQ=42.56;MQ0=0;MQRankSum=-11.905;QD=0.19;ReadPosRankSum=3.289;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3.01:0,3,45 0/0:3,0:3:9.03:0,9,135 0/0:1,0:1:3.01:0,3,45 0/0:3,0:3:9.02:0,9,116 0/0:1,0:1:3.01:0,3,45 0/0:1,0:1:3.01:0,3,34 0/0:2,0:2:6.02:0,6,82 0/0:6,0:6:18.06:0,18,247 ./. 0/0:3,0:3:9.03:0,9,113 0/0:4,0:4:9.03:0,9,135 0/0:46,0:46:51.71:0,52,556 0/0:69,1:70:54.17:0,54,1197 0/0:36,0:36:36.47:0,36,529 0/0:48,0:48:57.93:0,58,593 0/0:48,0:48:28.53:0,29,691 0/0:64,0:64:51.83:0,52,1100 0/0:59,0:60:77.29:0,77,1183 0/1:52,1:53:5.60:6,0,666 0/0:85,0:85:61.37:0,61,1508 0/0:57,1:59:84.74:0,85,1105 0/0:62,1:63:46.67:0,47,917 0/0:46,1:48:25.03:0,25,754 0/0:61,0:61:99:0,112,1459 0/0:46,0:47:71.26:0,71,1142 0/0:41,0:41:69:0,69,741 0/0:68,3:71:39.08:0,39,1212 0/0:53,0:53:32.32:0,32,611 0/0:65,0:65:99:0,103,1163 0/0:43,0:42:66.53:0,67,738 0/0:53,0:53:75.54:0,76,954 0/0:76,0:76:63.22:0,63,1190 0/0:48,0:49:47.04:0,47,848 0/0:53,0:53:40.29:0,40,1011 0/0:79,0:79:64.13:0,64,1261 0/0:101,0:101:99:0,159,1967 0/0:36,0:36:15.55:0,16,463 0/0:85,2:87:20.23:0,20,1213 0/0:67,0:67:4.40:0,4,1202 0/0:38,0:38:13.92:0,14,513 0/0:34,1:36:48.75:0,49,564 0/0:48,0:48:22.94:0,23,739 0/0:51,1:53:86.20:0,86,1100 0/1:44,2:46:43.64:44,0,546 0/0:71,0:71:69.35:0,69,1087 0/1:27,0:27:1.04:1,0,336 0/0:49,0:49:24.80:0,25,897 0/0:74,0:74:18.01:0,18,1084 0/0:72,1:73:12.09:0,12,1021 0/0:55,0:56:20.22:0,20,820 0/1:44,1:44:9.88:10,0,464 0/0:52,0:52:38.17:0,38,734 0/0:47,1:47:64.35:0,64,756 0/1:32,1:33:30.94:31,0,343 0/0:32,0:32:29.05:0,29,643 0/1:37,1:38:28.01:28,0,446 0/1:45,1:46:47.35:47,0,464 0/0:51,0:51:22.95:0,23,887 -chr1 1159175 . G C 12381.61 . AC=47;AF=0.4123;AN=114;BaseQRankSum=-13.988;DP=2603;Dels=0.01;FS=959.340;HRun=4;HaplotypeScore=13.4110;InbreedingCoeff=-0.7559;MQ=42.56;MQ0=0;MQRankSum=-22.983;QD=4.80;ReadPosRankSum=11.432;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3.01:0,3,38 0/0:3,0:3:9.03:0,9,113 0/0:1,0:1:3.01:0,3,41 0/0:2,1:3:6.02:0,6,81 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,38 0/0:2,0:2:6.02:0,6,82 0/0:6,0:6:18.06:0,18,229 ./. 0/0:3,0:3:9.03:0,9,113 0/0:4,0:4:9.03:0,9,122 0/1:17,27:46:99:146,0,172 0/1:30,39:69:99:303,0,571 0/1:18,18:36:89.30:89,0,120 0/1:23,24:48:99:233,0,295 0/1:25,23:48:99:192,0,382 0/1:34,30:64:99:357,0,506 0/1:31,28:59:99:131,0,560 0/1:24,28:52:99:262,0,341 0/1:48,36:85:99:232,0,795 0/1:30,27:58:99:277,0,556 0/1:32,29:62:99:291,0,421 0/1:22,25:47:99:288,0,340 0/1:36,23:61:99:263,0,698 0/1:28,17:47:71.69:72,0,605 0/1:14,27:41:99:258,0,308 0/1:33,35:68:99:382,0,619 0/1:26,27:53:99:204,0,352 0/1:27,36:65:99:229,0,452 0/1:22,21:43:99:151,0,275 0/1:26,27:53:99:207,0,499 0/1:43,33:76:99:317,0,656 0/1:23,25:49:99:214,0,345 0/1:22,30:53:99:231,0,438 0/1:41,37:78:99:244,0,668 0/1:41,59:101:99:882,0,835 0/1:13,23:36:99:250,0,296 0/1:35,47:84:99:425,0,630 0/1:35,32:67:99:314,0,722 0/1:19,18:38:99:221,0,291 0/1:15,20:35:99:206,0,279 0/1:17,31:48:99:341,0,214 0/1:29,23:52:99:264,0,595 0/1:17,27:44:99:344,0,274 0/1:32,38:71:99:403,0,524 0/1:11,16:27:99:139,0,185 0/1:25,23:49:99:170,0,442 0/1:38,34:73:99:371,0,574 0/1:31,39:72:99:473,0,484 0/1:24,32:56:99:350,0,376 0/1:18,23:44:99:241,0,318 0/1:23,28:52:99:154,0,341 0/1:21,25:47:99:225,0,310 0/1:10,22:32:99:136,0,231 0/1:19,13:32:23.25:23,0,287 0/1:17,20:37:99:235,0,192 0/1:13,32:45:99:394,0,267 0/1:23,28:51:99:248,0,507 -chr1 1159175 . G GC 1388.08 . AC=33;AF=0.2895;AN=114;BaseQRankSum=15.983;DP=2657;FS=479.390;HRun=4;HaplotypeScore=447.3152;InbreedingCoeff=-0.4239;MQ=42.88;MQ0=0;MQRankSum=-14.282;QD=0.74;ReadPosRankSum=11.216;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3.01:0,3,36 0/0:3,0:3:9.03:0,9,108 0/0:1,0:1:3.01:0,3,36 0/0:4,0:4:6.01:0,6,67 0/0:1,0:1:3.01:0,3,36 0/0:1,0:1:3.01:0,3,36 0/0:3,0:3:6.02:0,6,72 0/0:6,0:6:18.05:0,18,214 ./. 0/0:3,0:3:9.02:0,9,102 0/0:4,0:4:9.03:0,9,108 0/0:46,0:46:22.99:0,23,441 0/0:71,0:71:26.72:0,27,863 0/1:37,0:37:33.48:33,0,310 0/1:47,2:49:7.69:8,0,433 0/1:48,0:48:41.23:41,0,492 0/1:65,0:66:99:117,0,656 0/0:58,2:60:53.52:0,54,865 0/0:56,0:56:7.98:0,8,523 0/1:84,0:84:22.09:22,0,1001 0/1:60,0:60:0.43:0,0,776 0/1:67,1:68:23.85:24,0,776 0/1:50,0:50:68.11:68,0,534 0/0:63,0:63:19.21:0,19,1011 0/0:48,0:48:18.56:0,19,795 0/1:41,0:41:29.19:29,0,469 0/0:73,1:74:20.39:0,20,943 0/0:54,0:54:29.20:0,29,466 0/1:65,2:67:4.44:4,0,634 0/0:44,0:43:44.13:0,44,519 0/1:56,1:57:67.85:68,0,673 0/1:81,0:81:42.20:42,0,950 0/0:52,0:52:13.59:0,14,641 0/1:54,1:55:5.80:6,0,629 0/1:80,0:80:12.14:12,0,918 0/1:101,0:101:84.97:85,0,1182 0/1:36,0:36:36.07:36,0,354 0/1:86,2:89:91.48:91,0,778 0/1:66,0:67:99:126,0,954 0/1:38,0:38:4.45:4,0,413 0/0:37,0:37:24.67:0,25,423 0/1:47,1:48:86.42:86,0,441 0/0:53,0:53:4.61:0,5,744 0/1:45,0:45:99:109,0,371 0/1:72,0:72:26.65:27,0,742 0/1:27,0:27:0.34:0,0,279 0/1:49,0:49:29.80:30,0,640 0/1:73,1:75:44.53:45,0,732 0/1:74,0:74:30.13:30,0,718 0/0:54,1:56:1.61:0,2,604 0/1:44,0:45:53.38:53,0,371 0/1:55,0:55:99:144,0,462 0/0:46,1:46:24.11:0,24,490 0/1:33,0:33:49.64:50,0,263 0/1:32,1:33:12.91:13,0,450 0/1:41,0:41:55.88:56,0,361 0/1:45,0:45:99:132,0,342 0/1:51,0:51:10.80:11,0,656 -chr1 1159179 . A C 7593.73 . AC=46;AF=0.3898;AN=118;BaseQRankSum=-14.894;DP=2793;Dels=0.01;FS=168.118;HRun=3;HaplotypeScore=10.8241;InbreedingCoeff=-0.6865;MQ=44.03;MQ0=0;MQRankSum=-23.118;QD=2.84;ReadPosRankSum=9.565;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,34 0/0:3,0:3:9.03:0,9,117 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:12.04:0,12,155 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,123 0/0:4,0:4:12.04:0,12,165 0/0:6,1:7:18.06:0,18,228 0/0:2,0:2:6.02:0,6,81 0/0:3,0:3:9.02:0,9,104 0/0:6,0:6:15.05:0,15,188 0/1:29,21:50:35.98:36,0,323 0/1:43,29:74:99:157,0,439 0/1:13,26:39:99:100,0,204 0/1:22,30:54:71.33:71,0,386 0/1:29,23:52:99:118,0,341 0/1:33,36:70:99:293,0,450 0/1:37,29:66:27.49:27,0,679 0/1:30,28:58:85.72:86,0,551 0/1:45,39:84:99:209,0,506 0/1:35,29:64:99:170,0,707 0/1:39,34:73:99:176,0,710 0/1:24,29:54:99:203,0,417 0/1:39,30:69:99:226,0,685 0/1:29,20:50:76.59:77,0,516 0/1:19,24:43:99:100,0,343 0/1:39,37:76:98.25:98,0,716 0/1:24,32:57:90:90,0,297 0/1:33,37:70:99:141,0,495 0/1:24,23:48:81.82:82,0,462 0/1:32,29:61:99:139,0,563 0/1:48,32:81:92.19:92,0,750 0/1:31,25:56:99:138,0,458 0/1:26,29:55:99:164,0,462 0/0:46,34:81:21.75:0,22,664 0/1:50,54:106:99:463,0,747 0/1:18,20:38:99:220,0,302 0/1:41,49:90:99:365,0,481 0/1:37,31:69:99:293,0,678 0/1:20,18:38:86.84:87,0,305 0/1:22,18:40:73.21:73,0,346 0/1:18,30:49:99:283,0,296 0/1:28,26:54:97.36:97,0,572 0/1:18,24:42:99:220,0,231 0/1:35,36:73:99:265,0,539 0/1:14,14:29:67.66:68,0,188 0/1:26,22:48:76.99:77,0,437 0/1:38,37:76:99:209,0,550 0/1:33,48:82:99:259,0,548 0/1:26,32:60:99:242,0,302 0/1:20,28:49:99:243,0,330 0/1:25,30:56:99:185,0,385 0/1:18,30:48:99:203,0,238 0/1:12,19:32:99:123,0,255 0/1:19,15:35:52.35:52,0,298 0/1:21,22:43:99:121,0,287 0/1:16,29:45:99:287,0,195 0/1:28,24:54:99:166,0,596 -chr1 1159179 . A AC 430.63 . AC=15;AF=0.1293;AN=116;BaseQRankSum=17.141;DP=2801;FS=268.128;HRun=3;HaplotypeScore=446.6273;InbreedingCoeff=-0.1719;MQ=43.85;MQ0=0;MQRankSum=-15.854;QD=0.50;ReadPosRankSum=8.601;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,37 ./. 0/0:3,0:3:9.03:0,9,112 0/0:1,0:1:3.01:0,3,37 0/0:4,0:4:12.04:0,12,149 0/0:2,0:2:3.01:0,3,37 0/0:3,0:3:9.03:0,9,111 0/0:4,0:4:12.04:0,12,149 0/0:7,0:7:18.06:0,18,223 0/0:2,0:2:6.02:0,6,72 0/0:3,0:3:9.03:0,9,112 0/0:7,0:7:15.05:0,15,186 0/0:47,1:50:49.93:0,50,596 0/0:71,2:73:21.31:0,21,956 0/0:38,1:39:7.82:0,8,445 0/0:54,0:54:21.41:0,21,677 0/1:50,1:51:40.39:40,0,642 0/1:68,0:68:22.89:23,0,911 0/0:65,1:66:57.10:0,57,1098 0/0:60,1:61:10.27:0,10,746 0/0:82,1:85:63.65:0,64,1264 0/0:64,0:64:47.22:0,47,1032 0/0:72,1:73:49.68:0,50,1151 0/0:53,0:54:9.15:0,9,700 0/0:69,0:69:41.13:0,41,1271 0/0:53,0:53:50.10:0,50,1019 0/0:43,0:43:5.21:0,5,575 0/0:79,0:79:80.96:0,81,1298 0/0:56,0:57:21.19:0,21,593 0/0:67,0:68:23.85:0,24,897 0/0:48,0:47:42.09:0,42,713 0/0:61,0:61:39.08:0,39,1002 0/0:84,1:86:9.22:0,9,1288 0/0:56,0:56:46.74:0,47,900 0/0:56,0:56:62.96:0,63,919 0/1:81,2:84:15.96:16,0,1090 0/1:107,2:109:57.82:58,0,1451 0/0:39,0:39:6.76:0,7,475 0/1:89,0:89:68.04:68,0,903 0/1:70,0:70:5.09:5,0,1103 0/0:37,2:40:7.97:0,8,515 0/0:39,0:40:45.50:0,45,594 0/1:48,0:48:25.84:26,0,519 0/0:52,1:53:17.29:0,17,794 0/1:45,0:45:99:133,0,401 0/0:72,2:74:22.77:0,23,878 0/1:29,0:29:2.16:2,0,335 0/1:48,0:48:3.15:3,0,684 0/0:77,1:78:5.17:0,5,913 0/0:82,0:82:4.57:0,5,998 0/0:60,0:60:19.33:0,19,731 0/1:48,0:47:16.17:16,0,420 0/1:55,0:55:99:104,0,592 0/0:46,1:46:46.25:0,46,554 0/1:33,0:33:5.48:5,0,386 0/0:36,0:36:24.63:0,25,533 0/1:42,1:43:25.02:25,0,501 0/1:45,0:45:74.54:75,0,379 0/0:54,0:54:33.74:0,34,768 -chr1 1159182 . G C 2435.95 . AC=35;AF=0.3017;AN=116;BaseQRankSum=-22.569;DP=2867;Dels=0.01;FS=332.999;HRun=4;HaplotypeScore=9.7305;InbreedingCoeff=-0.4479;MQ=44.51;MQ0=0;MQRankSum=-21.997;QD=1.18;ReadPosRankSum=7.752;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:3,0:3:9.03:0,9,109 0/0:1,0:1:3.01:0,3,41 0/0:5,0:5:15.05:0,15,194 0/0:4,0:4:12.04:0,12,162 0/0:3,0:3:9.03:0,9,123 0/0:4,0:4:12.04:0,12,165 0/0:10,0:10:30.08:0,30,370 0/0:3,0:3:9.03:0,9,122 0/0:3,0:3:9.03:0,9,107 0/0:6,1:7:18.05:0,18,218 0/1:28,24:52:75.28:75,0,414 0/1:41,31:75:19.30:19,0,860 0/1:22,20:42:85:85,0,391 0/0:31,26:57:35.43:0,35,640 0/1:30,23:53:62.10:62,0,613 0/1:41,29:71:38.17:38,0,810 0/0:44,23:67:62.53:0,63,970 0/1:38,23:63:34.22:34,0,815 0/1:53,30:84:3.26:3,0,924 0/1:39,23:64:9.47:9,0,887 0/1:52,24:76:10.16:10,0,1078 0/1:32,23:55:84.86:85,0,548 0/1:47,19:69:79.08:79,0,1060 0/0:44,13:57:69.53:0,70,1027 0/0:24,16:40:3.79:0,4,536 0/0:49,31:81:53.11:0,53,1143 0/1:35,21:58:17.01:17,0,460 0/0:39,31:71:1.53:0,2,872 0/1:27,20:48:2.19:2,0,509 0/0:42,21:63:3.16:0,3,762 0/0:52,30:84:18.51:0,19,1117 0/0:36,20:56:63.14:0,63,699 0/0:32,25:57:32.83:0,33,871 0/0:57,30:90:32.46:0,32,1131 0/1:54,57:112:99:275,0,1323 0/1:17,19:37:99:121,0,422 0/1:37,47:86:99:209,0,682 0/1:46,23:70:99:127,0,923 0/1:26,13:40:18.78:19,0,562 0/0:25,15:40:29.46:0,29,579 0/1:20,26:47:54.40:54,0,415 0/1:29,23:53:99:130,0,672 0/1:24,22:46:99:173,0,403 0/1:38,34:73:99:143,0,651 0/1:17,11:29:6.37:6,0,236 0/1:33,16:50:4.91:5,0,617 0/1:44,32:78:99:164,0,873 0/1:47,35:83:99:122,0,912 0/1:30,30:61:61.65:62,0,656 0/1:25,19:47:27.70:28,0,456 0/1:28,24:53:99:116,0,507 0/1:28,24:52:15.91:16,0,539 0/1:19,15:34:22.94:23,0,436 0/1:21,15:36:45.19:45,0,352 0/1:25,18:44:56.34:56,0,465 0/1:16,27:44:99:227,0,270 0/1:28,30:58:12.96:13,0,752 -chr1 1159182 . G GC 290.6 . AC=11;AF=0.0948;AN=116;BaseQRankSum=18.934;DP=2960;FS=357.719;HRun=4;HaplotypeScore=463.0417;InbreedingCoeff=-0.1293;MQ=44.74;MQ0=0;MQRankSum=-17.632;QD=0.45;ReadPosRankSum=5.626;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,34 ./. 0/0:3,0:3:9.03:0,9,102 0/0:1,0:1:3.01:0,3,34 0/0:5,0:5:15.04:0,15,170 0/0:4,0:4:12.03:0,12,135 0/0:3,0:3:9.03:0,9,102 0/0:5,0:5:12.03:0,12,136 0/0:10,0:10:30.08:0,30,337 0/0:3,0:3:9.03:0,9,101 0/0:3,0:3:9.03:0,9,101 0/0:7,0:7:18.05:0,18,204 0/0:52,1:53:23.87:0,24,482 0/0:79,1:80:45.57:0,46,1018 0/0:46,1:47:21.71:0,22,490 0/0:57,1:58:28.34:0,28,696 0/1:56,0:56:7.80:8,0,710 0/1:73,0:73:8.89:9,0,913 0/0:67,1:69:64.55:0,65,1059 0/0:64,0:64:40.27:0,40,903 0/0:87,1:88:58.09:0,58,1235 0/0:67,0:67:67.35:0,67,1025 0/0:77,0:77:45.97:0,46,1206 0/0:57,1:58:2.56:0,3,695 0/0:70,1:71:50.75:0,51,1221 0/0:58,0:57:74.02:0,74,1108 0/1:43,0:43:10.77:11,0,529 0/0:82,2:84:78.60:0,79,1236 0/0:58,2:61:26.90:0,27,648 0/0:73,0:73:50.76:0,51,993 0/0:49,2:50:58.47:0,58,671 0/0:63,0:63:56.06:0,56,1026 0/0:88,1:89:38.25:0,38,1283 0/0:56,1:57:35.68:0,36,831 0/0:60,0:60:60.44:0,60,962 0/0:91,0:91:53.66:0,54,1260 0/1:116,0:116:65.04:65,0,1460 0/0:41,0:41:27.22:0,27,484 0/1:89,0:89:28.75:29,0,833 0/0:76,0:76:63.73:0,64,1150 0/0:41,0:41:49.93:0,50,641 0/0:40,0:41:50.29:0,50,601 0/0:50,0:50:2.11:0,2,490 0/0:54,0:55:47.09:0,47,781 0/1:48,0:48:99:125,0,473 0/0:73,0:73:1.17:0,1,763 0/1:27,2:29:26.45:26,0,299 0/1:50,1:51:14.97:15,0,737 0/0:82,0:82:43.71:0,44,1013 0/0:86,0:86:62.13:0,62,1133 0/0:63,0:64:20.42:0,20,726 0/0:51,0:50:14.98:0,15,440 0/1:55,0:55:99:112,0,568 0/0:52,1:52:38.62:0,39,648 0/1:34,1:35:17.96:18,0,432 0/0:37,0:37:39.74:0,40,511 0/0:44,1:45:7.27:0,7,547 0/1:47,0:47:26.78:27,0,399 0/0:58,1:59:17.71:0,18,756 -chr1 1159186 . CA C 59.87 . AC=4;AF=0.0345;AN=116;BaseQRankSum=16.532;DP=3075;FS=138.229;HRun=1;HaplotypeScore=462.1606;InbreedingCoeff=-0.0421;MQ=45.70;MQ0=0;MQRankSum=-13.262;QD=0.31;ReadPosRankSum=-6.897;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_truncation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,45 ./. 0/0:3,0:3:9.03:0,9,135 0/0:1,0:1:3.01:0,3,45 0/0:6,0:6:18.06:0,18,263 0/0:6,0:6:18.06:0,18,255 0/0:3,0:3:9.03:0,9,135 0/0:7,0:7:21.07:0,21,296 0/0:15,0:15:45.15:0,45,634 0/0:3,0:3:9.03:0,9,135 0/0:7,0:7:21.07:0,21,278 0/0:9,0:9:26.12:0,26,352 0/0:57,0:58:39.69:0,40,849 0/0:78,3:81:74.16:0,74,1616 0/0:46,0:46:61.90:0,62,830 0/0:60,0:60:80.10:0,80,1158 0/0:58,0:58:31.69:0,32,1103 0/0:74,0:74:77.97:0,78,1415 0/0:73,1:74:77.39:0,77,1734 0/0:64,0:64:77.12:0,77,1426 0/0:91,0:91:31.28:0,31,1737 0/0:67,0:67:99:0,119,1623 0/0:80,0:79:99:0,107,1853 0/0:62,0:62:24.72:0,25,1220 0/0:72,1:73:67.84:0,68,1679 0/0:63,0:62:99:0,108,1674 0/0:47,0:47:55.69:0,56,961 0/0:87,0:87:88.23:0,88,1856 0/0:64,0:64:99:0,101,1188 0/0:76,1:77:99:0,99,1615 0/0:50,0:49:54.84:0,55,984 0/0:65,0:65:87.91:0,88,1478 0/0:87,2:90:97.96:0,98,1962 0/0:58,0:58:99:0,114,1474 0/0:65,0:65:99:0,124,1573 0/0:91,1:92:99:0,130,1898 0/0:118,0:119:95.73:0,96,2448 0/0:42,0:42:17.85:0,18,757 0/0:93,0:93:24.55:0,25,1263 0/0:78,0:77:77.36:0,77,1814 0/0:45,0:45:64.85:0,65,1017 0/0:40,0:40:34.53:0,35,812 0/0:52,0:52:33.76:0,34,848 0/0:60,0:60:54.98:0,55,1208 0/1:52,0:52:65.63:66,0,743 0/0:75,1:76:63.17:0,63,1183 0/1:32,0:32:3.37:3,0,446 0/0:51,1:52:55.22:0,55,1133 0/0:83,2:85:67.17:0,67,1686 0/0:85,1:86:27.82:0,28,1568 0/1:63,0:63:5.63:6,0,1047 0/0:54,1:54:42.23:0,42,829 0/0:57,0:57:7.97:0,8,978 0/0:54,0:53:25.22:0,25,881 0/0:36,0:37:27.63:0,28,728 0/0:34,1:35:47.12:0,47,644 0/0:48,0:48:43.42:0,43,951 0/1:47,0:47:67.37:67,0,627 0/0:60,0:60:72.49:0,72,1178 -chr1 1159187 . A C 8669.24 . AC=47;AF=0.4052;AN=116;BaseQRankSum=-11.349;DP=3075;Dels=0.01;FS=50.216;HRun=4;HaplotypeScore=10.3138;InbreedingCoeff=-0.7071;MQ=45.70;MQ0=0;MQRankSum=-25.197;QD=2.88;ReadPosRankSum=-1.026;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:3,0:3:9.02:0,9,108 0/0:1,0:1:3.01:0,3,41 0/0:6,0:6:18.06:0,18,239 0/0:6,0:6:18.06:0,18,246 0/0:3,0:3:9.03:0,9,123 0/0:7,0:7:21.07:0,21,282 0/0:15,0:15:42.13:0,42,533 0/0:3,0:3:9.03:0,9,120 0/0:7,0:7:21.07:0,21,276 0/0:8,0:9:24.08:0,24,317 0/1:25,32:57:99:113,0,356 0/1:43,35:78:99:176,0,790 0/1:20,26:46:63.35:63,0,401 0/1:28,31:60:65.91:66,0,570 0/1:29,29:58:99:175,0,533 0/1:35,38:74:99:326,0,616 0/1:46,26:73:93.49:93,0,771 0/1:33,29:64:61.87:62,0,687 0/1:46,45:91:99:287,0,654 0/1:39,28:67:60.74:61,0,749 0/1:51,29:80:99:173,0,939 0/1:32,30:62:99:219,0,536 0/1:40,30:72:99:342,0,526 0/1:39,22:63:69.69:70,0,711 0/1:23,24:47:99:173,0,454 0/1:46,40:87:99:134,0,733 0/1:32,31:64:99:153,0,481 0/1:42,34:76:99:237,0,799 0/1:24,25:49:44.53:45,0,431 0/1:34,31:65:99:129,0,685 0/1:49,39:88:99:154,0,886 0/1:35,23:58:33.64:34,0,491 0/1:36,29:65:99:162,0,825 0/1:50,39:91:99:123,0,848 0/1:60,58:119:99:663,0,1207 0/1:22,19:42:99:180,0,473 0/1:44,46:93:99:423,0,578 0/1:48,30:78:99:122,0,981 0/1:29,16:45:65.78:66,0,540 0/1:24,16:40:99:136,0,351 0/1:23,29:52:99:289,0,348 0/1:34,25:60:99:216,0,595 0/1:27,24:52:99:311,0,281 0/1:36,39:75:99:246,0,580 0/1:15,17:32:63.46:63,0,220 0/1:35,16:51:99:102,0,383 0/1:46,36:83:99:243,0,712 0/1:43,40:85:99:383,0,580 0/1:24,38:63:99:176,0,347 0/1:22,31:54:99:124,0,481 0/1:34,23:57:99:220,0,505 0/1:24,29:54:99:228,0,303 0/1:21,16:37:99:102,0,423 0/1:18,16:34:59.63:60,0,191 0/1:24,24:48:99:177,0,450 0/1:18,29:47:99:329,0,364 0/1:29,31:60:99:242,0,670 -chr1 1159187 . A AC 38.33 . AC=3;AF=0.0259;AN=116;BaseQRankSum=18.228;DP=3113;FS=209.724;HRun=4;HaplotypeScore=455.4440;InbreedingCoeff=-0.0431;MQ=45.73;MQ0=0;MQRankSum=-16.454;QD=0.25;ReadPosRankSum=-6.893;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:3.01:0,3,36 ./. 0/0:3,0:3:9.03:0,9,108 0/0:1,0:1:3.01:0,3,36 0/0:6,0:6:18.06:0,18,216 0/0:6,0:6:18.05:0,18,214 0/0:3,0:3:9.03:0,9,108 0/0:8,0:8:21.06:0,21,252 0/0:15,0:15:45.14:0,45,535 0/0:5,0:5:9.03:0,9,108 0/0:6,0:6:18.05:0,18,210 0/0:9,0:9:27.08:0,27,321 0/0:61,0:61:41.07:0,41,673 0/0:84,0:84:77.67:0,78,1277 0/0:48,1:49:35.70:0,36,565 0/0:60,0:60:28.53:0,29,841 0/0:59,0:59:33.35:0,33,925 0/0:74,0:74:11.76:0,12,1012 0/0:74,0:74:99:0,136,1443 0/0:64,1:65:69.32:0,69,1109 0/0:91,0:91:99:0,109,1480 0/0:70,0:70:86.20:0,86,1209 0/0:80,0:79:69.43:0,69,1414 0/0:60,1:61:18.93:0,19,908 0/0:72,1:74:87.38:0,87,1303 0/0:64,0:63:99:0,119,1388 0/0:48,0:48:0.53:0,1,719 0/0:86,0:86:99:0,127,1508 0/0:65,1:66:52.31:0,52,926 0/0:76,3:79:99:0,100,1270 0/0:51,0:51:16.05:0,16,711 0/0:65,0:65:44.38:0,44,1116 0/0:89,0:90:40.23:0,40,1547 0/0:59,0:59:75.14:0,75,1158 0/0:64,1:65:74.45:0,74,1152 0/0:93,0:93:81.33:0,81,1469 0/0:115,2:117:70.61:0,71,1885 0/0:42,0:43:46.09:0,46,647 0/0:91,2:93:20.91:0,21,990 0/0:78,0:77:94.52:0,95,1433 0/0:48,0:48:64.43:0,64,850 0/0:40,0:40:53.72:0,54,630 0/0:52,0:52:23.03:0,23,669 0/0:60,0:60:67.06:0,67,978 0/1:51,0:51:22.33:22,0,584 0/0:77,0:78:28:0,28,887 0/0:32,0:32:6.26:0,6,375 0/0:52,0:53:32.34:0,32,811 0/0:86,1:87:31.92:0,32,1282 0/0:87,0:87:75.02:0,75,1248 0/0:62,0:62:54.05:0,54,791 0/0:56,0:55:39.49:0,39,628 0/1:57,0:57:85.78:86,0,759 0/0:54,0:53:35.33:0,35,719 0/0:37,0:37:20.05:0,20,590 0/0:35,0:35:41:0,41,480 0/0:49,0:49:29.29:0,29,765 0/1:46,1:47:14.57:15,0,481 0/0:63,0:63:55.62:0,56,948 -chr1 1159191 . A C 4227.25 . AC=45;AF=0.3814;AN=118;BaseQRankSum=-16.791;DP=3098;Dels=0.00;FS=55.651;HRun=4;HaplotypeScore=21.4245;InbreedingCoeff=-0.6257;MQ=46.09;MQ0=0;MQRankSum=-20.550;QD=1.47;ReadPosRankSum=-6.333;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|3),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|3),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|3),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|3),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:6.02:0,6,80 0/0:1,0:1:3.01:0,3,41 0/0:5,0:5:15.04:0,15,181 0/0:1,0:1:3.01:0,3,41 0/0:6,0:6:18.04:0,18,222 0/0:7,0:7:21.07:0,21,286 0/0:3,0:3:9.03:0,9,121 0/0:8,0:8:24.08:0,24,323 0/0:16,1:17:48.14:0,48,611 0/0:7,0:7:21.07:0,21,284 0/0:6,0:6:18.05:0,18,227 0/0:10,0:10:30.10:0,30,395 0/1:30,25:57:24.94:25,0,472 0/1:52,31:84:20.57:21,0,766 0/1:25,23:49:70:70,0,564 0/1:34,26:60:45.41:45,0,568 0/1:36,22:59:78.62:79,0,703 0/1:36,36:73:66.72:67,0,732 0/1:43,29:72:5.53:6,0,895 0/1:32,30:62:67.10:67,0,798 0/1:46,44:91:99:145,0,763 0/1:39,33:73:86.10:86,0,915 0/1:46,31:80:26.20:26,0,949 0/1:30,30:61:99:171,0,541 0/1:49,28:79:99:231,0,914 0/0:40,21:63:36.82:0,37,902 0/1:27,23:50:99:105,0,509 0/1:49,36:85:99:124,0,802 0/1:41,25:66:93.61:94,0,597 0/1:45,29:75:99:165,0,931 0/1:32,19:51:46.27:46,0,665 0/1:40,26:67:77.58:78,0,795 0/0:55,33:90:34.22:0,34,1186 0/1:30,28:58:34.16:34,0,687 0/1:38,27:65:73.49:73,0,901 0/1:57,34:92:20.40:20,0,837 0/1:60,57:117:99:218,0,1236 0/1:22,18:41:67.94:68,0,512 0/1:42,50:93:99:215,0,577 0/1:45,30:77:51.09:51,0,1055 0/1:33,15:48:9.70:10,0,576 0/1:22,18:40:41.73:42,0,353 0/1:29,24:54:99:153,0,333 0/1:42,17:60:75.46:75,0,672 0/1:25,24:50:28.96:29,0,413 0/1:41,34:76:99:102,0,656 0/1:14,15:31:60.59:61,0,223 0/1:31,18:50:72.92:73,0,463 0/1:50,35:86:99:115,0,749 0/1:40,36:79:99:102,0,598 0/1:25,31:56:99:193,0,287 0/1:32,24:57:99:113,0,629 0/1:29,25:57:68.70:69,0,496 0/1:21,30:52:99:164,0,345 0/1:20,14:34:74:74,0,414 0/1:27,7:34:3.64:4,0,196 0/1:28,23:52:99:122,0,531 0/1:22,27:50:99:264,0,357 0/1:35,25:61:99:134,0,721 -chr1 1159485 . C T 1786.91 . AC=11;AF=0.0917;AN=120;BaseQRankSum=-1.460;DP=676;Dels=0.00;FS=1.200;HRun=0;HaplotypeScore=0.4563;InbreedingCoeff=0.0725;MQ=57.99;MQ0=0;MQRankSum=0.146;QD=16.39;ReadPosRankSum=0.465;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/1:2,1:3:27.95:28,0,58 0/0:7,0:7:21.07:0,21,272 0/0:5,0:5:15.04:0,15,180 0/0:6,0:6:15.05:0,15,192 0/0:20,0:20:60.19:0,60,781 0/0:14,1:15:0.89:0,1,457 0/1:21,16:37:99:527,0,698 0/0:9,0:9:24.07:0,24,300 0/0:37,0:37:99:0,111,1471 0/0:25,0:25:75.24:0,75,1010 0/0:17,0:17:51.17:0,51,693 0/0:11,0:11:30.10:0,30,404 0/0:17,0:17:51.16:0,51,663 0/0:6,0:6:15.05:0,15,205 0/1:6,6:12:99:187,0,189 0/0:9,0:9:27.08:0,27,338 0/0:11,0:11:30.09:0,30,389 0/0:9,0:9:18.05:0,18,231 0/0:10,0:10:30.10:0,30,400 0/0:12,0:12:30.09:0,30,375 0/0:6,0:6:18.04:0,18,211 0/0:12,0:12:30.09:0,30,370 0/0:12,0:12:36.11:0,36,462 0/0:11,0:11:33.11:0,33,432 0/0:9,0:9:21.06:0,21,258 0/0:13,0:13:36.11:0,36,457 0/0:11,0:11:33.10:0,33,423 0/0:6,0:6:18.06:0,18,234 0/0:12,0:12:36.10:0,36,442 0/1:3,5:8:94.14:168,0,94 0/0:21,0:21:60.19:0,60,778 0/0:12,0:12:36.11:0,36,452 0/0:9,0:9:21.07:0,21,281 0/0:11,0:11:30.10:0,30,397 0/1:6,5:11:99:146,0,166 0/1:4,3:7:90.56:91,0,131 0/0:13,0:13:33.09:0,33,405 0/0:18,0:18:48.12:0,48,606 0/0:5,0:5:9.03:0,9,109 0/0:19,0:19:48.12:0,48,585 0/0:15,0:15:36.11:0,36,460 0/0:9,0:9:27.06:0,27,319 0/0:3,0:3:9.03:0,9,114 0/0:11,0:11:27.07:0,27,342 0/1:3,5:8:86.47:173,0,86 0/0:8,0:9:24.08:0,24,303 0/0:15,0:15:33.09:0,33,405 0/0:3,0:3:9.03:0,9,102 0/0:10,0:10:24.07:0,24,300 1/1:0,12:12:33.10:407,33,0 0/0:5,0:5:15.04:0,15,182 0/0:9,0:9:21.05:0,21,257 0/0:7,0:7:21.05:0,21,263 0/0:11,0:11:33.11:0,33,427 0/0:9,0:9:18.05:0,18,217 0/1:2,6:8:47.94:197,0,48 0/0:10,0:10:27.08:0,27,340 0/0:9,0:9:24.07:0,24,298 0/1:2,1:3:26.23:26,0,52 0/0:5,0:5:15.03:0,15,169 -chr1 1159517 . T C 12932.29 . AC=115;AF=0.9583;AN=120;BaseQRankSum=1.742;DP=373;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.2819;InbreedingCoeff=0.1828;MQ=58.44;MQ0=0;MQRankSum=1.074;QD=35.14;ReadPosRankSum=1.392;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,3:3:9.03:113,9,0 1/1:0,5:5:15.03:175,15,0 1/1:0,4:4:12.03:139,12,0 1/1:0,3:3:6.01:62,6,0 1/1:0,10:10:30.10:399,30,0 1/1:0,8:8:24.07:305,24,0 1/1:0,13:13:39.12:489,39,0 1/1:0,8:8:24.08:317,24,0 1/1:0,18:18:51.16:670,51,0 1/1:0,14:14:42.14:548,42,0 1/1:0,9:9:24.08:316,24,0 0/0:4,1:5:12.03:0,12,144 1/1:0,9:9:27.06:327,27,0 1/1:0,6:6:15.05:207,15,0 1/1:0,6:6:18.06:226,18,0 1/1:0,4:4:12.04:143,12,0 1/1:0,6:6:15.05:197,15,0 1/1:0,5:5:15.04:173,15,0 1/1:0,3:3:9.03:125,9,0 1/1:0,10:10:30.08:375,30,0 1/1:0,4:4:12.03:148,12,0 1/1:0,9:9:24.06:293,24,0 1/1:0,5:5:9.03:124,9,0 1/1:0,2:2:6.02:74,6,0 1/1:0,3:3:6.02:82,6,0 1/1:0,7:7:21.05:256,21,0 1/1:0,7:7:21.07:267,21,0 1/1:0,3:3:9.03:117,9,0 1/1:0,6:6:18.05:233,18,0 1/1:0,6:6:15.05:194,15,0 1/1:0,7:7:21.07:284,21,0 1/1:0,3:3:9.03:123,9,0 1/1:0,5:5:12.04:166,12,0 1/1:0,11:11:27.06:310,27,0 1/1:0,4:4:12.04:149,12,0 1/1:0,5:5:15.05:193,15,0 1/1:0,8:8:24.08:303,24,0 1/1:0,14:14:39.12:514,39,0 1/1:0,3:3:9.03:112,9,0 1/1:0,12:12:30.10:383,30,0 0/1:2,4:6:64.76:102,0,65 1/1:0,5:5:15.05:195,15,0 1/1:0,2:2:6.02:74,6,0 1/1:0,7:7:18.06:248,18,0 1/1:0,4:4:12.04:153,12,0 1/1:0,6:6:18.06:236,18,0 1/1:0,11:11:33.08:392,33,0 1/1:0,1:1:3.01:33,3,0 0/1:1,4:5:13.62:118,0,14 1/1:0,7:7:18.05:217,18,0 1/1:0,4:4:12.04:155,12,0 1/1:0,8:8:18.04:215,18,0 1/1:0,3:3:9.03:123,9,0 1/1:0,5:5:15.05:202,15,0 1/1:0,6:6:18.06:228,18,0 1/1:0,6:6:18.06:230,18,0 1/1:0,4:4:12.04:150,12,0 0/1:3,1:4:26.56:27,0,76 1/1:0,2:2:6.02:73,6,0 1/1:0,4:4:12.03:130,12,0 -chr1 1159520 . C T 92.03 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.994;DP=360;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.2826;InbreedingCoeff=-0.0403;MQ=58.45;MQ0=0;MQRankSum=0.711;QD=13.15;ReadPosRankSum=0.622;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,107 0/0:4,0:4:12.02:0,12,143 0/0:4,0:4:9.03:0,9,106 0/0:4,0:4:9.01:0,9,86 0/0:10,0:10:30.10:0,30,389 0/0:7,0:7:18.06:0,18,234 0/0:15,0:15:42.13:0,42,540 0/0:7,0:7:21.07:0,21,266 0/0:18,0:18:54.15:0,54,698 0/0:15,0:15:42.13:0,42,537 0/0:9,0:9:24.08:0,24,313 0/0:4,0:4:12.04:0,12,158 0/0:8,0:8:24.08:0,24,309 0/0:6,0:6:15.05:0,15,200 0/0:6,0:6:18.06:0,18,237 0/0:3,0:3:9.03:0,9,107 0/0:6,0:6:15.05:0,15,191 0/0:4,0:4:12.04:0,12,149 0/0:3,0:3:9.03:0,9,123 0/0:8,0:8:24.08:0,24,314 0/0:3,0:3:9.03:0,9,117 0/0:9,0:9:21.06:0,21,268 0/0:4,0:5:12.04:0,12,160 0/0:2,0:2:3.01:0,3,30 0/0:3,0:3:6.02:0,6,77 0/0:6,0:6:15.05:0,15,198 0/0:6,0:6:18.04:0,18,209 0/0:2,0:2:6.02:0,6,82 0/0:6,0:6:18.05:0,18,230 0/0:6,0:6:18.04:0,18,210 0/0:8,0:8:24.08:0,24,313 0/0:4,0:4:9.03:0,9,124 0/0:5,0:5:12.04:0,12,167 0/0:8,0:8:18.05:0,18,220 0/0:4,0:4:9.03:0,9,119 0/0:4,0:4:12.04:0,12,160 0/0:8,0:8:24.07:0,24,299 0/0:13,0:13:36.12:0,36,489 0/0:3,0:3:9.03:0,9,118 0/0:11,0:11:27.09:0,27,348 0/0:6,0:6:18.06:0,18,236 0/0:4,0:4:12.04:0,12,151 0/0:2,0:2:6.01:0,6,66 0/0:7,0:7:18.06:0,18,249 0/0:5,0:5:15.03:0,15,176 0/0:6,0:6:18.06:0,18,242 0/0:11,0:11:33.10:0,33,418 0/0:1,0:1:3.01:0,3,33 0/0:5,0:5:15.04:0,15,172 0/1:3,4:7:92.72:139,0,93 0/0:4,0:4:12.04:0,12,156 0/0:8,0:8:15.04:0,15,184 0/0:3,0:3:9.03:0,9,122 0/0:5,0:5:15.05:0,15,202 0/0:6,0:6:18.06:0,18,220 0/0:6,0:6:18.06:0,18,230 0/0:5,0:5:12.04:0,12,149 0/0:3,0:3:9.03:0,9,102 0/0:2,0:2:6.02:0,6,73 0/0:4,0:4:12.04:0,12,151 -chr1 1159540 . G A 542.38 . AC=6;AF=0.0517;AN=116;BaseQRankSum=-0.694;DP=294;Dels=0.00;FS=4.088;HRun=0;HaplotypeScore=0.1520;InbreedingCoeff=0.0954;MQ=58.66;MQ0=0;MQRankSum=1.126;QD=17.50;ReadPosRankSum=0.267;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,116 0/0:3,0:3:6.02:0,6,80 0/0:6,0:6:18.05:0,18,229 0/0:3,0:3:6.02:0,6,72 0/0:8,0:8:24.08:0,24,324 0/0:5,0:5:15.05:0,15,202 0/0:13,0:13:39.13:0,39,517 0/0:10,0:10:30.09:0,30,391 0/0:12,0:12:36.12:0,36,490 0/0:17,0:17:51.16:0,51,674 1/1:0,7:7:18.05:228,18,0 0/0:5,0:5:15.05:0,15,202 0/1:3,5:8:99:172,0,99 0/0:4,0:4:9.03:0,9,129 0/0:5,0:5:15.05:0,15,199 0/0:1,0:1:3.01:0,3,42 0/0:4,0:4:12.04:0,12,166 0/1:2,2:4:68.30:71,0,68 0/0:2,0:2:6.02:0,6,84 0/0:7,0:7:21.07:0,21,283 0/0:2,0:2:6.02:0,6,80 0/0:7,0:7:21.06:0,21,262 0/0:4,0:4:9.03:0,9,120 0/0:4,0:4:9.03:0,9,120 0/0:3,0:3:9.01:0,9,103 0/0:5,0:5:15.05:0,15,198 0/0:4,0:4:12.04:0,12,163 0/0:3,0:3:9.03:0,9,121 0/0:2,0:2:6.02:0,6,78 0/0:3,0:3:9.03:0,9,116 0/0:5,0:5:15.04:0,15,194 0/0:2,0:2:6.02:0,6,77 0/0:2,0:2:6.02:0,6,80 0/1:5,2:7:54.60:55,0,184 0/0:3,0:3:9.03:0,9,114 0/0:4,0:4:12.04:0,12,164 0/0:7,0:7:21.07:0,21,289 0/0:10,0:12:24.08:0,24,332 0/0:2,0:2:6.02:0,6,80 0/0:8,0:8:21.07:0,21,284 0/0:5,0:5:15.05:0,15,198 0/1:1,4:5:26.19:132,0,26 0/0:2,0:2:6.02:0,6,77 0/0:5,0:5:12.04:0,12,166 0/0:4,0:4:12.04:0,12,151 0/0:4,0:4:12.04:0,12,160 0/0:12,0:12:33.10:0,33,423 ./. 0/0:6,0:6:15.05:0,15,199 0/0:5,0:5:15.04:0,15,196 0/0:5,0:5:15.05:0,15,193 0/0:6,0:6:12.04:0,12,154 0/0:1,0:1:3.01:0,3,42 0/0:3,0:3:9.03:0,9,118 0/0:5,0:5:15.05:0,15,201 0/0:1,0:1:3.01:0,3,33 0/0:4,0:4:12.03:0,12,140 0/0:2,0:2:6.02:0,6,78 ./. 0/0:3,0:3:9.03:0,9,124 -chr1 1159729 . T G 41.48 . AC=5;AF=0.119;AN=42;BaseQRankSum=0.407;DP=35;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;InbreedingCoeff=0.0685;MQ=55.69;MQ0=0;MQRankSum=-0.031;QD=10.37;ReadPosRankSum=0.470;EFF=DOWNSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000478938|),UPSTREAM(MODIFIER|||||SDF4|retained_intron|CODING|ENST00000494748|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000494748|||||retained_intron|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000478938|||||retained_intron|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:9.03:0,9,111 0/0:2,0:2:6.02:0,6,74 0/0:1,0:1:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,41 1/1:0,1:1:3.01:33,3,0 ./. 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.02:0,9,100 ./. ./. ./. ./. 0/1:1,1:2:30.96:31,0,32 ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:2,0:2:3.01:0,3,45 0/0:1,0:1:3.01:0,3,37 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:5,0:5:9.03:0,9,128 ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. 0/0:1,0:1:3.01:0,3,42 ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. -chr1 1163767 . C T 814.94 . AC=5;AF=0.0446;AN=112;BaseQRankSum=-1.291;DP=646;Dels=0.00;FS=1.287;HRun=0;HaplotypeScore=0.6392;InbreedingCoeff=0.1958;MQ=57.92;MQ0=0;MQRankSum=-5.203;QD=14.05;ReadPosRankSum=2.369;EFF=INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),INTRON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.01:0,6,67 0/0:9,0:9:27.07:0,27,316 0/0:9,0:9:21.07:0,21,266 0/0:5,0:5:9.03:0,9,116 0/0:20,0:20:51.17:0,51,676 0/0:17,0:17:48.15:0,48,610 0/0:36,0:36:93.30:0,93,1220 0/0:11,0:11:33.11:0,33,439 0/0:31,0:31:93.29:0,93,1217 0/0:47,0:47:99:0,126,1649 0/0:18,0:18:51.17:0,51,683 0/0:20,0:20:60.19:0,60,783 0/0:8,0:8:24.06:0,24,300 0/0:10,0:10:27.08:0,27,328 0/0:17,0:17:33.11:0,33,438 0/0:7,0:7:18.04:0,18,218 0/0:7,0:7:15.05:0,15,206 0/0:13,0:13:33.10:0,33,429 0/0:18,0:18:45.14:0,45,570 0/0:6,0:6:18.05:0,18,219 0/0:16,0:16:39.12:0,39,498 0/0:24,0:24:57.16:0,57,726 0/0:14,0:14:39.10:0,39,477 0/0:8,0:8:21.07:0,21,266 0/0:12,0:12:33.10:0,33,385 0/0:15,0:15:36.12:0,36,500 0/1:7,11:18:99:292,0,186 0/0:15,0:15:42.13:0,42,538 0/0:5,0:5:15.05:0,15,196 0/0:10,0:10:24.08:0,24,308 0/0:16,0:16:39.10:0,39,481 0/0:12,0:12:33.10:0,33,423 0/0:18,0:18:48.15:0,48,627 0/0:13,0:13:30.10:0,30,389 0/1:6,6:12:99:142,0,171 0/0:8,0:8:18.06:0,18,220 0/1:12,11:23:99:308,0,375 0/0:24,0:24:57.18:0,57,756 0/0:2,0:2:6.02:0,6,81 0/0:4,0:4:9.03:0,9,116 0/0:6,0:6:15.04:0,15,189 0/0:1,0:1:3.01:0,3,42 0/0:3,0:3:9.03:0,9,114 0/0:3,0:4:9.03:0,9,110 0/0:3,0:3:9.03:0,9,118 0/0:4,0:4:12.04:0,12,158 0/0:7,0:7:21.06:0,21,259 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:6.02:0,6,77 0/0:8,0:8:24.08:0,24,321 0/0:5,0:5:15.03:0,15,171 0/0:4,0:4:9.02:0,9,103 0/0:7,0:7:18.04:0,18,206 ./. 1/1:0,5:5:15.04:176,15,0 0/0:2,0:2:3.01:0,3,33 ./. ./. 0/0:2,0:2:6.02:0,6,75 ./. -chr1 1163773 . C T 190.62 . AC=2;AF=0.0182;AN=110;BaseQRankSum=-0.471;DP=694;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6224;InbreedingCoeff=0.4388;MQ=58.00;MQ0=0;MQRankSum=0.927;QD=23.83;ReadPosRankSum=2.443;EFF=INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),INTRON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.01:0,9,101 0/0:9,0:9:24.06:0,24,282 0/0:11,0:11:27.08:0,27,339 0/0:5,0:5:9.02:0,9,99 0/0:19,0:19:54.17:0,54,696 0/0:18,0:18:54.17:0,54,680 0/0:39,0:39:99:0,105,1374 0/0:12,0:12:36.10:0,36,445 0/0:40,0:40:99:0,117,1507 0/0:48,0:48:99:0,129,1686 0/0:16,0:16:42.13:0,42,539 0/0:20,0:20:60.16:0,60,729 0/0:15,0:15:42.13:0,42,539 0/0:12,0:12:33.09:0,33,412 0/0:20,0:22:48.12:0,48,577 0/0:8,0:8:18.06:0,18,245 0/0:6,0:6:15.03:0,15,187 0/0:13,0:13:33.10:0,33,421 0/0:17,0:17:45.10:0,45,541 0/0:7,0:7:18.06:0,18,227 0/0:18,0:18:36.11:0,36,469 0/0:28,0:28:66.15:0,66,824 0/0:15,0:15:33.10:0,33,410 0/0:10,0:10:27.07:0,27,318 0/0:12,0:12:30.08:0,30,350 0/0:14,0:15:33.10:0,33,428 0/0:17,0:17:36.08:0,36,409 0/0:17,0:17:45.13:0,45,556 0/0:8,0:8:21.07:0,21,279 0/0:11,0:11:27.09:0,27,349 0/0:15,0:15:36.10:0,36,441 0/0:12,0:12:30.09:0,30,387 0/0:18,0:18:48.14:0,48,609 0/0:13,0:13:30.08:0,30,366 0/0:12,0:12:30.08:0,30,364 0/0:9,0:9:21.06:0,21,247 0/0:24,0:24:69.20:0,69,827 0/0:24,0:24:54.17:0,54,708 0/0:2,0:2:3.01:0,3,39 0/0:4,0:4:12.03:0,12,145 0/0:6,0:6:18.03:0,18,210 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:6.02:0,6,81 0/0:4,0:4:9.02:0,9,109 0/0:3,0:3:9.03:0,9,116 0/0:4,0:4:12.04:0,12,154 0/0:8,0:8:24.08:0,24,304 ./. 0/0:2,0:2:6.02:0,6,76 1/1:0,8:8:21.04:257,21,0 0/0:6,0:6:15.04:0,15,176 0/0:4,0:4:9.01:0,9,87 0/0:8,0:8:21.06:0,21,239 ./. 0/0:5,0:5:15.04:0,15,175 0/0:2,0:2:3.01:0,3,33 ./. ./. 0/0:4,0:4:12.04:0,12,157 ./. -chr1 1163804 . C T 3932.35 . AC=16;AF=0.1356;AN=118;BaseQRankSum=-5.937;DP=1136;Dels=0.00;FS=0.471;HRun=0;HaplotypeScore=1.9937;InbreedingCoeff=-0.0388;MQ=57.51;MQ0=0;MQRankSum=2.984;QD=13.15;ReadPosRankSum=-2.512;EFF=INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),INTRON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=intron_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1 GT:AD:DP:GQ:PL 0/1:4,2:8:24.10:24,0,91 0/0:17,0:18:42.10:0,42,477 0/0:12,0:12:33.09:0,33,398 0/0:7,0:7:15.03:0,15,175 0/0:30,0:30:84.26:0,84,1071 0/0:40,0:40:99:0,108,1390 0/1:32,23:57:99:632,0,1006 0/0:23,0:23:60.17:0,60,721 0/0:73,0:73:99:0,208,2633 0/0:83,0:83:99:0,238,2966 1/1:0,20:20:57.15:654,57,0 0/0:29,0:29:72.22:0,72,907 0/1:20,21:41:99:595,0,605 0/0:21,0:21:57.17:0,57,723 0/1:14,15:30:99:351,0,312 0/1:9,6:15:99:152,0,211 0/0:13,0:13:33.11:0,33,431 0/1:9,13:23:99:310,0,252 0/0:25,0:25:63.17:0,63,789 0/0:15,0:16:36.12:0,36,481 0/0:27,0:28:72.19:0,72,891 0/0:28,2:30:27.45:0,27,833 0/0:22,0:22:51.12:0,51,633 0/0:16,0:16:36.11:0,36,443 0/0:18,1:19:51.14:0,51,595 0/0:23,0:23:54.17:0,54,711 0/0:20,0:20:51.14:0,51,613 0/0:24,0:25:51.14:0,51,627 0/0:15,0:15:33.09:0,33,432 0/1:8,12:20:99:296,0,209 0/0:22,0:24:54.15:0,54,666 0/0:21,0:21:45.14:0,45,602 0/0:23,0:23:57.12:0,57,696 0/1:10,9:19:99:213,0,243 0/1:9,9:18:99:170,0,158 0/1:11,10:21:99:182,0,314 0/0:30,0:30:78.21:0,78,943 0/0:35,0:35:90.27:0,90,1140 0/0:2,0:2:6.02:0,6,72 0/0:8,0:8:21.06:0,21,266 0/0:8,0:8:21.05:0,21,250 0/1:2,1:3:29.55:30,0,65 0/1:4,3:8:64.97:65,0,101 0/0:3,0:3:9.03:0,9,111 0/0:3,0:3:6.02:0,6,69 0/0:5,0:5:15.03:0,15,172 0/0:10,0:10:30.10:0,30,395 ./. 0/0:5,0:5:15.04:0,15,174 0/0:16,0:16:45.14:0,45,571 0/0:13,0:13:33.10:0,33,404 0/0:9,0:9:21.06:0,21,246 0/0:14,0:14:36.11:0,36,425 0/0:3,0:3:9.03:0,9,121 0/0:9,0:9:24.07:0,24,270 0/1:2,7:9:38.01:199,0,38 0/0:2,0:2:3.01:0,3,41 0/0:5,0:5:15.05:0,15,196 0/1:4,3:7:59.66:60,0,109 0/0:1,0:1:3.01:0,3,37 -chr1 1163811 . G GGACA 6953.39 . AC=15;AF=0.1271;AN=118;BaseQRankSum=-5.858;DP=1276;FS=21.541;HRun=0;HaplotypeScore=109.0684;InbreedingCoeff=-0.0171;MQ=57.57;MQ0=0;MQRankSum=-14.498;QD=29.97;ReadPosRankSum=1.598;EFF=INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),INTRON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,intron_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1 GT:AD:DP:GQ:PL 0/0:12,0:12:21.05:0,21,324 0/0:21,0:21:45.13:0,45,772 0/0:13,0:13:30.10:0,30,515 0/0:7,0:7:18.06:0,18,313 0/0:36,0:36:87.30:0,87,1563 0/0:49,0:49:99:0,129,2249 0/0:61,0:61:99:0,153,2641 0/1:23,5:28:99:679,0,663 0/0:83,0:83:99:0,220,3927 0/0:96,0:95:99:0,241,4257 0/0:25,0:25:69.19:0,69,1144 0/0:30,0:30:81.27:0,81,1420 0/0:50,0:50:99:0,135,2376 0/0:23,0:23:60.21:0,60,1101 0/0:35,0:35:93.30:0,93,1658 0/0:13,0:13:36.12:0,36,663 0/0:16,0:16:42.14:0,42,733 0/0:25,0:25:72.24:0,72,1256 0/0:28,0:28:78.27:0,78,1409 0/0:18,0:18:48.16:0,48,883 0/0:29,0:28:78.27:0,78,1431 0/0:36,0:36:99:0,105,1859 0/0:24,0:24:60.20:0,60,1080 0/1:12,6:18:99:457,0,449 0/1:12,9:21:99:791,0,381 0/0:26,0:26:72.24:0,72,1298 0/1:16,5:21:99:606,0,443 0/0:24,0:24:57.19:0,57,978 0/0:19,0:19:54.18:0,54,924 0/0:23,0:23:66.22:0,66,1187 0/0:26,0:26:78.26:0,78,1388 0/0:21,0:21:60.21:0,60,1104 0/0:23,0:23:63.21:0,63,1135 0/0:23,0:23:63.21:0,63,1108 0/1:9,8:17:99:482,0,374 0/1:16,10:26:99:928,0,459 0/1:28,7:35:99:803,0,902 0/0:38,0:38:99:0,102,1833 0/1:2,1:3:70.27:70,0,100 0/0:9,0:9:21.07:0,21,386 0/0:8,0:8:21.07:0,21,386 0/0:3,0:3:9.03:0,9,166 0/0:8,0:8:18.06:0,18,327 0/1:5,1:6:61.23:61,0,256 0/0:3,0:3:6.02:0,6,110 0/0:7,0:7:15.05:0,15,276 0/0:11,0:11:33.11:0,33,561 ./. 0/0:6,0:6:18.06:0,18,293 0/0:18,0:18:54.18:0,54,945 0/1:9,5:15:99:357,0,378 0/1:5,5:10:99:370,0,142 0/1:10,6:16:99:595,0,205 0/0:3,0:3:9.03:0,9,166 1/1:1,7:8:24.08:620,24,0 0/1:6,2:8:99:134,0,307 0/0:1,0:1:3.01:0,3,55 0/0:5,0:5:15.05:0,15,270 0/0:8,0:8:21.07:0,21,386 0/0:1,0:1:3.01:0,3,55 -chr1 1163964 . G A 5411.83 . AC=5;AF=0.0417;AN=120;BaseQRankSum=1.794;DP=3215;Dels=0.00;FS=17.078;HRun=0;HaplotypeScore=1.6463;InbreedingCoeff=0.3739;MQ=58.93;MQ0=0;MQRankSum=1.765;QD=20.19;ReadPosRankSum=-3.159;EFF=EXON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),EXON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D70|202|SDF4|protein_coding|CODING|ENST00000545427|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D70|348|SDF4|protein_coding|CODING|ENST00000263741|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D70|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=synonymous_variant|gaC/gaT|D|ENSG00000078808|SDF4|ENST00000403997|1/5|||5/243|protein_coding|1,synonymous_variant&NMD_transcript_variant|gaC/gaT|D|ENSG00000078808|SDF4|ENST00000465727|2/7|||70/254|nonsense_mediated_decay|1,synonymous_variant|gaC/gaT|D|ENSG00000078808|SDF4|ENST00000360001|2/7|||70/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|2/3||||processed_transcript|1,synonymous_variant|gaC/gaT|D|ENSG00000078808|SDF4|ENST00000545427|2/5|||70/202|protein_coding|1,synonymous_variant|gaC/gaT|D|ENSG00000078808|SDF4|ENST00000263741|2/7|||70/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1 GT:AD:DP:GQ:PL 0/0:22,0:23:60.14:0,60,705 0/0:40,0:40:99:0,117,1437 0/0:25,0:25:69.21:0,69,856 0/0:32,0:32:84.26:0,84,1059 0/0:92,0:92:99:0,277,3649 0/0:91,0:91:99:0,268,3497 0/0:150,0:150:99:0,442,5819 0/0:103,0:103:99:0,298,3853 0/0:202,0:202:99:0,578,7676 0/0:187,1:188:99:0,510,7207 1/1:0,76:76:99:2913,223,0 0/0:84,0:84:99:0,250,3301 0/1:64,47:111:99:1517,0,2209 0/0:44,0:44:99:0,126,1634 0/0:56,0:56:99:0,132,1702 0/0:44,0:45:99:0,111,1463 0/0:29,0:30:78.25:0,78,1040 0/1:25,22:47:99:498,0,749 0/0:49,0:51:99:0,114,1502 0/0:37,0:37:96.30:0,96,1273 0/0:40,0:40:99:0,108,1414 0/0:64,0:64:99:0,160,2119 0/0:36,0:38:84.26:0,84,1120 0/0:38,0:38:99:0,99,1276 0/0:34,0:34:78.25:0,78,1033 0/0:46,0:46:99:0,114,1505 0/0:48,0:48:99:0,123,1622 0/0:34,0:38:93.30:0,93,1250 0/0:51,0:52:99:0,120,1589 0/0:50,0:50:99:0,126,1657 0/0:56,0:56:99:0,132,1770 0/0:38,0:39:93.28:0,93,1202 0/0:44,0:44:99:0,102,1365 0/0:28,0:28:78.24:0,78,1002 0/0:30,0:30:81.26:0,81,1052 0/0:38,0:38:93.30:0,93,1240 0/0:43,0:43:99:0,105,1347 0/0:76,0:76:99:0,193,2574 0/0:26,0:26:51.16:0,51,682 0/0:60,0:60:99:0,123,1610 0/0:40,0:41:93.25:0,93,1213 0/1:18,16:34:99:485,0,457 0/0:29,0:29:66.21:0,66,881 0/0:43,0:44:99:0,111,1407 0/0:25,1:26:63.20:0,63,845 0/0:24,0:26:60.17:0,60,782 0/0:77,0:78:99:0,169,2222 0/0:22,0:22:54.15:0,54,689 0/0:42,0:42:99:0,99,1296 0/0:66,0:66:99:0,172,2225 0/0:51,0:51:99:0,132,1662 0/0:41,0:41:99:0,105,1308 0/0:52,0:52:99:0,132,1718 0/0:30,0:31:60.19:0,60,798 0/0:34,0:34:87.28:0,87,1135 0/0:55,0:55:99:0,126,1686 0/0:26,0:26:51.16:0,51,680 0/0:38,0:38:90.29:0,90,1203 0/0:37,0:37:81.24:0,81,1040 0/0:25,0:25:57.16:0,57,734 -chr1 1164031 . A G 2189.26 . AC=3;AF=0.0250;AN=120;BaseQRankSum=0.524;DP=3658;DS;Dels=0.00;FS=1.511;HRun=0;HaplotypeScore=1.4260;InbreedingCoeff=0.6581;MQ=58.98;MQ0=0;MQRankSum=-0.494;QD=25.46;ReadPosRankSum=2.486;EFF=EXON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),EXON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V48A|202|SDF4|protein_coding|CODING|ENST00000545427|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V48A|348|SDF4|protein_coding|CODING|ENST00000263741|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V48A|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,missense_variant&NMD_transcript_variant|gTa/gCa|V/A|ENSG00000078808|SDF4|ENST00000465727|2/7|benign(0.002)|tolerated(0.47)|48/254|nonsense_mediated_decay|1,missense_variant|gTa/gCa|V/A|ENSG00000078808|SDF4|ENST00000360001|2/7|benign(0)|tolerated(1)|48/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|2/3||||processed_transcript|1,missense_variant|gTa/gCa|V/A|ENSG00000078808|SDF4|ENST00000545427|2/5|benign(0.002)|tolerated(1)|48/202|protein_coding|1,missense_variant|gTa/gCa|V/A|ENSG00000078808|SDF4|ENST00000263741|2/7|benign(0.002)|tolerated(1)|48/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1 GT:AD:DP:GQ:PL 0/0:29,0:29:69.20:0,69,830 0/0:40,0:41:99:0,105,1254 0/0:44,0:44:99:0,117,1433 0/0:41,1:42:99:0,105,1251 0/0:106,0:107:99:0,289,3534 0/0:119,1:122:99:0,334,4151 0/0:197,0:197:99:0,539,6683 0/0:88,0:88:99:0,238,2807 0/0:237,0:237:99:0,680,8581 0/0:235,2:238:99:0,655,8361 0/0:115,0:115:99:0,328,4070 0/0:98,0:98:99:0,268,3342 0/0:127,0:128:99:0,361,4493 0/0:50,1:51:99:0,120,1510 0/0:54,1:56:99:0,132,1613 0/0:41,0:42:99:0,102,1313 0/0:38,0:38:87.24:0,87,1126 0/0:44,0:46:99:0,105,1349 0/0:58,0:58:99:0,135,1803 0/0:32,0:32:90.26:0,90,1124 0/0:53,0:56:99:0,126,1601 0/0:66,0:66:99:0,150,1948 0/0:45,0:46:99:0,105,1356 0/0:48,0:48:99:0,114,1440 0/0:40,0:41:99:0,102,1259 0/0:54,0:54:99:0,129,1657 0/0:57,0:57:99:0,141,1814 0/0:42,0:43:90.29:0,90,1189 0/0:64,0:64:99:0,150,1954 0/0:62,1:63:99:0,138,1769 0/0:58,0:58:99:0,135,1758 0/0:63,1:64:99:0,138,1740 0/0:47,0:48:99:0,114,1433 0/0:48,0:49:99:0,102,1354 0/0:42,0:44:99:0,99,1313 0/0:59,0:59:99:0,141,1857 0/0:57,0:59:99:0,150,1904 0/0:79,0:80:99:0,202,2551 0/0:30,0:31:63.20:0,63,813 0/0:55,1:57:99:0,120,1481 0/0:27,1:30:75.21:0,75,911 0/0:36,0:37:90.23:0,90,1116 0/0:36,0:36:90.27:0,90,1134 0/0:42,1:43:99:0,99,1190 0/1:14,14:28:99:359,0,331 0/0:35,0:35:78.22:0,78,966 0/0:58,0:61:99:0,129,1564 0/0:28,0:29:63.19:0,63,820 0/0:35,0:37:93.21:0,93,1099 1/1:0,58:58:99:1917,150,0 0/0:40,0:40:87.25:0,87,1100 0/0:33,0:35:84.22:0,84,1002 0/0:41,0:42:93.28:0,93,1159 0/0:42,0:44:87.25:0,87,1126 0/0:31,1:33:78.20:0,78,954 0/0:48,0:48:99:0,120,1530 0/0:20,0:20:48.14:0,48,594 0/0:40,0:42:99:0,99,1308 0/0:35,0:36:78.24:0,78,997 0/0:25,0:26:51.16:0,51,653 -chr1 1164072 . C T 1571.76 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-2.716;DP=2924;DS;Dels=0.00;FS=4.033;HRun=0;HaplotypeScore=1.7879;InbreedingCoeff=0.6581;MQ=59.08;MQ0=0;MQRankSum=-0.133;QD=23.11;ReadPosRankSum=3.483;EFF=EXON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),EXON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A34|202|SDF4|protein_coding|CODING|ENST00000545427|),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A34|348|SDF4|protein_coding|CODING|ENST00000263741|),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A34|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,synonymous_variant&NMD_transcript_variant|gcG/gcA|A|ENSG00000078808|SDF4|ENST00000465727|2/7|||34/254|nonsense_mediated_decay|1,synonymous_variant|gcG/gcA|A|ENSG00000078808|SDF4|ENST00000360001|2/7|||34/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|2/3||||processed_transcript|1,synonymous_variant|gcG/gcA|A|ENSG00000078808|SDF4|ENST00000545427|2/5|||34/202|protein_coding|1,synonymous_variant|gcG/gcA|A|ENSG00000078808|SDF4|ENST00000263741|2/7|||34/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1 GT:AD:DP:GQ:PL 0/0:21,0:21:51.12:0,51,593 0/0:46,0:47:99:0,129,1605 0/0:20,0:20:57.15:0,57,712 0/0:32,0:32:84.25:0,84,1042 0/0:87,0:87:99:0,259,3393 0/0:80,0:80:99:0,235,3101 0/0:152,0:152:99:0,424,5603 0/0:75,0:75:99:0,223,2908 0/0:181,0:182:99:0,512,6735 0/0:191,1:192:99:0,519,7277 0/0:76,0:76:99:0,226,2949 0/0:72,0:72:99:0,208,2719 0/0:78,0:78:99:0,226,2979 0/0:40,1:41:68.34:0,68,1312 0/0:48,0:48:99:0,120,1585 0/0:36,0:36:87.28:0,87,1169 0/0:32,0:32:75.21:0,75,958 0/0:44,0:44:93.29:0,93,1240 0/0:40,0:40:93.29:0,93,1244 0/0:30,0:30:81.21:0,81,1009 0/0:58,0:58:99:0,135,1771 0/0:44,0:44:99:0,120,1596 0/0:44,0:44:99:0,102,1347 0/0:37,0:37:87.28:0,87,1131 0/0:42,0:42:99:0,105,1381 0/0:41,0:41:99:0,108,1404 0/0:52,0:52:99:0,129,1695 0/0:41,0:41:87.27:0,87,1135 0/0:49,0:49:99:0,120,1509 0/0:49,0:49:99:0,129,1668 0/0:50,0:50:99:0,123,1625 0/0:50,0:51:99:0,126,1673 0/0:43,0:43:90.29:0,90,1219 0/0:47,0:47:99:0,102,1349 0/0:45,1:46:62.32:0,62,1297 0/0:47,0:48:99:0,108,1437 0/0:53,0:53:99:0,123,1649 0/0:74,0:76:99:0,196,2585 0/0:25,0:25:63.17:0,63,801 0/0:51,0:52:99:0,129,1642 0/0:27,0:28:78.22:0,78,995 0/0:27,0:28:72.23:0,72,925 0/0:27,0:27:66.21:0,66,883 0/0:29,0:29:72.20:0,72,905 0/1:14,5:19:99:105,0,373 0/0:33,0:33:81.26:0,81,1068 0/0:46,0:46:99:0,123,1579 0/0:25,0:25:60.19:0,60,761 0/0:29,0:29:72.23:0,72,946 1/1:0,47:49:99:1553,123,0 0/0:32,0:32:87.26:0,87,1079 0/0:21,0:21:54.15:0,54,693 0/0:29,0:29:72.23:0,72,936 0/0:26,0:27:63.20:0,63,829 0/0:37,0:38:84.27:0,84,1115 0/0:31,0:31:81.26:0,81,1047 0/0:19,0:19:48.16:0,48,632 0/0:38,0:38:93.29:0,93,1189 0/0:22,0:22:48.12:0,48,592 0/0:19,0:19:36.12:0,36,487 -chr1 1164090 . T C 1638.23 . AC=3;AF=0.0250;AN=120;BaseQRankSum=0.539;DP=2459;Dels=0.00;FS=3.268;HRun=1;HaplotypeScore=1.1248;InbreedingCoeff=0.6578;MQ=59.09;MQ0=0;MQRankSum=-1.281;QD=25.20;ReadPosRankSum=2.166;EFF=EXON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2),EXON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A28|202|SDF4|protein_coding|CODING|ENST00000545427|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A28|348|SDF4|protein_coding|CODING|ENST00000263741|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A28|362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,synonymous_variant&NMD_transcript_variant|gcA/gcG|A|ENSG00000078808|SDF4|ENST00000465727|2/7|||28/254|nonsense_mediated_decay|1,synonymous_variant|gcA/gcG|A|ENSG00000078808|SDF4|ENST00000360001|2/7|||28/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|2/3||||processed_transcript|1,synonymous_variant|gcA/gcG|A|ENSG00000078808|SDF4|ENST00000545427|2/5|||28/202|protein_coding|1,synonymous_variant|gcA/gcG|A|ENSG00000078808|SDF4|ENST00000263741|2/7|||28/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1 GT:AD:DP:GQ:PL 0/0:19,0:19:51.12:0,51,581 0/0:34,0:34:90.27:0,90,1096 0/0:25,0:25:63.19:0,63,761 0/0:20,0:21:51.15:0,51,610 0/0:65,0:66:99:0,181,2346 0/0:72,1:73:99:0,205,2573 0/0:118,0:119:99:0,346,4349 0/0:71,0:71:99:0,208,2681 0/0:161,0:162:99:0,460,5958 0/0:154,0:154:99:0,445,5702 0/0:62,0:62:99:0,181,2328 0/0:59,0:59:99:0,169,2198 0/0:74,0:75:99:0,211,2649 0/0:31,0:31:90.26:0,90,1150 0/0:38,0:38:96.30:0,96,1261 0/0:31,0:31:75.22:0,75,979 0/0:28,0:28:72.22:0,72,926 0/0:44,0:44:93.29:0,93,1222 0/0:34,0:34:75.22:0,75,976 0/0:25,0:25:63.18:0,63,812 0/0:52,0:52:99:0,120,1580 0/0:34,0:34:99:0,99,1267 0/0:39,1:40:99:0,102,1265 0/0:33,0:33:81.23:0,81,1041 0/0:37,0:37:93.29:0,93,1218 0/0:36,0:38:87.28:0,87,1151 0/0:43,0:44:96.31:0,96,1283 0/0:34,0:34:72.20:0,72,933 0/0:32,0:32:84.24:0,84,1038 0/0:38,0:38:93.29:0,93,1210 0/0:42,1:43:99:0,99,1292 0/0:41,0:41:90.29:0,90,1212 0/0:34,0:35:63.20:0,63,854 0/0:39,0:39:90.29:0,90,1205 0/0:42,0:42:96.28:0,96,1239 0/0:42,0:43:99:0,108,1423 0/0:43,0:43:99:0,108,1425 0/0:67,1:68:99:0,172,2234 0/0:16,0:16:42.10:0,42,518 0/0:39,0:39:99:0,102,1250 0/0:25,0:26:66.18:0,66,820 0/0:24,0:24:60.19:0,60,784 0/0:22,0:22:51.16:0,51,670 0/0:20,0:21:54.16:0,54,686 0/1:12,6:18:99:139,0,365 0/0:30,0:30:75.19:0,75,963 0/0:39,0:39:99:0,102,1287 0/0:19,0:19:42.13:0,42,532 0/0:22,0:23:54.17:0,54,715 1/1:0,47:47:99:1585,123,0 0/0:30,0:30:81.23:0,81,1002 0/0:20,0:20:48.15:0,48,617 0/0:23,0:24:57.17:0,57,737 0/0:21,0:21:51.17:0,51,671 0/0:28,0:28:69.20:0,69,880 0/0:23,0:23:57.17:0,57,749 0/0:13,0:13:36.09:0,36,457 0/0:35,0:35:93.25:0,93,1169 0/0:18,0:18:45.13:0,45,554 0/0:14,0:15:30.09:0,30,387 -chr1 1164179 . G A 833.67 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-0.622;DP=1063;Dels=0.00;FS=8.157;HRun=0;HaplotypeScore=0.7297;InbreedingCoeff=0.6212;MQ=58.97;MQ0=0;MQRankSum=1.079;QD=26.89;ReadPosRankSum=2.348;EFF=EXON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|),UTR_5_PRIME(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),UTR_5_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),UTR_5_PRIME(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),UTR_5_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727|2/7|||-/254|nonsense_mediated_decay|1,5_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000360001|2/7|||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|2/3||||processed_transcript|1,5_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000545427|2/5|||-/202|protein_coding|1,5_prime_UTR_variant|||ENSG00000078808|SDF4|ENST00000263741|2/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:12.04:0,12,145 0/0:9,0:10:24.08:0,24,315 0/0:15,0:16:42.12:0,42,518 0/0:10,0:10:30.09:0,30,382 0/0:27,0:27:78.26:0,78,1061 0/0:30,0:30:87.28:0,87,1168 0/0:51,0:51:99:0,150,2005 0/0:22,0:22:60.18:0,60,771 0/0:70,0:70:99:0,205,2725 0/0:69,0:69:99:0,208,2749 0/0:25,0:25:72.23:0,72,943 0/0:14,0:14:42.14:0,42,555 0/0:39,0:39:99:0,105,1386 0/0:14,0:14:42.14:0,42,558 0/0:20,0:20:57.18:0,57,754 0/0:9,0:9:27.09:0,27,351 0/0:11,0:11:33.11:0,33,430 0/0:17,0:17:48.15:0,48,625 0/0:17,0:17:45.14:0,45,590 0/0:14,0:14:39.13:0,39,522 0/0:15,0:15:39.11:0,39,486 0/0:19,1:20:48.15:0,48,636 0/0:21,0:21:57.18:0,57,738 0/0:19,0:19:51.16:0,51,662 0/0:14,0:14:33.11:0,33,444 0/0:16,0:16:45.15:0,45,610 0/0:13,0:13:36.11:0,36,469 0/0:13,0:13:36.09:0,36,462 0/0:16,0:16:45.14:0,45,594 0/0:17,0:17:48.16:0,48,632 0/0:15,0:15:42.13:0,42,528 0/0:15,0:15:42.13:0,42,545 0/0:12,0:12:30.10:0,30,414 0/0:7,0:7:21.05:0,21,268 0/0:11,0:11:30.09:0,30,392 0/0:17,0:18:45.15:0,45,598 0/0:15,0:15:42.14:0,42,565 0/0:28,0:28:84.27:0,84,1098 0/0:6,0:6:18.06:0,18,236 0/0:26,0:26:72.23:0,72,965 0/0:9,0:9:21.07:0,21,277 0/0:14,0:14:39.12:0,39,500 0/0:8,0:8:21.07:0,21,268 0/0:13,0:13:27.09:0,27,364 0/1:1,9:10:12.37:229,0,12 0/0:13,0:13:33.11:0,33,452 0/0:25,0:25:63.21:0,63,853 0/0:3,0:3:9.03:0,9,117 0/0:11,0:11:24.07:0,24,301 1/1:0,20:21:51.17:691,51,0 0/0:7,0:7:21.07:0,21,268 0/0:9,0:9:24.07:0,24,307 0/0:10,0:10:21.07:0,21,281 0/0:19,0:19:45.14:0,45,599 0/0:17,0:17:48.16:0,48,643 0/0:8,0:8:18.06:0,18,243 0/0:8,0:8:18.05:0,18,219 0/0:20,0:20:48.15:0,48,632 0/0:9,0:9:21.06:0,21,263 0/0:20,0:20:42.13:0,42,550 -chr1 1164250 . C CCA 210.26 . AC=2;AF=0.0167;AN=120;BaseQRankSum=0.248;DP=413;FS=0.000;HRun=0;HaplotypeScore=29.3469;InbreedingCoeff=0.3092;MQ=58.65;MQ0=0;MQRankSum=2.358;QD=26.28;ReadPosRankSum=0.652;EFF=EXON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|2),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|),UTR_5_PRIME(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|2),UTR_5_PRIME(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|2),UTR_5_PRIME(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|2),UTR_5_PRIME(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|2);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,5_prime_UTR_variant&NMD_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000465727|2/7|||-/254|nonsense_mediated_decay|1,5_prime_UTR_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000360001|2/7|||-/362|protein_coding|1,non_coding_exon_variant&nc_transcript_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000459994|2/3||||processed_transcript|1,5_prime_UTR_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000545427|2/5|||-/202|protein_coding|1,5_prime_UTR_variant&feature_elongation|||ENSG00000078808|SDF4|ENST00000263741|2/7|||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:18.05:0,18,236 0/0:7,0:7:17.89:0,18,235 0/0:6,0:6:12.04:0,12,177 0/0:6,0:6:12.04:0,12,176 0/0:10,0:10:27.09:0,27,398 0/0:14,0:14:33.11:0,33,476 0/0:10,0:10:30.10:0,30,442 0/0:10,0:10:21.07:0,21,309 0/0:22,0:22:60.20:0,60,884 0/0:31,0:31:84.28:0,84,1229 0/0:11,0:11:33.11:0,33,486 0/0:11,0:11:27.09:0,27,397 0/0:14,0:14:42.14:0,42,619 0/0:7,0:7:21.07:0,21,309 0/0:4,0:4:12.04:0,12,177 0/0:2,0:2:6.02:0,6,88 0/0:5,0:5:15.05:0,15,221 0/0:8,0:8:21.06:0,21,283 0/0:11,0:11:33.11:0,33,486 0/0:9,0:9:21.07:0,21,309 0/0:8,0:8:21.07:0,21,309 0/0:7,0:7:21.07:0,21,309 0/0:7,0:7:21.07:0,21,309 0/0:6,0:6:18.06:0,18,265 0/0:3,0:3:6.02:0,6,88 0/0:3,0:3:9.03:0,9,133 0/0:3,0:3:9.03:0,9,133 0/0:4,0:4:12.04:0,12,177 0/0:7,0:7:21.07:0,21,309 0/0:7,0:7:15.05:0,15,221 0/0:3,0:3:9.03:0,9,133 0/0:6,0:6:18.06:0,18,265 0/0:5,0:5:12.04:0,12,177 0/0:3,0:3:9.03:0,9,133 0/0:2,0:2:6.02:0,6,88 0/0:8,0:8:24.08:0,24,354 0/0:7,0:7:21.07:0,21,309 0/0:11,0:11:30.10:0,30,442 0/0:3,0:3:9.03:0,9,118 0/0:4,0:4:12.04:0,12,177 0/0:5,0:5:12.04:0,12,177 0/0:5,0:5:15.05:0,15,221 0/0:3,0:3:6.02:0,6,88 0/0:8,0:8:21.07:0,21,309 0/0:1,0:1:3.01:0,3,44 0/0:4,0:4:12.04:0,12,176 0/0:10,0:10:21.07:0,21,309 0/0:2,0:2:6.02:0,6,88 0/0:1,0:1:3.01:0,3,44 1/1:2,6:8:15.05:281,15,0 0/0:5,0:5:12.04:0,12,177 0/0:8,0:8:18.06:0,18,265 0/0:1,0:1:3.01:0,3,44 0/0:4,0:4:9.03:0,9,133 0/0:4,0:4:12.04:0,12,177 0/0:6,0:6:15.05:0,15,220 0/0:3,0:3:9.03:0,9,133 0/0:7,0:7:21.07:0,21,309 0/0:10,0:10:24.08:0,24,354 0/0:6,0:6:15.05:0,15,221 -chr1 1164687 . G C 63.9 . AC=4;AF=0.118;AN=34;BaseQRankSum=1.043;DP=28;Dels=0.00;FS=10.726;HRun=0;HaplotypeScore=0.2350;InbreedingCoeff=0.1906;MQ=58.33;MQ0=0;MQRankSum=0.241;QD=21.30;ReadPosRankSum=-1.685;EFF=INTRON(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|1),INTRON(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|1),INTRON(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|1),INTRON(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|1),INTRON(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|1),UPSTREAM(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,intron_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,intron_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,intron_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,upstream_gene_variant|||ENSG00000176022|B3GALT6|ENST00000379198||||-/329|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,2:2:6.02:81,6,0 0/0:2,0:2:6.02:0,6,79 ./. 0/0:2,0:2:6.02:0,6,79 ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. 0/0:3,0:3:6.02:0,6,87 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3:0,3,29 ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/0:1,0:2:3.01:0,3,39 ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. 0/0:3,0:3:6.02:0,6,87 0/0:1,0:1:3.01:0,3,33 ./. 0/0:2,0:2:6.02:0,6,76 ./. ./. ./. ./. ./. -chr1 1168180 . G C 380.06 . AC=9;AF=0.105;AN=86;BaseQRankSum=0.307;DP=108;Dels=0.00;FS=6.481;HRun=3;HaplotypeScore=0.2416;InbreedingCoeff=0.2106;MQ=56.49;MQ0=0;MQRankSum=1.066;QD=21.11;ReadPosRankSum=-1.425;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E174D|329|B3GALT6|protein_coding|CODING|ENST00000379198|),UPSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),UPSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),UPSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),UPSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,missense_variant|gaG/gaC|E/D|ENSG00000176022|B3GALT6|ENST00000379198|1/1|benign(0.012)|tolerated(0.54)|174/329|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3.01:0,3,38 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,68 0/0:6,0:6:18.06:0,18,232 0/0:3,0:3:9.03:0,9,123 0/0:6,0:6:18.06:0,18,236 0/0:4,0:4:9.03:0,9,120 0/0:9,0:9:27.09:0,27,359 0/0:7,0:7:21.07:0,21,276 1/1:0,5:5:15.05:200,15,0 0/0:2,0:2:6.02:0,6,81 0/1:5,2:7:64.41:64,0,119 ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,78 ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,40 ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,40 ./. 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,42 1/1:0,1:1:3.01:38,3,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 1/1:0,4:4:12.04:152,12,0 0/0:7,0:7:18.05:0,18,215 0/0:5,1:6:6.01:0,6,65 0/0:5,0:5:15.04:0,15,175 0/0:2,0:2:6.02:0,6,73 ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,72 0/0:1,0:1:3.01:0,3,40 -chr1 1168567 . G A 197.95 . AC=1;AF=0.0098;AN=102;BaseQRankSum=-1.549;DP=173;Dels=0.00;FS=11.564;HRun=1;HaplotypeScore=0.1898;InbreedingCoeff=-0.1063;MQ=57.97;MQ0=0;MQRankSum=0.710;QD=15.23;ReadPosRankSum=-0.901;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E303|329|B3GALT6|protein_coding|CODING|ENST00000379198|),UPSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),UPSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),UPSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),UPSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,synonymous_variant|gaG/gaA|E|ENSG00000176022|B3GALT6|ENST00000379198|1/1|||303/329|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,30 0/0:2,0:2:3.01:0,3,36 ./. 0/0:3,0:3:9.03:0,9,113 ./. 0/0:2,0:2:6.02:0,6,81 0/0:2,0:2:6.02:0,6,79 0/0:4,0:4:12.04:0,12,158 0/0:7,0:7:21.07:0,21,276 0/0:4,0:4:12.04:0,12,155 0/0:2,0:2:6.01:0,6,68 0/0:3,0:3:9.03:0,9,118 0/0:5,0:5:15.05:0,15,202 0/0:3,0:3:9.03:0,9,117 0/0:2,0:2:3.01:0,3,38 0/0:2,0:2:6.02:0,6,80 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,78 0/0:5,0:5:12.04:0,12,163 0/0:2,0:2:6.02:0,6,74 ./. 0/0:3,0:3:9.03:0,9,115 0/0:4,0:4:9.03:0,9,118 ./. 0/0:2,0:2:3.01:0,3,45 0/0:2,0:2:6.02:0,6,80 ./. 0/0:1,0:1:3.01:0,3,39 0/0:5,0:5:9.03:0,9,123 0/0:1,0:1:3.01:0,3,38 0/0:2,0:2:6.02:0,6,84 0/0:4,0:4:9.03:0,9,116 0/0:3,0:3:9.03:0,9,119 0/0:2,0:2:6.02:0,6,81 0/0:4,0:4:9.01:0,9,104 0/0:2,0:2:6.02:0,6,72 0/0:2,0:2:3.01:0,3,45 0/0:8,0:8:21.07:0,21,288 0/0:3,0:3:9.03:0,9,111 0/0:2,0:2:3.01:0,3,33 0/0:2,0:2:3.01:0,3,39 0/0:4,0:4:12.04:0,12,157 ./. 0/0:3,0:3:9.02:0,9,103 ./. 0/0:7,0:7:12.02:0,12,151 0/0:3,0:3:9.03:0,9,110 ./. 0/0:3,0:3:9.03:0,9,108 0/1:3,10:13:71.97:244,0,72 0/0:11,0:11:27.08:0,27,337 0/0:1,0:1:3.01:0,3,34 0/0:10,0:10:27.08:0,27,338 ./. 0/0:2,0:2:3.01:0,3,39 0/0:2,0:2:6.02:0,6,67 0/0:2,0:2:6.02:0,6,77 0/0:2,0:2:6.02:0,6,80 0/0:3,0:3:9.03:0,9,113 0/0:1,0:1:3.01:0,3,40 -chr1 1168843 . C T 395.96 . AC=2;AF=0.031;AN=64;BaseQRankSum=1.429;DP=826;Dels=0.00;FS=1.955;HRun=0;HaplotypeScore=1.3582;InbreedingCoeff=-0.0815;MQ=56.66;MQ0=0;MQRankSum=0.858;QD=9.90;ReadPosRankSum=0.063;EFF=UPSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),UPSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),UPSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),UPSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),UTR_3_PRIME(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|1);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000403997||||-/243|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,3_prime_UTR_variant|||ENSG00000176022|B3GALT6|ENST00000379198|1/1|||-/329|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,79 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,37 ./. ./. 0/0:1,0:1:3.01:0,3,30 ./. 0/1:2,1:3:32.56:33,0,39 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:3.01:0,3,31 ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:17,0:17:48.12:0,48,590 0/0:61,0:61:99:0,144,1831 0/0:34,0:34:78.23:0,78,1005 0/1:22,15:37:99:422,0,535 0/0:22,0:22:57.14:0,57,695 0/0:23,0:23:63.19:0,63,784 0/0:40,0:40:99:0,99,1236 0/0:49,0:49:99:0,129,1691 0/0:62,0:62:99:0,147,1861 0/0:18,0:18:39.12:0,39,482 0/0:45,0:45:93.29:0,93,1211 0/0:62,0:62:99:0,138,1714 0/0:50,0:50:99:0,117,1487 0/0:51,0:51:99:0,105,1346 0/0:41,0:41:99:0,111,1363 0/0:41,2:43:51.51:0,52,1128 0/0:25,0:25:63.20:0,63,802 0/0:32,0:32:75.23:0,75,956 0/0:18,0:18:39.12:0,39,485 0/0:21,0:21:48.13:0,48,604 0/0:27,0:27:57.18:0,57,744 0/0:34,0:34:66.21:0,66,880 -chr1 1169094 . G C 1587.89 . AC=1;AF=0.016;AN=62;BaseQRankSum=1.089;DP=2518;Dels=0.00;FS=10.659;HRun=0;HaplotypeScore=2.4242;InbreedingCoeff=-0.0613;MQ=58.81;MQ0=0;MQRankSum=1.439;QD=15.72;ReadPosRankSum=-1.308;EFF=UPSTREAM(MODIFIER||||202|SDF4|protein_coding|CODING|ENST00000545427|),UPSTREAM(MODIFIER||||348|SDF4|protein_coding|CODING|ENST00000263741|),UPSTREAM(MODIFIER||||362|SDF4|protein_coding|CODING|ENST00000360001|),UPSTREAM(MODIFIER|||||SDF4|nonsense_mediated_decay|CODING|ENST00000465727|),UPSTREAM(MODIFIER|||||SDF4|processed_transcript|CODING|ENST00000459994|),UTR_3_PRIME(MODIFIER||||329|B3GALT6|protein_coding|CODING|ENST00000379198|1);CSQ=upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000465727||||-/254|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000360001||||-/362|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000459994|||||processed_transcript|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000545427||||-/202|protein_coding|1,upstream_gene_variant|||ENSG00000078808|SDF4|ENST00000263741||||-/348|protein_coding|1,3_prime_UTR_variant|||ENSG00000176022|B3GALT6|ENST00000379198|1/1|||-/329|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.04:0,12,155 0/0:2,0:2:6.02:0,6,79 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:2,0:2:3.01:0,3,45 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:89,0:91:99:0,217,2861 0/0:185,0:186:99:0,479,6388 0/0:143,0:143:99:0,346,4611 0/0:99,0:99:99:0,253,3299 0/1:47,54:101:99:1632,0,1336 0/0:89,0:89:99:0,238,3222 0/0:126,0:127:99:0,310,4199 0/0:142,0:142:99:0,349,4731 0/0:187,0:187:99:0,485,6424 0/0:57,0:57:99:0,144,1948 0/0:122,0:123:99:0,298,3959 0/0:150,0:150:99:0,370,4960 0/0:124,0:124:99:0,328,4324 0/0:103,0:103:99:0,262,3533 0/0:108,0:109:99:0,271,3612 0/0:126,0:127:99:0,301,3981 0/0:104,0:106:99:0,256,3464 0/0:83,0:83:99:0,220,2950 0/0:79,0:79:99:0,178,2436 0/0:91,0:91:99:0,211,2887 0/0:110,0:110:99:0,271,3568 0/0:77,0:77:99:0,193,2571 -chr1 1177474 . A G 43.95 . AC=4;AF=0.105;AN=38;BaseQRankSum=-0.867;DP=27;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=0.0000;InbreedingCoeff=0.1376;MQ=58.27;MQ0=0;MQRankSum=0.685;QD=14.65;ReadPosRankSum=1.780;EFF=DOWNSTREAM(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),INTERGENIC(MODIFIER|||||||||);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:6.02:0,6,66 0/0:1,0:1:3.01:0,3,38 0/0:2,0:2:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,80 ./. ./. 1/1:0,1:1:3.01:39,3,0 0/0:1,0:2:3.01:0,3,41 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. ./. 0/0:2,0:2:6.01:0,6,64 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:6:64,6,0 ./. ./. 0/0:1,0:1:3.01:0,3,32 ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 -chr1 1177630 . A G 581.54 . AC=7;AF=0.092;AN=76;BaseQRankSum=-0.178;DP=115;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.1257;InbreedingCoeff=0.0962;MQ=57.55;MQ0=0;MQRankSum=0.915;QD=24.23;ReadPosRankSum=0.465;EFF=DOWNSTREAM(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),INTERGENIC(MODIFIER|||||||||);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3:0,3,29 0/0:1,0:1:3.01:0,3,36 0/0:1,0:1:3.01:0,3,32 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:2,0:2:6.02:0,6,81 0/0:2,0:2:6.02:0,6,80 ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,37 ./. 0/0:2,0:2:6.02:0,6,82 ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,76 0/0:7,1:8:18.06:0,18,237 0/0:6,0:6:18.06:0,18,222 0/1:3,6:9:57:212,0,57 0/0:6,0:6:15.05:0,15,208 ./. 0/0:4,0:4:12.01:0,12,141 0/0:5,0:5:15.04:0,15,193 0/0:9,0:9:27.08:0,27,342 1/1:0,2:2:6.02:80,6,0 0/0:3,0:3:6.02:0,6,87 1/1:0,9:9:27.08:338,27,0 0/0:8,0:8:24.08:0,24,317 0/0:4,0:4:12.04:0,12,160 0/0:6,0:6:18.06:0,18,233 0/0:4,0:4:12.03:0,12,135 0/0:2,0:2:6.02:0,6,76 0/1:1,1:2:30.96:31,0,36 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,39 0/1:1,1:2:26.48:26,0,36 0/0:1,0:1:3.01:0,3,33 -chr1 1177773 . C G 1999.45 . AC=2;AF=0.0179;AN=112;BaseQRankSum=0.305;DP=963;Dels=0.00;FS=3.764;HRun=0;HaplotypeScore=0.6634;InbreedingCoeff=0.3008;MQ=56.96;MQ0=0;MQRankSum=1.294;QD=32.25;ReadPosRankSum=-0.562;EFF=DOWNSTREAM(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),INTERGENIC(MODIFIER|||||||||);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.02:0,6,77 0/0:3,0:3:9.03:0,9,119 ./. 0/0:3,0:3:9.02:0,9,107 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 0/0:8,0:8:24.08:0,24,307 0/0:4,0:4:12.04:0,12,164 ./. 0/0:3,0:3:9.03:0,9,117 0/0:4,0:4:12.04:0,12,160 0/0:5,0:5:15.05:0,15,187 0/0:4,0:4:12.04:0,12,148 0/0:4,0:4:12.04:0,12,165 0/0:4,0:4:12.04:0,12,157 0/0:2,0:2:6.02:0,6,76 0/0:7,0:7:21.07:0,21,280 0/0:3,0:3:9.02:0,9,99 0/0:4,0:4:9.03:0,9,115 0/0:7,0:7:21.06:0,21,263 0/0:3,0:3:9.03:0,9,122 0/0:3,0:3:9.03:0,9,117 0/0:9,0:9:21.06:0,21,274 0/0:2,0:2:6.02:0,6,74 0/0:2,0:2:6.02:0,6,78 0/0:3,0:3:9.03:0,9,119 0/0:3,0:3:6.02:0,6,75 0/0:4,0:4:12.04:0,12,153 0/0:3,0:3:6:0,6,61 0/0:7,0:7:21.05:0,21,267 0/0:5,0:5:15.05:0,15,190 0/0:3,0:3:6.02:0,6,87 0/0:2,0:2:6.02:0,6,80 0/0:4,0:4:9.03:0,9,110 0/0:9,0:9:24.08:0,24,332 0/0:32,0:32:87.26:0,87,1102 0/0:61,0:61:99:0,165,2074 0/0:31,0:31:81.23:0,81,1019 0/0:23,0:23:66.21:0,66,866 0/0:40,0:40:99:0,102,1304 0/0:31,0:31:75.23:0,75,958 0/0:31,0:31:84.25:0,84,1063 0/0:37,0:37:93.28:0,93,1162 0/0:61,0:61:99:0,147,1818 0/0:31,0:31:75.22:0,75,941 0/0:24,0:24:66.19:0,66,822 1/1:0,61:62:99:2070,163,0 0/0:63,0:63:99:0,165,2023 0/0:41,0:41:99:0,108,1347 0/0:41,0:41:99:0,99,1224 0/0:44,0:44:99:0,99,1255 0/0:27,0:27:78.22:0,78,985 0/0:35,0:35:96.29:0,96,1196 0/0:32,0:33:87.27:0,87,1130 0/0:41,0:41:99:0,102,1316 0/0:21,0:21:60.17:0,60,734 0/0:19,0:19:51.14:0,51,636 -chr1 1177893 . C T 2555.63 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.263;DP=3336;Dels=0.00;FS=2.685;HRun=0;HaplotypeScore=1.5161;InbreedingCoeff=-0.0315;MQ=56.80;MQ0=0;MQRankSum=1.301;QD=12.84;ReadPosRankSum=-1.150;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|3),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|2),UTR_3_PRIME(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|8);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|3/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000184163|FAM132A|ENST00000330388|8/8|||-/302|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000478606|2/2||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,69 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:9.03:0,9,114 0/0:3,0:3:9.02:0,9,103 0/0:6,0:6:18.06:0,18,237 0/0:3,0:3:9.03:0,9,119 0/0:13,0:13:39.12:0,39,513 0/0:6,0:6:18.06:0,18,229 0/0:17,0:17:51.17:0,51,691 0/0:4,0:4:9.03:0,9,124 0/0:6,0:6:18.06:0,18,227 0/0:1,0:1:3.01:0,3,34 0/0:3,0:3:9.03:0,9,119 0/0:23,0:23:69.21:0,69,898 0/0:29,0:29:81.26:0,81,1068 0/0:9,0:9:27.08:0,27,343 0/0:17,0:17:45.12:0,45,575 0/0:24,0:24:72.22:0,72,928 0/0:26,0:26:72.24:0,72,967 0/0:23,0:23:63.20:0,63,834 0/0:17,0:17:48.16:0,48,627 0/0:18,0:18:54.18:0,54,715 0/0:15,0:15:42.12:0,42,540 0/0:17,0:17:42.12:0,42,558 0/0:23,0:23:66.22:0,66,891 0/0:25,0:25:69.21:0,69,869 0/0:17,1:18:5.93:0,6,572 0/0:15,0:15:39.13:0,39,519 0/0:12,0:12:36.11:0,36,460 0/0:22,0:22:60.20:0,60,810 0/0:22,0:22:60.20:0,60,802 0/0:14,0:14:39.13:0,39,506 0/0:19,0:19:54.17:0,54,705 0/0:19,0:19:48.16:0,48,647 0/0:15,0:15:39.12:0,39,512 0/1:12,9:21:99:273,0,374 0/0:9,0:9:21.07:0,21,270 0/0:25,0:25:69.22:0,69,905 0/0:102,0:102:99:0,250,3164 0/0:201,0:202:99:0,502,6291 0/0:136,0:136:99:0,346,4428 0/0:110,0:110:99:0,277,3486 0/0:130,0:131:99:0,322,4118 0/0:86,0:86:99:0,220,2755 0/0:121,0:121:99:0,298,3826 0/0:140,0:140:99:0,361,4608 0/0:202,1:204:99:0,515,6542 0/0:52,0:52:99:0,147,1871 0/0:101,0:101:99:0,253,3220 0/0:202,0:202:99:0,515,6531 0/1:92,86:178:99:2347,0,2563 0/0:140,0:140:99:0,373,4708 0/0:147,0:147:99:0,382,4842 0/0:127,0:127:99:0,307,3975 0/0:95,0:97:99:0,226,2907 0/0:113,0:114:99:0,283,3608 0/0:83,0:84:99:0,214,2723 0/0:130,0:130:99:0,304,3852 0/0:93,0:93:99:0,250,3144 0/0:92,0:93:99:0,223,2806 -chr1 1177918 . CT C 3669.24 . AC=4;AF=0.0333;AN=120;BaseQRankSum=7.568;DP=3999;DS;FS=3.238;HRun=1;HaplotypeScore=287.5611;InbreedingCoeff=-0.0451;MQ=56.98;MQ0=0;MQRankSum=0.885;QD=11.87;ReadPosRankSum=-0.015;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|3),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|2),UTR_3_PRIME(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|8);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000184163|FAM132A|ENST00000462849|3/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,3_prime_UTR_variant&feature_truncation|||ENSG00000184163|FAM132A|ENST00000330388|8/8|||-/302|protein_coding|1,non_coding_exon_variant&nc_transcript_variant&feature_truncation|||ENSG00000184163|FAM132A|ENST00000478606|2/2||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,91 0/0:6,0:6:15.04:0,15,209 0/0:2,0:2:6.02:0,6,92 0/0:2,0:2:6.02:0,6,90 0/0:5,0:5:15.05:0,15,205 0/0:4,0:4:9.03:0,9,131 0/0:14,0:14:33.11:0,33,500 0/0:7,0:7:21.07:0,21,298 0/0:16,0:16:45.15:0,45,645 0/0:9,0:9:22.89:0,23,299 0/0:10,0:10:24.08:0,24,354 0/0:3,0:3:3.01:0,3,46 0/0:5,0:5:12.04:0,12,173 0/0:32,0:32:84.27:0,84,1229 0/1:19,18:37:99:595,0,715 0/0:10,0:10:27.01:0,27,363 0/0:25,0:25:72.20:0,72,1031 0/0:33,0:33:93.26:0,93,1375 0/0:32,0:32:93.28:0,93,1365 0/0:27,0:27:75.25:0,75,1127 0/0:31,0:31:87.28:0,87,1269 0/0:32,0:32:90.30:0,90,1352 0/0:26,0:26:72.24:0,72,1086 0/0:25,0:25:75.12:0,75,1097 0/0:24,0:24:72.22:0,72,1039 0/0:32,0:32:93.29:0,93,1366 0/0:36,0:36:99:0,99,1458 0/0:24,0:24:66.22:0,66,960 0/0:20,0:20:60.20:0,60,919 0/0:30,0:29:90.30:0,90,1361 0/0:33,0:32:93.31:0,93,1388 0/0:19,0:19:57.19:0,57,843 0/0:34,0:34:99:0,102,1511 0/0:28,0:28:78.22:0,78,1154 0/0:20,0:20:57.11:0,57,787 0/1:19,15:34:99:532,0,586 0/0:16,0:16:48.12:0,48,682 0/0:44,0:44:99:0,126,1822 0/0:112,0:112:99:0,286,4131 0/0:201,0:201:99:0,527,7667 0/0:160,0:160:99:0,416,6181 0/0:123,0:123:99:0,319,4689 0/0:157,0:156:99:0,412,6013 0/0:114,0:115:99:0,298,4417 0/0:138,0:138:99:0,367,5378 0/0:152,0:152:99:0,399,5803 0/0:250,0:250:99:0,644,9432 0/0:64,0:64:99:0,166,2448 0/0:133,0:131:99:0,340,5001 0/0:219,1:219:99:0,559,8146 0/0:197,1:197:99:0,497,7226 0/0:154,0:155:99:0,390,5668 0/0:155,0:155:99:0,381,5600 0/0:155,0:154:99:0,424,6075 0/0:118,0:118:99:0,306,4449 0/1:82,39:122:99:1441,0,2373 0/0:103,0:103:99:0,265,3825 0/0:143,0:142:99:0,379,5453 0/1:83,32:116:99:1101,0,2583 0/0:119,0:119:99:0,310,4585 -chr1 1177919 . T C 61.88 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-3.136;DP=3999;DS;Dels=0.03;FS=1.983;HRun=6;HaplotypeScore=4.0470;InbreedingCoeff=-0.0307;MQ=56.98;MQ0=0;MQRankSum=0.755;QD=0.41;ReadPosRankSum=-5.282;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|3),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|2),UTR_3_PRIME(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|8);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|3/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000184163|FAM132A|ENST00000330388|8/8|||-/302|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000478606|2/2||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,63 0/0:5,1:6:15.03:0,15,158 0/0:2,0:2:6.01:0,6,59 0/0:2,0:2:3.01:0,3,39 0/0:4,1:5:12.03:0,12,144 0/0:3,1:4:3.01:0,3,33 0/0:13,1:14:24.05:0,24,272 0/0:7,0:7:18.05:0,18,218 0/0:15,1:16:39.11:0,39,483 0/0:9,0:9:18.06:0,18,246 0/0:9,1:10:21.04:0,21,239 0/0:3,0:3:3.01:0,3,41 0/0:4,0:5:12.03:0,12,149 0/0:32,0:32:75.16:0,75,855 0/0:19,0:19:48.14:0,48,616 0/0:10,0:10:21.05:0,21,247 0/0:25,0:25:69.19:0,69,850 0/0:33,0:33:84.22:0,84,1016 0/0:32,0:32:90.23:0,90,1081 0/0:27,0:27:63.19:0,63,788 0/0:31,0:31:78.21:0,78,962 0/0:32,0:32:84.23:0,84,1031 0/0:26,0:26:66.20:0,66,829 0/0:25,0:25:66.19:0,66,840 0/0:24,0:24:66.17:0,66,797 0/0:32,0:32:87.20:0,87,1019 0/0:36,0:36:90.27:0,90,1147 0/0:24,0:24:60.18:0,60,759 0/0:20,0:20:54.15:0,54,689 0/0:30,0:30:78.21:0,78,991 0/0:33,0:33:84.23:0,84,1017 0/0:18,1:19:51.12:0,51,601 0/0:34,0:34:81.23:0,81,1041 0/0:28,0:28:72.19:0,72,901 0/0:20,0:20:48.11:0,48,578 0/1:15,4:19:86.59:87,0,450 0/0:16,0:16:42.13:0,42,535 0/0:44,0:44:99:0,117,1458 0/0:108,3:112:99:0,244,2998 0/0:194,6:201:99:0,421,5051 0/0:155,5:160:99:0,358,4494 0/0:119,4:123:99:0,265,3190 0/0:150,6:157:99:0,346,4186 0/0:109,2:115:99:0,250,3077 0/0:128,7:138:99:0,278,3819 0/0:148,3:152:99:0,309,3984 0/0:243,5:250:99:0,560,6826 0/0:60,3:64:99:0,138,1678 0/0:128,4:133:99:0,274,3409 0/0:209,7:218:99:0,475,5672 0/0:188,9:197:99:0,421,5280 0/0:146,7:155:99:0,337,4034 0/0:147,6:155:99:0,304,3589 0/0:148,4:155:99:0,352,4301 0/0:112,5:118:99:0,256,3129 0/0:70,9:82:24.33:0,24,1755 0/0:98,4:103:99:0,208,2535 0/0:134,6:143:99:0,285,3866 0/1:72,8:84:40.44:40,0,1839 0/0:112,5:120:99:0,226,3153 -chr1 1178047 . T C 1725.37 . AC=1;AF=0.0085;AN=118;BaseQRankSum=0.230;DP=3874;DS;Dels=0.00;FS=5.482;HRun=1;HaplotypeScore=3.6848;InbreedingCoeff=-0.0204;MQ=57.02;MQ0=0;MQRankSum=-0.683;QD=10.59;ReadPosRankSum=1.820;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|7),INTRON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|2),INTRON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|1);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,78 0/0:4,0:4:12.03:0,12,142 ./. 0/0:5,1:6:15.05:0,15,200 0/0:3,1:4:6.01:0,6,70 0/0:12,2:14:27.09:0,27,354 0/0:1,1:2:3.01:0,3,34 0/0:14,1:15:33.11:0,33,436 0/0:13,1:14:39.11:0,39,478 0/0:3,1:4:9.03:0,9,107 0/0:5,0:5:12.04:0,12,154 0/0:5,0:5:12.04:0,12,157 0/0:34,1:35:72.19:0,72,890 0/0:51,1:52:99:0,108,1358 0/0:26,3:29:57.14:0,57,687 0/0:38,1:39:78.22:0,78,948 0/0:50,0:51:99:0,117,1466 0/0:45,2:48:99:0,99,1251 0/0:52,0:53:96.27:0,96,1234 0/0:53,1:55:99:0,108,1348 0/0:60,1:61:99:0,123,1547 0/0:43,2:45:84.22:0,84,1031 0/0:41,0:42:72.18:0,72,864 0/0:48,2:50:99:0,102,1248 0/0:45,3:49:93.26:0,93,1179 0/0:35,1:36:81.25:0,81,1025 0/0:22,0:22:51.15:0,51,609 0/0:45,1:47:96.27:0,96,1169 0/0:47,0:47:99:0,111,1386 0/0:47,0:47:99:0,99,1230 0/0:38,0:38:81.23:0,81,994 0/0:58,1:59:99:0,120,1476 0/0:43,2:45:87.27:0,87,1123 0/0:29,0:29:54.11:0,54,673 0/0:49,0:49:99:0,102,1272 0/0:47,0:48:99:0,99,1235 0/0:66,1:68:99:0,150,1826 0/0:93,2:97:99:0,199,2412 0/0:162,4:169:99:0,361,4258 0/0:162,3:165:99:0,349,4247 0/0:103,4:108:99:0,214,2595 0/0:106,5:111:99:0,207,2513 0/0:95,2:97:99:0,220,2586 0/0:92,1:95:99:0,208,2614 0/0:113,5:119:99:0,268,3250 0/0:174,8:184:99:0,376,4483 0/0:71,3:74:99:0,144,1751 0/0:118,1:120:99:0,238,2836 0/1:81,80:162:99:1773,0,1751 0/0:156,5:163:99:0,355,4296 0/0:161,2:166:99:0,334,4004 0/0:137,2:141:99:0,301,3582 0/0:103,1:109:99:0,226,2705 0/0:94,8:104:99:0,202,2486 0/0:100,4:105:99:0,192,2334 0/0:62,2:66:99:0,153,1900 0/0:103,2:106:99:0,223,2751 0/0:94,2:97:99:0,217,2693 0/0:93,0:95:99:0,208,2499 -chr1 1178244 . G C 483.23 . AC=2;AF=0.0167;AN=120;BaseQRankSum=1.151;DP=1605;Dels=0.00;FS=2.186;HRun=1;HaplotypeScore=1.4521;InbreedingCoeff=0.7073;MQ=59.01;MQ0=0;MQRankSum=0.273;QD=32.22;ReadPosRankSum=-0.751;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|2),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Gta|L261V|302|FAM132A|protein_coding|CODING|ENST00000330388|);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|2/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,missense_variant|Cta/Gta|L/V|ENSG00000184163|FAM132A|ENST00000330388|7/8|benign(0.001)|tolerated(0.98)|261/302|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000478606|1/2||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:9.02:0,9,104 0/0:4,0:4:12.04:0,12,157 0/0:2,0:2:6.02:0,6,73 0/0:10,0:10:30.10:0,30,395 0/0:5,0:5:15.05:0,15,201 0/0:11,0:11:33.10:0,33,428 0/0:8,0:8:24.08:0,24,309 0/0:21,0:21:60.19:0,60,790 0/0:6,0:6:18.06:0,18,235 0/0:8,0:8:24.08:0,24,325 0/0:9,0:9:27.09:0,27,356 0/0:16,0:16:48.15:0,48,624 0/0:48,0:48:99:0,120,1582 0/0:45,0:45:99:0,99,1349 0/0:25,0:25:69.22:0,69,910 0/0:40,0:41:99:0,102,1340 0/0:60,0:61:99:0,144,1927 0/0:41,0:41:90.30:0,90,1225 0/0:36,0:36:99:0,99,1314 0/0:51,0:51:99:0,123,1653 0/0:53,0:53:99:0,108,1471 0/0:65,0:65:99:0,166,2192 0/0:39,0:40:96.31:0,96,1290 0/0:51,0:51:99:0,126,1654 0/0:67,1:68:99:0,150,2031 0/0:45,0:46:99:0,111,1480 0/0:15,0:15:39.12:0,39,504 0/0:41,0:41:99:0,105,1375 0/0:50,0:50:99:0,129,1708 0/0:65,0:65:99:0,166,2225 0/0:50,0:50:99:0,117,1593 0/0:48,0:48:99:0,108,1441 0/0:46,0:46:99:0,105,1425 0/0:39,0:39:87.29:0,87,1218 0/0:39,0:39:99:0,102,1344 0/0:39,0:39:99:0,108,1425 0/0:73,0:73:99:0,184,2468 0/0:7,0:7:21.04:0,21,255 0/0:16,0:16:39.13:0,39,526 0/0:16,0:16:45.14:0,45,585 0/0:10,0:10:27.09:0,27,349 0/0:13,0:13:39.13:0,39,515 0/0:8,0:8:24.07:0,24,311 0/0:14,0:14:33.11:0,33,443 0/0:16,0:16:42.13:0,42,540 0/0:31,0:31:75.24:0,75,973 0/0:7,0:7:21.06:0,21,265 0/0:12,0:12:30.10:0,30,398 1/1:0,15:15:42.14:555,42,0 0/0:25,0:25:66.19:0,66,854 0/0:18,0:18:51.16:0,51,654 0/0:19,0:19:57.18:0,57,726 0/0:14,0:14:39.12:0,39,497 0/0:15,0:15:33.11:0,33,449 0/0:12,0:12:36.11:0,36,459 0/0:16,0:16:39.13:0,39,536 0/0:18,0:18:45.15:0,45,620 0/0:14,0:14:39.13:0,39,511 0/0:8,0:8:18.05:0,18,232 -chr1 1178245 . C T 4066.47 . AC=15;AF=0.1250;AN=120;BaseQRankSum=-1.548;DP=1603;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.3636;InbreedingCoeff=0.1530;MQ=59.01;MQ0=0;MQRankSum=1.224;QD=13.51;ReadPosRankSum=-1.253;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|2),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|1),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T260|302|FAM132A|protein_coding|CODING|ENST00000330388|);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|2/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,synonymous_variant|acG/acA|T|ENSG00000184163|FAM132A|ENST00000330388|7/8|||260/302|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000478606|1/2||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,40 0/0:4,0:4:9.02:0,9,105 0/0:4,0:4:12.04:0,12,147 0/0:2,0:2:6.02:0,6,79 0/0:10,0:10:30.10:0,30,396 0/0:5,0:5:15.05:0,15,201 0/0:11,0:11:33.08:0,33,417 0/0:7,0:7:21.07:0,21,275 0/0:21,0:21:60.20:0,60,800 0/0:6,0:6:18.06:0,18,236 1/1:0,8:8:24.06:303,24,0 0/0:9,0:9:24.08:0,24,317 0/1:8,6:14:99:166,0,238 0/0:48,0:48:99:0,120,1548 0/1:24,21:45:99:466,0,651 0/0:24,0:24:66.21:0,66,861 0/0:41,0:41:99:0,105,1376 0/1:37,25:62:99:666,0,964 0/0:41,0:41:90.30:0,90,1229 0/0:36,0:36:99:0,99,1298 0/0:52,0:52:99:0,126,1692 0/0:52,0:52:99:0,102,1408 0/0:65,0:66:99:0,168,2211 0/0:41,0:41:99:0,102,1346 0/0:51,0:51:99:0,126,1649 0/0:69,0:69:99:0,156,2109 0/0:46,0:46:99:0,114,1514 0/0:16,0:16:39.13:0,39,522 0/0:40,0:41:99:0,105,1383 0/0:50,0:50:99:0,132,1748 0/0:64,0:64:99:0,163,2192 0/0:50,0:50:99:0,117,1568 0/0:48,0:48:99:0,108,1456 0/1:26,20:46:99:532,0,674 0/0:38,0:38:84.28:0,84,1166 0/1:27,12:39:99:276,0,837 0/0:39,0:39:99:0,108,1410 0/0:74,0:74:99:0,184,2440 0/0:7,0:7:21.06:0,21,261 0/0:16,0:16:39.13:0,39,524 0/0:16,0:16:42.14:0,42,551 0/1:3,7:10:48.58:238,0,49 0/0:13,0:13:39.12:0,39,507 0/0:8,0:8:24.08:0,24,321 0/1:7,7:14:99:211,0,169 0/0:15,0:15:39.12:0,39,508 0/0:30,0:30:69.22:0,69,917 0/1:3,4:7:83.75:133,0,84 0/0:12,0:12:30.10:0,30,399 1/1:0,16:16:45.15:596,45,0 0/0:25,0:25:66.21:0,66,863 0/0:18,0:18:51.16:0,51,647 0/0:19,0:19:57.18:0,57,726 0/1:13,1:14:0.19:0,0,420 0/0:15,0:15:33.11:0,33,452 0/1:6,6:12:99:190,0,187 0/0:15,0:15:36.12:0,36,495 0/0:18,0:18:45.15:0,45,613 0/1:5,9:14:99:289,0,141 0/0:8,0:8:18.06:0,18,235 -chr1 1178453 . G A 466.91 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-3.075;DP=1354;Dels=0.00;FS=5.034;HRun=0;HaplotypeScore=0.8964;InbreedingCoeff=0.6716;MQ=57.75;MQ0=0;MQRankSum=1.619;QD=23.35;ReadPosRankSum=0.909;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|1),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|1),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C240|302|FAM132A|protein_coding|CODING|ENST00000330388|);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,synonymous_variant|tgC/tgT|C|ENSG00000184163|FAM132A|ENST00000330388|6/8|||240/302|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000478606|1/2||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,109 0/0:6,0:6:15.05:0,15,193 0/0:1,0:1:3.01:0,3,36 0/0:3,0:3:9.03:0,9,114 0/0:6,0:6:15.05:0,15,202 0/0:4,0:4:12.04:0,12,155 0/0:9,0:9:24.08:0,24,319 0/0:13,0:13:36.12:0,36,486 0/0:18,0:18:51.17:0,51,686 0/0:10,0:10:30.09:0,30,387 0/0:4,0:4:12.04:0,12,162 0/0:10,0:10:30.10:0,30,397 0/0:15,0:15:45.12:0,45,558 0/0:49,0:49:99:0,114,1536 0/0:47,0:47:99:0,120,1554 0/0:31,0:31:60.19:0,60,803 0/0:32,0:32:75.24:0,75,995 0/0:45,0:45:99:0,102,1374 0/0:51,0:51:99:0,117,1556 0/0:34,0:34:81.26:0,81,1064 0/0:38,0:40:90.25:0,90,1157 0/0:55,0:55:99:0,132,1740 0/0:37,0:37:93.29:0,93,1213 0/0:33,0:33:78.23:0,78,988 0/0:37,0:37:93.28:0,93,1200 0/0:38,0:38:90.28:0,90,1146 0/0:36,0:37:90.29:0,90,1196 0/0:25,0:25:54.17:0,54,717 0/0:29,0:29:69.22:0,69,930 0/0:31,0:31:75.24:0,75,1001 0/0:33,0:33:72.21:0,72,911 0/0:46,0:46:99:0,114,1481 0/0:43,0:43:99:0,102,1353 0/0:49,0:49:99:0,117,1484 0/0:32,0:32:81.26:0,81,1075 0/0:33,0:34:78.23:0,78,1010 0/0:58,0:58:99:0,138,1790 0/0:67,0:67:99:0,150,2003 0/0:7,0:7:15.04:0,15,179 0/0:22,0:23:60.17:0,60,731 0/0:11,0:11:30.09:0,30,378 0/0:8,0:8:21.06:0,21,269 0/0:5,0:5:12.04:0,12,160 0/0:9,0:9:27.08:0,27,331 0/0:7,0:7:18.06:0,18,229 0/0:16,0:16:45.13:0,45,557 0/0:13,0:13:33.10:0,33,429 0/0:5,0:5:15.05:0,15,192 0/0:10,0:10:21.07:0,21,274 1/1:1,19:20:45.10:538,45,0 0/0:10,0:10:30.09:0,30,348 0/0:14,0:15:39.12:0,39,496 0/0:12,0:12:30.09:0,30,371 0/0:8,0:8:21.06:0,21,263 0/0:11,0:11:24.08:0,24,319 0/0:16,0:16:39.10:0,39,486 0/0:6,0:6:18.06:0,18,229 0/0:9,0:9:24.06:0,24,281 0/0:7,0:7:21.07:0,21,286 0/0:10,0:10:21.07:0,21,287 -chr1 1178482 . A G 2936.1 . AC=13;AF=0.1121;AN=116;BaseQRankSum=2.434;DP=1386;Dels=0.00;FS=2.627;HRun=0;HaplotypeScore=0.8846;InbreedingCoeff=0.1962;MQ=57.58;MQ0=0;MQRankSum=-0.397;QD=11.84;ReadPosRankSum=1.190;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|1),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C231R|302|FAM132A|protein_coding|CODING|ENST00000330388|);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,missense_variant|Tgt/Cgt|C/R|ENSG00000184163|FAM132A|ENST00000330388|6/8|benign(0)|tolerated(1)|231/302|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000478606|1/2||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3:0,3,29 0/0:6,0:6:12.03:0,12,142 ./. ./. 0/0:7,0:7:21.05:0,21,251 0/0:10,0:10:27.09:0,27,343 0/0:9,0:9:27.08:0,27,329 0/0:8,0:8:21.06:0,21,250 0/0:16,0:16:48.15:0,48,608 0/0:15,0:15:39.11:0,39,461 1/1:0,5:5:15.04:186,15,0 0/0:7,0:8:18.05:0,18,220 0/1:8,5:13:99:164,0,268 0/0:39,0:41:93.26:0,93,1202 0/1:25,20:46:99:474,0,601 0/0:27,0:28:63.15:0,63,735 0/0:32,0:32:69.21:0,69,899 0/1:26,19:45:99:463,0,658 0/0:60,0:60:99:0,123,1583 0/0:37,0:39:81.21:0,81,1037 0/0:40,0:40:78.20:0,78,976 0/0:58,0:59:99:0,135,1707 0/0:38,0:39:96.26:0,96,1197 0/0:37,0:38:72.19:0,72,862 0/0:39,0:39:99:0,99,1214 0/0:37,0:38:93.26:0,93,1145 0/0:47,0:47:99:0,99,1283 0/0:23,0:24:54.14:0,54,647 0/0:27,0:29:66.21:0,66,847 0/0:36,0:37:81.26:0,81,1091 0/0:30,0:32:69.22:0,69,888 0/0:43,0:44:93.20:0,93,1179 0/0:45,0:45:99:0,102,1297 0/1:33,20:53:99:525,0,854 0/0:36,0:36:84.20:0,84,1047 0/1:20,17:37:99:426,0,524 0/0:52,1:53:99:0,117,1504 0/0:58,1:60:99:0,105,1574 0/0:4,0:5:12.04:0,12,144 0/0:21,0:22:48.11:0,48,583 0/0:13,0:13:33.07:0,33,394 0/1:5,3:8:99:100,0,134 0/0:5,0:6:15.04:0,15,176 0/0:10,0:10:27.08:0,27,323 0/1:6,2:8:53.96:54,0,124 0/0:13,1:14:33.10:0,33,406 0/0:15,0:15:42.13:0,42,515 0/1:4,3:7:82.11:82,0,89 0/0:11,0:11:30.09:0,30,356 1/1:0,17:17:36.10:448,36,0 0/0:13,0:13:33.10:0,33,396 0/0:18,0:18:45.13:0,45,550 0/0:15,0:15:30.06:0,30,351 0/0:7,0:7:18:0,18,190 0/0:10,0:10:21.03:0,21,244 0/1:3,6:9:73.32:192,0,73 0/0:9,0:9:21.06:0,21,258 0/0:11,0:12:24.06:0,24,268 0/0:5,0:5:15.05:0,15,191 0/0:8,0:8:18.05:0,18,219 -chr1 1178571 . C G 79.76 . AC=15;AF=0.1364;AN=110;BaseQRankSum=-6.811;DP=485;Dels=0.00;FS=26.762;HRun=6;HaplotypeScore=2.2448;InbreedingCoeff=-0.0971;MQ=52.03;MQ0=0;MQRankSum=-8.725;QD=0.69;ReadPosRankSum=1.393;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|1),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|5),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,76 0/0:2,0:2:3.01:0,3,33 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,121 0/0:11,0:11:33.10:0,33,436 0/0:3,0:3:9.03:0,9,120 0/0:3,0:3:9.03:0,9,123 0/0:1,0:1:3.01:0,3,34 0/0:3,0:3:9.03:0,9,118 0/0:9,1:10:18.04:0,18,197 0/0:9,4:13:21.07:0,21,284 0/0:6,1:7:18.05:0,18,222 0/0:12,0:13:21.04:0,21,240 0/1:8,4:12:4.59:5,0,237 0/0:13,1:14:24.07:0,24,294 0/0:9,1:11:4.39:0,4,283 0/0:7,3:10:15.05:0,15,187 0/0:17,3:21:13.41:0,13,389 0/0:10,3:13:21.07:0,21,276 0/0:9,1:10:18.05:0,18,218 0/0:13,2:15:24.06:0,24,295 0/0:10,2:12:15.04:0,15,180 0/0:13,1:14:30.09:0,30,379 0/0:9,1:10:18.06:0,18,219 0/0:10,0:11:12.04:0,12,158 0/0:13,1:14:8.40:0,8,311 0/0:16,3:20:27.07:0,27,339 0/1:13,1:14:3.61:4,0,219 0/0:14,1:15:21.07:0,21,263 0/0:9,5:14:2.38:0,2,274 0/0:6,2:8:15.02:0,15,160 0/1:12,2:14:17.29:17,0,312 0/0:13,3:17:4.35:0,4,249 0/0:18,2:20:36.08:0,36,427 0/0:2,0:3:3:0,3,25 0/1:4,2:7:12.67:13,0,79 1/1:0,3:3:6.01:60,6,0 0/0:5,0:5:12.04:0,12,148 0/0:5,0:5:12.04:0,12,154 0/1:2,2:5:21.65:22,0,33 0/1:2,2:4:24.41:24,0,65 0/1:5,4:9:7.64:8,0,175 0/1:5,6:11:12.66:13,0,104 ./. 0/1:4,2:6:18.39:18,0,130 0/1:1,3:4:18.68:19,0,31 0/1:7,5:13:7.64:8,0,163 0/1:6,3:9:9.61:10,0,166 0/0:6,1:7:9.03:0,9,105 ./. 0/0:4,1:5:9.03:0,9,105 0/1:3,2:5:12.66:13,0,102 ./. 0/0:3,3:6:6.02:0,6,70 0/0:3,0:3:9.03:0,9,106 0/0:4,0:5:6.02:0,6,76 -chr1 1178576 . T G 181.67 . AC=17;AF=0.1574;AN=108;BaseQRankSum=-5.916;DP=438;Dels=0.01;FS=1.537;HRun=5;HaplotypeScore=3.1212;InbreedingCoeff=-0.0423;MQ=51.34;MQ0=0;MQRankSum=-4.551;QD=1.36;ReadPosRankSum=1.353;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|1),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|5),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.02:0,6,74 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,82 0/0:7,0:7:21.07:0,21,273 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.02:0,6,79 0/0:8,0:8:12.03:0,12,136 0/1:8,4:12:7.63:8,0,178 0/0:4,0:4:9.03:0,9,116 0/0:9,3:12:21.03:0,21,233 0/0:8,2:10:15.04:0,15,185 0/0:8,3:11:18.05:0,18,213 0/0:8,2:10:18.06:0,18,232 0/0:8,1:9:15.03:0,15,168 0/0:18,1:19:33.08:0,33,381 0/0:8,2:11:21.03:0,21,238 0/1:7,3:10:1.63:2,0,201 0/1:11,2:14:5.57:6,0,215 0/1:8,3:11:6.65:7,0,149 0/0:11,0:13:18.05:0,18,221 0/0:7,2:9:15.05:0,15,188 0/0:8,2:10:15.04:0,15,175 0/0:9,3:12:15.04:0,15,168 0/0:14,6:20:18.60:0,19,262 0/0:11,1:12:15.03:0,15,172 0/1:13,2:15:4.61:5,0,196 0/0:11,1:13:18.03:0,18,216 0/0:7,1:8:9.01:0,9,92 0/1:10,3:13:12.37:12,0,208 0/0:16,3:19:27.07:0,27,318 0/0:11,7:18:1.36:0,1,232 0/0:2,1:3:3.01:0,3,35 0/0:3,2:5:9.02:0,9,102 1/1:0,3:3:6.02:67,6,0 0/0:4,1:5:9.02:0,9,111 0/0:2,2:4:6.02:0,6,81 0/1:2,3:5:16.69:17,0,20 0/1:2,2:4:18.68:19,0,35 0/1:6,3:9:10.66:11,0,123 0/1:3,7:10:39.30:39,0,95 ./. 0/1:2,2:4:24.42:24,0,57 0/1:2,3:5:18.68:19,0,29 1/1:5,8:13:9.01:88,9,0 0/0:6,1:7:6.01:0,6,67 ./. ./. 0/0:4,1:5:3.01:0,3,33 0/1:3,2:5:18.68:19,0,35 0/0:1,0:1:2.98:0,3,22 0/0:2,4:6:6.02:0,6,67 0/0:2,0:2:3.01:0,3,41 0/0:3,1:4:3.01:0,3,41 -chr1 1178586 . T G 169.37 . AC=15;AF=0.150;AN=100;BaseQRankSum=-5.907;DP=387;Dels=0.00;FS=26.401;HRun=4;HaplotypeScore=3.0709;InbreedingCoeff=-0.2409;MQ=49.88;MQ0=0;MQRankSum=-7.180;QD=1.44;ReadPosRankSum=1.347;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|1),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|5),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000462849|1/3||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,41 ./. 0/0:3,0:3:9.03:0,9,118 0/0:1,0:1:3.01:0,3,38 ./. 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:6.02:0,6,81 0/0:9,0:9:20.99:0,21,205 0/1:6,3:9:15.64:16,0,91 ./. 0/0:10,1:11:21.06:0,21,246 0/0:5,1:6:9:0,9,86 0/0:7,0:7:12.01:0,12,118 0/0:6,1:7:12.03:0,12,137 0/0:5,4:9:6.01:0,6,63 0/0:17,0:17:35.99:0,36,366 0/0:11,2:13:30.04:0,30,337 0/0:4,2:6:9.03:0,9,105 0/0:11,1:13:21.01:0,21,212 0/1:8,3:11:12.37:12,0,186 0/0:7,3:11:15.02:0,15,164 0/0:7,1:8:15.05:0,15,193 0/0:7,4:11:18.02:0,18,191 0/0:7,3:10:18.02:0,18,180 0/0:15,4:20:10.37:0,10,357 0/0:9,2:11:24.03:0,24,243 0/0:12,3:15:27.04:0,27,313 0/1:9,1:10:6.53:7,0,220 0/1:5,2:7:31.38:31,0,106 0/1:7,4:11:9.58:10,0,158 0/0:14,2:16:30.05:0,30,327 0/0:13,4:17:21.41:0,21,292 0/0:2,1:3:3.01:0,3,31 0/0:4,2:6:9.02:0,9,103 0/1:1,3:4:24.41:58,0,24 0/0:3,1:4:3.01:0,3,40 0/0:4,0:4:6.02:0,6,78 0/1:3,3:6:27.42:27,0,28 0/0:2,2:4:6.01:0,6,67 0/1:5,4:9:21.42:21,0,88 0/1:6,5:11:31.36:31,0,110 0/0:1,1:2:3.01:0,3,31 0/1:2,2:4:24.43:24,0,51 0/1:3,2:5:20.60:21,0,60 0/1:7,5:12:11.60:12,0,131 0/1:6,2:8:7.71:8,0,119 ./. ./. 0/1:3,2:5:21.65:22,0,26 0/0:1,3:4:2.99:0,3,23 0/0:2,1:3:6:0,6,58 0/1:2,3:5:22.55:23,0,47 0/0:1,0:1:3.01:0,3,38 ./. -chr1 1178925 . G A 1946.86 . AC=13;AF=0.1102;AN=118;BaseQRankSum=-1.965;DP=1010;Dels=0.00;FS=8.294;HRun=0;HaplotypeScore=0.9315;InbreedingCoeff=0.1268;MQ=57.94;MQ0=0;MQRankSum=0.962;QD=13.91;ReadPosRankSum=-0.443;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A180V|302|FAM132A|protein_coding|CODING|ENST00000330388|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000468365|3/3||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,missense_variant|gCc/gTc|A/V|ENSG00000184163|FAM132A|ENST00000330388|5/8|possibly_damaging(0.558)|tolerated(0.06)|180/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3:25,3,0 0/0:2,0:2:6.02:0,6,77 0/0:3,0:3:9.03:0,9,114 0/0:2,0:2:6.02:0,6,71 0/0:5,0:5:15.05:0,15,195 0/0:3,0:3:6.02:0,6,80 0/0:5,0:5:12.04:0,12,160 0/0:2,0:2:6.02:0,6,69 0/0:6,0:6:18.06:0,18,233 0/0:5,0:5:15.03:0,15,182 1/1:0,3:3:9.03:120,9,0 ./. 0/1:1,2:3:32.20:72,0,32 0/0:10,0:10:30.10:0,30,401 0/1:3,6:9:62.28:159,0,62 0/0:15,0:15:39.13:0,39,517 0/0:12,0:12:33.11:0,33,441 0/1:5,4:9:99:127,0,174 0/0:29,0:29:78.24:0,78,1044 0/0:7,0:7:18.05:0,18,237 0/0:10,0:10:27.09:0,27,368 0/0:14,0:14:36.11:0,36,444 0/0:14,0:14:33.10:0,33,422 0/0:13,0:13:33.11:0,33,443 0/0:20,0:20:54.18:0,54,729 0/0:16,0:16:39.12:0,39,515 0/0:15,0:15:39.13:0,39,532 0/0:9,0:10:27.06:0,27,333 0/0:8,0:8:21.07:0,21,283 0/0:9,0:9:27.09:0,27,359 0/0:10,0:10:24.08:0,24,327 0/0:10,0:10:27.09:0,27,346 0/0:15,0:16:39.13:0,39,520 0/1:11,5:16:99:116,0,353 0/0:12,0:12:30.10:0,30,404 0/1:6,6:12:99:210,0,163 0/0:11,0:11:30.09:0,30,380 0/0:12,0:12:30.10:0,30,406 0/0:27,0:27:66.21:0,66,848 0/0:53,0:53:99:0,132,1680 0/0:35,0:35:72.23:0,72,956 0/1:9,15:24:99:454,0,275 0/0:22,0:22:51.17:0,51,673 0/0:19,0:19:51.14:0,51,648 0/0:8,0:8:24.08:0,24,303 0/0:24,0:24:69.20:0,69,874 0/0:36,0:36:93.29:0,93,1195 0/1:9,7:16:99:228,0,225 0/0:24,0:24:66.19:0,66,852 0/0:47,0:47:99:0,108,1368 0/0:43,0:43:99:0,105,1368 0/0:41,0:41:84.26:0,84,1111 0/0:41,0:41:99:0,102,1288 0/0:32,0:32:84.24:0,84,1070 0/0:26,0:26:63.20:0,63,836 0/1:8,11:20:99:327,0,254 0/0:20,0:20:45.12:0,45,582 0/0:31,0:31:69.22:0,69,918 0/1:16,11:27:99:277,0,415 0/0:35,0:35:87.26:0,87,1126 -chr1 1178935 . G A 255.43 . AC=1;AF=0.0085;AN=118;BaseQRankSum=0.108;DP=915;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6695;InbreedingCoeff=-0.0264;MQ=58.14;MQ0=0;MQRankSum=0.476;QD=14.19;ReadPosRankSum=1.215;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|4),INTRON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|2),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,34 0/0:2,0:2:3.01:0,3,40 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,68 0/0:5,0:5:15.04:0,15,185 0/0:2,0:2:3.01:0,3,38 0/0:6,0:6:15.05:0,15,199 0/0:2,0:2:6.02:0,6,79 0/0:5,0:5:12.04:0,12,162 0/0:6,0:6:18.06:0,18,233 0/0:4,0:4:12.04:0,12,161 ./. 0/0:4,0:4:12.04:0,12,163 0/0:9,0:9:27.09:0,27,354 0/0:7,0:7:18.03:0,18,220 0/0:12,0:12:33.11:0,33,432 0/0:11,0:11:30.10:0,30,407 0/0:8,0:8:24.07:0,24,298 0/0:29,0:29:78.25:0,78,1029 0/0:6,0:6:15.05:0,15,201 0/0:10,0:11:27.09:0,27,356 0/0:12,0:12:33.10:0,33,421 0/0:11,0:11:30.09:0,30,383 0/0:13,0:13:30.10:0,30,407 0/0:17,0:17:45.14:0,45,582 0/0:14,0:14:36.11:0,36,474 0/0:14,0:14:39.13:0,39,510 0/0:13,0:13:36.11:0,36,445 0/0:7,0:8:21.07:0,21,271 0/0:8,0:8:24.07:0,24,306 0/0:9,0:9:24.07:0,24,307 0/0:9,0:9:27.08:0,27,336 0/0:13,0:13:36.12:0,36,471 0/0:15,0:15:36.12:0,36,482 0/0:10,0:10:27.09:0,27,362 0/0:10,0:10:30.10:0,30,402 0/0:12,0:12:30.10:0,30,410 0/0:11,0:11:30.10:0,30,382 0/0:21,1:22:26.76:0,27,717 0/0:46,0:46:99:0,126,1593 0/0:30,0:31:63.20:0,63,839 0/0:22,0:22:63.16:0,63,771 0/0:21,0:21:45.13:0,45,571 0/1:8,10:18:99:303,0,222 0/0:9,0:9:24.07:0,24,293 0/0:22,0:22:63.20:0,63,808 0/0:35,0:35:84.26:0,84,1068 0/0:13,0:13:33.10:0,33,416 0/0:20,0:20:54.14:0,54,691 0/0:45,0:45:99:0,102,1281 0/0:38,0:38:90.28:0,90,1173 0/0:36,0:36:84.21:0,84,1070 0/0:35,0:35:87.27:0,87,1104 0/0:29,0:29:78.24:0,78,999 0/0:21,0:21:48.15:0,48,632 0/0:17,0:17:45.14:0,45,582 0/0:16,0:16:39.12:0,39,505 0/0:30,0:30:75.22:0,75,941 0/0:25,0:25:66.21:0,66,853 0/0:32,0:32:81.23:0,81,1045 -chr1 1179030 . G A 765.15 . AC=11;AF=0.0982;AN=112;BaseQRankSum=-0.728;DP=324;Dels=0.00;FS=3.299;HRun=0;HaplotypeScore=0.2197;InbreedingCoeff=0.1064;MQ=58.27;MQ0=0;MQRankSum=-0.685;QD=17.39;ReadPosRankSum=0.230;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|4),INTRON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|2),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,39 ./. 0/1:2,1:3:25.32:25,0,69 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,41 0/0:7,0:7:18.06:0,18,241 0/0:8,0:8:24.08:0,24,310 1/1:0,2:2:6.02:80,6,0 0/0:3,0:3:9.03:0,9,122 0/0:2,0:2:6.02:0,6,78 0/0:6,0:6:18.06:0,18,249 0/1:2,1:3:32.73:33,0,74 ./. 0/0:6,0:6:18.06:0,18,241 0/0:1,0:2:3.01:0,3,41 0/0:3,0:3:9.03:0,9,117 ./. 0/0:8,0:8:24.08:0,24,321 0/0:7,0:7:21.07:0,21,277 0/0:2,0:2:6.02:0,6,82 0/0:4,0:4:9.03:0,9,115 0/0:4,0:4:12.04:0,12,156 0/0:5,0:5:15.05:0,15,200 0/0:2,0:2:6.02:0,6,82 0/0:3,0:3:9.03:0,9,124 0/0:3,0:3:9.03:0,9,117 0/0:4,0:4:12.04:0,12,163 0/0:6,0:6:18.06:0,18,235 0/0:2,0:2:6.02:0,6,80 0/0:4,0:4:12.04:0,12,168 0/1:1,1:2:28.33:28,0,36 ./. 0/1:1,3:4:26.54:104,0,27 0/0:6,0:6:18.06:0,18,237 0/0:8,0:8:21.07:0,21,277 0/0:6,0:6:15.05:0,15,200 0/0:15,0:15:45.14:0,45,560 0/0:20,0:20:51.16:0,51,664 0/1:2,6:8:62.47:173,0,62 0/0:3,0:3:9.03:0,9,115 0/0:8,0:8:24.08:0,24,309 1/1:1,4:5:12.04:161,12,0 0/0:7,0:7:21.07:0,21,281 0/0:12,0:13:30.09:0,30,385 0/0:1,0:1:3.01:0,3,42 0/0:4,0:4:12.04:0,12,163 0/0:22,0:22:66.21:0,66,851 0/0:13,0:13:39.13:0,39,521 0/0:13,0:13:36.12:0,36,489 0/0:14,0:14:39.13:0,39,527 0/0:8,0:8:24.08:0,24,313 0/0:4,0:4:9.03:0,9,117 0/1:6,8:14:99:278,0,167 0/0:5,0:5:15.05:0,15,203 0/0:8,0:8:21.07:0,21,279 0/1:2,1:3:33.20:33,0,73 0/0:3,0:3:9.03:0,9,117 -chr1 1179309 . G A 1486.6 . AC=12;AF=0.1017;AN=118;BaseQRankSum=-0.202;DP=527;Dels=0.00;FS=5.698;HRun=0;HaplotypeScore=0.2810;InbreedingCoeff=0.1431;MQ=57.09;MQ0=0;MQRankSum=0.038;QD=15.65;ReadPosRankSum=-0.459;EFF=DOWNSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|4),INTRON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|2),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,downstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL 0/1:3,2:5:31.62:32,0,58 0/0:3,0:3:9.03:0,9,109 0/0:4,0:4:12.04:0,12,150 0/0:6,0:6:18.05:0,18,214 0/0:6,0:6:18.04:0,18,228 0/0:12,0:12:33.10:0,33,421 0/0:25,0:25:75.23:0,75,976 0/0:8,0:8:24.08:0,24,315 0/0:17,0:17:48.15:0,48,625 0/0:22,0:22:60.20:0,60,803 1/1:0,13:13:39.12:476,39,0 0/0:9,0:9:24.07:0,24,300 0/1:14,6:20:99:187,0,424 0/0:9,0:9:21.07:0,21,285 0/1:4,9:14:99:244,0,122 0/0:11,0:11:24.08:0,24,320 0/0:13,0:13:39.12:0,39,490 0/1:2,5:7:61.94:159,0,62 0/0:2,0:2:6.02:0,6,80 0/0:11,0:11:24.08:0,24,336 0/0:11,0:11:24.04:0,24,284 0/0:24,0:24:54.17:0,54,717 0/0:10,0:10:21.06:0,21,278 0/0:8,0:8:15.05:0,15,210 0/0:13,0:13:30.08:0,30,379 0/0:7,0:7:15.05:0,15,189 0/0:11,0:11:27.06:0,27,328 0/0:8,0:8:18.06:0,18,235 0/0:15,0:15:36.12:0,36,476 0/0:4,0:4:9.03:0,9,123 0/0:15,0:15:33.10:0,33,427 0/0:11,0:11:30.10:0,30,408 0/0:4,0:4:12.04:0,12,143 0/1:3,7:10:57.13:188,0,57 0/0:7,0:7:15.05:0,15,203 0/1:4,8:12:71.48:147,0,71 0/0:10,0:10:27.08:0,27,337 0/0:15,0:15:36.12:0,36,481 0/0:5,0:5:12.04:0,12,163 0/0:8,0:8:21.05:0,21,255 0/0:6,0:6:15.05:0,15,208 0/1:4,6:10:99:128,0,131 0/0:2,0:2:3.01:0,3,33 0/0:5,0:5:6.02:0,6,86 0/0:3,0:3:9.02:0,9,108 0/0:8,0:9:18.05:0,18,227 0/0:9,0:9:24.05:0,24,283 0/1:1,1:2:23.61:24,0,31 0/0:9,0:9:15.04:0,15,175 0/0:10,0:10:24.08:0,24,314 0/0:5,0:5:15.04:0,15,180 0/0:2,0:2:6.02:0,6,76 0/0:10,0:11:30.09:0,30,389 0/0:3,0:3:6.02:0,6,82 0/0:4,0:4:9.03:0,9,117 ./. 0/0:2,0:2:6.02:0,6,84 0/0:1,0:1:3.01:0,3,42 1/1:0,2:2:6.02:67,6,0 0/0:4,0:4:9.01:0,9,91 -chr1 1179416 . A C 387.28 . AC=8;AF=0.0690;AN=116;BaseQRankSum=-8.770;DP=848;Dels=0.00;FS=181.958;HRun=3;HaplotypeScore=0.9454;InbreedingCoeff=-0.0952;MQ=53.74;MQ0=0;MQRankSum=-2.436;QD=3.25;ReadPosRankSum=-1.967;EFF=EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|2),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V150G|302|FAM132A|protein_coding|CODING|ENST00000330388|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000468365|2/3||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000486627|2/2||||retained_intron|1,missense_variant|gTg/gGg|V/G|ENSG00000184163|FAM132A|ENST00000330388|4/8|possibly_damaging(0.839)|deleterious(0)|150/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL ./. 0/0:2,1:4:6.01:0,6,66 0/0:6,0:6:12.04:0,12,157 0/0:4,1:5:9.03:0,9,115 0/1:4,4:8:72.51:73,0,117 0/1:7,5:12:65.78:66,0,150 0/1:9,7:16:73.57:74,0,237 0/0:5,5:10:12.04:0,12,154 0/1:20,7:27:25.62:26,0,660 0/1:12,5:17:40.74:41,0,385 0/1:10,7:17:94.92:95,0,339 0/1:9,7:16:99:127,0,236 0/0:10,4:14:11.42:0,11,372 0/0:18,1:19:42.12:0,42,526 0/0:15,2:17:33.09:0,33,383 0/0:14,1:15:30.05:0,30,356 0/0:22,3:25:27.44:0,27,602 0/0:18,4:22:14.43:0,14,415 0/0:16,1:17:27.07:0,27,333 0/0:14,2:16:30.08:0,30,368 0/0:23,2:25:24.48:0,24,613 0/0:27,6:34:66.14:0,66,789 0/0:17,2:19:36.03:0,36,377 0/0:16,2:18:36.05:0,36,408 0/0:21,4:25:36.09:0,36,444 0/0:19,1:20:42.11:0,42,512 0/0:11,3:14:18.05:0,18,207 0/0:14,0:15:36.11:0,36,445 0/0:14,8:22:27.07:0,27,334 0/0:11,4:15:33.10:0,33,421 0/0:18,5:23:42.10:0,42,517 0/0:21,5:26:36.08:0,36,444 0/0:8,3:11:12.01:0,12,126 0/0:16,1:17:27.05:0,27,313 0/0:14,0:14:21.07:0,21,288 0/0:12,1:13:21.04:0,21,245 0/0:23,3:28:26.45:0,26,576 0/0:36,4:40:81.13:0,81,947 0/0:1,1:2:3.01:0,3,31 0/0:12,2:14:30.08:0,30,359 0/0:11,4:15:30.08:0,30,370 0/0:7,0:7:15.05:0,15,202 ./. 0/0:3,1:4:6.01:0,6,68 0/0:9,2:11:24.08:0,24,312 0/0:9,2:11:15.04:0,15,177 0/0:14,4:18:30.08:0,30,350 0/0:5,1:6:12.03:0,12,128 0/0:6,1:7:15.05:0,15,182 0/0:11,3:14:30.06:0,30,350 0/0:6,2:8:9.03:0,9,111 0/0:6,1:7:12.01:0,12,132 0/0:11,1:12:30.06:0,30,354 0/0:12,0:12:21.07:0,21,272 0/0:6,2:8:12.04:0,12,152 0/0:3,0:3:6.02:0,6,80 0/0:5,0:5:15.04:0,15,179 0/0:4,0:4:6.02:0,6,80 0/0:4,3:7:9.02:0,9,97 0/1:3,3:6:17.66:18,0,70 -chr1 1179532 . C T 490.97 . AC=2;AF=0.0167;AN=120;BaseQRankSum=1.132;DP=1835;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0586;InbreedingCoeff=-0.0210;MQ=57.90;MQ0=0;MQRankSum=1.423;QD=10.45;ReadPosRankSum=0.071;EFF=EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|2),EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|2),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|3),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000468365|2/3||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000486627|2/2||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:6,0:6:12.03:0,12,139 0/0:15,0:15:39.10:0,39,461 0/0:4,0:4:12.04:0,12,150 0/0:8,0:8:24.07:0,24,290 0/0:12,0:12:36.12:0,36,478 0/0:17,0:17:48.13:0,48,615 0/0:23,0:23:66.21:0,66,877 0/0:15,0:15:45.13:0,45,557 0/0:35,0:35:99:0,99,1308 0/0:35,0:35:99:0,102,1343 0/0:17,0:17:45.14:0,45,585 0/0:9,0:9:21.07:0,21,280 0/0:27,0:27:81.25:0,81,1029 0/0:55,0:55:99:0,138,1834 0/0:62,0:62:99:0,162,2114 0/1:24,13:38:99:366,0,633 0/0:53,0:53:99:0,129,1682 0/0:43,0:43:99:0,114,1429 0/0:61,0:62:99:0,150,1961 0/0:57,1:58:99:0,115,1900 0/0:65,0:65:99:0,156,2039 0/0:66,0:66:99:0,166,2132 0/0:53,0:53:99:0,138,1779 0/0:39,0:39:90.25:0,90,1161 0/0:48,1:49:99:0,129,1626 0/0:45,0:45:99:0,114,1496 0/0:53,0:53:99:0,141,1838 0/0:38,0:38:99:0,105,1365 0/0:77,0:77:99:0,184,2403 0/0:46,0:46:99:0,111,1424 0/0:58,0:58:99:0,153,1990 0/0:46,1:47:85.76:0,86,1557 0/0:63,0:63:99:0,169,2156 0/0:51,0:51:99:0,129,1646 0/0:47,0:47:99:0,114,1507 0/0:52,0:52:99:0,129,1698 0/0:64,0:64:99:0,159,2066 0/0:84,1:85:99:0,186,2834 0/0:4,0:4:12.04:0,12,161 0/0:22,0:22:57.16:0,57,708 0/0:18,0:18:48.14:0,48,586 0/0:7,0:7:18.06:0,18,233 0/1:2,7:9:54.49:190,0,54 0/0:7,0:7:15.04:0,15,189 0/0:10,0:10:30.08:0,30,378 0/0:13,0:14:33.09:0,33,386 0/0:20,0:20:51.12:0,51,624 0/0:4,0:4:12.04:0,12,143 0/0:8,0:8:18.05:0,18,215 0/0:17,0:17:45.14:0,45,563 0/0:11,0:11:24.08:0,24,317 0/0:5,0:5:12.03:0,12,139 0/0:12,0:12:27.08:0,27,342 0/0:17,0:17:39.12:0,39,501 0/0:11,0:11:24.07:0,24,307 0/0:8,0:8:15.05:0,15,204 0/0:6,0:6:15.03:0,15,187 0/0:5,0:5:15.04:0,15,179 0/0:13,0:13:27.07:0,27,339 0/0:14,0:14:30.09:0,30,383 -chr1 1179747 . C T 48.72 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.106;DP=2070;Dels=0.00;FS=5.993;HRun=0;HaplotypeScore=1.5289;InbreedingCoeff=-0.0284;MQ=59.19;MQ0=0;MQRankSum=-1.469;QD=6.96;ReadPosRankSum=1.335;EFF=INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|2),INTRON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|1),INTRON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|1),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=intron_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:7,0:7:15.03:0,15,172 0/0:14,0:14:36.09:0,36,449 0/0:14,0:14:42.13:0,42,532 0/0:15,0:15:36.12:0,36,467 0/0:20,0:20:57.19:0,57,769 0/0:32,0:32:90.29:0,90,1194 0/0:47,0:47:99:0,135,1776 0/0:34,0:34:96.25:0,96,1191 0/0:67,0:67:99:0,193,2541 0/0:63,0:63:99:0,184,2396 0/0:42,0:42:99:0,120,1574 0/0:26,0:26:69.20:0,69,871 0/0:58,0:58:99:0,165,2126 0/0:45,0:45:99:0,111,1412 0/0:75,0:78:99:0,193,2504 0/0:34,0:34:93.26:0,93,1139 0/0:67,0:67:99:0,153,2034 0/0:87,0:87:99:0,220,2852 0/0:57,0:57:99:0,138,1801 0/0:60,0:60:99:0,150,1990 0/0:59,0:59:99:0,147,1894 0/0:68,0:68:99:0,172,2268 0/0:53,0:53:99:0,135,1702 0/0:48,0:48:99:0,126,1673 0/0:53,0:53:99:0,141,1858 0/0:48,0:48:99:0,114,1467 0/0:55,0:55:99:0,132,1778 0/0:43,0:43:99:0,105,1363 0/0:84,0:84:99:0,220,2791 0/0:64,0:64:99:0,153,2032 0/0:79,0:79:99:0,196,2594 0/0:43,0:43:99:0,108,1429 0/0:68,0:68:99:0,166,2171 0/0:78,0:78:99:0,208,2580 0/0:45,0:45:99:0,114,1511 0/0:58,0:58:99:0,132,1777 0/0:59,0:59:99:0,150,2015 0/0:86,0:86:99:0,208,2743 0/0:2,0:2:6.02:0,6,84 0/0:8,0:8:18.06:0,18,246 0/0:9,0:9:24.08:0,24,308 0/0:3,0:3:9.01:0,9,103 0/0:5,0:5:9.02:0,9,110 0/0:1,0:1:3.01:0,3,33 0/0:6,0:6:18.04:0,18,215 0/0:4,0:4:12.04:0,12,156 0/0:12,0:12:24.08:0,24,332 0/0:2,0:2:6.02:0,6,75 0/0:5,0:5:12.02:0,12,142 0/0:5,0:5:12.04:0,12,145 0/0:10,0:10:24.07:0,24,299 0/0:5,0:5:9.03:0,9,120 0/0:5,0:5:12.03:0,12,132 0/1:4,3:7:96.25:96,0,124 0/0:3,0:3:6.02:0,6,77 0/0:4,0:4:9.02:0,9,114 0/0:1,0:1:3.01:0,3,38 0/0:7,0:7:12.04:0,12,174 0/0:2,0:2:6.02:0,6,72 0/0:5,0:5:12.04:0,12,160 -chr1 1179800 . G A 782.26 . AC=2;AF=0.0172;AN=116;BaseQRankSum=-3.138;DP=2073;Dels=0.00;FS=2.190;HRun=0;HaplotypeScore=1.3315;InbreedingCoeff=-0.0420;MQ=59.44;MQ0=0;MQRankSum=-0.175;QD=9.78;ReadPosRankSum=0.512;EFF=EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|1),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G85|302|FAM132A|protein_coding|CODING|ENST00000330388|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000486627|1/2||||retained_intron|1,synonymous_variant|ggC/ggT|G|ENSG00000184163|FAM132A|ENST00000330388|2/8|||85/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:15,0:15:30.10:0,30,390 0/0:13,0:14:30.10:0,30,385 0/0:15,0:15:33.10:0,33,418 0/0:12,0:12:33.08:0,33,396 0/0:48,0:48:99:0,129,1691 0/0:28,0:28:78.25:0,78,1018 0/0:67,0:67:99:0,178,2294 0/0:34,1:35:55.91:0,56,1069 0/0:92,1:94:99:0,219,3286 0/0:86,0:88:99:0,244,3156 0/0:39,0:39:99:0,114,1500 0/0:46,0:46:99:0,126,1654 0/0:86,0:86:99:0,232,2984 0/0:49,0:49:99:0,117,1461 0/1:39,35:77:99:818,0,975 0/0:28,0:28:69.18:0,69,876 0/0:49,0:49:99:0,114,1465 0/0:74,0:74:99:0,181,2313 0/0:42,0:43:99:0,99,1287 0/0:49,0:50:99:0,114,1477 0/0:58,0:58:99:0,132,1671 0/0:49,0:49:99:0,120,1503 0/0:58,0:58:99:0,120,1526 0/0:50,0:50:99:0,108,1393 0/0:46,0:46:99:0,108,1391 0/0:50,0:50:99:0,111,1418 0/0:53,0:53:99:0,120,1564 0/0:40,0:40:99:0,99,1187 0/0:67,0:70:99:0,159,1987 0/0:54,0:54:99:0,135,1733 0/0:76,0:76:99:0,174,2211 0/0:45,0:45:99:0,102,1356 0/0:69,0:69:99:0,160,2097 0/0:77,0:77:99:0,196,2477 0/0:46,0:46:99:0,99,1287 0/0:57,0:57:99:0,126,1657 0/0:62,0:62:99:0,132,1768 0/0:78,0:78:99:0,190,2507 0/0:2,0:2:3.01:0,3,45 0/0:6,0:6:18.06:0,18,233 0/0:3,0:4:9.02:0,9,98 0/0:2,0:2:6.02:0,6,74 0/0:3,0:4:9.03:0,9,118 ./. 0/0:4,0:4:12.04:0,12,159 0/0:4,0:4:12.04:0,12,154 0/0:7,0:8:15.05:0,15,203 0/0:3,0:3:6.02:0,6,85 0/0:4,0:4:9.03:0,9,122 0/0:5,0:5:12.04:0,12,156 0/0:7,0:7:18.05:0,18,221 0/0:2,0:3:3.01:0,3,32 0/0:3,0:4:6:0,6,51 0/0:3,0:3:3:0,3,25 0/0:2,0:2:6.02:0,6,74 0/1:1,2:3:28.33:28,0,36 ./. 0/0:5,0:5:15.04:0,15,186 0/0:2,0:2:6.02:0,6,84 0/0:2,0:2:6.02:0,6,79 -chr1 1179983 . G A 2866.16 . AC=17;AF=0.1417;AN=120;BaseQRankSum=-1.868;DP=688;Dels=0.00;FS=0.855;HRun=0;HaplotypeScore=0.3402;InbreedingCoeff=0.3638;MQ=59.13;MQ0=0;MQRankSum=0.378;QD=21.71;ReadPosRankSum=-2.062;EFF=EXON(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|1),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|1),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|);CSQ=upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000184163|FAM132A|ENST00000486627|1/2||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL 0/1:4,3:7:85.52:86,0,120 0/0:9,0:9:27.08:0,27,336 0/0:10,0:10:30.10:0,30,387 0/0:14,0:14:30.09:0,30,369 0/0:31,0:31:93.29:0,93,1233 0/0:22,0:22:63.20:0,63,836 0/0:45,0:45:99:0,132,1749 0/0:25,0:25:69.23:0,69,917 0/0:53,0:53:99:0,157,2089 0/0:59,1:60:99:0,139,2279 1/1:0,24:24:72.23:954,72,0 0/0:25,0:25:75.24:0,75,989 0/1:21,31:52:99:979,0,650 0/0:5,0:5:15.05:0,15,198 0/1:4,5:9:99:125,0,136 0/0:9,0:9:24.08:0,24,322 0/0:4,0:4:12.04:0,12,156 1/1:0,9:9:27.09:357,27,0 0/0:13,0:13:39.13:0,39,514 0/0:11,0:11:33.07:0,33,402 0/0:11,0:11:30.10:0,30,403 0/0:9,0:9:27.09:0,27,346 0/0:10,0:10:21.01:0,21,237 0/0:12,0:12:33.10:0,33,417 0/0:9,0:9:15.05:0,15,202 0/0:10,0:10:30.09:0,30,373 0/0:10,0:10:27.09:0,27,352 0/0:6,0:6:15.05:0,15,195 0/0:9,0:9:24.08:0,24,314 0/0:7,0:7:21.07:0,21,277 0/0:10,0:10:27.07:0,27,338 0/0:5,0:5:15.05:0,15,199 0/0:9,0:9:24.07:0,24,309 0/1:6,4:10:99:130,0,213 0/0:5,0:5:12.04:0,12,154 0/1:2,2:4:67.18:68,0,67 0/0:11,0:11:33.11:0,33,444 0/0:16,0:16:45.12:0,45,579 0/0:1,0:1:3.01:0,3,33 0/0:6,0:6:15.05:0,15,202 0/0:7,0:7:12.04:0,12,168 0/1:1,1:2:33.99:34,0,35 0/0:3,0:3:6.02:0,6,76 0/0:3,0:3:6.02:0,6,87 0/0:3,0:3:6.02:0,6,87 0/0:4,0:4:12.04:0,12,158 0/0:5,0:5:15.05:0,15,190 1/1:0,1:1:3.01:39,3,0 0/0:4,0:4:9.03:0,9,124 1/1:0,8:8:15.01:161,15,0 0/0:6,0:6:15.05:0,15,193 0/0:4,0:4:9.02:0,9,108 0/0:10,0:10:24.08:0,24,310 0/0:2,0:2:6.02:0,6,82 0/0:5,0:5:12.04:0,12,157 0/1:2,2:4:62.67:63,0,68 0/0:3,0:3:6.02:0,6,85 0/0:2,0:2:3.01:0,3,45 1/1:0,2:2:6.02:74,6,0 0/0:3,0:3:6.02:0,6,85 -chr1 1181372 . C T 142.78 . AC=9;AF=0.205;AN=44;BaseQRankSum=0.940;DP=56;Dels=0.00;FS=10.677;HRun=0;HaplotypeScore=0.1214;InbreedingCoeff=0.3107;MQ=57.48;MQ0=0;MQRankSum=0.070;QD=20.40;ReadPosRankSum=1.361;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|1),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|);CSQ=upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,downstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL 0/0:6,0:6:15.02:0,15,160 0/0:5,0:5:12.04:0,12,147 0/0:5,0:5:15.05:0,15,193 0/0:6,0:6:15.04:0,15,184 0/0:1,0:1:3.01:0,3,41 1/1:0,1:1:3.01:39,3,0 0/1:1,2:3:32.20:70,0,32 0/0:3,0:3:9.01:0,9,98 0/0:5,0:5:15.01:0,15,169 ./. 0/0:2,0:2:6.02:0,6,74 0/0:2,0:2:6.02:0,6,80 0/0:7,0:7:21.07:0,21,276 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3:0,3,26 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,37 ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. -chr1 1181751 . T C 107.96 . AC=6;AF=0.130;AN=46;BaseQRankSum=0.029;DP=35;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0398;InbreedingCoeff=0.0106;MQ=56.62;MQ0=0;MQRankSum=0.202;QD=15.42;ReadPosRankSum=0.375;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),INTRON(MODIFIER||||302|FAM132A|protein_coding|CODING|ENST00000330388|1),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000462849|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000468365|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000478606|),UPSTREAM(MODIFIER|||||FAM132A|retained_intron|CODING|ENST00000486627|);CSQ=upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000468365|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000462849|||||retained_intron|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000486627|||||retained_intron|1,intron_variant|||ENSG00000184163|FAM132A|ENST00000330388||||-/302|protein_coding|1,downstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,upstream_gene_variant|||ENSG00000184163|FAM132A|ENST00000478606|||||retained_intron|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:3.01:0,3,33 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,40 ./. 0/0:3,0:3:9.02:0,9,111 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. 0/0:2,0:2:6.02:0,6,73 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,38 ./. 1/1:0,1:1:3.01:39,3,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 1/1:0,2:2:6.02:82,6,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/1:1,1:2:31.78:34,0,32 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,32 0/1:1,1:2:27.42:27,0,30 ./. -chr1 1190061 . A G 343.05 . AC=12;AF=0.176;AN=68;BaseQRankSum=1.182;DP=113;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0935;InbreedingCoeff=0.3239;MQ=57.93;MQ0=0;MQRankSum=0.135;QD=20.18;ReadPosRankSum=-0.224;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|),DOWNSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),DOWNSTREAM(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|),DOWNSTREAM(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|7),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|7),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000349431|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|7/7|||-/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 1/1:1,1:2:3.01:40,3,0 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,40 ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. 0/0:2,0:2:3.01:0,3,32 ./. ./. ./. 0/1:2,1:3:21.56:22,0,71 ./. ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. 0/0:1,0:1:2.99:0,3,23 ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. ./. ./. 0/0:5,0:5:15.05:0,15,201 0/0:9,0:9:27.07:0,27,340 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,82 0/1:1,2:3:33.20:72,0,33 0/0:2,0:2:6.02:0,6,84 1/1:0,4:4:12.04:164,12,0 0/0:5,0:5:15.05:0,15,197 0/0:15,0:15:39.12:0,39,503 1/1:0,1:1:3.01:41,3,0 0/0:3,0:3:6.02:0,6,80 1/1:0,3:3:6.02:82,6,0 0/0:6,0:6:12.04:0,12,157 0/0:3,0:3:9.03:0,9,122 0/0:3,0:3:6.01:0,6,65 0/0:6,0:6:15.04:0,15,191 0/0:5,0:5:15.04:0,15,183 0/0:4,0:4:12.04:0,12,164 0/0:5,0:5:15.04:0,15,180 0/0:3,0:3:6.02:0,6,84 0/0:4,0:4:12.04:0,12,162 0/0:3,0:3:9.03:0,9,121 -chr1 1190166 . G A 197.18 . AC=1;AF=0.017;AN=58;BaseQRankSum=1.290;DP=332;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.5654;InbreedingCoeff=-0.0510;MQ=56.96;MQ0=0;MQRankSum=0.784;QD=10.38;ReadPosRankSum=-0.832;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|),DOWNSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),DOWNSTREAM(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|),DOWNSTREAM(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|7),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|7),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000349431|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|7/7|||-/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:18.06:0,18,230 ./. 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:9.03:0,9,121 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,34 ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. 0/0:13,0:13:36.12:0,36,474 0/0:17,0:17:42.12:0,42,513 0/0:11,0:12:30.08:0,30,357 0/1:9,10:19:99:241,0,197 0/0:12,0:12:33.09:0,33,407 0/0:14,0:14:33.09:0,33,405 0/0:17,0:17:51.15:0,51,633 0/0:11,0:13:21.07:0,21,275 0/0:34,0:34:81.25:0,81,1025 0/0:8,0:8:24.06:0,24,290 0/0:13,0:13:33.10:0,33,424 0/0:12,0:12:33.09:0,33,404 0/0:14,0:14:33.11:0,33,433 0/0:11,0:11:30.09:0,30,374 0/0:15,0:15:42.11:0,42,498 0/0:20,0:20:42.13:0,42,521 0/0:14,0:14:39.12:0,39,479 0/0:9,0:9:21.07:0,21,264 0/0:15,0:15:39.13:0,39,508 0/0:14,0:14:36.11:0,36,449 0/0:7,0:7:18.06:0,18,237 0/0:12,0:12:30.09:0,30,369 -chr1 1190206 . G A 197.94 . AC=1;AF=0.015;AN=68;BaseQRankSum=-0.934;DP=520;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7388;InbreedingCoeff=-0.0641;MQ=57.17;MQ0=0;MQRankSum=2.013;QD=15.23;ReadPosRankSum=-0.458;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|),DOWNSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),DOWNSTREAM(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|),DOWNSTREAM(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|7),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|7),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000349431|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|7/7|||-/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.02:0,6,69 0/0:2,0:2:6.02:0,6,80 0/0:2,0:2:6.02:0,6,70 ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,77 ./. 0/0:3,0:3:9.03:0,9,119 ./. 0/0:1,0:1:3.01:0,3,38 ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,35 ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. 0/0:20,0:20:51.17:0,51,684 0/0:34,0:34:78.22:0,78,993 0/0:27,0:27:63.19:0,63,826 0/0:26,0:26:63.20:0,63,817 0/0:15,0:15:36.10:0,36,458 0/0:16,0:16:39.11:0,39,477 0/0:20,0:20:54.16:0,54,669 0/0:21,0:21:48.15:0,48,614 0/0:48,0:48:99:0,123,1605 0/1:5,8:13:99:243,0,155 0/0:20,0:20:54.18:0,54,719 0/0:33,0:34:78.25:0,78,1026 0/0:26,0:26:72.23:0,72,950 0/0:15,0:15:36.08:0,36,432 0/0:20,0:20:48.14:0,48,595 0/0:33,0:33:78.23:0,78,992 0/0:26,0:26:66.21:0,66,863 0/0:13,0:13:27.08:0,27,347 0/0:20,0:20:54.16:0,54,685 0/0:20,0:20:42.13:0,42,545 0/0:14,0:14:36.12:0,36,481 0/0:19,0:19:51.16:0,51,649 -chr1 1190207 . C T 432.13 . AC=7;AF=0.100;AN=70;BaseQRankSum=-1.418;DP=529;Dels=0.00;FS=4.930;HRun=0;HaplotypeScore=0.6967;InbreedingCoeff=0.1975;MQ=57.18;MQ0=0;MQRankSum=0.339;QD=9.39;ReadPosRankSum=1.134;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|),DOWNSTREAM(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|),DOWNSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),DOWNSTREAM(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|),DOWNSTREAM(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|7),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|7),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000349431|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|7/7|||-/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/1:1,1:2:32.56:33,0,34 0/0:2,0:2:6.02:0,6,74 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:6.02:0,6,70 ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,80 ./. 0/0:3,0:3:9.03:0,9,124 ./. 0/0:1,0:1:3:0,3,26 ./. 1/1:0,1:1:3.01:41,3,0 ./. 0/0:1,0:1:3:0,3,26 ./. ./. 1/1:0,1:1:3.01:37,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,37 ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. 0/0:20,0:20:51.17:0,51,680 0/0:38,0:38:84.23:0,84,1053 0/0:28,1:29:29.21:0,29,818 0/1:15,11:26:99:258,0,402 0/1:9,7:16:99:159,0,231 0/0:16,0:16:39.12:0,39,484 0/0:20,0:20:54.15:0,54,665 0/0:20,0:20:45.14:0,45,585 0/0:46,0:46:99:0,123,1568 0/0:13,0:13:33.11:0,33,445 0/0:22,0:22:60.18:0,60,771 0/0:34,0:34:75.24:0,75,1009 0/0:26,0:26:75.24:0,75,973 0/0:15,0:15:39.11:0,39,468 0/0:20,0:20:48.15:0,48,601 0/0:34,0:34:78.22:0,78,992 0/0:28,0:28:66.21:0,66,872 0/0:13,0:13:27.08:0,27,339 0/0:20,0:20:54.13:0,54,671 0/0:20,0:20:42.13:0,42,559 0/0:14,0:14:36.10:0,36,473 0/0:19,0:19:51.16:0,51,649 -chr1 1190481 . G A 116.73 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.156;DP=714;Dels=0.00;FS=12.015;HRun=1;HaplotypeScore=0.6509;InbreedingCoeff=-0.0173;MQ=59.06;MQ0=0;MQRankSum=-0.238;QD=6.49;ReadPosRankSum=1.991;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|),DOWNSTREAM(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|7),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|7),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|6),UTR_3_PRIME(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|6),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|7),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|8);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000339385|6/6|||-/224|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036|8/8|||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000349431|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000348298|7/7|||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|7/7|||-/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000400929|6/6|||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,76 0/0:2,0:2:6.01:0,6,66 0/0:2,0:2:6.02:0,6,70 0/0:5,0:5:15.04:0,15,188 0/0:6,0:6:18.06:0,18,236 0/0:3,0:3:9.03:0,9,122 0/0:13,0:13:39.13:0,39,522 0/0:9,0:9:27.07:0,27,343 0/0:9,0:9:27.09:0,27,352 0/0:26,0:26:75.24:0,75,995 0/0:9,0:9:24.08:0,24,313 0/0:4,0:4:12.04:0,12,157 0/0:16,0:16:42.13:0,42,542 0/0:14,0:14:39.13:0,39,508 0/0:12,0:12:33.11:0,33,450 0/0:8,0:8:21.06:0,21,269 0/0:11,0:11:33.08:0,33,419 0/0:10,0:10:30.08:0,30,389 0/0:17,0:17:48.15:0,48,637 0/0:6,0:6:12.04:0,12,170 0/0:13,0:13:39.13:0,39,519 0/0:14,0:14:42.11:0,42,526 0/0:14,0:14:39.10:0,39,491 0/0:6,0:6:18.06:0,18,239 0/0:10,0:10:27.09:0,27,353 0/0:5,0:5:15.05:0,15,205 0/0:14,0:14:42.14:0,42,567 0/0:7,0:7:21.07:0,21,280 0/0:11,0:11:33.11:0,33,442 0/0:9,0:9:27.09:0,27,369 0/0:12,0:12:36.12:0,36,473 0/0:9,0:9:27.09:0,27,372 0/0:6,0:6:18.06:0,18,228 0/0:10,0:10:27.09:0,27,360 0/0:7,0:7:18.06:0,18,240 0/0:6,0:6:18.06:0,18,251 0/0:11,0:11:33.11:0,33,444 0/0:18,0:18:51.16:0,51,679 0/0:13,0:13:36.11:0,36,470 0/0:20,0:20:54.17:0,54,705 0/0:19,0:19:45.15:0,45,584 0/0:18,0:18:48.16:0,48,638 0/0:15,0:15:36.12:0,36,482 0/0:15,0:15:39.12:0,39,500 0/0:10,0:10:30.09:0,30,386 0/0:19,0:19:51.16:0,51,656 0/0:25,0:25:75.23:0,75,966 0/0:5,0:5:15.05:0,15,192 0/0:14,0:14:42.13:0,42,550 0/1:11,7:18:99:164,0,380 0/0:17,0:17:51.16:0,51,658 0/0:16,0:16:39.12:0,39,517 0/0:12,0:12:36.12:0,36,468 0/0:22,0:22:54.15:0,54,700 0/0:14,0:14:33.11:0,33,454 0/0:13,0:13:39.09:0,39,483 0/0:13,0:13:36.11:0,36,445 0/0:20,0:20:57.17:0,57,730 0/0:18,0:18:51.16:0,51,666 0/0:12,0:12:36.11:0,36,461 -chr1 1190523 . C T 321.56 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-1.643;DP=1091;Dels=0.00;FS=3.027;HRun=0;HaplotypeScore=0.7506;InbreedingCoeff=-0.0300;MQ=58.89;MQ0=0;MQRankSum=-0.522;QD=7.31;ReadPosRankSum=-0.760;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|),DOWNSTREAM(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|7),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|7),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|6),UTR_3_PRIME(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|6),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|7),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|8);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000339385|6/6|||-/224|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036|8/8|||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000349431|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000348298|7/7|||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|7/7|||-/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000400929|6/6|||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12.04:0,12,157 0/0:2,0:2:6.02:0,6,79 0/0:3,0:3:9.03:0,9,119 0/1:5,3:8:90.05:90,0,174 0/0:7,0:7:21.07:0,21,284 0/0:6,0:6:18.06:0,18,244 0/0:11,0:11:33.10:0,33,427 0/0:7,0:7:15.05:0,15,200 0/0:18,0:18:51.17:0,51,676 0/0:28,0:28:75.24:0,75,979 0/0:7,0:7:21.07:0,21,283 0/0:5,0:5:15.05:0,15,196 0/0:7,0:8:21.06:0,21,253 0/0:19,0:19:57.18:0,57,749 0/0:20,0:20:51.15:0,51,663 0/0:15,0:15:45.14:0,45,591 0/0:17,0:17:45.13:0,45,588 0/0:18,0:18:51.15:0,51,653 0/0:23,0:23:60.19:0,60,785 0/1:4,7:11:99:162,0,125 0/0:29,0:29:78.25:0,78,1045 0/0:21,0:21:63.20:0,63,826 0/0:21,0:21:60.15:0,60,768 0/0:15,0:15:42.13:0,42,546 0/0:17,0:17:51.16:0,51,667 0/0:9,0:9:24.08:0,24,315 0/0:21,0:21:63.20:0,63,819 0/0:12,0:12:33.11:0,33,436 0/0:21,0:21:51.17:0,51,696 0/0:16,0:16:36.12:0,36,506 0/0:16,0:17:48.15:0,48,628 0/0:13,0:13:39.13:0,39,516 0/0:10,0:10:30.10:0,30,407 0/0:12,0:12:33.05:0,33,401 0/0:9,0:9:21.06:0,21,270 0/0:12,0:12:33.09:0,33,413 0/0:20,0:20:57.13:0,57,726 0/0:31,0:31:90.29:0,90,1196 0/0:14,0:14:39.12:0,39,493 0/0:40,0:41:99:0,105,1373 0/0:23,0:23:57.18:0,57,766 0/0:27,0:28:66.21:0,66,858 0/0:26,0:26:72.22:0,72,943 0/0:22,0:22:54.15:0,54,713 0/0:19,0:19:42.13:0,42,547 0/0:25,0:25:57.17:0,57,722 0/0:40,0:41:99:0,108,1412 0/0:9,0:9:21.06:0,21,275 0/0:21,0:21:54.17:0,54,725 0/0:29,0:30:81.25:0,81,1048 0/0:26,0:26:69.22:0,69,931 0/0:20,0:20:48.15:0,48,638 0/1:18,7:25:99:149,0,497 0/0:35,0:35:93.29:0,93,1200 0/0:19,0:19:48.15:0,48,629 0/0:17,0:17:45.15:0,45,603 0/0:23,0:23:57.18:0,57,744 0/0:37,0:37:90.29:0,90,1217 0/0:25,0:25:66.21:0,66,876 0/0:21,0:21:51.17:0,51,693 -chr1 1190544 . G A 120.24 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.624;DP=1337;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.7866;InbreedingCoeff=-0.0117;MQ=58.85;MQ0=0;MQRankSum=-0.513;QD=4.01;ReadPosRankSum=1.551;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|7),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|7),UTR_3_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|6),UTR_3_PRIME(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|6),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|7),UTR_3_PRIME(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|7),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|8);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000339385|6/6|||-/224|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036|8/8|||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000349431|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000348298|7/7|||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|7/7|||-/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000400929|6/6|||-/207|protein_coding|1,3_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000360466|7/7|||-/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.01:0,12,121 0/0:6,0:6:18.06:0,18,230 0/0:7,0:7:21.06:0,21,267 0/0:7,0:7:21.04:0,21,245 0/0:10,0:10:27.09:0,27,358 0/0:4,0:4:12.04:0,12,162 0/0:16,0:16:48.16:0,48,636 0/0:2,0:2:6.02:0,6,78 0/0:17,0:17:51.16:0,51,661 0/0:19,0:19:54.16:0,54,700 0/0:11,0:11:30.10:0,30,391 0/0:6,0:6:18.06:0,18,240 0/0:6,0:6:18.04:0,18,217 0/0:23,0:23:66.22:0,66,884 0/0:33,0:33:84.26:0,84,1071 0/0:20,0:20:57.18:0,57,738 0/0:21,1:22:51.16:0,51,675 0/0:26,0:26:66.18:0,66,819 0/0:22,0:22:57.18:0,57,738 0/0:16,0:16:42.14:0,42,569 0/0:31,0:31:78.24:0,78,1008 0/0:29,1:30:39.63:0,40,902 0/0:29,0:29:78.22:0,78,986 0/0:20,0:21:54.17:0,54,722 0/0:22,0:22:54.17:0,54,707 0/0:15,0:16:42.14:0,42,557 0/0:26,0:26:72.20:0,72,938 0/0:15,0:15:45.10:0,45,560 0/0:28,0:28:72.24:0,72,973 0/0:25,0:25:60.19:0,60,787 0/0:21,0:21:60.18:0,60,769 0/0:14,0:14:39.13:0,39,525 0/0:12,0:12:36.11:0,36,456 0/0:18,0:18:39.12:0,39,503 0/0:11,1:12:30.09:0,30,385 0/0:21,0:21:48.14:0,48,642 0/0:26,0:26:60.20:0,60,811 0/0:38,0:38:99:0,108,1425 0/0:17,0:17:45.14:0,45,565 0/0:46,0:46:99:0,111,1479 0/0:25,0:25:60.19:0,60,793 0/0:29,0:29:75.23:0,75,964 0/0:27,0:27:72.22:0,72,929 0/0:28,0:28:69.21:0,69,900 0/0:17,0:17:39.13:0,39,527 0/0:29,0:29:63.18:0,63,778 0/0:45,0:45:99:0,105,1369 0/0:15,0:15:30.10:0,30,410 0/0:25,0:25:63.20:0,63,832 0/0:41,0:41:99:0,108,1365 0/0:32,0:32:81.25:0,81,1081 0/0:28,0:28:75.24:0,75,962 0/1:21,9:30:99:168,0,534 0/0:42,0:42:96.27:0,96,1231 0/0:31,0:31:66.21:0,66,877 0/0:24,0:24:57.18:0,57,752 0/0:24,0:24:54.17:0,54,716 0/0:46,0:46:99:0,111,1460 0/0:26,1:28:63.18:0,63,815 0/0:24,0:24:51.17:0,51,708 -chr1 1190685 . G A 695.66 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.799;DP=3117;Dels=0.00;FS=3.835;HRun=0;HaplotypeScore=1.7262;InbreedingCoeff=-0.0084;MQ=59.01;MQ0=0;MQRankSum=1.046;QD=13.38;ReadPosRankSum=-1.664;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),EXON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|2),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H174|207|UBE2J2|protein_coding|CODING|ENST00000347370|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H174|207|UBE2J2|protein_coding|CODING|ENST00000348298|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H174|207|UBE2J2|protein_coding|CODING|ENST00000400929|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H191|224|UBE2J2|protein_coding|CODING|ENST00000339385|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H226|259|UBE2J2|protein_coding|CODING|ENST00000349431|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H226|259|UBE2J2|protein_coding|CODING|ENST00000360466|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H242|275|UBE2J2|protein_coding|CODING|ENST00000400930|),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|8),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|8),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|7);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,synonymous_variant|caC/caT|H|ENSG00000160087|UBE2J2|ENST00000339385|6/6|||191/224|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215|7/7|||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036|8/8|||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,synonymous_variant|caC/caT|H|ENSG00000160087|UBE2J2|ENST00000349431|7/7|||226/259|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000467339|2/2||||processed_transcript|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,synonymous_variant|caC/caT|H|ENSG00000160087|UBE2J2|ENST00000348298|7/7|||174/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,synonymous_variant|caC/caT|H|ENSG00000160087|UBE2J2|ENST00000347370|7/7|||174/207|protein_coding|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390|8/8|||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,synonymous_variant|caC/caT|H|ENSG00000160087|UBE2J2|ENST00000400930|8/8|||242/275|protein_coding|1,synonymous_variant|caC/caT|H|ENSG00000160087|UBE2J2|ENST00000400929|6/6|||174/207|protein_coding|1,synonymous_variant|caC/caT|H|ENSG00000160087|UBE2J2|ENST00000360466|7/7|||226/259|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:14,0:14:39.11:0,39,472 0/0:23,0:23:63.18:0,63,765 0/0:13,0:13:39.11:0,39,467 0/0:14,0:14:39.12:0,39,489 0/0:35,0:35:99:0,99,1318 0/0:39,0:39:99:0,117,1554 0/0:71,0:71:99:0,214,2794 0/0:26,0:26:78.25:0,78,1010 0/0:86,0:86:99:0,250,3305 0/0:80,0:80:99:0,229,3034 0/0:31,0:31:90.29:0,90,1197 0/0:29,0:29:87.28:0,87,1153 0/0:53,0:53:99:0,156,2051 0/0:63,0:64:99:0,153,2046 0/0:70,0:70:99:0,178,2274 0/0:42,0:42:93.28:0,93,1187 0/0:47,0:48:99:0,123,1641 0/0:72,0:72:99:0,172,2285 0/0:61,0:62:99:0,138,1838 0/0:54,0:55:99:0,126,1665 0/0:62,0:62:99:0,162,2137 0/0:60,1:61:99:0,113,1827 0/0:56,0:56:99:0,138,1822 0/0:46,0:46:99:0,117,1513 0/0:55,0:55:99:0,144,1873 0/0:36,0:37:96.31:0,96,1263 0/0:58,0:58:99:0,138,1843 0/0:51,0:51:99:0,129,1710 0/0:62,0:62:99:0,166,2163 0/0:48,0:48:99:0,123,1583 0/0:75,0:75:99:0,211,2733 0/0:51,0:51:99:0,132,1721 0/0:53,2:55:93.68:0,94,1765 0/0:46,0:46:99:0,114,1477 0/0:47,0:47:99:0,108,1454 0/0:62,0:62:99:0,138,1885 0/0:76,0:76:99:0,184,2398 0/0:87,0:89:99:0,217,2903 0/0:34,1:35:59.86:0,60,1151 0/0:75,0:77:99:0,196,2511 0/0:42,0:42:99:0,111,1432 0/0:52,0:52:99:0,141,1784 0/0:47,0:47:99:0,126,1651 0/0:38,0:38:87.28:0,87,1155 0/0:38,0:38:96.31:0,96,1274 0/0:58,0:58:99:0,163,2072 0/0:79,0:80:99:0,202,2610 0/0:36,0:37:96.30:0,96,1215 0/0:53,0:53:99:0,153,1999 0/0:82,0:82:99:0,220,2811 0/0:84,0:84:99:0,235,2994 0/0:68,0:68:99:0,168,2137 0/0:46,0:46:99:0,120,1531 0/1:28,24:52:99:743,0,686 0/0:51,0:51:99:0,132,1696 0/0:46,0:46:99:0,120,1573 0/0:28,0:28:69.21:0,69,893 0/0:57,0:57:99:0,141,1847 0/0:43,0:43:99:0,117,1545 0/0:38,0:38:93.29:0,93,1239 -chr1 1190913 . CT C 3484.23 . AC=11;AF=0.0917;AN=120;BaseQRankSum=10.114;DP=1539;FS=1.866;HRun=3;HaplotypeScore=78.4459;InbreedingCoeff=0.1110;MQ=58.86;MQ0=0;MQRankSum=0.337;QD=15.98;ReadPosRankSum=0.968;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|6),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|6),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|6),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|5),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|5),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|6),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|6),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|7),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|7),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|7),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|4),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|1),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/1:6,7:13:99:261,0,137 0/0:19,0:19:48.63:0,49,691 0/0:15,0:15:42.14:0,42,595 0/0:9,0:9:24.08:0,24,340 0/0:22,0:22:62.70:0,63,874 0/0:33,0:32:90.30:0,90,1290 0/0:57,0:57:99:0,160,2280 0/0:30,0:30:78.26:0,78,1124 0/0:86,0:86:99:0,250,3539 0/0:85,0:85:99:0,247,3507 0/0:40,0:40:99:0,111,1578 0/0:33,0:33:96.32:0,96,1366 0/1:29,18:47:99:604,0,938 0/0:18,0:18:54.18:0,54,768 0/0:15,0:15:45.15:0,45,648 0/1:10,3:13:99:100,0,350 0/0:16,0:16:45.15:0,45,648 0/1:11,5:16:99:144,0,334 0/0:16,0:16:45.15:0,45,648 0/1:12,1:13:1.09:1,0,439 0/0:18,0:18:51.17:0,51,735 0/0:17,0:17:51.17:0,51,724 0/0:22,0:22:57.19:0,57,811 0/1:9,7:16:99:250,0,298 0/0:18,0:18:51.17:0,51,725 0/0:15,0:15:45.15:0,45,648 0/0:23,0:23:63.21:0,63,886 0/0:15,0:15:42.14:0,42,605 0/0:25,0:25:75.25:0,75,1072 0/0:19,0:19:54.17:0,54,760 0/0:22,0:22:63.21:0,63,908 0/0:19,0:19:51.17:0,51,735 0/0:18,0:18:51.17:0,51,735 0/0:18,0:18:52.41:0,52,724 0/0:16,0:16:45.15:0,45,639 0/0:13,0:13:36.12:0,36,519 0/0:24,0:24:60.19:0,60,845 0/0:26,0:26:78.26:0,78,1124 0/0:17,0:17:48.16:0,48,672 0/0:39,0:39:99:0,111,1600 0/0:27,0:27:78.26:0,78,1112 0/1:14,6:20:99:241,0,400 0/1:12,9:21:99:238,0,458 0/0:16,0:16:45.15:0,45,638 0/1:10,9:19:99:316,0,283 0/0:29,0:29:81.20:0,81,1129 0/0:44,0:44:99:0,114,1623 0/0:22,0:22:63.21:0,63,898 0/0:28,0:28:81.27:0,81,1157 1/1:4,36:40:99:1331,108,0 0/0:43,0:43:99:0,120,1728 0/0:42,0:42:99:0,111,1572 0/0:28,0:28:81.27:0,81,1155 0/0:22,0:22:57.19:0,57,812 0/0:31,0:31:87.29:0,87,1242 0/0:32,0:32:90.29:0,90,1255 0/0:15,0:15:42.14:0,42,604 0/0:26,0:26:72.24:0,72,1023 0/0:16,0:16:48.16:0,48,691 0/0:22,0:22:63.21:0,63,907 -chr1 1191290 . C T 273.07 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.037;DP=1868;Dels=0.00;FS=4.676;HRun=1;HaplotypeScore=1.1539;InbreedingCoeff=-0.0090;MQ=58.69;MQ0=0;MQRankSum=0.087;QD=11.38;ReadPosRankSum=0.846;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|6),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|6),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|6),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|5),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|5),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|6),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|6),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|7),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|7),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|7),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|4),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|1),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:11,0:11:30.10:0,30,399 0/0:15,0:15:45.13:0,45,565 0/0:4,0:4:12.04:0,12,152 0/0:12,0:12:36.11:0,36,465 0/0:11,0:11:30.10:0,30,405 0/0:9,0:9:24.08:0,24,329 0/0:22,0:22:66.21:0,66,883 0/0:14,0:14:42.14:0,42,567 0/0:44,0:44:99:0,132,1786 0/0:35,0:35:99:0,99,1345 0/0:12,0:12:36.12:0,36,489 0/0:12,0:12:33.11:0,33,441 0/0:17,0:17:51.17:0,51,695 0/0:53,0:53:99:0,150,1966 0/0:54,0:54:99:0,144,1904 0/0:36,0:36:99:0,108,1403 0/0:44,0:44:99:0,126,1671 0/0:51,0:51:99:0,150,1954 0/0:40,0:40:99:0,120,1587 0/0:37,0:37:99:0,108,1411 0/0:37,0:37:99:0,102,1373 0/0:50,0:50:99:0,138,1812 0/0:34,0:34:99:0,102,1361 0/0:35,0:35:99:0,102,1342 0/0:39,0:39:99:0,111,1477 0/0:40,0:40:99:0,111,1469 0/0:35,0:35:99:0,102,1356 0/0:33,0:33:96.31:0,96,1263 0/0:49,0:49:99:0,132,1752 0/0:43,0:43:99:0,117,1554 0/0:70,0:70:99:0,205,2715 0/0:31,0:31:84.27:0,84,1115 0/0:38,0:38:99:0,105,1375 0/0:42,0:42:99:0,123,1572 0/0:29,0:29:75.25:0,75,1008 0/0:33,0:33:96.31:0,96,1259 0/0:49,0:49:99:0,144,1898 0/0:53,0:53:99:0,153,2040 0/0:30,0:30:75.23:0,75,964 0/0:36,0:36:99:0,99,1300 0/0:35,0:35:99:0,99,1283 0/0:25,0:25:66.20:0,66,825 0/0:27,0:27:72.22:0,72,931 0/0:23,0:23:54.17:0,54,714 0/1:13,11:24:99:321,0,430 0/0:19,0:19:54.17:0,54,708 0/0:40,0:40:99:0,111,1452 0/0:15,0:15:42.13:0,42,541 0/0:20,0:20:57.18:0,57,718 0/0:35,0:35:90.29:0,90,1169 0/0:38,0:38:99:0,99,1241 0/0:21,0:22:60.19:0,60,784 0/0:21,0:21:63.20:0,63,822 0/0:42,0:42:99:0,117,1521 0/0:28,0:28:81.25:0,81,1016 0/0:23,0:23:60.19:0,60,781 0/0:22,0:22:57.19:0,57,763 0/0:28,0:28:75.23:0,75,941 0/0:26,0:26:60.19:0,60,770 0/0:16,0:16:45.15:0,45,594 -chr1 1191589 . G A 716.56 . AC=1;AF=0.0083;AN=120;BaseQRankSum=1.146;DP=2848;Dels=0.00;FS=11.254;HRun=0;HaplotypeScore=1.5890;InbreedingCoeff=-0.0084;MQ=59.49;MQ0=0;MQRankSum=0.568;QD=9.55;ReadPosRankSum=0.273;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),EXON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|1),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|4),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|4),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|5),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|5),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|3),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|3),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000467339|1/2||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:40,0:40:99:0,114,1460 0/0:25,0:25:72.23:0,72,954 0/0:15,0:15:45.14:0,45,592 0/0:27,0:27:81.24:0,81,1041 0/0:37,0:37:99:0,111,1514 0/0:22,0:22:66.22:0,66,902 0/0:45,0:45:99:0,132,1780 0/0:31,0:31:90.29:0,90,1214 0/0:70,0:70:99:0,211,2863 0/0:59,0:59:99:0,175,2345 0/0:28,0:28:84.28:0,84,1146 0/0:32,0:32:96.31:0,96,1263 0/0:36,0:36:99:0,108,1450 0/0:55,0:56:99:0,159,2107 0/0:82,0:82:99:0,244,3259 0/0:53,0:53:99:0,160,2173 0/0:55,0:55:99:0,163,2178 0/0:71,0:71:99:0,208,2818 0/1:50,25:75:99:764,0,1748 0/0:73,0:73:99:0,214,2912 0/0:66,0:66:99:0,196,2640 0/0:84,0:84:99:0,250,3358 0/0:68,0:69:99:0,202,2701 0/0:63,0:64:99:0,187,2503 0/0:73,0:73:99:0,217,2845 0/0:56,0:56:99:0,169,2282 0/0:79,0:80:99:0,232,3090 0/0:48,0:48:99:0,144,1926 0/0:78,0:78:99:0,235,3208 0/0:68,0:68:99:0,196,2600 0/0:86,0:86:99:0,256,3433 0/0:70,0:70:99:0,205,2717 0/0:71,0:71:99:0,205,2744 0/0:66,0:66:99:0,199,2664 0/0:62,0:64:99:0,181,2415 0/0:71,0:72:99:0,211,2857 0/0:83,0:84:99:0,250,3340 0/0:92,0:92:99:0,274,3705 0/0:29,0:29:81.27:0,81,1114 0/0:62,0:62:99:0,184,2464 0/0:33,0:33:93.29:0,93,1195 0/0:26,0:26:75.24:0,75,996 0/0:27,0:27:81.27:0,81,1092 0/0:22,0:22:66.22:0,66,886 0/0:28,0:29:84.27:0,84,1132 0/0:35,0:35:99:0,105,1385 0/0:50,0:50:99:0,147,1959 0/0:13,0:13:36.11:0,36,468 0/0:26,0:26:78.25:0,78,1041 0/0:27,0:27:81.26:0,81,1080 0/0:23,0:23:69.22:0,69,911 0/0:11,0:11:33.10:0,33,417 0/0:29,0:29:84.27:0,84,1125 0/0:21,0:21:63.18:0,63,820 0/0:35,0:35:99:0,105,1420 0/0:26,0:26:75.21:0,75,962 0/0:26,0:26:75.24:0,75,998 0/0:27,0:27:78.23:0,78,1039 0/0:33,0:33:99:0,99,1301 0/0:15,0:15:45.15:0,45,607 -chr1 1191651 . A G 329.19 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.637;DP=1304;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5306;InbreedingCoeff=-0.0104;MQ=59.58;MQ0=0;MQRankSum=0.314;QD=16.46;ReadPosRankSum=1.231;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),EXON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|1),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|4),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|4),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|5),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|5),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|3),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|3),UPSTREAM(MODIFIER|||||RP5-902P8.12|lincRNA|NON_CODING|ENST00000565563|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000260179|RP5-902P8.12|ENST00000565563|||||lincRNA|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000467339|1/2||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:13,0:13:39.12:0,39,501 0/0:15,0:15:45.12:0,45,566 0/0:13,0:13:39.13:0,39,512 0/0:15,0:15:45.15:0,45,589 0/0:18,0:18:54.18:0,54,736 0/0:16,0:16:48.15:0,48,639 0/0:24,0:24:72.24:0,72,973 0/0:17,0:17:48.16:0,48,655 0/0:32,0:32:96.32:0,96,1305 0/0:48,0:48:99:0,144,1959 0/0:12,0:12:36.12:0,36,492 0/0:10,0:10:30.10:0,30,404 0/0:29,0:29:87.29:0,87,1185 0/0:29,0:29:84.27:0,84,1093 0/0:45,0:45:99:0,132,1731 0/0:13,0:13:36.11:0,36,474 0/0:30,0:30:84.27:0,84,1085 0/0:30,0:30:84.27:0,84,1094 0/0:38,0:38:99:0,111,1427 0/0:29,0:29:84.25:0,84,1079 0/0:32,0:32:90.29:0,90,1148 0/0:33,0:33:96.31:0,96,1242 0/0:26,0:26:75.24:0,75,968 0/0:24,0:24:72.23:0,72,940 0/0:31,0:32:90.29:0,90,1170 0/0:25,0:25:69.21:0,69,907 0/0:36,0:36:99:0,105,1383 0/0:23,0:23:69.21:0,69,887 0/0:38,0:38:99:0,111,1429 0/0:42,0:42:99:0,123,1576 0/0:34,0:34:96.31:0,96,1259 0/0:27,0:27:81.26:0,81,1048 0/0:37,0:37:99:0,111,1451 0/0:31,0:31:87.28:0,87,1131 0/0:26,0:26:78.25:0,78,1017 0/0:24,0:24:69.21:0,69,897 0/0:39,0:39:99:0,108,1399 0/0:51,0:51:99:0,147,1917 0/0:12,0:12:36.11:0,36,455 0/0:24,0:24:72.23:0,72,940 0/0:11,0:11:30.10:0,30,401 0/0:11,0:11:30.10:0,30,403 0/0:13,0:13:39.13:0,39,507 0/0:9,0:9:27.08:0,27,335 0/0:9,0:9:24.08:0,24,322 0/0:18,0:18:54.18:0,54,710 0/1:9,11:20:99:377,0,301 0/0:7,0:7:21.07:0,21,262 0/0:8,0:8:24.08:0,24,314 0/0:9,0:9:27.09:0,27,359 0/0:11,0:11:30.10:0,30,391 0/0:2,0:2:6.02:0,6,74 0/0:13,0:13:36.12:0,36,474 0/0:10,0:10:27.08:0,27,332 0/0:12,0:12:36.09:0,36,459 0/0:9,0:9:27.09:0,27,353 0/0:11,0:11:30.10:0,30,393 0/0:11,0:11:30.09:0,30,378 0/0:9,0:9:27.09:0,27,355 0/0:9,0:9:24.08:0,24,319 -chr1 1192105 . C A 38.15 . AC=5;AF=0.081;AN=62;BaseQRankSum=0.672;DP=78;Dels=0.00;FS=4.123;HRun=11;HaplotypeScore=0.3295;InbreedingCoeff=-0.0659;MQ=39.13;MQ0=0;MQRankSum=-1.521;QD=4.77;ReadPosRankSum=-0.389;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|4),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|4),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|5),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|5),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|3),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|3),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,33 ./. 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:3:0,3,29 0/0:6,0:6:18.02:0,18,189 0/0:4,0:4:12.03:0,12,140 0/0:6,0:6:18.05:0,18,197 0/0:1,0:1:3.01:0,3,33 0/0:8,0:8:21.03:0,21,238 0/0:13,0:13:39.11:0,39,435 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,67 0/0:4,0:4:9.02:0,9,100 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:2.98:0,3,22 ./. ./. 0/0:2,0:2:6.02:0,6,67 ./. 0/1:1,1:2:27.42:27,0,36 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,117 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,42 ./. 0/0:1,0:1:3.01:0,3,40 0/1:1,1:2:27.42:27,0,27 0/0:1,0:1:3.01:0,3,33 0/1:2,1:3:27.42:27,0,27 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. 1/1:0,1:1:3.01:33,3,0 -chr1 1192268 . G A 34.31 . AC=9;AF=0.0763;AN=118;BaseQRankSum=-2.951;DP=712;Dels=0.00;FS=86.476;HRun=23;HaplotypeScore=4.3915;InbreedingCoeff=-0.1175;MQ=40.22;MQ0=0;MQRankSum=-4.056;QD=0.35;ReadPosRankSum=-6.599;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|4),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|4),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|5),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|5),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|3),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|3),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:14,0:14:42.12:0,42,487 0/0:6,0:6:18.05:0,18,206 0/0:6,0:6:18.05:0,18,215 0/0:11,1:12:30.08:0,30,332 0/0:23,0:23:69.21:0,69,842 0/0:14,1:15:42.13:0,42,510 0/0:37,1:38:77.90:0,78,1270 0/0:20,0:20:60.18:0,60,712 0/0:44,1:45:99:0,102,1591 0/0:50,3:53:59.17:0,59,1716 0/0:18,1:19:20.73:0,21,595 0/0:20,0:20:60.18:0,60,715 0/0:41,0:41:99:0,117,1425 0/0:16,0:16:48.14:0,48,548 0/0:15,1:16:9.56:0,10,474 0/0:12,0:12:36.10:0,36,406 0/0:12,0:12:36.10:0,36,421 0/1:8,1:9:6.36:6,0,239 0/0:11,0:11:33.09:0,33,368 0/0:18,0:18:54.15:0,54,623 0/1:6,2:8:42.81:43,0,172 0/0:13,0:13:39.10:0,39,433 0/1:7,1:8:9.37:9,0,214 0/0:10,0:11:30.09:0,30,358 0/0:14,1:15:11.70:0,12,454 0/0:16,1:17:17.71:0,18,502 0/1:7,1:8:12.37:12,0,184 0/0:9,0:9:27.08:0,27,306 0/1:19,2:21:3.69:4,0,587 0/0:13,0:14:39.09:0,39,432 0/0:23,1:24:38.77:0,39,754 0/0:12,0:12:36.10:0,36,399 0/1:16,2:19:12.71:13,0,497 0/1:16,2:19:15.75:16,0,441 0/0:7,0:7:21.06:0,21,234 0/0:11,1:12:2.67:0,3,352 0/0:7,1:8:21.06:0,21,240 0/0:18,1:20:52.01:0,52,564 ./. 0/0:2,0:2:6.02:0,6,67 0/0:4,0:4:12.03:0,12,136 0/0:2,0:2:6.02:0,6,67 0/0:3,0:3:9.03:0,9,105 0/0:2,0:2:6.01:0,6,63 0/0:5,0:5:12.02:0,12,124 0/1:2,1:3:24.41:24,0,58 0/0:5,0:5:12.04:0,12,141 0/0:3,1:4:5.23:0,5,40 0/0:4,0:4:12.03:0,12,134 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:3.01:0,3,33 0/1:1,1:2:23.61:27,0,24 0/0:2,0:2:6.02:0,6,67 0/0:2,1:3:6.02:0,6,72 0/0:1,1:2:3.01:0,3,33 0/0:2,0:2:6.02:0,6,67 0/0:3,0:3:9.02:0,9,100 0/0:2,0:2:3.01:0,3,33 0/0:2,1:3:5.89:0,6,54 0/0:1,1:2:3.01:0,3,35 -chr1 1192321 . C A 197.5 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.375;DP=1985;Dels=0.00;FS=2.097;HRun=0;HaplotypeScore=2.7167;InbreedingCoeff=-0.0116;MQ=52.62;MQ0=0;MQRankSum=0.704;QD=10.97;ReadPosRankSum=-0.366;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|),DOWNSTREAM(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|),DOWNSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|5),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|4),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|4),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|5),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|5),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|6),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|3),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|3),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/1:9,9:18:99:245,0,182 0/0:21,0:21:63.19:0,63,785 0/0:18,1:19:39.10:0,39,471 0/0:22,0:22:48.09:0,48,537 0/0:38,0:38:99:0,102,1368 0/0:41,0:41:99:0,108,1444 0/0:75,0:75:99:0,199,2544 0/0:54,0:54:99:0,138,1815 0/0:109,0:109:99:0,277,3592 0/0:103,0:103:99:0,253,3202 0/0:46,0:47:99:0,120,1552 0/0:40,0:40:96.27:0,96,1212 0/0:68,1:69:99:0,150,1930 0/0:38,0:39:75.24:0,75,986 0/0:51,0:53:99:0,117,1523 0/0:29,0:29:48.12:0,48,592 0/0:37,0:37:75.24:0,75,992 0/0:47,0:47:81.26:0,81,1050 0/0:52,0:52:93.28:0,93,1229 0/0:47,0:48:96.29:0,96,1210 0/0:34,0:34:66.20:0,66,839 0/0:36,0:36:60.17:0,60,793 0/0:35,0:35:66.20:0,66,826 0/0:45,0:45:99:0,105,1297 0/0:35,0:35:66.22:0,66,887 0/0:38,0:38:72.21:0,72,901 0/0:47,0:47:99:0,102,1312 0/0:28,0:28:57.14:0,57,717 0/0:46,0:46:69.19:0,69,871 0/0:36,0:36:78.23:0,78,1006 0/0:61,0:61:99:0,126,1623 0/0:40,0:40:87.27:0,87,1127 0/0:45,0:45:69.20:0,69,883 0/0:48,0:48:87.27:0,87,1112 0/0:32,1:33:63.17:0,63,784 0/0:36,0:37:66.20:0,66,860 0/0:39,0:40:96.30:0,96,1253 0/0:56,0:56:99:0,117,1505 0/0:12,0:12:24.08:0,24,318 0/0:14,0:15:30.09:0,30,396 0/0:16,0:16:33.10:0,33,429 0/0:10,0:10:27.09:0,27,348 0/0:11,0:11:30.07:0,30,368 0/0:11,0:11:24.08:0,24,330 0/0:10,0:10:18.06:0,18,234 0/0:15,0:15:33.11:0,33,449 0/0:28,0:28:57.19:0,57,773 0/0:10,0:10:27.09:0,27,348 0/0:12,0:12:21.07:0,21,276 0/0:15,0:15:42.12:0,42,539 0/0:15,0:15:36.11:0,36,466 0/0:10,0:10:24.05:0,24,288 0/0:17,0:17:39.06:0,39,450 0/0:15,0:15:36.11:0,36,460 0/0:18,0:18:33.11:0,33,435 0/0:9,0:9:24.08:0,24,331 0/0:17,0:17:33.11:0,33,438 0/0:8,0:8:9.02:0,9,110 0/0:7,0:7:18.06:0,18,236 0/0:2,0:2:6.02:0,6,76 -chr1 1192515 . A G 9144.94 . AC=10;AF=0.0833;AN=120;BaseQRankSum=-2.796;DP=4520;Dels=0.00;FS=4.056;HRun=0;HaplotypeScore=2.8736;InbreedingCoeff=0.1273;MQ=57.88;MQ0=0;MQRankSum=7.716;QD=16.19;ReadPosRankSum=-1.141;EFF=DOWNSTREAM(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|),DOWNSTREAM(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|4),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|4),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|4),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|3),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|4),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|4),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|5),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|2),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|2),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/1:13,6:19:99:132,0,406 0/0:24,0:24:63.20:0,63,809 0/0:19,0:19:57.18:0,57,722 0/0:18,0:18:54.14:0,54,677 0/0:41,0:41:99:0,117,1571 0/0:43,0:43:99:0,126,1691 0/0:80,0:80:99:0,232,3047 0/0:43,0:43:99:0,123,1625 0/0:113,0:113:99:0,331,4357 0/0:104,0:104:99:0,310,4059 0/0:54,0:54:99:0,156,2025 0/0:40,0:40:99:0,117,1534 0/1:23,34:57:99:1152,0,767 0/0:100,0:100:99:0,253,3303 0/0:117,0:117:99:0,283,3714 0/1:45,37:82:99:917,0,1342 0/0:85,0:85:99:0,214,2807 0/1:54,53:107:99:1419,0,1536 0/0:92,0:93:99:0,244,3128 0/0:108,0:108:99:0,280,3674 0/0:113,0:113:99:0,274,3587 0/0:118,0:118:99:0,295,3882 0/0:95,0:95:99:0,238,3140 0/1:42,41:83:99:1117,0,1253 0/0:101,0:101:99:0,274,3597 0/0:77,0:77:99:0,208,2670 0/0:86,0:87:99:0,223,2880 0/0:73,0:73:99:0,193,2487 0/0:110,0:110:99:0,283,3708 0/0:120,0:120:99:0,304,4027 0/0:131,0:131:99:0,343,4504 0/0:73,0:73:99:0,181,2375 0/0:127,0:127:99:0,328,4322 0/0:122,0:122:99:0,322,4198 0/0:80,0:80:99:0,211,2775 0/0:93,0:93:99:0,238,3168 0/0:125,0:125:99:0,319,4177 0/0:153,0:153:99:0,382,5096 0/0:53,0:53:99:0,147,1913 0/0:85,0:85:99:0,232,2939 0/0:84,0:84:99:0,232,3048 0/1:28,21:49:99:634,0,823 0/1:24,25:49:99:768,0,686 0/0:43,0:43:99:0,111,1438 0/1:25,34:59:99:972,0,639 0/0:61,0:61:99:0,160,2058 0/0:103,0:103:99:0,268,3495 0/0:36,0:36:99:0,102,1321 0/0:74,0:74:99:0,171,2199 1/1:0,60:60:99:2034,159,0 0/0:69,0:69:99:0,175,2284 0/0:48,0:48:99:0,132,1696 0/0:73,2:75:99:0,151,2496 0/0:56,0:56:99:0,147,1883 0/0:61,0:61:99:0,147,1961 0/0:45,0:45:99:0,126,1638 0/0:40,0:40:99:0,111,1422 0/0:59,0:59:99:0,135,1811 0/0:45,0:45:99:0,117,1501 0/0:37,0:37:96.31:0,96,1264 -chr1 1192767 . C G 279.19 . AC=5;AF=0.0424;AN=118;BaseQRankSum=-0.503;DP=1028;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=10.9757;InbreedingCoeff=-0.0595;MQ=43.48;MQ0=0;MQRankSum=0.689;QD=3.49;ReadPosRankSum=-0.850;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,107 0/0:6,0:6:18.06:0,18,238 0/0:4,0:4:12.04:0,12,158 0/0:2,0:2:6.02:0,6,79 0/0:6,0:6:15.05:0,15,204 0/0:9,0:9:24.08:0,24,315 0/0:14,0:14:39.13:0,39,526 0/0:10,0:10:27.09:0,27,365 0/0:11,0:11:24.08:0,24,329 0/0:16,0:16:39.13:0,39,526 0/0:9,0:9:18.06:0,18,236 0/0:8,0:8:24.08:0,24,318 0/1:5,5:10:99:106,0,177 0/0:21,0:21:21.06:0,21,246 0/0:12,0:12:18.04:0,18,204 0/1:10,4:14:24.41:68,0,24 0/0:17,0:17:21.05:0,21,246 0/1:12,5:17:49.62:50,0,124 0/0:19,0:19:15.04:0,15,176 0/0:16,0:16:24.06:0,24,282 0/0:26,0:26:33.08:0,33,380 0/0:20,0:20:21.05:0,21,239 0/0:15,0:15:15.04:0,15,181 0/0:12,0:12:12.03:0,12,146 0/0:20,0:20:18.05:0,18,209 0/0:21,0:21:27.06:0,27,300 0/0:14,0:14:18.04:0,18,210 0/0:13,0:13:12.01:0,12,114 0/0:18,0:18:30.06:0,30,338 0/0:20,0:20:9.03:0,9,118 0/0:28,0:28:27.09:0,27,344 0/0:21,0:21:18.05:0,18,207 0/0:16,0:16:21.06:0,21,262 0/0:18,0:18:24.04:0,24,270 0/0:14,0:14:18.04:0,18,207 0/0:16,0:16:18.05:0,18,213 0/0:20,0:20:9.03:0,9,111 0/0:32,0:32:42.08:0,42,470 0/0:11,0:11:6.01:0,6,66 0/0:18,0:18:21.07:0,21,266 0/0:29,0:29:51.11:0,51,564 0/1:8,5:13:57.11:57,0,83 0/1:22,3:25:53.64:102,0,54 0/0:18,0:18:12.03:0,12,141 0/0:19,0:19:45.09:0,45,511 0/0:26,0:26:24.05:0,24,280 0/0:36,0:36:30.06:0,30,336 0/0:16,0:16:15.03:0,15,167 0/0:15,0:15:12.04:0,12,157 0/0:30,0:30:42.12:0,42,525 0/0:36,0:36:48.11:0,48,540 0/0:24,0:24:24.06:0,24,280 0/0:25,0:25:27.08:0,27,342 0/0:27,0:27:30.08:0,30,353 0/0:31,0:31:27.05:0,27,302 0/0:15,0:15:27.05:0,27,304 0/0:8,0:8:12.03:0,12,136 0/0:20,0:20:30.09:0,30,368 ./. 0/0:6,0:6:3.01:0,3,40 -chr1 1192769 . CG C 46.23 . AC=14;AF=0.1167;AN=120;BaseQRankSum=7.490;DP=929;FS=8.084;HRun=1;HaplotypeScore=182.4593;InbreedingCoeff=-0.1268;MQ=41.55;MQ0=0;MQRankSum=-2.659;QD=0.18;ReadPosRankSum=0.739;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,76 0/0:3,0:3:9.03:0,9,144 0/0:3,0:3:9.03:0,9,132 0/0:2,0:2:6.02:0,6,96 0/0:5,0:5:12.04:0,12,192 0/0:6,0:6:15.05:0,15,222 0/0:9,0:9:24.08:0,24,374 0/0:6,0:6:15.05:0,15,225 0/0:8,0:8:15.05:0,15,240 0/0:13,0:13:30.10:0,30,461 0/0:7,1:8:15.05:0,15,226 0/0:4,0:4:12.04:0,12,180 0/0:8,0:8:20.66:0,21,297 0/1:20,0:20:15.04:15,0,207 0/1:11,0:11:10.64:11,0,156 0/0:15,0:15:7.95:0,8,119 0/0:14,0:14:2.88:0,3,122 0/0:15,0:15:12.58:0,13,200 0/1:15,1:16:14.71:25,0,15 0/1:15,1:16:1.14:1,0,285 0/0:26,0:26:5.03:0,5,287 0/0:16,1:17:1.19:0,1,91 0/0:14,0:14:11.55:0,12,154 0/0:11,1:12:12.04:0,12,177 0/0:18,0:18:11.06:0,11,132 0/1:19,0:19:13.85:14,0,93 0/0:10,0:10:8.06:0,8,102 0/0:11,1:12:9.13:0,9,95 0/0:16,2:18:12.04:0,12,341 0/0:19,1:20:5.28:0,5,80 0/1:26,1:27:24.02:24,0,224 0/0:18,0:18:10.74:0,11,148 0/1:15,0:15:1.72:2,0,193 0/0:16,0:16:20.53:0,21,171 0/0:13,1:14:5.79:0,6,183 0/0:15,1:16:14.91:0,15,222 0/0:19,0:19:6.89:0,7,83 0/0:25,2:27:19.66:0,20,304 0/0:10,1:11:6.47:0,6,73 0/0:17,0:17:15.05:0,15,239 0/1:26,0:26:26.12:26,0,296 0/1:10,0:10:1.47:1,0,51 0/0:21,0:21:3.01:0,3,48 0/0:19,0:19:7.26:0,7,100 0/0:17,0:17:32.08:0,32,451 0/0:24,1:25:21.06:0,21,231 0/0:31,1:32:4.59:0,5,129 0/1:13,1:15:10.87:11,0,44 0/0:14,1:15:9.31:0,9,130 0/0:28,0:28:44.73:0,45,556 0/0:32,1:33:25:0,25,402 0/1:18,4:22:33.44:33,0,144 0/0:25,1:26:11.14:0,11,358 0/1:26,0:26:22.11:22,0,217 0/0:28,0:28:22.44:0,22,249 0/0:14,0:14:2.45:0,2,212 0/0:8,0:8:0.80:0,1,103 0/1:18,0:18:3.35:3,0,233 0/1:8,2:10:0:0,0,0 0/0:6,0:6:3.01:0,3,48 -chr1 1192770 . GCCA G 709.55 . AC=36;AF=0.3051;AN=118;BaseQRankSum=7.682;DP=910;FS=3.236;HRun=0;HaplotypeScore=185.0135;InbreedingCoeff=-0.3195;MQ=40.92;MQ0=0;MQRankSum=-5.310;QD=1.24;ReadPosRankSum=5.795;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,29 0/0:3,0:3:8.76:0,9,82 0/1:3,0:3:0:0,0,0 0/0:2,0:2:2.97:0,3,21 0/0:5,0:5:9.02:0,9,106 0/1:6,0:6:0.08:0,0,98 0/0:9,0:9:17.40:0,17,172 0/0:6,0:6:9.01:0,9,95 0/0:8,0:8:12.02:0,12,130 0/0:11,0:11:17.99:0,18,186 0/0:7,0:7:7.81:0,8,70 0/0:3,0:3:8.99:0,9,99 0/1:8,0:8:13.44:13,0,128 0/0:18,0:19:10.29:0,10,100 0/1:10,0:10:6.60:14,0,7 0/1:15,0:15:18.32:18,0,50 0/1:13,0:13:3.90:4,0,59 0/0:15,0:15:5.82:0,6,90 1/1:14,2:16:7.06:40,7,0 0/1:15,0:15:9.76:10,0,42 0/1:24,0:25:49.27:49,0,67 0/1:17,0:17:33.34:33,0,53 0/1:12,0:14:31.23:31,0,74 0/1:12,0:12:4.56:5,0,109 0/1:17,0:17:20.29:20,0,24 0/1:18,0:19:39.20:55,0,39 0/1:11,0:11:18.64:19,0,26 0/1:13,0:13:19.17:34,0,19 0/1:17,0:18:10.52:11,0,157 0/0:20,0:20:0.35:0,0,29 0/1:25,0:25:9.12:9,0,93 0/0:18,0:18:0.12:0,0,28 0/1:14,0:14:3.54:4,0,74 0/1:15,1:16:48.70:61,0,49 0/0:13,0:14:13.09:0,13,103 0/0:15,0:15:7.11:0,7,66 0/0:17,0:18:3.39:0,3,28 0/1:27,0:27:28.07:28,0,111 0/1:10,0:11:16.11:16,0,43 0/0:17,0:17:8.88:0,9,80 0/1:25,0:25:88.11:137,0,88 0/1:10,0:11:7.16:37,0,7 0/0:21,0:21:3.01:0,3,33 0/1:19,0:19:14.05:14,0,29 0/0:14,0:15:17.22:0,17,167 0/1:21,2:24:24.61:98,0,25 0/1:31,1:32:50.36:50,0,69 0/1:15,0:15:4.06:4,0,23 0/0:14,1:15:4.98:0,5,60 0/0:27,0:28:43.26:0,43,342 0/1:32,0:33:11.72:12,0,213 0/1:21,0:21:7.39:7,0,81 0/0:26,0:26:5.23:0,5,161 0/0:25,0:26:2.32:0,2,101 0/1:28,0:28:23.03:23,0,98 0/1:14,0:14:27.66:28,0,80 0/0:7,0:7:4.81:0,5,18 0/1:18,0:18:33.11:33,0,38 ./. 1/1:6,0:6:0.47:1,0,0 -chr1 1192771 . CCA C 1171.87 . AC=44;AF=0.3729;AN=118;BaseQRankSum=10.317;DP=897;FS=2.917;HRun=0;HaplotypeScore=180.9024;InbreedingCoeff=-0.3867;MQ=40.58;MQ0=0;MQRankSum=-6.072;QD=1.66;ReadPosRankSum=5.982;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,29 0/0:3,0:3:8.76:0,9,82 0/1:2,0:2:0:0,0,0 0/0:2,0:2:2.97:0,3,21 0/0:5,0:5:9.01:0,9,94 0/1:6,0:6:0.11:0,0,97 0/0:9,0:9:14.57:0,15,166 0/0:5,0:5:9.01:0,9,93 0/0:8,0:8:12.02:0,12,128 0/0:10,1:11:17.97:0,18,182 0/0:7,0:7:7.86:0,8,70 0/0:3,0:3:8.99:0,9,88 0/1:7,1:8:11.59:12,0,127 0/1:19,0:19:2.19:2,0,88 0/1:10,0:10:6.20:24,0,6 0/1:15,0:15:24.73:43,0,25 0/1:11,2:13:43.16:43,0,52 0/0:14,1:15:4.24:0,4,87 1/1:15,1:16:7.27:90,7,0 0/1:15,0:15:19.53:20,0,38 0/1:24,1:25:55.85:57,0,56 0/1:15,2:17:22.08:22,0,45 0/1:13,1:14:50.76:51,0,73 0/1:11,1:12:17.35:17,0,96 0/1:17,0:17:3.02:3,0,24 0/1:18,1:19:28.31:39,0,28 0/1:10,1:11:24.48:33,0,24 0/1:13,0:13:16.70:17,0,19 0/1:17,1:18:37.14:37,0,117 0/0:18,1:19:4.55:0,5,37 0/1:24,1:25:14.49:14,0,83 0/1:18,0:18:5.17:5,0,22 0/1:13,0:13:1.11:1,0,74 0/1:16,0:16:31.40:109,0,31 0/0:13,0:13:3.99:0,4,67 0/0:14,1:15:7.50:0,8,66 0/1:18,0:18:4.30:4,0,22 0/1:26,0:26:15.15:15,0,94 0/1:10,1:11:10.55:11,0,29 0/0:17,0:17:8.93:0,9,80 0/1:23,1:24:54:128,0,54 1/1:11,0:11:4.28:38,4,0 0/1:21,0:21:5.23:5,0,27 0/1:18,1:19:26.06:27,0,26 0/0:15,0:15:5.24:0,5,124 0/1:23,0:23:24.24:57,0,24 0/1:28,4:32:37.93:89,0,38 0/1:15,0:15:18.55:29,0,19 0/1:15,0:15:6.22:6,0,53 0/0:28,0:28:27.28:0,27,312 0/1:31,1:32:99:102,0,154 0/1:20,1:21:21.41:21,0,78 0/1:25,0:25:15.50:15,0,151 0/1:25,1:26:46.69:47,0,92 0/1:27,1:28:68.95:69,0,85 0/1:13,1:14:59.43:59,0,65 0/0:6,0:6:2.22:0,2,8 0/1:16,0:16:22.75:29,0,23 ./. 1/1:6,0:6:0.47:1,0,0 -chr1 1192772 . CA C 1504.33 . AC=45;AF=0.3879;AN=116;BaseQRankSum=10.581;DP=873;FS=9.989;HRun=1;HaplotypeScore=179.8239;InbreedingCoeff=-0.4727;MQ=39.95;MQ0=0;MQRankSum=-6.732;QD=2.06;ReadPosRankSum=6.533;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,29 0/0:3,0:3:8.76:0,9,81 ./. 0/0:1,0:1:2.98:0,3,21 0/0:4,0:4:8.96:0,9,83 0/1:6,0:6:0.14:0,0,96 0/1:8,0:8:5.23:5,0,148 0/0:4,0:4:9.02:0,9,92 0/0:7,0:7:12.03:0,12,126 0/0:9,0:9:17.99:0,18,179 0/0:6,0:6:8.05:0,8,69 0/0:3,0:3:8.99:0,9,84 0/0:7,0:7:3.38:0,3,129 0/1:19,0:19:26.21:26,0,87 0/1:8,1:9:6.11:35,0,6 0/1:12,1:14:14.77:51,0,15 0/1:12,1:13:26.26:26,0,50 0/0:15,0:15:3.80:0,4,85 1/1:15,1:16:7.25:59,7,0 0/1:12,1:13:37.21:43,0,37 0/1:22,1:23:40.36:40,0,56 0/1:16,1:17:39.57:40,0,44 0/1:14,0:14:27.90:28,0,71 0/1:12,0:12:2.16:2,0,84 0/0:15,1:16:1.56:0,2,27 0/1:19,0:19:22.26:44,0,22 0/1:7,3:10:21.99:37,0,22 0/1:11,2:13:9.94:10,0,20 0/1:17,0:17:30.08:30,0,93 0/0:18,1:19:1.38:0,1,29 0/1:22,2:24:35.23:35,0,81 0/1:16,2:18:12.62:13,0,27 0/1:13,0:13:16.56:17,0,73 0/1:13,4:17:20.74:146,0,21 0/1:12,1:13:16.99:17,0,50 0/1:15,0:15:13.56:14,0,55 0/1:18,0:18:10.02:10,0,21 0/1:26,0:26:28:28,0,82 0/1:11,0:11:4.52:5,0,29 0/0:15,0:15:8.94:0,9,79 0/1:22,1:23:43.96:136,0,44 1/1:10,1:11:7.31:49,7,0 0/1:20,1:21:9.53:10,0,25 0/1:19,0:19:21.91:22,0,26 0/1:14,0:14:12.62:13,0,97 0/1:21,1:22:23.62:40,0,24 0/1:29,3:32:14.48:76,0,14 0/1:15,0:15:18.18:49,0,18 0/1:14,1:15:30.52:31,0,52 0/0:28,0:28:11.57:0,12,285 0/1:30,2:32:99:108,0,135 0/1:22,1:23:71.22:87,0,71 0/1:23,2:25:50.95:51,0,149 0/1:25,0:25:82.77:83,0,90 0/1:27,2:29:58.58:59,0,74 0/1:11,3:14:47.44:96,0,47 0/1:6,0:6:1.98:18,0,2 0/1:14,1:15:32.59:42,0,33 0/1:10,0:10:0.01:0,0,0 ./. -chr1 1192773 . AC A 268.82 . AC=52;AF=0.4815;AN=108;BaseQRankSum=1.061;DP=867;FS=7.111;HRun=15;HaplotypeScore=182.8712;InbreedingCoeff=0.1639;MQ=39.70;MQ0=0;MQRankSum=-1.275;QD=0.46;ReadPosRankSum=4.858;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_truncation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. 0/0:4,0:4:0:0,0,0 0/0:5,0:5:0:0,0,0 0/0:7,0:7:2.37:0,2,8 ./. 0/1:7,0:7:0:0,0,0 0/1:9,0:9:0:0,0,0 0/1:6,0:6:0:0,0,0 0/0:3,0:3:0:0,0,0 0/0:7,0:7:0.47:0,0,1 1/1:17,0:17:2.03:6,2,0 0/0:9,0:9:1.25:0,1,3 0/1:14,0:14:7.88:8,0,22 1/1:13,0:13:1.99:6,2,0 0/0:14,1:15:0.34:0,0,7 1/1:16,0:16:2.27:6,2,0 1/1:12,0:13:0.85:2,1,0 0/0:23,0:23:1.05:0,1,23 1/1:17,0:17:3.57:20,4,0 1/1:13,0:14:3.74:12,4,0 0/0:12,0:12:4.79:0,5,26 1/1:15,0:16:2.04:6,2,0 0/1:18,0:18:1.50:2,0,32 1/1:10,0:10:2.99:9,3,0 1/1:13,0:13:1.93:5,2,0 0/0:17,0:17:1.17:0,1,39 0/0:18,1:19:4.85:0,5,23 0/0:23,0:23:2.24:0,2,8 0/1:19,0:19:13.72:14,0,22 0/0:13,0:14:5.04:0,5,32 1/1:17,0:17:12.52:72,13,0 0/0:13,0:13:7.96:0,8,34 0/0:15,0:15:2.86:0,3,25 1/1:18,0:18:2.66:19,3,0 0/1:23,0:25:6.32:6,0,18 0/1:11,0:11:0.33:0,0,21 0/1:16,0:16:0:0,0,0 0/1:21,1:22:24.62:25,0,25 0/1:9,1:11:1.83:16,0,2 0/0:20,1:21:2.60:0,3,10 1/1:19,0:19:2.24:7,2,0 0/0:14,0:14:2.44:0,2,47 1/1:21,1:22:5.69:16,6,0 0/1:31,0:32:13.77:14,0,41 0/0:15,0:15:0.67:0,1,2 1/1:14,0:14:2.90:16,3,0 0/0:28,0:28:17.10:0,17,64 0/1:32,0:32:17.72:18,0,46 0/1:22,0:23:2.93:3,0,20 1/1:25,0:25:3.84:24,4,0 0/1:24,0:26:7.82:8,0,11 0/1:28,1:29:1.73:35,0,2 0/1:14,0:14:2.15:25,0,2 1/1:6,0:6:2.89:16,3,0 1/1:14,0:15:4.41:18,4,0 0/1:10,0:10:0:0,0,0 ./. -chr1 1192776 . C G 174.83 . AC=3;AF=0.0273;AN=110;BaseQRankSum=-0.288;DP=833;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=8.8403;InbreedingCoeff=-0.0771;MQ=38.73;MQ0=0;MQRankSum=2.194;QD=3.64;ReadPosRankSum=-1.689;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:6.02:0,6,82 0/0:5,0:5:12.04:0,12,156 0/0:7,0:7:18.06:0,18,239 0/0:3,0:3:6.02:0,6,80 0/0:5,0:5:6.02:0,6,82 0/0:7,0:7:12.04:0,12,154 0/0:5,0:5:6.02:0,6,78 0/0:3,0:3:9.03:0,9,113 0/0:6,0:6:12.04:0,12,162 0/0:18,0:18:12.04:0,12,156 0/0:9,0:9:9.01:0,9,99 0/0:13,0:13:15.02:0,15,158 0/0:13,0:13:12.04:0,12,144 0/0:14,0:14:15.04:0,15,174 0/0:16,0:16:9.03:0,9,102 0/0:12,0:12:18.05:0,18,220 0/0:22,0:22:21.06:0,21,253 0/0:14,1:16:9.01:0,9,96 0/0:14,0:14:15.04:0,15,177 0/1:10,1:11:24.94:25,0,99 ./. 0/0:17,1:18:12.03:0,12,135 0/0:9,0:9:6.02:0,6,67 0/0:13,0:13:6.02:0,6,71 0/0:17,0:17:27.08:0,27,326 0/0:20,0:20:9.03:0,9,112 0/0:22,0:22:9.03:0,9,109 0/0:20,0:20:18.05:0,18,213 0/0:12,0:12:9.03:0,9,115 0/0:17,0:17:27.06:0,27,306 0/0:12,0:12:12.03:0,12,136 0/0:14,0:14:12.02:0,12,138 0/0:18,0:18:9.02:0,9,98 0/0:23,0:23:15.05:0,15,192 0/0:11,0:11:9.01:0,9,93 0/0:15,0:15:6.02:0,6,77 0/0:22,0:22:30.05:0,30,325 0/0:11,0:11:6.01:0,6,63 0/0:21,0:21:9.03:0,9,105 0/0:19,0:19:12.03:0,12,138 0/1:10,2:12:20.52:21,0,154 0/0:22,0:22:9.03:0,9,107 0/0:30,0:31:18.05:0,18,211 0/0:14,0:14:6.02:0,6,67 0/0:13,0:13:6:0,6,60 0/1:17,8:25:51.48:206,0,51 0/0:31,0:31:39.10:0,39,446 0/0:23,0:23:21.06:0,21,246 0/0:24,0:24:27.08:0,27,329 0/0:23,0:23:21.06:0,21,243 0/0:26,0:26:18.04:0,18,198 0/0:13,0:13:24.07:0,24,292 0/0:7,0:7:6.02:0,6,72 0/0:15,0:15:15.05:0,15,180 ./. ./. -chr1 1192786 . C A 471.53 . AC=12;AF=0.1154;AN=104;BaseQRankSum=-6.703;DP=722;Dels=0.00;FS=2.215;HRun=0;HaplotypeScore=1.5194;InbreedingCoeff=0.1443;MQ=35.94;MQ0=0;MQRankSum=0.095;QD=3.27;ReadPosRankSum=2.115;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. 0/0:2,0:2:3.01:0,3,41 ./. 0/0:2,0:2:3.01:0,3,41 ./. 0/0:4,0:4:3.01:0,3,40 ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:5,0:5:12.04:0,12,164 0/0:16,0:16:6.02:0,6,77 0/0:8,0:8:3.01:0,3,33 0/0:12,0:12:15.04:0,15,167 0/0:11,0:11:12.03:0,12,142 0/0:12,0:12:6.02:0,6,70 0/0:15,0:15:12.03:0,12,132 0/0:10,0:10:9.03:0,9,102 0/0:18,0:18:15.05:0,15,179 0/0:15,0:15:6.02:0,6,67 0/0:11,0:11:6.02:0,6,67 1/1:4,6:10:5.99:51,6,0 0/0:15,0:15:3.01:0,3,33 0/0:17,0:17:18.05:0,18,202 1/1:5,8:13:12.01:118,12,0 0/0:11,0:11:3.01:0,3,33 0/0:13,0:13:15.05:0,15,194 0/0:20,0:20:9.03:0,9,107 0/0:21,0:21:3.01:0,3,39 0/0:16,0:16:9.03:0,9,109 0/0:12,0:12:9.03:0,9,116 0/1:10,6:16:39.73:40,0,175 1/1:6,5:11:9.02:91,9,0 0/0:11,1:12:12.03:0,12,133 0/1:12,4:16:24.41:54,0,24 0/0:23,0:23:15.05:0,15,185 0/0:11,0:11:9.03:0,9,101 0/0:14,0:14:6.02:0,6,71 0/0:19,0:19:30.09:0,30,343 0/0:8,0:8:15.04:0,15,174 0/0:20,0:20:6.02:0,6,69 0/0:15,0:15:12.03:0,12,141 0/0:8,0:8:15.04:0,15,172 0/0:19,0:19:15.04:0,15,167 0/0:32,0:32:30.08:0,30,341 0/0:16,0:16:12.04:0,12,144 0/0:12,0:12:6.02:0,6,68 0/0:19,0:19:9:0,9,86 0/1:20,7:28:56.60:57,0,276 0/0:19,0:19:21.06:0,21,241 0/1:9,7:16:22.63:23,0,31 0/0:20,0:20:15.04:0,15,172 0/1:10,12:24:38.11:110,0,38 0/1:7,3:10:79.41:79,0,89 0/0:6,0:6:3:0,3,28 0/0:13,0:13:15.04:0,15,171 0/0:10,0:10:3.01:0,3,33 ./. -chr1 1192786 . C CA 288.17 . AC=16;AF=0.1455;AN=110;BaseQRankSum=0.649;DP=716;FS=2.212;HRun=0;HaplotypeScore=181.3815;InbreedingCoeff=0.2496;MQ=36.10;MQ0=0;MQRankSum=-1.597;QD=1.84;ReadPosRankSum=-0.511;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,34 ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 ./. 0/0:2,0:2:3.01:0,3,35 ./. 0/0:4,0:4:3.01:0,3,34 0/1:3,0:3:0:0,0,0 0/1:3,0:3:0:0,0,0 0/0:1,0:1:3:0,3,26 0/0:5,0:5:12.02:0,12,135 0/0:16,0:16:5.95:0,6,58 0/0:7,0:7:2.84:0,3,14 0/0:12,0:12:12.91:0,13,133 0/0:12,0:12:8.87:0,9,83 0/0:12,0:12:5.77:0,6,74 0/0:15,0:15:11.73:0,12,96 0/0:10,0:10:9.01:0,9,90 0/0:18,0:18:14.59:0,15,109 0/0:15,0:15:5.40:0,5,32 0/0:11,0:11:6.33:0,6,36 1/1:9,2:11:1.51:48,2,0 0/0:15,0:15:1.64:0,2,13 0/0:17,0:17:17.30:0,17,138 1/1:12,1:13:4.50:71,5,0 0/0:11,0:11:3.37:0,3,16 0/0:13,0:13:14.85:0,15,153 0/0:20,0:20:9.62:0,10,95 0/0:21,0:21:2.51:0,3,28 0/0:16,0:16:11.85:0,12,100 0/0:12,0:12:9.03:0,9,103 0/1:16,0:16:18.52:19,0,97 1/1:10,2:12:7.62:27,8,0 0/0:12,0:12:11.35:0,11,99 0/1:15,1:16:26.85:36,0,27 0/0:22,0:22:15.25:0,15,139 0/0:11,0:11:8.54:0,9,85 0/0:14,0:14:6.01:0,6,64 0/0:19,0:19:30.22:0,30,247 0/0:7,0:7:11.89:0,12,110 0/0:19,0:19:5.80:0,6,65 0/0:15,0:15:11.42:0,11,72 0/0:8,0:8:15.02:0,15,168 0/0:19,0:19:12.05:0,12,78 0/0:32,0:32:29.33:0,29,236 0/0:16,0:16:11.55:0,12,135 0/0:11,0:11:5.76:0,6,52 0/0:19,0:19:1.64:0,2,73 0/1:23,2:27:57.66:58,0,136 0/0:19,0:19:17.44:0,17,127 0/1:15,1:16:9.06:9,0,17 0/0:20,0:20:17.57:0,18,133 1/1:14,6:23:13.37:117,13,0 0/1:10,0:10:4.55:60,0,5 0/0:6,0:6:2.50:0,2,9 0/0:12,0:12:9.88:0,10,77 0/0:10,0:10:3:0,3,26 0/1:7,0:7:0:0,0,0 -chr1 1192787 . C G 453.3 . AC=12;AF=0.120;AN=100;BaseQRankSum=2.173;DP=716;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.4128;InbreedingCoeff=0.1641;MQ=36.10;MQ0=0;MQRankSum=-0.721;QD=4.08;ReadPosRankSum=0.454;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:2,0:2:3.01:0,3,41 ./. 0/0:4,0:4:3.01:0,3,40 ./. ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,5:5:12.04:163,12,0 0/0:16,0:16:6.02:0,6,76 ./. 0/1:9,3:12:51.83:52,0,84 0/0:12,0:12:9.03:0,9,107 1/1:6,6:12:6.02:69,6,0 0/0:15,0:15:12.03:0,12,134 0/0:10,0:10:9.02:0,9,99 0/0:18,0:18:15.04:0,15,174 0/0:15,0:15:6.02:0,6,67 0/0:11,0:11:6.02:0,6,67 0/0:11,0:11:12.04:0,12,144 0/0:15,0:15:3.01:0,3,33 0/0:17,0:17:18.05:0,18,198 0/0:13,0:13:18.05:0,18,205 0/0:11,0:11:3.01:0,3,33 0/0:13,0:13:15.05:0,15,190 0/0:19,0:20:9.02:0,9,93 0/0:21,0:21:3.01:0,3,39 0/1:14,2:16:13.67:14,0,62 0/0:12,0:12:9.03:0,9,114 0/1:9,7:16:99:100,0,122 0/0:12,0:12:12.03:0,12,132 0/0:12,0:12:15.04:0,15,176 0/0:16,0:16:9.02:0,9,100 0/0:22,0:22:15.04:0,15,179 0/0:11,0:11:9.03:0,9,105 0/0:14,0:14:6.02:0,6,70 0/0:19,0:19:30.08:0,30,337 0/1:3,4:7:21.40:21,0,97 0/0:17,2:19:6.02:0,6,65 0/0:15,0:15:12.04:0,12,146 0/1:6,2:8:18.39:18,0,124 0/0:19,0:19:15.03:0,15,158 0/0:31,0:32:30.05:0,30,320 0/1:12,4:16:54.83:55,0,64 0/0:11,0:11:6.02:0,6,68 1/1:7,12:19:9.03:110,9,0 0/0:26,0:27:42.11:0,42,490 0/0:19,0:19:21.06:0,21,234 0/0:15,1:16:9.03:0,9,111 0/0:20,0:20:15.04:0,15,168 0/0:23,0:23:15.04:0,15,178 0/0:10,0:10:12.04:0,12,145 ./. 0/0:12,0:12:15.04:0,15,169 0/0:10,0:10:3.01:0,3,33 ./. -chr1 1192787 . C CG 374.1 . AC=17;AF=0.1545;AN=110;BaseQRankSum=0.800;DP=712;FS=0.000;HRun=0;HaplotypeScore=181.2272;InbreedingCoeff=0.2381;MQ=36.30;MQ0=0;MQRankSum=-3.098;QD=2.65;ReadPosRankSum=-1.333;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant&feature_elongation|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. 0/0:1,0:1:3.01:0,3,37 ./. 0/0:2,0:2:3.01:0,3,35 ./. 0/0:4,0:4:3.01:0,3,33 0/1:3,0:3:0:0,0,0 0/1:3,0:3:0:0,0,0 0/0:1,0:1:0:0,0,0 1/1:5,0:5:12.04:139,12,0 0/0:16,0:16:5.94:0,6,55 0/0:7,0:7:1.82:0,2,5 0/1:9,0:12:12.98:69,0,13 0/0:12,0:12:8.93:0,9,76 1/1:10,0:12:6.02:67,6,0 0/0:15,0:15:11.85:0,12,95 0/0:10,0:10:9.01:0,9,87 0/0:18,0:18:14.43:0,14,105 0/0:15,0:15:5.95:0,6,42 0/0:12,0:12:6.33:0,6,36 0/0:11,0:11:12.01:0,12,125 0/0:15,0:15:2.90:0,3,16 0/0:17,0:17:17.33:0,17,138 0/0:13,0:13:17.95:0,18,164 0/0:10,0:10:3.37:0,3,17 0/0:14,0:14:14.86:0,15,151 0/0:20,0:20:9.93:0,10,81 0/0:21,0:21:2.25:0,2,28 0/1:14,2:16:4.88:5,0,51 0/0:12,0:12:9.02:0,9,102 0/1:15,1:16:13.76:87,0,14 0/0:12,0:12:11.41:0,11,143 0/0:12,0:12:14.74:0,15,140 0/0:16,0:16:8.71:0,9,83 0/0:21,0:22:15.27:0,15,136 0/0:11,0:11:8.57:0,9,89 0/0:14,0:14:9.01:0,9,90 0/0:18,0:18:30.32:0,30,258 0/1:7,0:7:12.41:12,0,57 0/1:15,2:18:18.61:19,0,21 0/0:15,0:15:11.49:0,11,77 0/1:8,0:8:7.71:8,0,107 0/0:19,0:19:12.16:0,12,70 0/0:30,0:30:26.33:0,26,217 0/1:15,1:16:38.22:38,0,52 0/0:11,0:11:5.76:0,6,51 1/1:16,0:19:7.03:87,7,0 0/0:27,0:27:41.48:0,41,390 0/0:19,0:19:15.85:0,16,119 0/0:16,0:16:8.47:0,8,69 0/0:19,0:19:15.29:0,15,115 0/0:23,0:23:15.44:0,15,89 0/0:10,0:10:11.22:0,11,68 1/1:6,0:6:1.55:4,2,0 0/0:11,0:11:9.12:0,9,75 0/0:10,0:10:3.01:0,3,30 0/0:7,0:7:0.47:0,0,1 -chr1 1192789 . T C 74.78 . AC=1;AF=0.0098;AN=102;BaseQRankSum=-1.047;DP=679;Dels=0.00;FS=0.000;HRun=15;HaplotypeScore=1.3798;InbreedingCoeff=-0.0743;MQ=36.78;MQ0=0;MQRankSum=-1.425;QD=9.35;ReadPosRankSum=1.189;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:2,0:2:3.01:0,3,39 0/0:1,0:1:3:0,3,26 0/0:3,0:3:3.01:0,3,35 ./. ./. ./. 0/0:5,0:5:15.04:0,15,183 0/0:14,1:15:6.02:0,6,70 0/0:6,1:7:3.01:0,3,35 0/0:9,0:10:12.03:0,12,134 0/0:10,1:11:6.02:0,6,73 0/0:12,0:12:18.01:0,18,178 0/0:15,0:15:8.99:0,9,83 0/0:10,0:10:3.01:0,3,33 0/0:18,0:18:15.02:0,15,152 0/0:14,1:15:6.02:0,6,67 0/0:11,0:11:6.02:0,6,67 0/0:11,0:11:15.02:0,15,155 0/0:13,0:13:3.01:0,3,33 0/0:17,0:17:18.03:0,18,190 0/0:12,1:13:27.05:0,27,286 0/0:10,0:10:3.01:0,3,33 0/0:14,0:14:18.05:0,18,216 0/0:19,1:20:6.02:0,6,67 0/0:20,1:21:3.01:0,3,38 0/0:15,0:15:6.02:0,6,67 0/0:10,0:10:9.02:0,9,104 0/0:15,0:15:30.09:0,30,348 0/0:12,0:12:18.05:0,18,201 0/0:12,0:12:18.04:0,18,195 0/0:15,0:15:12.02:0,12,122 0/0:20,0:20:15.05:0,15,180 0/0:11,0:11:9.03:0,9,102 0/0:11,0:12:9.03:0,9,102 0/0:18,0:18:27.05:0,27,295 0/0:7,0:7:18.05:0,18,209 0/0:17,0:17:15:0,15,146 0/0:14,1:15:12.01:0,12,117 0/1:2,6:8:18.39:121,0,18 0/0:17,1:18:9.02:0,9,100 0/0:28,0:29:24.07:0,24,278 0/0:15,1:16:15.02:0,15,156 0/0:10,0:10:3.01:0,3,33 0/0:15,1:16:15.02:0,15,160 0/0:23,2:25:36.10:0,36,420 0/0:17,0:17:15.04:0,15,161 0/0:15,0:15:18.05:0,18,210 0/0:17,1:18:12.03:0,12,139 0/0:22,1:23:27.01:0,27,278 0/0:9,1:10:15.02:0,15,157 ./. 0/0:9,0:9:9.03:0,9,105 0/0:9,0:9:3.01:0,3,32 ./. -chr1 1192796 . G A 212.87 . AC=4;AF=0.0364;AN=110;BaseQRankSum=-1.973;DP=615;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.2937;InbreedingCoeff=-0.0566;MQ=38.68;MQ0=0;MQRankSum=-0.959;QD=4.09;ReadPosRankSum=-2.635;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1),UPSTREAM(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000467339|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000467339|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. 0/0:2,0:2:6.02:0,6,82 ./. 0/0:2,0:2:6.02:0,6,75 0/0:1,0:1:3.01:0,3,39 0/0:3,0:3:9.03:0,9,111 0/0:5,0:5:15.05:0,15,189 0/0:1,0:1:3.01:0,3,40 ./. 0/0:5,0:5:15.05:0,15,189 0/0:13,0:13:39.07:0,39,421 0/0:8,0:8:21.06:0,21,236 0/0:11,0:11:30.08:0,30,334 0/0:9,0:9:24.07:0,24,267 0/0:10,0:10:30.08:0,30,334 0/0:12,0:12:36.10:0,36,404 0/0:9,0:9:24.05:0,24,260 0/0:17,0:17:45.13:0,45,510 0/0:12,0:12:36.10:0,36,399 0/0:9,0:9:24.06:0,24,262 0/0:11,0:11:30.07:0,30,337 0/0:13,0:13:36.10:0,36,401 0/0:15,0:15:45.13:0,45,507 0/0:13,0:13:33.09:0,33,372 0/0:9,0:9:27.08:0,27,311 0/0:13,0:13:39.11:0,39,460 0/0:15,0:15:39.08:0,39,423 0/0:18,0:18:48.14:0,48,545 0/1:12,4:16:47.60:48,0,292 0/0:11,0:11:33.10:0,33,383 0/1:7,6:13:99:150,0,143 0/0:11,0:11:33.09:0,33,364 0/0:10,0:10:27.08:0,27,309 0/0:13,0:13:39.11:0,39,436 0/0:20,0:20:57.16:0,57,658 0/0:8,0:8:24.07:0,24,273 0/0:11,0:11:27.05:0,27,299 0/0:16,0:16:45.12:0,45,503 0/0:6,0:6:15.04:0,15,170 0/0:16,0:16:48.13:0,48,538 0/0:12,0:12:33.10:0,33,388 0/1:6,3:9:15.38:15,0,154 0/0:15,0:15:42.11:0,42,460 0/0:27,0:27:66.19:0,66,750 0/1:10,4:14:88.87:89,0,271 0/0:9,0:9:27.08:0,27,306 0/0:13,1:14:5.51:0,6,341 0/0:24,0:24:57.16:0,57,654 0/0:13,0:13:39.11:0,39,438 0/0:16,0:16:42.12:0,42,483 0/0:15,0:16:39.10:0,39,433 0/0:21,0:21:63.16:0,63,711 0/0:10,0:10:24.07:0,24,280 0/0:7,0:7:15.03:0,15,160 0/0:7,0:7:18.05:0,18,204 0/0:7,0:7:21.06:0,21,234 0/0:6,0:6:18.05:0,18,210 -chr1 1198510 . G A 538.65 . AC=2;AF=0.0179;AN=112;BaseQRankSum=2.023;DP=404;Dels=0.00;FS=3.013;HRun=0;HaplotypeScore=0.4208;InbreedingCoeff=-0.0639;MQ=57.33;MQ0=0;MQRankSum=1.298;QD=17.96;ReadPosRankSum=1.405;EFF=DOWNSTREAM(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|),EXON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|3),INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|3/3||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,1:3:3.01:0,3,41 0/0:3,0:3:6.02:0,6,74 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:6.02:0,6,69 0/0:4,0:4:9.03:0,9,116 ./. 0/0:5,0:5:9.03:0,9,124 0/0:5,0:5:12.04:0,12,157 0/0:3,0:3:6.02:0,6,81 0/0:3,0:3:9.03:0,9,124 0/0:4,0:4:3.01:0,3,41 0/0:3,0:3:9.03:0,9,120 0/0:4,0:4:9.03:0,9,123 0/0:12,0:12:27.08:0,27,334 0/1:7,14:21:99:425,0,223 0/0:3,0:3:9.02:0,9,102 0/0:11,0:11:27.08:0,27,338 0/0:8,0:8:24.08:0,24,313 0/0:19,0:19:51.17:0,51,671 0/0:12,0:13:36.11:0,36,449 0/0:11,0:11:30.10:0,30,391 0/0:11,0:11:33.10:0,33,412 0/0:10,0:10:27.09:0,27,357 0/0:7,0:7:18.06:0,18,236 0/0:13,0:13:30.10:0,30,402 0/0:6,0:6:15.05:0,15,190 0/0:7,0:7:18.04:0,18,206 0/0:6,0:6:15.01:0,15,169 0/0:8,0:8:21.07:0,21,278 0/0:12,0:12:33.09:0,33,405 0/0:18,0:18:48.14:0,48,597 0/1:3,6:9:39.88:178,0,40 0/0:9,0:9:24.07:0,24,302 0/0:14,0:14:36.10:0,36,448 0/0:10,0:10:24.08:0,24,326 0/0:10,0:10:27.08:0,27,336 0/0:14,0:15:36.09:0,36,438 0/0:24,0:24:66.21:0,66,860 0/0:6,0:6:18.03:0,18,213 0/0:2,0:2:6.02:0,6,79 0/0:4,0:4:12.04:0,12,151 0/0:7,0:7:18.04:0,18,215 0/0:3,0:3:9.03:0,9,116 0/0:4,0:4:12.04:0,12,155 0/0:4,0:4:12.03:0,12,128 0/0:4,0:4:12.04:0,12,162 0/0:8,0:8:24.06:0,24,293 ./. 0/0:1,0:1:3.01:0,3,34 0/0:6,0:6:18.05:0,18,223 0/0:4,0:4:12.04:0,12,152 0/0:1,0:1:3.01:0,3,42 0/0:5,0:5:15.05:0,15,195 ./. 0/0:1,0:1:3.01:0,3,39 0/0:7,0:7:18.05:0,18,228 0/0:4,0:4:12.04:0,12,154 0/0:2,0:2:6.02:0,6,82 0/0:1,0:1:3.01:0,3,41 ./. -chr1 1198578 . C T 938.59 . AC=4;AF=0.0333;AN=120;BaseQRankSum=-0.880;DP=1202;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.1589;InbreedingCoeff=0.4530;MQ=59.30;MQ0=0;MQRankSum=0.985;QD=21.33;ReadPosRankSum=-2.169;EFF=DOWNSTREAM(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|),EXON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|3),INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|3/3||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:12,0:12:33.10:0,33,419 0/0:9,0:9:27.08:0,27,328 0/0:15,0:15:42.14:0,42,566 0/0:7,0:7:21.05:0,21,254 0/0:5,0:5:15.05:0,15,206 0/0:6,0:6:18.05:0,18,231 0/0:8,0:8:24.08:0,24,324 0/0:10,0:10:30.10:0,30,411 0/0:14,0:14:42.14:0,42,571 0/0:32,0:32:93.31:0,93,1264 0/0:9,0:9:27.09:0,27,367 0/0:8,0:8:24.08:0,24,326 1/1:0,7:7:21.07:279,21,0 0/0:28,0:28:75.23:0,75,961 0/0:47,0:47:99:0,132,1762 0/0:16,0:16:45.14:0,45,591 0/0:35,0:37:99:0,102,1325 0/1:9,21:30:99:695,0,194 0/0:37,0:37:99:0,102,1348 0/0:30,0:30:87.26:0,87,1125 0/0:28,0:28:75.25:0,75,1017 0/0:36,0:37:90.29:0,90,1194 0/0:36,0:36:99:0,102,1333 0/0:29,0:29:81.26:0,81,1069 0/0:27,0:29:78.25:0,78,1042 0/0:24,0:24:66.20:0,66,854 0/0:31,0:31:90.29:0,90,1196 0/0:18,0:18:54.17:0,54,706 0/0:36,0:37:99:0,105,1393 0/0:38,0:38:99:0,108,1430 0/0:35,0:35:96.30:0,96,1271 0/0:20,0:21:57.18:0,57,750 0/0:38,0:38:99:0,114,1511 0/0:48,0:48:99:0,138,1802 0/0:20,0:21:57.18:0,57,752 0/0:34,0:34:96.30:0,96,1242 0/0:46,0:46:99:0,132,1717 0/0:54,0:54:99:0,144,1925 0/0:11,0:11:24.07:0,24,311 0/0:12,0:12:33.11:0,33,446 0/0:11,0:11:33.11:0,33,422 0/1:5,2:7:61.17:61,0,168 0/0:11,0:11:27.09:0,27,350 0/0:9,0:9:24.08:0,24,318 0/0:10,0:10:24.08:0,24,330 0/0:13,0:13:36.12:0,36,481 0/0:21,0:21:60.16:0,60,762 0/0:8,0:8:18.06:0,18,243 0/0:7,0:7:21.07:0,21,278 0/0:12,0:12:33.11:0,33,439 0/0:19,0:19:57.18:0,57,751 0/0:8,0:8:24.08:0,24,318 0/0:10,0:10:24.08:0,24,322 0/0:10,0:10:24.08:0,24,319 0/0:9,0:9:24.08:0,24,319 0/0:10,0:10:21.07:0,21,289 0/0:8,0:8:21.04:0,21,254 0/0:6,0:6:18.06:0,18,236 0/0:13,0:13:39.12:0,39,517 0/0:5,0:6:12.04:0,12,161 -chr1 1198618 . T A 9157.74 . AC=14;AF=0.1167;AN=120;BaseQRankSum=0.445;DP=2253;Dels=0.00;FS=1.666;HRun=1;HaplotypeScore=1.0999;InbreedingCoeff=0.1893;MQ=59.34;MQ0=0;MQRankSum=0.163;QD=16.59;ReadPosRankSum=2.122;EFF=DOWNSTREAM(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|),EXON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|3),INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|4),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|3),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|2),INTRON(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|3),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|3),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|4),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|4),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|2),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|1);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|3/3||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:20,0:20:57.14:0,57,711 0/0:10,0:10:30.07:0,30,350 0/0:14,0:14:39.12:0,39,505 0/0:4,0:4:12.02:0,12,134 0/0:15,0:15:45.15:0,45,615 0/0:16,0:16:48.16:0,48,648 0/0:22,0:22:66.22:0,66,898 0/0:11,0:11:33.11:0,33,452 0/0:20,0:20:60.20:0,60,811 0/0:33,0:33:99:0,99,1331 0/0:18,0:18:54.18:0,54,738 0/0:16,0:16:48.16:0,48,647 0/0:14,0:14:42.14:0,42,571 0/0:51,0:51:99:0,132,1751 0/0:74,1:75:99:0,202,2690 0/0:37,0:37:99:0,105,1382 0/0:74,0:74:99:0,196,2623 0/0:64,0:65:99:0,178,2346 0/0:71,0:72:99:0,193,2489 0/0:60,0:60:99:0,169,2245 0/0:62,0:62:99:0,163,2194 0/0:66,0:66:99:0,187,2470 0/0:67,0:68:99:0,184,2471 0/1:29,29:58:99:815,0,882 0/0:73,0:73:99:0,202,2696 0/0:51,0:51:99:0,141,1887 1/1:0,52:52:99:1876,141,0 0/0:46,0:47:99:0,129,1696 0/0:78,0:78:99:0,217,2900 0/0:70,0:70:99:0,196,2601 0/0:74,0:74:99:0,211,2805 0/1:23,23:46:99:717,0,643 0/0:63,0:65:99:0,169,2270 0/1:47,41:88:99:1348,0,1428 0/1:32,22:54:99:714,0,1062 0/1:40,25:65:99:657,0,1208 0/1:44,35:79:99:1139,0,1244 0/0:101,0:101:99:0,289,3831 0/0:14,0:14:39.13:0,39,524 0/0:24,0:24:63.20:0,63,830 0/0:25,0:25:69.22:0,69,930 0/0:15,0:16:42.14:0,42,557 0/0:18,0:18:51.15:0,51,648 0/0:12,0:12:36.12:0,36,473 0/1:10,11:21:99:363,0,268 0/0:16,0:16:39.12:0,39,510 0/0:30,0:30:75.24:0,75,987 0/0:11,0:11:30.10:0,30,393 0/0:15,0:15:33.11:0,33,438 0/0:23,0:23:63.19:0,63,812 0/1:17,20:37:99:573,0,477 0/0:11,0:11:30.10:0,30,401 0/1:15,9:24:99:217,0,428 0/0:22,0:22:63.18:0,63,774 1/1:0,13:14:36.11:458,36,0 0/1:5,9:14:99:280,0,171 0/0:17,0:17:48.15:0,48,619 0/0:12,0:12:36.11:0,36,466 0/0:19,0:19:54.17:0,54,719 0/0:14,0:14:30.09:0,30,387 -chr1 1203116 . G A 525.11 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.823;DP=1403;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.4562;InbreedingCoeff=-0.0106;MQ=58.08;MQ0=0;MQRankSum=2.079;QD=11.93;ReadPosRankSum=2.071;EFF=DOWNSTREAM(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|),INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|2),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|2),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|2),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|2),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|2),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|1),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|2),UPSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),UPSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|2),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|2),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|2),UTR_5_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|2);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|||||retained_intron|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215|2/7|||-/44|nonsense_mediated_decay|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294|2/6|||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,5_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|2/7|||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752|2/6|||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:18.03:0,18,211 0/0:7,0:7:15.04:0,15,175 0/0:9,0:9:27.07:0,27,323 0/0:2,0:2:6.02:0,6,81 0/0:9,0:9:24.08:0,24,313 0/0:11,0:11:27.09:0,27,351 0/0:29,0:31:87.28:0,87,1143 0/0:11,0:11:33.10:0,33,426 0/0:25,0:25:75.23:0,75,961 0/0:37,0:37:99:0,108,1347 0/0:13,0:13:36.11:0,36,459 0/0:10,0:10:30.10:0,30,404 0/0:15,0:15:45.14:0,45,593 0/0:21,0:21:60.19:0,60,765 0/0:26,0:26:75.24:0,75,999 0/0:11,0:11:30.10:0,30,403 0/0:24,0:24:69.21:0,69,905 0/0:14,0:14:42.12:0,42,545 0/0:23,0:23:69.22:0,69,918 0/0:32,0:33:87.28:0,87,1157 0/0:22,0:22:63.20:0,63,829 0/0:37,0:38:99:0,102,1357 0/0:24,0:24:72.24:0,72,959 0/0:31,0:31:90.29:0,90,1194 0/0:26,0:26:75.24:0,75,995 0/0:29,0:29:78.25:0,78,1028 0/0:35,0:35:93.30:0,93,1222 0/0:17,0:17:51.16:0,51,677 0/0:29,0:29:84.27:0,84,1103 0/0:22,0:22:63.19:0,63,812 0/0:36,0:36:99:0,105,1396 0/0:19,0:19:54.18:0,54,714 0/0:25,0:25:72.23:0,72,937 0/0:29,0:29:81.26:0,81,1055 0/0:12,0:12:30.10:0,30,407 0/0:24,0:24:72.22:0,72,934 0/0:38,0:38:99:0,105,1390 0/0:35,0:35:87.29:0,87,1177 0/0:24,1:25:66.20:0,66,834 0/0:42,0:44:99:0,105,1352 0/0:24,0:24:66.20:0,66,829 0/0:26,0:26:69.21:0,69,899 0/0:14,0:14:33.11:0,33,444 0/0:21,0:21:51.14:0,51,627 0/0:15,0:16:45.14:0,45,563 0/0:38,0:38:93.27:0,93,1186 0/0:33,0:34:87.26:0,87,1070 0/0:18,0:18:36.11:0,36,466 0/0:27,0:28:69.21:0,69,878 0/1:25,19:44:99:573,0,773 0/0:27,0:28:78.24:0,78,1002 0/0:28,0:29:78.23:0,78,1022 0/0:40,0:40:99:0,105,1356 0/0:13,0:13:33.10:0,33,436 0/0:22,0:22:66.20:0,66,821 0/0:29,0:29:66.20:0,66,845 0/0:18,0:18:51.15:0,51,641 0/0:21,0:21:54.17:0,54,711 0/0:23,0:23:60.19:0,60,793 0/0:15,0:15:39.09:0,39,494 -chr1 1203167 . C T 1087.43 . AC=2;AF=0.0167;AN=120;BaseQRankSum=1.333;DP=2258;Dels=0.00;FS=8.468;HRun=1;HaplotypeScore=1.5625;InbreedingCoeff=0.8365;MQ=57.71;MQ0=0;MQRankSum=-0.200;QD=28.62;ReadPosRankSum=-1.052;EFF=DOWNSTREAM(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|),INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|2),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|2),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|2),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|2),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|2),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|2),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|3),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|1),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|2),UPSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),UPSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|2),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|2),UTR_3_PRIME(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|2),UTR_5_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|2);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|||||retained_intron|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215|2/7|||-/44|nonsense_mediated_decay|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294|2/6|||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,5_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|2/7|||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752|2/6|||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.05:0,15,178 0/0:2,0:2:3.01:0,3,39 0/0:8,0:8:21.07:0,21,276 0/0:7,0:7:21.07:0,21,273 0/0:20,0:20:54.18:0,54,714 0/0:17,0:17:48.15:0,48,629 0/0:25,0:25:66.21:0,66,868 0/0:9,0:9:27.09:0,27,363 0/0:30,0:30:90.29:0,90,1184 0/0:30,0:30:78.25:0,78,1004 0/0:19,0:19:54.17:0,54,711 0/0:12,0:12:36.12:0,36,475 0/0:30,0:30:84.27:0,84,1105 0/0:45,0:45:99:0,117,1531 0/0:39,0:40:99:0,108,1389 0/0:16,0:16:45.14:0,45,585 0/0:39,0:39:99:0,108,1356 0/0:26,0:26:72.22:0,72,927 0/0:48,0:48:99:0,135,1795 0/0:58,0:58:99:0,163,2131 0/0:46,0:46:99:0,123,1549 0/0:57,0:57:99:0,150,1949 0/0:36,0:36:99:0,105,1349 0/0:50,0:50:99:0,138,1787 0/0:37,0:37:99:0,108,1342 0/0:41,0:41:99:0,120,1566 0/0:53,1:54:99:0,119,1899 0/0:42,0:42:99:0,114,1514 0/0:46,0:46:99:0,126,1609 0/0:36,0:36:99:0,102,1321 0/0:61,0:61:99:0,169,2154 0/0:34,0:34:99:0,99,1247 0/0:32,0:32:96.31:0,96,1278 0/0:45,0:45:99:0,123,1576 0/0:33,0:33:81.26:0,81,1060 0/0:42,0:43:99:0,114,1487 0/0:49,0:49:99:0,126,1676 0/0:55,0:55:99:0,150,2008 0/0:39,0:39:87.23:0,87,1120 0/0:74,0:74:99:0,169,2220 0/0:47,1:48:99:0,120,1559 0/0:41,0:41:99:0,102,1298 0/0:32,0:33:87.27:0,87,1105 0/0:39,0:39:96.30:0,96,1211 0/0:33,1:34:46.05:0,46,1044 0/0:45,0:45:99:0,108,1431 0/0:61,0:62:99:0,166,2113 0/0:20,0:20:39.12:0,39,498 0/0:52,0:52:99:0,120,1580 0/0:86,0:86:99:0,226,2883 0/0:51,0:51:99:0,135,1761 0/0:42,0:42:99:0,108,1394 0/0:63,0:63:99:0,153,1986 0/0:40,0:40:96.30:0,96,1248 1/1:0,37:38:90.28:1159,90,0 0/0:39,0:39:99:0,105,1349 0/0:32,0:32:84.27:0,84,1095 0/0:32,0:32:81.24:0,81,1043 0/0:32,0:32:81.26:0,81,1047 0/0:32,0:33:81.26:0,81,1065 -chr1 1203271 . G A 523.79 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.124;DP=5255;Dels=0.00;FS=0.700;HRun=0;HaplotypeScore=3.4063;InbreedingCoeff=-0.0084;MQ=58.09;MQ0=0;MQRankSum=0.171;QD=10.48;ReadPosRankSum=-1.486;EFF=EXON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|2),EXON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|2),EXON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|2),EXON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|2),EXON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|2),EXON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|2),EXON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|2),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|1),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A34|100|UBE2J2|protein_coding|CODING|ENST00000422076|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A34|195|UBE2J2|protein_coding|CODING|ENST00000435198|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A34|259|UBE2J2|protein_coding|CODING|ENST00000349431|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A34|259|UBE2J2|protein_coding|CODING|ENST00000360466|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A34|275|UBE2J2|protein_coding|CODING|ENST00000400930|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A34|42|UBE2J2|protein_coding|CODING|ENST00000488418|),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A34|70|UBE2J2|protein_coding|CODING|ENST00000502382|),UPSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),UPSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|),UTR_5_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|2),UTR_5_PRIME(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|2);CSQ=synonymous_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000502382|3/5|||34/71|protein_coding|1,synonymous_variant&NMD_transcript_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000477894|2/6|||34/100|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|2/3||||retained_intron|1,synonymous_variant&NMD_transcript_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000473215|2/7|||34/44|nonsense_mediated_decay|1,synonymous_variant&NMD_transcript_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000503294|2/6|||34/44|nonsense_mediated_decay|1,synonymous_variant&NMD_transcript_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000464036|2/8|||34/105|nonsense_mediated_decay|1,synonymous_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000488418|2/2|||34/43|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000422076|2/5|||34/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,synonymous_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000349431|2/7|||34/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,5_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000348298|2/7|||-/207|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,5_prime_UTR_variant|||ENSG00000160087|UBE2J2|ENST00000347370|2/7|||-/207|protein_coding|1,synonymous_variant&NMD_transcript_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000450390|2/8|||34/43|nonsense_mediated_decay|1,synonymous_variant&NMD_transcript_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000466752|2/6|||34/44|nonsense_mediated_decay|1,synonymous_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000400930|2/8|||34/275|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000360466|2/7|||34/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,synonymous_variant|gcC/gcT|A|ENSG00000160087|UBE2J2|ENST00000435198|2/7|||34/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:11,0:11:30.09:0,30,367 0/0:26,0:26:66.19:0,66,789 0/0:16,0:16:45.14:0,45,572 0/0:17,0:17:48.15:0,48,593 0/0:46,0:46:99:0,129,1649 0/0:39,0:39:99:0,111,1440 0/0:69,0:69:99:0,199,2527 0/0:28,0:29:84.25:0,84,1050 0/0:48,0:49:99:0,144,1931 0/0:86,0:86:99:0,244,3165 0/0:38,0:38:99:0,108,1415 0/0:37,0:37:99:0,111,1378 0/0:56,0:57:99:0,165,2050 0/0:112,1:114:99:0,256,3365 0/0:127,0:128:99:0,313,4084 0/0:70,0:70:99:0,178,2371 0/0:107,0:107:99:0,262,3482 0/0:130,2:132:99:0,259,3867 0/0:126,1:127:99:0,310,4093 0/0:132,0:132:99:0,328,4349 0/0:103,0:103:99:0,238,3155 0/0:154,0:154:99:0,361,4736 0/0:112,0:112:99:0,256,3394 0/0:137,0:137:99:0,334,4412 0/0:90,0:91:99:0,229,3023 0/0:125,0:126:99:0,292,3901 0/0:120,0:120:99:0,295,3890 0/0:79,1:80:99:0,167,2512 0/0:149,0:151:99:0,370,4819 0/0:129,0:129:99:0,316,4142 0/0:137,0:138:99:0,361,4778 0/0:104,0:105:99:0,247,3254 0/0:114,0:114:99:0,280,3706 0/0:124,2:126:99:0,232,3928 0/0:92,0:92:99:0,211,2787 0/0:139,0:139:99:0,340,4507 0/0:155,0:155:99:0,370,4932 0/0:161,0:161:99:0,385,5110 0/0:63,0:63:99:0,138,1797 0/0:93,0:93:99:0,223,2909 0/0:73,0:75:99:0,187,2366 0/0:65,0:65:99:0,150,1919 0/0:68,1:69:99:0,169,2128 0/0:63,0:63:99:0,141,1853 0/0:68,0:68:99:0,166,2167 0/0:83,1:85:99:0,166,2407 0/0:112,0:112:99:0,268,3448 0/1:20,29:49:99:572,0,539 0/0:70,0:70:99:0,168,2102 0/0:138,0:138:99:0,331,4338 0/0:91,0:92:99:0,226,2917 0/0:71,0:71:99:0,172,2226 0/0:119,0:120:99:0,283,3648 0/0:73,0:73:99:0,175,2242 0/0:77,0:77:99:0,193,2476 0/0:76,1:78:99:0,175,2260 0/0:49,0:49:99:0,114,1509 0/0:70,0:70:99:0,150,1958 0/0:48,0:48:99:0,120,1544 0/0:63,0:63:99:0,156,2071 -chr1 1203387 . G A 3095.18 . AC=4;AF=0.0333;AN=120;BaseQRankSum=-1.839;DP=3379;Dels=0.00;FS=3.622;HRun=0;HaplotypeScore=1.5906;InbreedingCoeff=0.4826;MQ=57.66;MQ0=0;MQRankSum=0.825;QD=17.10;ReadPosRankSum=1.782;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|1),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|1),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|1),INTRON(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|1),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|1),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|1),UPSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),UPSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:12,0:12:33.10:0,33,424 0/0:16,0:16:39.11:0,39,479 0/0:19,0:19:48.14:0,48,600 0/0:11,0:11:33.08:0,33,390 0/0:29,0:29:87.28:0,87,1163 0/0:30,0:30:81.23:0,81,1018 0/0:55,1:56:99:0,156,2058 0/0:26,1:28:72.23:0,72,951 0/0:52,0:52:99:0,150,1910 0/0:69,0:69:99:0,193,2480 0/0:37,0:37:99:0,108,1404 0/0:25,0:25:69.22:0,69,890 0/0:36,0:36:99:0,102,1320 0/0:76,0:79:99:0,165,2153 0/0:75,0:76:99:0,184,2422 0/0:62,0:62:99:0,153,2016 0/0:84,0:84:99:0,196,2575 0/0:81,0:81:99:0,208,2673 0/0:81,0:81:99:0,196,2599 0/0:67,0:67:99:0,181,2363 0/0:71,0:71:99:0,166,2187 0/0:84,0:84:99:0,214,2758 0/0:73,0:73:99:0,172,2214 0/1:47,31:78:99:821,0,1360 0/0:67,0:67:99:0,165,2162 0/0:78,0:80:99:0,181,2372 0/0:74,1:77:99:0,172,2240 0/0:54,0:54:99:0,123,1608 0/0:96,0:96:99:0,241,3201 0/0:78,0:79:99:0,196,2513 0/0:91,0:91:99:0,220,2885 0/0:62,0:63:99:0,159,2062 0/0:69,0:70:99:0,175,2272 0/0:85,0:86:99:0,205,2684 0/0:63,0:65:99:0,141,1879 0/0:85,0:86:99:0,202,2652 0/0:87,0:87:99:0,217,2805 0/0:111,0:112:99:0,262,3435 0/0:43,0:43:99:0,105,1340 0/0:65,0:66:99:0,175,2196 0/0:60,0:61:99:0,138,1825 0/0:37,0:37:90.26:0,90,1154 0/0:46,0:46:99:0,117,1521 0/0:28,0:28:63.18:0,63,790 0/1:22,12:35:99:297,0,656 0/0:50,0:50:99:0,126,1625 0/0:81,0:81:99:0,196,2464 0/0:20,0:20:54.15:0,54,662 0/0:33,0:33:87.24:0,87,1085 1/1:1,66:68:99:2077,134,0 0/0:52,0:53:99:0,114,1487 0/0:48,0:48:99:0,117,1490 0/0:45,0:46:99:0,105,1385 0/0:58,0:59:99:0,126,1678 0/0:31,0:31:78.22:0,78,1004 0/0:34,0:34:87.28:0,87,1154 0/0:28,0:28:72.22:0,72,931 0/0:60,0:60:99:0,135,1777 0/0:37,0:38:93.29:0,93,1179 0/0:45,0:45:96.27:0,96,1247 -chr1 1203464 . G A 885.88 . AC=5;AF=0.0417;AN=120;BaseQRankSum=-4.027;DP=1394;Dels=0.00;FS=13.230;HRun=0;HaplotypeScore=0.4057;InbreedingCoeff=-0.0494;MQ=51.99;MQ0=0;MQRankSum=3.105;QD=10.42;ReadPosRankSum=-0.558;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|1),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|1),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|1),INTRON(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|1),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|1),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|1),UPSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),UPSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,41 0/0:7,0:7:21.05:0,21,235 0/0:3,0:3:9.02:0,9,102 0/0:5,0:5:15.05:0,15,179 0/0:19,0:19:54.17:0,54,675 0/0:15,0:15:42.13:0,42,521 0/0:17,0:17:48.15:0,48,605 0/0:13,0:13:36.11:0,36,460 0/0:14,0:14:39.12:0,39,474 0/0:22,0:22:66.20:0,66,812 0/0:8,0:8:24.07:0,24,281 0/0:6,0:6:15.05:0,15,186 0/1:6,13:19:99:349,0,130 0/0:36,1:37:99:0,102,1247 0/0:25,0:25:69.20:0,69,860 0/1:4,5:9:96.59:102,0,97 0/0:16,0:16:48.15:0,48,614 0/1:14,9:23:99:234,0,374 0/0:32,0:32:84.25:0,84,1042 0/0:22,0:22:63.19:0,63,780 0/0:27,0:28:69.21:0,69,867 0/0:31,0:31:90.27:0,90,1115 0/0:14,1:15:8.16:0,8,493 0/0:24,0:24:69.22:0,69,879 0/0:18,0:18:51.10:0,51,588 0/0:28,0:28:69.21:0,69,869 0/0:27,0:27:72.22:0,72,881 0/0:14,0:14:33.10:0,33,421 0/0:20,0:20:60.15:0,60,701 0/0:30,0:30:81.24:0,81,998 0/0:34,0:34:87.25:0,87,1041 0/0:18,0:19:54.13:0,54,643 0/0:20,0:21:60.17:0,60,728 0/0:27,0:27:78.21:0,78,939 0/0:29,0:30:81.25:0,81,1029 0/0:25,0:25:72.22:0,72,912 0/0:27,0:27:75.20:0,75,929 0/0:39,0:40:99:0,99,1212 0/0:31,0:31:72.20:0,72,883 0/0:41,0:41:99:0,105,1294 0/0:42,0:42:99:0,99,1286 0/1:9,7:16:99:212,0,277 0/1:12,4:18:92.87:93,0,358 0/0:16,0:16:42.10:0,42,507 0/0:25,0:27:63.20:0,63,823 0/0:25,0:25:60.19:0,60,784 0/0:57,0:58:99:0,135,1691 0/0:11,0:11:30.09:0,30,344 0/0:21,0:22:51.16:0,51,633 0/0:33,1:35:55.01:0,55,1038 0/0:35,0:36:96.26:0,96,1186 0/0:43,0:44:99:0,102,1246 0/0:17,0:18:45.13:0,45,544 0/0:31,0:32:78.24:0,78,1006 0/0:19,0:19:48.14:0,48,582 0/0:28,0:29:66.17:0,66,796 0/0:21,0:21:51.16:0,51,647 0/0:33,1:34:55.71:0,56,1030 0/0:22,0:22:51.16:0,51,630 0/0:26,0:26:54.17:0,54,729 -chr1 1203573 . C T 46.79 . AC=2;AF=0.0169;AN=118;BaseQRankSum=-2.029;DP=398;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3328;InbreedingCoeff=-0.0477;MQ=57.94;MQ0=0;MQRankSum=0.064;QD=3.90;ReadPosRankSum=-2.020;EFF=INTRON(MODIFIER||||100|UBE2J2|protein_coding|CODING|ENST00000422076|1),INTRON(MODIFIER||||195|UBE2J2|protein_coding|CODING|ENST00000435198|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000347370|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000348298|1),INTRON(MODIFIER||||207|UBE2J2|protein_coding|CODING|ENST00000400929|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000349431|1),INTRON(MODIFIER||||259|UBE2J2|protein_coding|CODING|ENST00000360466|1),INTRON(MODIFIER||||275|UBE2J2|protein_coding|CODING|ENST00000400930|1),INTRON(MODIFIER||||42|UBE2J2|protein_coding|CODING|ENST00000488418|1),INTRON(MODIFIER||||70|UBE2J2|protein_coding|CODING|ENST00000502382|2),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000450390|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000464036|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000466752|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000473215|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000477894|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000503294|1),INTRON(MODIFIER|||||UBE2J2|nonsense_mediated_decay|CODING|ENST00000509720|1),INTRON(MODIFIER|||||UBE2J2|processed_transcript|CODING|ENST00000491779|1),INTRON(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000461142|1),UPSTREAM(MODIFIER||||224|UBE2J2|protein_coding|CODING|ENST00000339385|),UPSTREAM(MODIFIER|||||UBE2J2|retained_intron|CODING|ENST00000471154|);CSQ=intron_variant|||ENSG00000160087|UBE2J2|ENST00000502382||||-/71|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000477894||||-/100|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000339385||||-/224|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000461142|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000473215||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000503294||||-/44|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000464036||||-/105|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000488418||||-/43|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000422076||||-/101|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000491779|||||processed_transcript|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000349431||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000509720||||-/60|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000348298||||-/207|protein_coding|1,upstream_gene_variant|||ENSG00000160087|UBE2J2|ENST00000471154|||||retained_intron|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000347370||||-/207|protein_coding|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000450390||||-/43|nonsense_mediated_decay|1,intron_variant&NMD_transcript_variant|||ENSG00000160087|UBE2J2|ENST00000466752||||-/44|nonsense_mediated_decay|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400930||||-/275|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000360466||||-/259|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000400929||||-/207|protein_coding|1,intron_variant|||ENSG00000160087|UBE2J2|ENST00000435198||||-/196|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,34 0/0:8,0:8:12.04:0,12,157 0/0:2,0:2:6.02:0,6,77 0/0:4,0:4:12.04:0,12,157 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,113 0/1:3,4:7:90.04:90,0,101 ./. 0/0:7,0:7:21.07:0,21,281 0/0:10,0:10:30.10:0,30,390 0/0:2,0:2:6.02:0,6,79 0/0:2,0:2:3.01:0,3,35 0/0:4,0:4:12.03:0,12,144 0/1:4,1:5:19.31:19,0,137 0/0:8,0:8:21.07:0,21,289 0/0:6,0:6:18.06:0,18,228 0/0:7,0:7:21.07:0,21,278 0/0:12,0:12:36.12:0,36,486 0/0:8,0:8:24.08:0,24,319 0/0:4,0:4:12.04:0,12,161 0/0:6,0:6:18.06:0,18,241 0/0:9,0:9:27.09:0,27,365 0/0:5,0:5:9.03:0,9,119 0/0:5,0:5:15.05:0,15,198 0/0:6,0:6:18.06:0,18,236 0/0:5,0:5:15.05:0,15,207 0/0:4,0:4:12.04:0,12,166 0/0:3,0:3:6.02:0,6,84 0/0:5,0:5:12.04:0,12,166 0/0:8,0:8:24.08:0,24,324 0/0:2,0:2:6.02:0,6,70 0/0:7,0:7:21.07:0,21,270 0/0:8,0:8:21.07:0,21,289 0/0:3,0:3:9.01:0,9,101 0/0:5,0:5:12.04:0,12,161 0/0:5,0:5:12.03:0,12,144 0/0:7,0:7:21.07:0,21,263 0/0:12,0:12:33.11:0,33,434 0/0:8,0:8:21.07:0,21,277 0/0:14,0:14:36.11:0,36,467 0/0:10,0:10:21.06:0,21,272 0/0:7,0:7:21.07:0,21,285 0/0:6,0:6:18.06:0,18,233 0/0:5,0:5:15.05:0,15,198 0/0:7,0:7:18.06:0,18,242 0/0:7,0:7:21.07:0,21,281 0/0:15,0:15:39.12:0,39,510 0/0:3,0:3:6.01:0,6,70 0/0:8,0:8:21.06:0,21,272 0/0:21,0:21:51.16:0,51,661 0/0:9,0:9:27.07:0,27,349 0/0:10,0:10:24.08:0,24,308 0/0:5,0:6:12.04:0,12,155 0/0:12,0:12:30.10:0,30,409 0/0:7,0:7:18.05:0,18,233 0/0:14,0:14:36.11:0,36,472 0/0:6,0:6:15.05:0,15,197 0/0:2,0:2:6.02:0,6,84 0/0:8,0:8:24.07:0,24,307 0/0:6,0:6:18.05:0,18,220 -chr1 1219382 . C G 517.5 . AC=1;AF=0.0085;AN=118;BaseQRankSum=-1.346;DP=1303;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.5737;InbreedingCoeff=-0.0262;MQ=56.33;MQ0=0;MQRankSum=-0.677;QD=16.69;ReadPosRankSum=0.201;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),EXON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),EXON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q126E|802|SCNN1D|protein_coding|CODING|ENST00000379116|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q28E|704|SCNN1D|protein_coding|CODING|ENST00000325425|),START_GAINED(LOW||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),STOP_GAINED(HIGH|NONSENSE|tCa/tGa|S29*|138|SCNN1D|protein_coding|CODING|ENST00000470022|),UTR_5_PRIME(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),UTR_5_PRIME(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6);CSQ=5_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000338555|3/15|||-/638|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000467651|3/4||||processed_transcript|1,missense_variant&NMD_transcript_variant|Cag/Gag|Q/E|ENSG00000162572|SCNN1D|ENST00000379101|5/17|benign(0.028)||126/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,missense_variant|Cag/Gag|Q/E|ENSG00000162572|SCNN1D|ENST00000325425|2/15|benign(0.007)|deleterious(0)|28/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,stop_gained|tCa/tGa|S/*|ENSG00000162572|SCNN1D|ENST00000470022|3/4|||29/139|protein_coding|1,5_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000400928|2/14|||-/638|protein_coding|1,missense_variant|Cag/Gag|Q/E|ENSG00000162572|SCNN1D|ENST00000379116|5/18|benign(0.007)|deleterious(0)|126/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:6.02:0,6,75 0/0:3,0:3:6.02:0,6,73 0/0:5,0:5:15.05:0,15,200 0/0:2,0:2:6.02:0,6,70 0/0:4,0:4:12.03:0,12,141 0/0:4,0:4:12.04:0,12,155 0/0:4,0:4:9.03:0,9,111 0/0:4,0:4:12.04:0,12,155 0/0:1,0:1:3.01:0,3,33 ./. 0/0:4,0:4:12.03:0,12,129 0/0:16,0:16:27.08:0,27,361 0/0:23,0:24:51.14:0,51,662 0/0:15,0:15:36.12:0,36,489 0/0:21,0:21:42.14:0,42,579 0/0:21,0:21:36.12:0,36,496 0/0:11,0:11:27.08:0,27,350 0/0:19,0:19:45.14:0,45,587 0/0:23,0:23:42.14:0,42,570 0/0:23,0:23:42.14:0,42,598 0/0:13,0:13:33.10:0,33,421 0/0:17,0:17:39.12:0,39,500 0/0:21,0:21:48.15:0,48,621 0/0:21,0:21:45.14:0,45,595 0/0:10,0:10:21.07:0,21,283 0/0:11,0:11:21.07:0,21,297 0/0:24,0:24:45.15:0,45,617 0/0:21,0:21:42.14:0,42,579 0/0:8,0:8:18.06:0,18,237 0/0:5,0:5:9.03:0,9,125 0/0:14,0:14:30.10:0,30,407 0/0:32,0:32:69.22:0,69,905 0/0:16,0:16:33.11:0,33,442 0/0:8,0:8:12.04:0,12,166 0/0:24,0:24:54.17:0,54,723 0/0:29,0:29:60.19:0,60,808 0/0:21,0:22:51.16:0,51,676 0/0:64,0:64:99:0,144,1812 0/0:44,0:44:90.29:0,90,1192 0/0:35,0:35:72.21:0,72,934 0/0:31,0:31:66.20:0,66,861 0/0:38,0:38:87.27:0,87,1112 0/0:36,0:36:84.27:0,84,1109 0/0:29,0:29:72.22:0,72,902 0/0:81,0:81:99:0,168,2211 0/0:13,0:13:33.10:0,33,400 0/0:38,0:38:87.27:0,87,1128 0/1:9,22:31:99:565,0,274 0/0:47,0:47:99:0,102,1293 0/0:24,0:25:60.18:0,60,722 0/0:41,0:41:87.27:0,87,1112 0/0:43,0:43:96.28:0,96,1206 0/0:40,1:41:96.28:0,96,1183 0/0:19,0:19:45.14:0,45,597 0/0:36,0:36:78.25:0,78,1020 0/0:48,0:48:99:0,111,1398 0/0:22,0:22:45.14:0,45,603 0/0:36,0:36:78.25:0,78,1018 -chr1 1219477 . T G 61.09 . AC=10;AF=0.0962;AN=104;BaseQRankSum=-2.023;DP=228;Dels=0.02;FS=0.000;HRun=9;HaplotypeScore=1.3848;InbreedingCoeff=0.0086;MQ=48.26;MQ0=0;MQRankSum=-5.204;QD=1.61;ReadPosRankSum=5.116;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,splice_region_variant&intron_variant&nc_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. 0/0:2,0:2:3.01:0,3,33 0/0:5,0:5:15.03:0,15,171 0/0:2,0:2:6.02:0,6,82 0/0:5,0:5:9.02:0,9,95 0/0:4,1:5:9.03:0,9,112 0/0:8,1:9:21.05:0,21,258 0/0:3,0:3:9.02:0,9,94 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,64 0/0:2,0:2:5.99:0,6,60 ./. 0/0:4,0:5:12.04:0,12,145 0/0:4,0:4:9.03:0,9,124 0/0:5,0:5:15.05:0,15,188 0/0:2,0:2:6.01:0,6,63 0/0:3,1:4:6.01:0,6,64 0/1:1,2:3:27.42:27,0,34 0/0:4,0:5:9.01:0,9,93 0/0:3,0:3:9.03:0,9,119 0/0:2,0:3:3.01:0,3,41 0/1:3,1:4:21.40:21,0,104 0/1:1,1:2:19.69:20,0,20 0/0:2,1:3:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:4,1:5:9.03:0,9,110 0/0:5,0:5:12.04:0,12,156 ./. 0/0:2,1:3:6.02:0,6,71 0/0:6,0:6:15.04:0,15,176 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,38 0/0:3,0:3:9.03:0,9,116 1/1:0,1:1:3.01:33,3,0 0/0:3,0:3:6.02:0,6,72 0/0:10,2:12:12.03:0,12,129 0/1:8,2:10:18.43:18,0,110 0/0:4,1:5:9.02:0,9,102 0/0:9,1:10:15.03:0,15,178 0/0:1,1:2:3.01:0,3,40 0/0:4,0:4:9.03:0,9,110 1/1:2,1:3:3.01:33,3,0 0/0:6,0:6:9.03:0,9,121 0/0:3,1:4:6.02:0,6,70 0/0:6,0:6:18.05:0,18,221 0/0:5,0:5:15.04:0,15,180 0/0:5,1:6:12.04:0,12,155 0/0:2,0:2:3.01:0,3,38 ./. 0/0:3,2:5:6.01:0,6,61 0/1:4,1:5:21.40:21,0,89 0/0:2,1:3:6.01:0,6,66 0/1:8,2:10:9.38:9,0,206 0/0:4,2:6:6.02:0,6,71 0/0:2,1:3:3.01:0,3,38 0/0:4,0:4:9.03:0,9,115 -chr1 1219487 . T G 252.82 . AC=16;AF=0.178;AN=90;BaseQRankSum=-6.004;DP=169;Dels=0.04;FS=31.669;HRun=9;HaplotypeScore=0.8999;InbreedingCoeff=-0.0964;MQ=41.70;MQ0=0;MQRankSum=-5.947;QD=4.29;ReadPosRankSum=5.203;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. 0/0:2,0:2:3.01:0,3,37 0/0:4,0:4:12.04:0,12,154 0/0:1,0:1:3.01:0,3,39 0/0:3,2:5:9.03:0,9,121 0/0:4,1:5:12.04:0,12,148 0/0:6,0:6:18.06:0,18,232 0/0:2,0:2:6.02:0,6,81 ./. 0/0:2,0:2:6.02:0,6,73 0/0:2,0:2:6.02:0,6,72 0/0:1,0:1:3.01:0,3,33 0/1:1,1:2:27.42:27,0,27 0/0:1,0:1:3.01:0,3,40 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,39 0/0:2,2:4:6.02:0,6,74 1/1:0,3:3:3:25,3,0 0/1:1,3:4:20.66:21,0,33 0/0:1,1:2:3.01:0,3,38 0/1:1,1:2:27.42:27,0,27 0/1:1,1:2:18.68:19,0,33 0/0:1,1:2:2.99:0,3,23 0/0:2,1:3:6.01:0,6,68 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:2,0:2:5.99:0,6,62 0/0:6,0:6:12.04:0,12,147 ./. 0/1:1,1:2:27.42:27,0,34 0/0:2,0:2:6.02:0,6,76 ./. ./. 0/0:1,0:1:3.01:0,3,35 ./. ./. 0/1:4,3:9:39.35:39,0,58 0/1:5,4:9:18.39:18,0,117 0/0:2,0:2:3.01:0,3,40 0/0:4,4:8:9.03:0,9,111 0/0:2,1:3:6.02:0,6,69 0/0:2,0:2:6:0,6,61 0/0:2,1:5:3.01:0,3,33 0/0:4,0:4:6.02:0,6,79 0/0:2,1:3:3.01:0,3,37 0/0:1,0:1:3.01:0,3,33 0/0:1,1:2:3.01:0,3,33 0/0:5,0:5:6.02:0,6,75 ./. ./. 0/0:4,3:7:2.99:0,3,23 1/1:1,3:4:3:29,3,0 ./. 0/1:5,3:8:41.03:41,0,145 0/1:2,7:9:21.43:70,0,21 0/1:1,1:2:18.68:19,0,34 ./. -chr1 1219489 . A G 510.67 . AC=22;AF=0.244;AN=90;BaseQRankSum=-4.579;DP=161;Dels=0.04;FS=3.458;HRun=6;HaplotypeScore=0.5978;InbreedingCoeff=-0.2229;MQ=40.79;MQ0=0;MQRankSum=-5.372;QD=6.01;ReadPosRankSum=7.135;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. 0/0:2,0:2:3.01:0,3,40 0/0:3,0:3:9.03:0,9,121 0/0:1,0:1:3.01:0,3,41 0/0:3,2:5:9.03:0,9,121 0/0:5,0:5:12.04:0,12,150 0/0:5,0:5:15.05:0,15,190 0/0:2,0:2:6.02:0,6,81 ./. 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,32 ./. 0/1:1,2:3:24.41:58,0,24 0/0:1,0:1:3.01:0,3,40 ./. 0/0:1,0:1:3.01:0,3,39 0/1:3,1:4:17.66:18,0,68 1/1:0,3:3:6.01:59,6,0 0/1:2,2:4:26.23:55,0,26 0/1:1,1:2:27.42:27,0,32 0/1:1,1:2:27.42:27,0,27 0/1:1,1:2:25.53:27,0,26 0/0:1,1:2:3.01:0,3,34 0/0:3,1:4:6.02:0,6,71 0/0:1,0:1:3.01:0,3,30 ./. ./. 0/0:2,0:2:3.01:0,3,35 0/0:5,1:6:12.04:0,12,146 ./. 0/1:1,1:2:27.42:27,0,35 0/0:1,0:1:3.01:0,3,34 ./. ./. 0/0:1,0:1:3.01:0,3,35 1/1:1,1:2:3:26,3,0 ./. 0/1:3,5:8:51.83:52,0,85 0/1:5,4:9:16.51:17,0,121 0/0:2,0:2:3.01:0,3,38 0/1:5,3:8:21.40:21,0,99 0/0:1,1:2:3.01:0,3,33 0/0:2,0:2:3.01:0,3,40 0/1:3,2:5:24.58:25,0,27 0/0:4,0:4:9.03:0,9,108 0/1:2,1:3:19.67:20,0,33 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:3.01:0,3,33 0/1:1,2:4:27.42:27,0,32 ./. ./. 0/0:3,1:6:3.01:0,3,33 1/1:0,3:3:3.01:33,3,0 0/0:1,1:2:3.01:0,3,33 0/1:5,2:7:46.94:47,0,117 0/1:2,8:10:21.40:87,0,21 0/1:1,1:2:16.68:17,0,35 ./. -chr1 1219495 . GT G 259.6 . AC=33;AF=0.434;AN=76;BaseQRankSum=1.135;DP=118;FS=0.000;HRun=1;HaplotypeScore=47.6513;InbreedingCoeff=0.0098;MQ=32.06;MQ0=0;MQRankSum=-2.879;QD=3.05;ReadPosRankSum=1.806;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. 0/1:1,0:1:0:0,0,0 0/0:2,0:2:2.80:0,3,13 ./. 0/0:1,0:1:3.01:0,3,35 ./. ./. 0/0:1,0:1:3.01:0,3,36 ./. ./. 0/1:3,0:3:17.03:33,0,17 ./. ./. ./. 0/1:3,0:3:7.32:7,0,32 0/1:3,0:3:3.60:4,0,4 0/1:4,0:4:3.24:9,0,3 0/0:1,0:1:2.97:0,3,20 1/1:1,0:1:2.92:17,3,0 1/1:2,0:2:4.25:36,4,0 0/0:3,0:3:0.99:0,1,33 0/1:3,0:3:17.51:18,0,27 0/0:1,0:1:2.04:0,2,6 ./. 1/1:1,0:1:2.22:7,2,0 0/0:1,0:1:3:0,3,26 1/1:2,0:2:2.68:11,3,0 ./. 0/1:2,0:2:11.62:12,0,24 ./. ./. ./. 1/1:1,0:1:2.84:14,3,0 1/1:1,1:2:5.16:25,5,0 0/0:2,0:2:5.01:0,5,27 0/1:9,0:9:39.95:40,0,51 0/0:5,0:5:3.19:0,3,59 ./. 0/1:5,2:7:12.10:12,0,52 0/0:3,0:3:3.01:0,3,31 0/0:2,0:2:4.25:0,4,37 1/1:3,1:4:2.59:23,3,0 0/1:2,1:3:0.48:0,0,1 0/1:4,0:4:3.61:4,0,35 ./. 0/1:2,0:2:0:0,0,0 1/1:5,0:5:7.57:49,8,0 ./. ./. 0/1:7,0:7:34.40:35,0,34 0/0:4,0:4:4.88:0,5,20 0/0:1,0:1:2.99:0,3,23 0/1:4,0:4:27.04:27,0,34 0/1:9,1:10:8.53:9,0,43 0/0:2,0:2:3.01:0,3,33 1/1:2,0:2:2.84:14,3,0 -chr1 1219503 . GTT G 181.28 . AC=26;AF=0.481;AN=54;BaseQRankSum=1.078;DP=79;FS=0.000;HRun=2;HaplotypeScore=43.9645;InbreedingCoeff=0.2483;MQ=29.00;MQ0=0;MQRankSum=1.524;QD=4.90;ReadPosRankSum=-0.049;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:0.47:0,0,1 ./. ./. ./. ./. 0/1:0,1:1:0:0,0,0 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:1,1:2:5.23:43,5,0 ./. 0/0:0,1:1:0.47:0,0,1 ./. ./. 0/1:1,1:2:5.43:6,0,5 0/0:2,1:3:8.76:0,9,95 0/0:1,0:1:3.01:0,3,55 1/1:0,1:1:2.98:22,3,0 1/1:1,1:2:5.72:33,6,0 0/1:1,1:2:4.06:4,0,48 ./. ./. ./. 1/1:1,0:1:0.47:1,0,0 ./. 0/0:1,0:1:3.01:0,3,37 ./. 1/1:1,0:1:2.99:23,3,0 ./. ./. ./. 1/1:0,1:1:2.98:21,3,0 0/1:2,0:2:1.41:1,0,26 0/0:1,1:2:3.99:0,4,15 0/1:6,2:8:44.63:45,0,142 1/1:2,0:2:1.81:5,2,0 ./. 0/0:5,1:6:5.75:0,6,42 ./. ./. 0/0:1,1:3:0.60:0,1,4 ./. 1/1:0,1:1:3:27,3,0 ./. ./. 1/1:2,3:5:8:52,8,0 ./. ./. 0/0:5,1:6:0.83:0,1,95 0/1:2,2:4:0.11:0,0,8 ./. 0/0:1,0:1:2.99:0,3,24 0/0:5,3:8:4.04:0,4,85 ./. 1/1:0,2:2:0.50:4,1,0 -chr1 1219508 . GTGA G 294.79 . AC=34;AF=0.586;AN=58;BaseQRankSum=0.768;DP=70;FS=4.559;HRun=0;HaplotypeScore=41.3138;InbreedingCoeff=0.0804;MQ=29.00;MQ0=0;MQRankSum=2.030;QD=5.67;ReadPosRankSum=0.867;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. 1/1:1,0:1:2.37:8,2,0 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:2,0:2:5.91:38,6,0 ./. 0/0:1,0:1:0:0,0,0 ./. ./. 1/1:1,0:1:2.80:13,3,0 0/1:2,1:3:17.35:17,0,22 0/0:1,0:1:3.01:0,3,63 1/1:1,0:1:3:27,3,0 1/1:0,1:1:2.92:17,3,0 0/1:3,0:3:15.41:15,0,56 ./. ./. ./. 1/1:1,0:1:2.50:9,2,0 ./. 0/0:1,0:1:3:0,3,25 ./. 0/1:1,0:1:0:0,0,0 ./. ./. ./. 1/1:0,1:1:2.88:15,3,0 0/1:2,0:2:2.13:2,0,28 0/1:2,0:2:11.72:12,0,12 0/1:5,1:6:72.98:73,0,100 1/1:1,1:2:2.27:10,2,0 ./. 0/0:5,0:5:1.81:0,2,8 0/0:1,0:2:0:0,0,0 ./. 0/0:2,1:3:1.30:0,1,9 0/1:1,0:1:0:0,0,0 1/1:0,0:1:3:27,3,0 ./. 0/1:2,0:2:0:0,0,0 1/1:4,1:5:7.72:45,8,0 ./. ./. 0/1:3,0:4:12.56:19,0,13 0/1:4,0:4:3.42:3,0,13 ./. 0/0:1,0:1:2.37:0,2,8 1/1:4,0:6:5.90:36,6,0 ./. 1/1:1,1:2:3.99:14,4,0 -chr1 1219522 . GTC G 520.05 . AC=42;AF=0.750;AN=56;BaseQRankSum=-1.486;DP=62;FS=0.000;HRun=0;HaplotypeScore=40.8056;InbreedingCoeff=0.1654;MQ=29.00;MQ0=0;MQRankSum=0.412;QD=10.61;ReadPosRankSum=2.095;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:38,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 1/1:1,1:2:3.84:13,4,0 ./. 0/0:0,1:1:0.47:0,0,1 ./. ./. 1/1:0,1:1:3.01:43,3,0 0/0:1,1:2:2.72:0,3,12 ./. 1/1:0,1:1:2.92:17,3,0 1/1:0,1:1:2.90:16,3,0 1/1:1,1:2:2.92:51,3,0 1/1:1,0:1:1.82:5,2,0 ./. ./. 1/1:1,0:1:3.01:47,3,0 0/0:1,0:1:2.74:0,3,12 ./. ./. ./. ./. ./. ./. 1/1:0,1:1:2.94:18,3,0 1/1:0,1:1:2.04:6,2,0 1/1:0,2:2:5.98:54,6,0 0/1:1,2:3:35.24:55,0,35 0/0:2,2:4:2.65:0,3,16 ./. 1/1:1,1:2:0.47:1,0,0 ./. ./. 0/0:1,1:2:2.04:0,2,6 ./. 1/1:0,1:1:2.99:24,3,0 ./. 1/1:1,1:2:2.22:7,2,0 1/1:4,2:6:6.62:59,7,0 1/1:1,1:2:3.01:43,3,0 ./. 0/1:0,3:3:5.92:17,0,6 0/1:4,1:5:4.37:36,0,4 0/1:1,0:1:0:0,0,0 1/1:2,0:2:2.03:4,2,0 1/1:4,2:6:2.96:20,3,0 ./. 1/1:0,2:2:5.75:43,6,0 -chr1 1219534 . GTT G 272.36 . AC=31;AF=0.534;AN=58;BaseQRankSum=0.856;DP=61;FS=0.000;HRun=2;HaplotypeScore=38.8244;InbreedingCoeff=0.3057;MQ=29.00;MQ0=0;MQRankSum=1.124;QD=6.64;ReadPosRankSum=0.386;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. 0/0:1,0:1:2.50:0,2,9 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:0,1:1:0.47:0,0,1 ./. ./. 1/1:0,0:1:1.82:5,2,0 0/0:2,0:2:2.74:0,3,12 ./. 0/1:0,0:1:0:0,0,0 0/1:1,0:1:0:0,0,0 1/1:0,2:2:1.73:5,2,0 0/0:1,0:1:3:0,3,28 ./. ./. 0/0:1,0:1:1.55:0,2,4 1/1:0,1:1:2.98:21,3,0 ./. ./. ./. ./. ./. ./. 1/1:1,0:1:2.50:9,2,0 1/1:1,0:1:2.04:6,2,0 0/1:0,0:2:7.68:27,0,8 0/0:2,0:3:2.80:0,3,13 0/1:1,0:3:0.23:0,0,0 ./. 0/0:1,0:1:0.89:0,1,2 ./. 1/1:0,1:1:3:26,3,0 1/1:0,3:4:8.93:73,9,0 0/1:0,1:1:0:0,0,0 0/0:1,0:1:1.25:0,1,3 ./. 1/1:1,2:4:8.09:43,8,0 1/1:4,0:6:11.11:56,11,0 0/0:1,0:2:3.01:0,3,33 ./. 0/1:0,3:3:5.90:23,0,6 0/0:3,1:4:3.17:0,3,60 0/1:1,0:1:0:0,0,0 1/1:2,0:2:4.56:36,5,0 1/1:2,1:5:3.01:32,3,0 ./. 1/1:1,0:1:2.84:14,3,0 -chr1 1219556 . GTT G 904.28 . AC=38;AF=0.826;AN=46;BaseQRankSum=2.314;DP=45;FS=0.000;HRun=2;HaplotypeScore=34.7120;InbreedingCoeff=0.2326;MQ=29.00;MQ0=0;MQRankSum=-0.104;QD=23.80;ReadPosRankSum=0.656;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:46,3,0 ./. ./. 1/1:1,0:1:2.80:13,3,0 1/1:0,1:1:3.01:42,3,0 ./. 0/0:1,0:1:0:0,0,0 ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 0/0:1,0:1:2.99:0,3,24 ./. ./. ./. ./. ./. ./. 1/1:1,0:1:3.01:37,3,0 1/1:0,2:2:4.26:50,4,0 0/0:0,1:1:0:0,0,0 1/1:2,1:3:5.78:58,6,0 0/0:1,0:1:3.01:0,3,30 ./. 1/1:1,0:1:3.01:46,3,0 1/1:1,0:1:3.01:40,3,0 1/1:4,0:4:12.04:149,12,0 1/1:0,1:1:3.01:45,3,0 ./. ./. 1/1:2,2:4:9.83:90,10,0 1/1:1,2:3:7.73:57,8,0 1/1:0,1:1:2.99:24,3,0 ./. 1/1:1,1:2:4.82:37,5,0 1/1:1,3:4:11.06:106,11,0 1/1:1,0:1:1.82:5,2,0 1/1:0,1:1:2.96:19,3,0 1/1:2,3:5:6.02:78,6,0 ./. ./. -chr1 1219565 . GTT G 199.22 . AC=18;AF=0.450;AN=40;BaseQRankSum=1.357;DP=40;FS=3.680;HRun=2;HaplotypeScore=38.8961;InbreedingCoeff=0.2109;MQ=29.00;MQ0=0;MQRankSum=-0.222;QD=7.38;ReadPosRankSum=-1.209;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000453732|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:1,0:1:3.01:33,3,0 ./. ./. ./. 0/0:0,1:1:0.47:0,0,1 ./. 1/1:1,0:1:0.47:1,0,0 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:0.47:0,0,1 0/0:1,0:1:2.92:0,3,17 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:2.74:0,3,12 1/1:1,1:2:2.98:21,3,0 1/1:1,0:1:0.47:1,0,0 0/1:2,0:2:0.23:0,0,0 0/0:1,0:1:3.01:0,3,54 ./. 0/0:1,0:1:3:0,3,27 0/0:1,0:1:0.89:0,1,2 0/1:4,0:4:0.12:39,0,0 0/0:1,0:1:2.84:0,3,14 ./. ./. 1/1:4,0:4:4.77:18,5,0 0/0:3,0:3:2.08:0,2,21 ./. ./. 0/1:3,0:3:8.91:9,0,46 1/1:1,2:3:6.02:91,6,0 ./. 1/1:0,1:1:2.04:6,2,0 0/1:5,0:5:24.44:65,0,24 ./. ./. -chr1 1220765 . C T 169.99 . AC=1;AF=0.011;AN=92;BaseQRankSum=0.603;DP=202;Dels=0.00;FS=9.170;HRun=0;HaplotypeScore=0.1511;InbreedingCoeff=-0.0821;MQ=58.15;MQ0=0;MQRankSum=1.246;QD=18.89;ReadPosRankSum=0.238;EFF=DOWNSTREAM(MODIFIER|||||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000230415|RP5-902P8.10|ENST00000434139|||||lincRNA|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:2,0:2:6.02:0,6,82 ./. ./. 0/0:2,0:2:6.02:0,6,82 ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. 0/0:4,0:4:12.04:0,12,162 0/0:2,0:2:6.02:0,6,76 0/0:2,0:2:6.01:0,6,68 0/0:2,0:2:3.01:0,3,45 0/0:4,0:4:12.04:0,12,162 0/0:4,0:4:9.03:0,9,124 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,72 0/0:1,0:1:2.99:0,3,24 0/0:5,0:5:15.05:0,15,197 0/0:1,0:1:3.01:0,3,42 ./. ./. 0/0:3,0:3:9.03:0,9,119 ./. 0/0:2,0:2:3.01:0,3,31 0/0:3,0:3:6.02:0,6,83 0/0:3,0:3:9.02:0,9,109 0/0:3,0:3:9.03:0,9,122 ./. 0/0:3,0:3:9.02:0,9,109 0/0:2,0:2:6.02:0,6,76 0/0:3,0:3:9.03:0,9,118 0/0:7,0:7:21.07:0,21,264 0/0:10,0:10:24.08:0,24,309 0/0:10,0:10:24.07:0,24,304 0/0:5,0:5:15.05:0,15,202 0/0:6,0:6:18.06:0,18,240 0/0:3,0:3:9.03:0,9,112 0/0:4,0:4:12.04:0,12,145 0/0:13,0:13:39.12:0,39,498 0/0:19,0:19:51.13:0,51,637 0/0:4,0:4:12.04:0,12,158 0/0:9,0:9:24.08:0,24,312 0/1:2,7:9:46.05:216,0,46 0/0:7,0:7:21.05:0,21,269 0/0:6,0:6:18.06:0,18,246 0/0:4,0:4:12.04:0,12,163 0/0:4,0:4:9.03:0,9,125 0/0:1,0:1:3.01:0,3,40 0/0:5,0:5:15.05:0,15,196 0/0:8,0:8:24.08:0,24,306 0/0:6,0:6:18.06:0,18,228 0/0:2,0:2:6.02:0,6,81 0/0:3,0:3:9.03:0,9,117 -chr1 1220822 . G A 282.41 . AC=1;AF=0.0096;AN=104;BaseQRankSum=-0.135;DP=459;Dels=0.00;FS=7.514;HRun=0;HaplotypeScore=0.1948;InbreedingCoeff=-0.0472;MQ=57.39;MQ0=0;MQRankSum=-0.080;QD=14.12;ReadPosRankSum=0.116;EFF=INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|2),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|5),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),INTRON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:4,0:4:12.03:0,12,142 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,34 ./. 0/0:1,0:1:3.01:0,3,37 ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:5,0:5:12.04:0,12,157 0/0:7,0:7:21.07:0,21,283 0/0:4,0:4:12.04:0,12,149 0/0:4,0:4:12.04:0,12,156 0/0:3,0:3:9.03:0,9,115 0/0:8,0:8:21.07:0,21,274 0/0:4,1:5:12.04:0,12,152 0/0:4,0:4:9.01:0,9,102 0/0:8,0:8:21.06:0,21,265 0/0:5,0:5:9.03:0,9,114 0/0:9,0:9:27.09:0,27,364 0/0:9,0:9:21.07:0,21,274 0/0:3,0:3:9.03:0,9,112 0/0:5,0:5:12.04:0,12,163 0/0:2,0:2:6.02:0,6,82 0/0:8,0:8:21.06:0,21,250 ./. 0/0:6,0:6:18.05:0,18,235 0/0:2,0:2:6.02:0,6,78 0/0:4,0:4:9.02:0,9,101 0/0:11,0:11:30.09:0,30,392 0/0:2,0:2:6.02:0,6,72 0/0:3,0:3:6.02:0,6,87 0/0:2,0:2:6.02:0,6,75 0/0:8,0:8:21.06:0,21,263 0/0:18,0:18:45.14:0,45,591 0/0:19,0:19:54.14:0,54,665 0/0:17,0:17:48.15:0,48,605 0/0:21,0:21:57.17:0,57,706 0/0:17,0:17:42.12:0,42,556 0/0:9,0:9:27.08:0,27,342 0/0:13,0:13:30.10:0,30,391 0/0:23,0:23:63.19:0,63,803 0/0:24,1:25:63.19:0,63,803 0/0:7,0:8:21.06:0,21,259 0/0:18,0:18:51.15:0,51,642 0/1:9,10:20:99:329,0,238 0/0:21,0:22:57.18:0,57,753 0/0:15,0:15:45.13:0,45,576 0/0:13,0:13:39.13:0,39,507 0/0:13,0:13:30.10:0,30,391 0/0:9,0:9:24.07:0,24,298 0/0:11,0:11:33.10:0,33,409 0/0:11,0:11:30.09:0,30,380 0/0:6,0:6:15.05:0,15,189 0/0:7,0:7:18.06:0,18,228 0/0:8,0:8:21.04:0,21,252 -chr1 1220954 . G A 9088.59 . AC=17;AF=0.1574;AN=108;BaseQRankSum=-2.368;DP=1910;Dels=0.00;FS=13.820;HRun=0;HaplotypeScore=1.1187;InbreedingCoeff=0.4214;MQ=58.61;MQ0=0;MQRankSum=-0.837;QD=20.20;ReadPosRankSum=-1.798;EFF=EXON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|4),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A24T|669|SCNN1D|protein_coding|CODING|ENST00000379110|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S156|802|SCNN1D|protein_coding|CODING|ENST00000379116|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S58|704|SCNN1D|protein_coding|CODING|ENST00000325425|);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000467651|4/4||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,synonymous_variant|tcG/tcA|S|ENSG00000162572|SCNN1D|ENST00000325425|3/15|||58/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,synonymous_variant|tcG/tcA|S|ENSG00000162572|SCNN1D|ENST00000379116|6/18|||156/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:2,0:2:6.02:0,6,79 ./. 0/0:2,0:2:3.01:0,3,38 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.02:0,6,79 ./. ./. ./. 0/0:24,0:24:57.19:0,57,787 0/0:38,0:39:93.29:0,93,1218 0/0:13,0:13:36.12:0,36,482 0/0:17,0:17:45.14:0,45,588 0/0:15,0:15:36.11:0,36,472 0/0:32,0:32:78.23:0,78,1028 0/0:21,0:21:45.12:0,45,584 0/0:25,1:26:30.47:0,30,858 0/0:43,0:43:99:0,102,1337 0/0:19,0:19:45.14:0,45,579 0/1:18,8:26:99:194,0,439 0/0:23,0:23:54.17:0,54,701 0/0:20,0:20:39.13:0,39,527 1/1:0,15:15:39.12:505,39,0 0/0:20,0:20:51.16:0,51,674 0/0:17,1:19:15.52:0,16,519 0/0:31,0:31:75.24:0,75,1020 0/0:37,0:37:93.27:0,93,1217 0/1:14,8:22:99:224,0,332 0/0:24,0:24:60.17:0,60,782 1/1:0,27:27:81.24:1034,81,0 0/1:14,17:31:99:517,0,390 0/0:24,0:24:54.17:0,54,734 0/1:15,13:29:99:376,0,384 0/0:39,0:39:90.30:0,90,1238 0/0:59,0:59:99:0,144,1807 0/0:81,0:81:99:0,202,2576 0/0:61,0:63:99:0,141,1881 0/0:46,0:47:99:0,114,1485 0/0:55,0:55:99:0,123,1653 0/0:40,0:40:87.27:0,87,1154 1/1:0,33:33:75.24:963,75,0 0/0:72,0:72:99:0,159,2110 0/0:105,0:106:99:0,256,3258 0/1:16,14:30:99:379,0,409 0/0:69,0:69:99:0,150,2032 1/1:0,71:72:99:2149,169,0 0/0:61,0:61:99:0,138,1747 0/0:68,2:71:99:0,115,1986 0/1:27,38:65:99:880,0,792 0/0:50,1:51:70.54:0,71,1342 1/1:0,55:56:99:1473,111,0 0/1:24,18:44:99:395,0,664 0/0:54,0:54:99:0,129,1715 0/0:46,0:46:99:0,99,1312 0/0:34,0:34:78.24:0,78,1028 0/0:51,0:52:99:0,120,1551 -chr1 1221001 . A G 1982.19 . AC=3;AF=0.0273;AN=110;BaseQRankSum=-1.350;DP=1904;Dels=0.00;FS=4.488;HRun=1;HaplotypeScore=1.2454;InbreedingCoeff=0.3709;MQ=58.84;MQ0=0;MQRankSum=-1.238;QD=25.09;ReadPosRankSum=0.484;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q172R|802|SCNN1D|protein_coding|CODING|ENST00000379116|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cGg|Q74R|704|SCNN1D|protein_coding|CODING|ENST00000325425|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A39|669|SCNN1D|protein_coding|CODING|ENST00000379110|);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,missense_variant|cAg/cGg|Q/R|ENSG00000162572|SCNN1D|ENST00000325425|3/15|benign(0.108)|deleterious(0.04)|74/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,missense_variant|cAg/cGg|Q/R|ENSG00000162572|SCNN1D|ENST00000379116|6/18|benign(0.108)|deleterious(0.01)|172/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:9.02:0,9,108 ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 0/0:5,0:5:15.05:0,15,201 0/0:2,0:2:6.02:0,6,75 ./. 0/0:2,0:2:3.01:0,3,31 ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:35,0:35:93.30:0,93,1249 0/0:49,0:49:99:0,111,1509 0/0:18,0:18:42.10:0,42,532 0/0:18,0:18:42.12:0,42,548 0/0:27,0:27:57.18:0,57,756 0/0:34,0:34:84.27:0,84,1120 0/0:23,0:23:63.17:0,63,795 0/0:38,0:38:87.28:0,87,1187 0/0:44,0:44:99:0,105,1401 0/0:26,0:26:66.21:0,66,875 0/0:35,0:35:84.26:0,84,1110 0/0:29,0:29:66.21:0,66,898 0/0:29,0:29:66.20:0,66,866 0/0:24,0:24:63.18:0,63,818 0/0:31,0:32:72.23:0,72,960 0/0:25,0:25:63.17:0,63,804 0/0:38,0:38:93.29:0,93,1214 0/0:37,0:37:84.26:0,84,1111 0/0:33,0:33:75.24:0,75,1010 0/0:33,0:34:69.23:0,69,960 0/0:43,0:43:93.30:0,93,1244 0/0:38,0:38:81.24:0,81,1091 0/0:33,0:33:69.22:0,69,960 0/0:39,0:39:96.29:0,96,1272 0/0:41,0:41:96.28:0,96,1283 0/0:44,0:46:99:0,105,1385 0/0:66,0:66:99:0,165,2165 0/0:51,0:51:99:0,135,1757 0/0:52,0:52:99:0,123,1653 0/0:47,0:47:99:0,111,1501 0/0:37,0:37:87.28:0,87,1169 0/1:12,21:33:99:518,0,319 0/0:62,0:62:99:0,147,1951 0/0:88,0:88:99:0,211,2722 0/0:20,0:21:54.15:0,54,686 0/0:52,1:53:76.15:0,76,1518 1/1:0,46:46:99:1549,120,0 0/0:62,0:62:99:0,150,1975 0/0:67,0:67:99:0,156,2083 0/0:63,0:64:99:0,141,1836 0/0:47,0:47:99:0,111,1494 0/0:44,0:44:99:0,105,1413 0/0:36,0:37:90.28:0,90,1195 0/0:40,0:40:99:0,99,1313 0/0:34,0:35:84.27:0,84,1109 0/0:30,0:30:72.23:0,72,950 0/0:38,0:38:84.27:0,84,1122 -chr1 1221018 . C T 150.26 . AC=1;AF=0.0088;AN=114;BaseQRankSum=1.476;DP=1708;Dels=0.00;FS=1.441;HRun=0;HaplotypeScore=0.9012;InbreedingCoeff=-0.0297;MQ=58.90;MQ0=0;MQRankSum=0.438;QD=6.83;ReadPosRankSum=2.382;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H178Y|802|SCNN1D|protein_coding|CODING|ENST00000379116|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Tac|H80Y|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A45V|669|SCNN1D|protein_coding|CODING|ENST00000379110|);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,missense_variant|Cac/Tac|H/Y|ENSG00000162572|SCNN1D|ENST00000325425|3/15|benign(0.022)|tolerated(0.53)|80/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,missense_variant|Cac/Tac|H/Y|ENSG00000162572|SCNN1D|ENST00000379116|6/18|benign(0.022)|tolerated(0.15)|178/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,74 ./. ./. 0/0:4,0:4:12.04:0,12,164 0/0:1,0:1:3.01:0,3,41 0/0:5,0:5:15.05:0,15,190 0/0:2,0:2:6.02:0,6,75 ./. 0/0:1,0:1:3.01:0,3,30 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,82 0/0:33,0:33:87.29:0,87,1189 0/0:47,1:48:99:0,120,1607 0/0:19,0:19:48.15:0,48,624 0/0:24,0:24:60.19:0,60,793 0/0:23,0:23:57.16:0,57,757 0/0:37,0:37:84.27:0,84,1134 0/1:14,8:22:99:198,0,396 0/0:37,0:37:87.27:0,87,1177 0/0:43,0:43:99:0,102,1350 0/0:25,0:25:60.19:0,60,799 0/0:33,0:33:81.25:0,81,1064 0/0:24,1:25:32.74:0,33,765 0/0:29,0:29:69.22:0,69,931 0/0:27,0:27:66.22:0,66,894 0/0:28,0:28:66.22:0,66,899 0/0:26,0:26:66.16:0,66,829 0/0:40,0:40:99:0,99,1304 0/0:33,0:33:84.24:0,84,1086 0/0:32,0:32:72.24:0,72,982 0/0:30,0:30:72.24:0,72,977 0/0:46,0:46:96.29:0,96,1276 0/0:34,0:34:78.26:0,78,1071 0/0:35,0:36:75.25:0,75,1041 0/0:39,0:39:99:0,99,1319 0/0:40,0:40:99:0,102,1358 0/0:36,0:36:90.29:0,90,1158 0/0:59,0:59:99:0,141,1812 0/0:40,0:40:99:0,117,1477 0/0:41,0:41:99:0,105,1370 0/0:34,0:34:93.30:0,93,1233 0/0:35,0:35:87.26:0,87,1134 0/0:28,0:28:81.23:0,81,1000 0/0:48,0:48:99:0,117,1513 0/0:75,0:75:99:0,184,2337 0/0:16,0:16:39.12:0,39,484 0/0:37,0:37:87.29:0,87,1191 0/0:40,0:40:99:0,102,1303 0/0:59,0:59:99:0,153,1961 0/0:52,0:52:99:0,126,1664 0/0:61,0:61:99:0,141,1835 0/0:37,0:37:96.30:0,96,1254 0/0:34,0:34:90.29:0,90,1199 0/0:32,0:32:81.23:0,81,1057 0/0:33,0:33:87.28:0,87,1145 0/0:29,0:29:75.24:0,75,989 0/0:29,0:29:72.23:0,72,935 0/0:22,1:24:27.98:0,28,791 -chr1 1221054 . G T 326.69 . AC=1;AF=0.0086;AN=116;BaseQRankSum=-1.105;DP=1276;Dels=0.00;FS=1.144;HRun=1;HaplotypeScore=0.9866;InbreedingCoeff=-0.0243;MQ=58.76;MQ0=0;MQRankSum=-1.148;QD=13.07;ReadPosRankSum=0.107;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|7),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|3),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|6),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,34 ./. 0/0:4,0:4:12.03:0,12,140 0/0:1,0:1:3.01:0,3,30 0/0:4,0:4:12.04:0,12,160 0/0:4,0:4:12.04:0,12,161 0/0:5,0:5:15.04:0,15,189 0/0:2,0:2:6.02:0,6,82 0/0:3,0:3:6.02:0,6,82 0/0:3,0:3:9.03:0,9,124 0/0:1,0:1:3.01:0,3,41 ./. 0/0:3,0:3:9.03:0,9,124 0/0:29,0:29:72.23:0,72,961 0/0:38,0:38:99:0,99,1335 0/0:21,0:21:48.15:0,48,642 0/0:24,0:24:60.20:0,60,821 0/0:22,0:22:54.17:0,54,720 0/0:36,0:36:90.29:0,90,1196 0/0:19,0:20:48.12:0,48,612 0/0:24,0:24:72.24:0,72,964 0/0:31,0:31:81.26:0,81,1081 0/0:21,0:21:51.17:0,51,682 0/0:22,0:22:51.17:0,51,687 0/0:20,0:20:48.15:0,48,633 0/0:26,0:26:60.19:0,60,813 0/0:24,0:24:54.18:0,54,734 0/0:27,0:27:66.22:0,66,892 0/0:23,0:24:51.16:0,51,675 0/0:25,0:25:60.20:0,60,820 0/0:27,0:27:63.20:0,63,851 0/0:28,2:31:24.46:0,24,851 0/0:30,0:30:78.25:0,78,1023 0/0:40,0:40:99:0,105,1372 0/0:27,0:27:66.21:0,66,896 0/0:26,0:26:63.20:0,63,843 0/0:26,0:26:69.22:0,69,925 0/0:30,0:30:75.24:0,75,1022 0/0:21,0:21:60.17:0,60,767 0/0:40,0:40:99:0,111,1422 0/0:29,0:29:84.27:0,84,1090 0/0:29,0:29:78.24:0,78,1006 0/0:23,0:23:63.20:0,63,840 0/0:23,0:23:63.18:0,63,803 0/0:16,0:16:42.13:0,42,533 0/0:27,0:27:78.25:0,78,1027 0/0:48,0:48:99:0,126,1618 0/0:11,0:11:30.08:0,30,359 0/0:24,0:24:66.21:0,66,869 0/1:12,13:25:99:374,0,401 0/0:40,0:40:99:0,117,1487 0/0:35,0:35:99:0,99,1270 0/0:40,0:40:99:0,114,1510 0/0:21,0:21:54.17:0,54,704 0/0:18,0:18:42.14:0,42,568 0/0:22,0:22:54.18:0,54,728 0/0:25,0:25:69.22:0,69,915 0/0:20,0:20:60.19:0,60,781 0/0:23,0:23:57.18:0,57,773 0/0:14,0:14:39.13:0,39,513 -chr1 1221055 . A G 407.9 . AC=1;AF=0.0085;AN=118;BaseQRankSum=-2.031;DP=1272;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.9531;InbreedingCoeff=-0.0269;MQ=58.74;MQ0=0;MQRankSum=-1.920;QD=14.57;ReadPosRankSum=-0.545;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|7),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|3),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|6),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,38 ./. 0/0:4,0:4:12.04:0,12,156 0/0:1,0:1:3.01:0,3,36 0/0:4,0:4:12.04:0,12,158 0/0:5,0:5:15.05:0,15,195 0/0:6,0:6:18.04:0,18,221 0/0:2,0:2:6.02:0,6,82 0/0:3,0:3:6.02:0,6,82 0/0:3,0:3:9.03:0,9,122 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,118 0/0:30,0:30:75.24:0,75,997 0/0:38,0:38:99:0,99,1311 0/0:21,0:21:51.13:0,51,646 0/0:23,0:23:60.19:0,60,802 0/0:22,0:22:54.17:0,54,712 0/0:36,0:36:90.28:0,90,1174 0/0:19,0:20:45.15:0,45,600 0/0:23,0:23:69.21:0,69,906 0/0:31,0:31:78.25:0,78,1036 0/0:21,0:21:51.15:0,51,667 0/0:22,0:22:51.16:0,51,675 0/0:19,0:19:45.12:0,45,585 0/0:26,0:26:60.19:0,60,813 0/0:24,0:24:54.17:0,54,730 0/0:26,0:26:66.22:0,66,878 0/0:23,1:24:45.15:0,45,612 0/0:26,0:26:63.20:0,63,846 0/0:27,0:27:63.20:0,63,844 0/0:30,0:30:63.21:0,63,871 0/0:30,0:30:75.24:0,75,983 0/0:39,0:39:99:0,102,1350 0/0:26,0:26:66.21:0,66,892 0/0:26,0:26:63.21:0,63,850 0/0:25,0:25:69.22:0,69,911 0/0:29,0:30:69.23:0,69,945 0/0:20,0:21:57.18:0,57,748 0/0:39,0:39:99:0,108,1360 0/0:29,0:29:84.25:0,84,1061 0/0:29,0:29:72.22:0,72,937 0/0:22,0:23:63.18:0,63,834 0/0:22,0:23:63.18:0,63,792 0/0:16,0:16:45.14:0,45,569 0/0:27,1:28:38.25:0,38,961 0/0:47,0:48:99:0,126,1626 0/0:11,0:11:30.07:0,30,372 0/0:23,0:23:63.20:0,63,836 0/1:13,15:28:99:455,0,380 0/0:39,0:39:99:0,111,1415 0/0:35,1:36:93.28:0,93,1219 0/0:40,0:40:99:0,114,1506 0/0:19,0:20:51.16:0,51,666 0/0:18,0:18:42.14:0,42,563 0/0:21,0:21:51.17:0,51,693 0/0:24,0:25:69.22:0,69,906 0/0:19,0:19:57.18:0,57,752 0/0:23,0:23:57.18:0,57,772 0/0:13,1:14:39.12:0,39,501 -chr1 1221138 . G A 2422.14 . AC=12;AF=0.1000;AN=120;BaseQRankSum=1.373;DP=714;Dels=0.00;FS=4.157;HRun=0;HaplotypeScore=0.6978;InbreedingCoeff=0.2209;MQ=58.20;MQ0=0;MQRankSum=0.824;QD=19.38;ReadPosRankSum=-0.027;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|7),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|3),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|6),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,70 0/0:5,0:5:15.02:0,15,166 0/0:3,0:3:9.03:0,9,115 0/0:2,0:2:6.02:0,6,80 0/0:4,0:4:12.04:0,12,158 0/0:2,0:2:6.02:0,6,81 0/0:15,0:15:45.13:0,45,579 0/0:9,0:9:24.08:0,24,312 0/0:9,0:9:27.09:0,27,357 0/0:12,0:12:33.10:0,33,422 0/0:4,0:4:12.04:0,12,160 0/0:4,0:4:12.04:0,12,149 0/0:9,0:9:27.08:0,27,345 0/0:19,0:19:51.17:0,51,684 0/0:15,0:15:45.15:0,45,599 0/0:9,0:9:27.08:0,27,341 0/0:8,0:8:21.07:0,21,285 0/0:9,0:9:27.07:0,27,347 0/0:9,0:9:21.06:0,21,261 0/0:5,0:5:15.05:0,15,183 0/0:8,0:8:24.08:0,24,324 0/0:16,0:16:45.13:0,45,584 0/0:10,0:11:24.08:0,24,328 0/1:2,2:4:60.79:63,0,61 0/0:8,0:8:24.07:0,24,308 0/0:7,0:7:18.03:0,18,221 1/1:0,8:8:24.08:331,24,0 0/0:9,0:9:27.09:0,27,354 0/0:7,0:7:21.07:0,21,268 0/0:14,0:14:39.13:0,39,514 0/0:18,0:19:54.17:0,54,707 0/1:6,4:10:99:141,0,131 0/0:7,0:7:21.07:0,21,273 0/1:7,6:13:99:190,0,234 0/1:1,8:9:21.16:224,0,21 0/0:7,0:7:21.07:0,21,289 0/1:6,8:14:99:273,0,160 0/0:16,0:16:48.15:0,48,629 0/0:16,0:16:39.12:0,39,502 0/0:23,0:23:63.20:0,63,819 0/0:23,0:23:66.22:0,66,882 0/0:21,0:21:60.18:0,60,787 0/0:18,0:18:45.14:0,45,598 0/0:17,0:19:45.14:0,45,587 0/1:10,7:17:99:188,0,301 0/0:18,0:18:51.16:0,51,663 0/0:32,0:32:84.25:0,84,1077 0/0:5,0:6:12.04:0,12,159 0/0:13,0:13:33.11:0,33,437 0/0:23,0:23:66.18:0,66,814 0/0:19,0:19:54.15:0,54,661 0/0:16,0:16:45.14:0,45,563 0/1:5,12:17:99:416,0,136 0/0:11,0:11:33.10:0,33,414 1/1:1,16:17:45.12:551,45,0 0/1:5,11:16:99:222,0,157 0/0:14,0:14:30.10:0,30,410 0/0:9,0:9:27.08:0,27,340 0/0:11,0:11:27.09:0,27,352 0/0:13,0:13:36.10:0,36,449 -chr1 1221164 . T C 91.02 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.693;DP=688;Dels=0.00;FS=9.028;HRun=0;HaplotypeScore=0.7707;InbreedingCoeff=-0.0208;MQ=57.89;MQ0=0;MQRankSum=0.498;QD=11.38;ReadPosRankSum=-0.855;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|7),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|3),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|6),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,33 0/0:5,0:5:12.03:0,12,139 0/0:3,0:3:9.03:0,9,112 0/0:4,0:4:12.04:0,12,150 0/0:4,0:4:12.04:0,12,149 0/0:3,0:4:9.02:0,9,111 0/0:17,0:17:51.15:0,51,630 0/0:5,0:5:15.05:0,15,188 0/0:13,0:13:39.11:0,39,498 0/0:14,0:14:42.11:0,42,509 0/0:7,0:7:21.07:0,21,274 0/0:4,0:4:12.04:0,12,150 0/0:9,0:9:24.06:0,24,290 0/0:10,0:10:30.09:0,30,389 0/0:10,0:10:30.09:0,30,386 0/0:5,0:5:15.02:0,15,172 0/0:8,0:8:24.07:0,24,299 0/0:7,0:7:21.04:0,21,244 0/0:8,0:8:15.05:0,15,202 0/0:4,0:4:12.04:0,12,153 0/0:6,0:6:18.06:0,18,239 0/0:11,0:11:33.09:0,33,429 0/0:6,0:6:18.06:0,18,237 0/0:2,0:2:6.02:0,6,78 0/0:6,0:6:18.06:0,18,242 0/0:9,0:9:27.06:0,27,332 0/0:3,0:3:9.03:0,9,125 0/0:7,0:7:21.07:0,21,273 0/0:6,0:6:18.06:0,18,234 0/0:14,0:14:36.12:0,36,469 0/0:15,0:15:39.12:0,39,502 0/0:5,0:5:15.05:0,15,192 0/0:5,0:5:15.05:0,15,200 0/1:2,6:8:61.50:139,0,61 0/0:6,0:6:15.04:0,15,189 0/0:7,0:7:21.05:0,21,256 0/0:10,0:10:30.10:0,30,407 0/0:12,0:12:36.12:0,36,471 0/0:12,0:12:33.08:0,33,409 0/0:22,0:22:57.15:0,57,702 0/0:22,0:22:51.16:0,51,678 0/0:24,0:24:63.20:0,63,817 0/0:16,0:16:42.13:0,42,542 0/0:15,0:15:39.12:0,39,491 0/0:24,0:24:60.18:0,60,765 0/0:24,0:24:60.17:0,60,733 0/0:37,0:37:93.28:0,93,1150 0/0:7,0:7:18.06:0,18,223 0/0:13,0:13:33.10:0,33,423 0/0:25,0:25:69.19:0,69,849 0/0:24,0:24:66.20:0,66,821 0/0:17,0:17:48.15:0,48,621 0/0:17,0:17:48.15:0,48,610 0/0:16,0:16:45.13:0,45,546 0/0:13,0:13:33.08:0,33,393 0/0:18,0:18:42.10:0,42,529 0/0:20,0:20:42.12:0,42,524 0/0:13,0:15:36.07:0,36,428 0/0:8,0:9:21.06:0,21,262 0/0:18,0:18:45.13:0,45,573 -chr1 1221276 . C T 104.85 . AC=1;AF=0.0085;AN=118;BaseQRankSum=-1.022;DP=641;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.3777;InbreedingCoeff=-0.0348;MQ=57.84;MQ0=0;MQRankSum=1.773;QD=6.55;ReadPosRankSum=0.299;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|7),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|3),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|6),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:6:0,6,62 0/0:3,0:3:9.03:0,9,117 0/0:3,0:3:9:0,9,102 0/0:4,0:4:9.03:0,9,118 0/0:7,0:7:18.06:0,18,229 0/0:7,0:7:21.06:0,21,258 0/0:21,0:21:60.18:0,60,771 0/0:10,0:10:24.08:0,24,319 0/0:16,0:16:45.11:0,45,548 0/0:13,0:13:39.12:0,39,505 0/0:4,0:4:12.04:0,12,156 0/0:8,0:8:24.08:0,24,301 0/0:8,0:8:24.05:0,24,280 0/0:5,0:5:15.04:0,15,195 0/0:7,0:7:18.06:0,18,236 0/0:3,0:3:9.03:0,9,110 0/0:3,0:3:6.02:0,6,75 0/0:4,0:4:12.03:0,12,146 0/0:6,0:6:15.05:0,15,191 0/0:2,0:2:6.02:0,6,69 0/0:4,0:4:12.04:0,12,162 0/0:6,0:6:18.06:0,18,242 0/0:2,0:2:6.02:0,6,77 0/0:4,0:4:12.04:0,12,153 0/0:4,0:4:12.04:0,12,148 0/0:5,0:5:15.03:0,15,180 0/0:5,0:5:12.04:0,12,169 0/0:4,0:4:9.03:0,9,122 0/0:6,0:6:15.05:0,15,197 0/0:3,0:3:9.03:0,9,117 0/0:7,0:7:18.05:0,18,230 0/0:3,0:3:9.03:0,9,108 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,123 0/0:4,0:4:9.03:0,9,115 ./. 0/0:3,0:3:6.02:0,6,86 0/0:5,0:5:15.05:0,15,198 0/0:17,0:17:36.08:0,36,452 0/0:24,0:25:60.18:0,60,801 0/0:21,0:21:54.16:0,54,688 0/0:16,0:16:45.15:0,45,587 0/0:24,0:24:57.17:0,57,747 0/0:13,0:13:21.06:0,21,266 0/1:10,6:16:99:152,0,291 0/0:29,0:29:66.19:0,66,848 0/0:25,0:25:66.21:0,66,846 0/0:7,0:7:18.05:0,18,211 0/0:23,0:24:51.14:0,51,657 0/0:21,0:22:57.17:0,57,726 0/0:36,0:37:90.28:0,90,1151 0/0:33,0:33:78.24:0,78,988 0/0:23,0:23:60.19:0,60,779 0/0:10,0:10:27.08:0,27,339 0/0:20,0:20:51.13:0,51,640 0/0:11,0:11:24.08:0,24,320 0/0:6,0:6:18.06:0,18,239 0/0:21,0:22:51.16:0,51,673 0/0:16,0:16:30.10:0,30,428 0/0:18,0:18:39.13:0,39,518 -chr1 1221302 . A G 519.74 . AC=2;AF=0.0167;AN=120;BaseQRankSum=1.538;DP=606;Dels=0.00;FS=12.594;HRun=0;HaplotypeScore=0.3788;InbreedingCoeff=-0.0395;MQ=57.80;MQ0=0;MQRankSum=0.895;QD=14.85;ReadPosRankSum=-0.140;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|7),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|3),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|6),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5);CSQ=splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.02:0,9,99 0/0:1,0:1:3.01:0,3,30 0/0:4,0:4:12.04:0,12,151 0/0:3,0:3:9.01:0,9,94 0/0:6,0:6:18.06:0,18,241 0/0:5,0:5:15.05:0,15,198 0/0:22,0:22:63.19:0,63,801 0/0:11,0:11:33.08:0,33,399 0/0:21,0:21:63.20:0,63,822 0/0:12,0:13:33.10:0,33,403 0/0:6,0:6:18.06:0,18,234 0/0:12,0:12:33.07:0,33,402 0/0:11,0:11:33.10:0,33,427 0/0:7,0:7:21.07:0,21,276 0/0:6,0:6:15.04:0,15,186 0/0:2,0:2:6.02:0,6,78 0/0:6,0:6:18.06:0,18,222 0/0:2,0:2:6.02:0,6,77 0/0:6,0:6:12.04:0,12,157 0/0:4,0:4:9.03:0,9,118 0/0:4,0:4:12.04:0,12,159 0/0:6,0:6:18.06:0,18,232 0/0:2,0:2:6.02:0,6,80 0/0:3,0:3:9.03:0,9,117 0/0:6,0:6:15.05:0,15,200 0/0:4,0:4:12.03:0,12,147 0/0:6,0:6:15.05:0,15,194 0/0:4,0:4:12.04:0,12,149 0/0:9,0:9:24.08:0,24,319 0/0:3,0:3:9.03:0,9,114 0/0:7,0:7:18.06:0,18,231 0/0:5,0:5:12.04:0,12,163 0/0:3,0:3:9.01:0,9,98 0/0:5,0:5:15.05:0,15,201 0/0:3,0:3:9.02:0,9,107 0/0:3,0:3:9.03:0,9,111 0/0:3,0:3:9.03:0,9,122 0/0:12,0:12:33.09:0,33,415 0/0:10,0:11:18.06:0,18,254 0/0:23,0:24:60.19:0,60,776 0/0:14,0:14:36.10:0,36,449 0/0:16,0:16:42.13:0,42,543 0/0:18,0:18:54.17:0,54,699 0/0:10,0:10:24.07:0,24,308 0/1:7,7:14:99:233,0,228 0/0:25,0:25:66.19:0,66,841 0/0:27,0:28:72.17:0,72,865 0/0:7,0:7:18.06:0,18,222 0/0:21,0:21:54.14:0,54,676 0/1:10,11:21:99:352,0,337 0/0:31,0:33:75.19:0,75,954 0/0:26,0:26:63.20:0,63,804 0/0:18,0:18:45.14:0,45,579 0/0:8,0:8:24.08:0,24,321 0/0:14,0:14:42.13:0,42,540 0/0:8,0:8:21.07:0,21,269 0/0:6,0:6:18.06:0,18,232 0/0:16,0:16:39.11:0,39,507 0/0:15,0:15:33.11:0,33,439 0/0:14,0:14:36.11:0,36,464 -chr1 1221488 . CAA C 470.7 . AC=1;AF=0.0083;AN=120;BaseQRankSum=3.941;DP=1231;FS=0.000;HRun=2;HaplotypeScore=83.4816;InbreedingCoeff=-0.0140;MQ=58.74;MQ0=0;MQRankSum=-0.574;QD=21.40;ReadPosRankSum=1.386;EFF=DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),EXON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|6),FRAME_SHIFT(HIGH||-|-115|669|SCNN1D|protein_coding|CODING|ENST00000379110|9),FRAME_SHIFT(HIGH||-|-120|138|SCNN1D|protein_coding|CODING|ENST00000470022|4),FRAME_SHIFT(HIGH||-|-150|704|SCNN1D|protein_coding|CODING|ENST00000325425|4),FRAME_SHIFT(HIGH||-|-248|802|SCNN1D|protein_coding|CODING|ENST00000379116|7),FRAME_SHIFT(HIGH||-|-84|638|SCNN1D|protein_coding|CODING|ENST00000338555|4),FRAME_SHIFT(HIGH||-|-84|638|SCNN1D|protein_coding|CODING|ENST00000400928|3);CSQ=frameshift_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555|4/15|||84/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,frameshift_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101|6/17|||216-217/328|nonsense_mediated_decay|1,frameshift_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425|4/15|||150/704|protein_coding|1,frameshift_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000470022|4/4|||120/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,frameshift_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928|3/14|||84/638|protein_coding|1,frameshift_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116|7/18|||248/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.05:0,15,304 0/0:8,0:8:21.05:0,21,389 0/0:6,0:6:18.06:0,18,330 0/0:1,0:1:3.01:0,3,61 0/0:23,0:23:69.23:0,69,1353 0/0:20,0:20:60.20:0,60,1165 0/0:39,0:39:99:0,108,2166 0/0:14,0:14:42.14:0,42,854 0/0:42,0:42:99:0,123,2432 0/0:30,0:30:90.30:0,90,1772 0/0:18,0:18:51.18:0,51,1035 0/0:21,0:21:63.22:0,63,1281 0/0:26,0:26:78.27:0,78,1545 0/0:28,0:28:81.28:0,81,1638 0/0:24,0:24:66.23:0,66,1342 0/0:22,0:22:66.23:0,66,1329 0/1:9,13:22:99:527,0,425 0/0:21,0:21:63.21:0,63,1258 0/0:30,0:29:84.29:0,84,1673 0/0:21,0:21:63.22:0,63,1281 0/0:26,0:26:78.26:0,78,1532 0/0:36,0:36:99:0,105,2140 0/0:22,0:22:63.21:0,63,1242 0/0:22,0:22:66.23:0,66,1342 0/0:26,0:25:75.26:0,75,1525 0/0:25,0:25:72.24:0,72,1434 0/0:31,0:31:87.30:0,87,1766 0/0:28,0:28:81.27:0,81,1591 0/0:29,0:29:81.28:0,81,1645 0/0:19,0:19:51.17:0,51,1008 0/0:42,0:42:99:0,111,2227 0/0:24,0:24:69.24:0,69,1381 0/0:32,0:32:96.33:0,96,1950 0/0:28,0:28:81.27:0,81,1615 0/0:18,0:18:51.18:0,51,1037 0/0:38,0:38:99:0,108,2201 0/0:32,0:32:93.32:0,93,1882 0/0:35,0:35:99:0,99,2026 0/0:15,0:15:45.15:0,45,915 0/0:17,0:17:51.17:0,51,968 0/0:15,0:15:45.15:0,45,915 0/0:10,0:10:30.10:0,30,607 0/0:14,0:14:33.11:0,33,669 0/0:14,0:14:36.12:0,36,732 0/0:8,0:8:24.08:0,24,488 0/0:16,0:16:45.15:0,45,914 0/0:23,0:23:63.22:0,63,1265 0/0:13,0:13:39.13:0,39,792 0/0:8,0:8:24.08:0,24,487 0/0:18,0:18:48.16:0,48,974 0/0:12,0:12:33.11:0,33,671 0/0:24,0:24:66.23:0,66,1338 0/0:16,0:16:39.13:0,39,792 0/0:16,0:16:45.15:0,45,856 0/0:9,0:9:27.09:0,27,548 0/0:17,0:17:48.16:0,48,976 0/0:2,0:2:6.02:0,6,122 0/0:12,0:12:33.11:0,33,668 0/0:13,0:13:36.12:0,36,728 0/0:5,0:5:12.04:0,12,242 -chr1 1221717 . C T 1847.63 . AC=12;AF=0.1053;AN=114;BaseQRankSum=0.132;DP=473;Dels=0.00;FS=1.107;HRun=0;HaplotypeScore=0.2958;InbreedingCoeff=0.1362;MQ=58.52;MQ0=0;MQRankSum=-0.162;QD=17.77;ReadPosRankSum=1.073;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|4),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|3),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|9),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|4),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|7),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|6);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3:0,3,25 0/0:5,0:5:15.05:0,15,187 0/0:1,0:1:3.01:0,3,35 0/0:3,0:3:9.03:0,9,121 0/0:8,0:8:24.07:0,24,303 0/0:11,0:11:30.10:0,30,391 0/0:4,0:5:9.03:0,9,119 0/0:6,0:6:12.04:0,12,155 0/0:15,0:16:39.12:0,39,498 0/0:7,0:7:21.07:0,21,283 0/0:8,0:8:24.06:0,24,297 0/0:5,0:5:12.04:0,12,152 0/0:6,0:6:18.06:0,18,235 0/0:16,0:16:45.12:0,45,543 0/0:13,0:13:30.09:0,30,381 0/0:13,0:13:36.12:0,36,468 0/0:9,0:9:27.09:0,27,356 0/0:14,0:14:33.11:0,33,441 0/0:13,0:13:36.09:0,36,438 0/0:14,0:14:42.14:0,42,562 0/0:14,0:14:39.12:0,39,493 0/0:12,0:12:36.11:0,36,462 0/1:7,6:13:99:210,0,133 0/0:15,0:15:42.14:0,42,556 0/0:19,0:19:57.18:0,57,732 1/1:0,16:16:42.14:551,42,0 0/0:5,0:5:12.04:0,12,164 0/0:16,0:16:42.13:0,42,540 0/0:10,0:10:24.07:0,24,300 0/0:15,0:15:39.13:0,39,533 0/1:6,9:15:99:276,0,157 0/0:9,0:9:27.09:0,27,353 0/1:5,5:10:99:133,0,169 0/1:11,9:20:99:290,0,341 0/0:10,0:10:30.10:0,30,395 0/1:5,6:11:86.78:213,0,87 0/0:17,0:17:45.14:0,45,596 0/0:4,0:4:12.01:0,12,131 0/0:5,0:5:15.05:0,15,188 0/0:3,0:3:6.02:0,6,82 0/0:5,0:5:12.04:0,12,146 0/0:1,0:1:3.01:0,3,41 ./. 0/1:1,1:2:31.78:32,0,35 0/0:6,0:6:15.05:0,15,202 0/0:2,0:2:6.02:0,6,81 0/0:2,0:2:6.02:0,6,83 0/0:2,0:2:6.02:0,6,77 0/0:5,0:5:15.04:0,15,187 0/0:4,0:4:6.02:0,6,75 0/0:4,0:4:12.04:0,12,150 0/1:2,1:3:32.73:33,0,72 0/0:4,0:4:9.03:0,9,118 1/1:0,6:6:18.06:223,18,0 0/1:6,2:8:55.30:55,0,178 0/0:1,0:1:3.01:0,3,40 0/0:4,0:4:9.03:0,9,118 ./. 0/0:1,0:1:3.01:0,3,33 -chr1 1221728 . G A 60.11 . AC=1;AF=0.0089;AN=112;BaseQRankSum=-0.547;DP=393;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.3050;InbreedingCoeff=-0.0498;MQ=58.52;MQ0=0;MQRankSum=0.131;QD=15.03;ReadPosRankSum=0.389;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|4),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|3),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|9),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|4),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|7),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|6);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.04:0,12,151 0/0:2,0:2:3.01:0,3,39 0/0:2,0:2:6.02:0,6,71 0/0:7,0:7:21.05:0,21,251 0/0:12,0:12:33.11:0,33,432 0/0:5,1:6:9.03:0,9,112 0/0:5,0:5:9:0,9,99 0/0:12,1:13:30.10:0,30,395 0/0:4,0:4:12.03:0,12,148 0/0:8,0:8:24.06:0,24,294 0/0:5,0:5:15.04:0,15,186 0/0:4,0:4:12.03:0,12,148 0/0:13,0:13:36.11:0,36,464 0/0:10,0:10:21.07:0,21,268 0/0:7,0:7:18.06:0,18,236 0/0:9,0:9:27.09:0,27,352 0/0:9,1:10:24.08:0,24,320 0/0:12,0:12:33.11:0,33,428 0/0:8,0:8:24.08:0,24,324 0/0:11,0:11:27.09:0,27,352 0/0:9,0:9:27.06:0,27,343 0/0:14,0:14:33.11:0,33,435 0/0:12,0:12:33.10:0,33,418 0/0:17,0:17:51.17:0,51,688 0/0:13,0:13:33.11:0,33,444 0/0:4,0:4:12.03:0,12,150 0/0:15,0:15:39.10:0,39,492 0/0:9,0:9:21.07:0,21,265 0/0:14,0:14:39.13:0,39,538 0/0:14,0:14:36.11:0,36,464 0/0:7,0:7:21.07:0,21,273 0/0:9,0:9:27.09:0,27,358 0/0:15,0:15:42.14:0,42,576 0/0:7,0:7:21.07:0,21,278 0/0:9,0:9:21.07:0,21,278 0/0:13,0:13:39.11:0,39,518 0/0:2,0:2:6.02:0,6,76 0/0:5,0:5:15.04:0,15,189 0/0:2,0:2:3.01:0,3,32 0/0:6,0:6:12.03:0,12,144 ./. ./. 0/0:1,0:1:3.01:0,3,42 0/0:4,0:4:9.03:0,9,120 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,39 0/1:1,3:4:26.54:107,0,27 0/0:3,0:3:9.03:0,9,107 0/0:4,0:4:12.04:0,12,157 0/0:3,0:3:9.01:0,9,103 0/0:4,0:4:12.03:0,12,143 0/0:5,0:5:12.04:0,12,161 0/0:5,0:5:12.04:0,12,152 0/0:2,0:2:6.02:0,6,80 0/0:3,0:3:6.02:0,6,78 ./. 0/0:1,0:1:3.01:0,3,33 -chr1 1222051 . A G 730.01 . AC=3;AF=0.0259;AN=116;BaseQRankSum=-1.656;DP=566;Dels=0.00;FS=1.481;HRun=4;HaplotypeScore=0.4452;InbreedingCoeff=0.4132;MQ=57.13;MQ0=0;MQRankSum=0.440;QD=29.20;ReadPosRankSum=-0.248;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|4),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|3),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|9),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|4),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|7),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|6);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:2,0:2:3:0,3,26 0/0:1,0:1:3:0,3,27 0/0:7,0:7:21.04:0,21,266 0/0:7,0:7:21.07:0,21,276 0/0:14,0:14:42.13:0,42,539 0/0:3,0:3:9.03:0,9,119 0/0:7,0:7:21.07:0,21,284 0/0:10,0:10:30.10:0,30,394 0/0:5,0:5:15.05:0,15,202 0/0:5,0:5:15.05:0,15,193 0/0:5,0:5:15.05:0,15,188 0/0:13,0:13:33.10:0,33,420 0/0:11,0:11:27.08:0,27,338 0/0:11,0:11:33.10:0,33,415 0/0:9,0:9:27.09:0,27,349 0/0:5,0:5:15.05:0,15,195 0/0:5,0:5:15.05:0,15,186 0/0:8,0:8:21.06:0,21,261 0/0:9,0:9:27.05:0,27,324 0/0:9,0:9:27.09:0,27,349 0/0:7,0:7:12.03:0,12,143 0/0:9,0:9:27.07:0,27,317 0/0:11,0:11:33.10:0,33,418 0/0:3,0:3:6.02:0,6,76 0/0:6,0:6:15.05:0,15,198 0/0:4,0:4:9.03:0,9,119 0/0:9,0:9:27.09:0,27,351 0/0:14,0:14:36.11:0,36,455 0/0:15,0:15:42.12:0,42,532 0/0:10,0:10:24.07:0,24,309 0/0:12,0:12:27.08:0,27,329 0/0:18,0:18:48.12:0,48,600 0/0:14,0:14:36.12:0,36,485 0/0:10,0:10:30.09:0,30,375 0/0:10,1:11:24.08:0,24,324 0/0:13,0:13:33.10:0,33,407 0/0:7,0:7:15.05:0,15,181 0/0:12,0:12:33.10:0,33,417 0/0:13,1:14:39.12:0,39,501 0/0:10,0:10:24.08:0,24,309 0/0:16,0:16:42.12:0,42,519 0/0:4,0:4:9.03:0,9,107 0/1:1,5:6:21.26:158,0,21 0/0:9,1:10:27.05:0,27,315 0/0:23,0:23:57.14:0,57,681 0/0:6,0:6:18.06:0,18,230 0/0:18,0:18:45.12:0,45,536 1/1:0,19:19:54.16:658,54,0 0/0:14,0:14:36.10:0,36,431 0/0:17,0:18:48.12:0,48,551 0/0:14,1:15:36.08:0,36,411 0/0:13,0:13:30.10:0,30,391 0/0:9,0:9:24.07:0,24,301 0/0:9,0:9:24.07:0,24,301 0/0:7,0:7:15.05:0,15,196 0/0:7,0:7:21.06:0,21,256 0/0:10,0:10:27.08:0,27,348 0/0:6,0:6:18.05:0,18,205 -chr1 1222267 . G C 6009.85 . AC=12;AF=0.1000;AN=120;BaseQRankSum=-0.365;DP=2056;Dels=0.00;FS=2.228;HRun=5;HaplotypeScore=2.3088;InbreedingCoeff=0.2341;MQ=56.92;MQ0=0;MQRankSum=1.028;QD=15.90;ReadPosRankSum=2.427;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),EXON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|7),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R180P|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R180P|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R211P|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R246P|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cCc|R344P|802|SCNN1D|protein_coding|CODING|ENST00000379116|);CSQ=missense_variant|cGc/cCc|R/P|ENSG00000162572|SCNN1D|ENST00000338555|5/15|possibly_damaging(0.646)|tolerated(0.29)|180/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,missense_variant&NMD_transcript_variant|Gcc/Ccc|A/P|ENSG00000162572|SCNN1D|ENST00000379101|7/17|unknown(0)||313/328|nonsense_mediated_decay|1,missense_variant|cGc/cCc|R/P|ENSG00000162572|SCNN1D|ENST00000325425|5/15|possibly_damaging(0.659)|tolerated(0.22)|246/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,missense_variant|cGc/cCc|R/P|ENSG00000162572|SCNN1D|ENST00000400928|4/14|possibly_damaging(0.646)|tolerated(0.29)|180/638|protein_coding|1,missense_variant|cGc/cCc|R/P|ENSG00000162572|SCNN1D|ENST00000379116|8/18|possibly_damaging(0.659)|tolerated(0.1)|344/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:6.02:0,6,77 0/0:3,0:3:6.02:0,6,77 0/0:5,0:5:12.04:0,12,141 0/0:3,0:3:6.02:0,6,73 0/0:20,0:20:60.18:0,60,749 0/0:12,0:12:33.10:0,33,421 0/0:21,0:21:60.19:0,60,761 0/0:9,0:9:27.08:0,27,340 0/0:27,1:28:43.60:0,44,991 0/0:37,0:37:96.30:0,96,1242 0/0:12,0:12:33.10:0,33,418 0/0:14,0:14:42.11:0,42,507 0/0:20,0:20:57.18:0,57,728 0/0:53,2:55:99:0,120,1573 0/0:62,0:62:99:0,135,1782 0/0:34,0:34:81.25:0,81,1050 0/0:45,0:45:99:0,114,1438 0/0:39,0:39:93.28:0,93,1209 0/0:56,0:56:99:0,123,1606 0/0:42,2:44:96.28:0,96,1220 0/0:47,0:47:99:0,117,1515 0/0:45,0:45:99:0,108,1379 0/0:43,0:43:96.28:0,96,1249 0/1:19,24:43:99:581,0,524 0/0:39,0:39:90.29:0,90,1200 0/0:40,0:40:87.27:0,87,1138 1/1:0,47:47:99:1463,114,0 0/0:24,0:24:60.19:0,60,780 0/0:58,0:58:99:0,132,1750 0/0:45,0:45:99:0,111,1416 0/0:54,0:54:99:0,141,1772 0/1:15,14:30:99:383,0,456 0/0:43,0:43:99:0,108,1312 0/1:29,20:49:99:513,0,680 0/1:18,23:41:99:582,0,395 0/0:56,0:57:99:0,129,1593 0/1:13,26:39:99:763,0,272 0/0:48,0:49:99:0,129,1660 0/0:26,1:27:69.17:0,69,819 0/0:52,3:55:99:0,114,1439 0/0:34,0:34:84.25:0,84,1063 0/0:36,1:37:78.23:0,78,998 0/0:29,0:29:69.21:0,69,839 0/0:21,0:21:51.14:0,51,614 0/1:16,12:28:99:231,0,459 0/0:31,0:31:66.19:0,66,819 0/0:49,1:51:99:0,126,1500 0/0:23,0:23:54.15:0,54,665 0/0:33,2:35:75.21:0,75,929 0/0:42,1:44:99:0,111,1362 0/0:46,3:50:99:0,114,1409 0/0:41,1:42:90.20:0,90,1074 0/1:21,18:39:99:410,0,509 0/0:23,2:25:15.02:0,15,560 1/1:0,33:34:72.22:921,72,0 0/1:18,10:28:99:164,0,401 0/0:24,1:25:51.13:0,51,639 0/0:22,1:24:54.17:0,54,682 0/0:27,1:29:63.17:0,63,769 0/0:27,1:28:57.18:0,57,744 -chr1 1222407 . C T 341.16 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.879;DP=1311;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0043;InbreedingCoeff=-0.0091;MQ=58.24;MQ0=0;MQRankSum=1.305;QD=17.96;ReadPosRankSum=0.457;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|5),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|4),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|10),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|5),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|8),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|7);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,upstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:8,0:8:21.06:0,21,259 0/0:7,0:7:18.05:0,18,220 0/0:8,0:8:18.04:0,18,209 0/0:7,0:7:21.06:0,21,266 0/0:16,0:16:48.16:0,48,642 0/0:19,0:19:57.18:0,57,752 0/0:38,0:38:99:0,114,1475 0/0:20,0:20:54.17:0,54,706 0/0:41,0:42:99:0,120,1580 0/0:42,0:42:99:0,120,1590 0/0:24,0:24:69.22:0,69,911 0/0:24,0:24:63.19:0,63,804 0/0:28,0:28:81.26:0,81,1042 0/0:29,0:29:81.25:0,81,1068 0/0:34,0:34:90.28:0,90,1165 0/0:20,0:20:57.16:0,57,730 0/0:14,0:14:36.12:0,36,470 0/0:23,0:23:69.21:0,69,876 0/0:27,0:27:78.25:0,78,1002 0/0:21,0:21:54.15:0,54,677 0/0:19,0:19:48.15:0,48,639 0/0:24,0:24:60.15:0,60,742 0/0:18,0:18:51.16:0,51,665 0/0:18,0:18:45.14:0,45,577 0/0:19,0:19:57.17:0,57,716 0/0:22,0:22:63.20:0,63,810 0/0:20,0:20:57.18:0,57,745 0/0:16,0:16:39.12:0,39,515 0/0:19,0:19:54.17:0,54,700 0/0:25,0:25:69.20:0,69,874 0/0:26,0:26:72.23:0,72,953 0/0:20,0:20:48.13:0,48,612 0/0:24,0:24:57.18:0,57,749 0/0:31,0:31:78.25:0,78,1028 0/0:13,0:13:39.11:0,39,499 0/0:26,0:26:72.23:0,72,958 0/0:25,0:25:63.20:0,63,822 0/0:27,0:27:75.24:0,75,976 0/0:7,0:7:18.06:0,18,249 0/0:31,0:31:81.24:0,81,1009 0/0:23,0:23:63.18:0,63,809 0/0:16,0:16:48.15:0,48,617 0/0:9,0:9:21.07:0,21,276 0/0:15,0:15:39.09:0,39,479 0/1:8,11:19:99:389,0,176 0/0:24,0:24:69.22:0,69,904 0/0:44,0:44:99:0,108,1373 0/0:16,0:16:42.13:0,42,551 0/0:21,0:21:54.16:0,54,674 0/0:36,0:36:93.29:0,93,1193 0/0:41,1:42:99:0,105,1326 0/0:24,0:24:54.16:0,54,694 0/0:29,0:29:75.24:0,75,961 0/0:23,0:23:60.16:0,60,757 0/0:18,0:18:48.11:0,48,570 0/0:18,0:18:54.16:0,54,698 0/0:11,0:11:33.08:0,33,422 0/0:20,0:21:48.15:0,48,628 0/0:6,0:6:18.06:0,18,240 0/0:15,0:15:39.12:0,39,492 -chr1 1222598 . C T 248.87 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.379;DP=1688;Dels=0.00;FS=2.854;HRun=0;HaplotypeScore=1.2495;InbreedingCoeff=-0.0104;MQ=58.05;MQ0=0;MQRankSum=0.950;QD=9.95;ReadPosRankSum=0.137;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A246V|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A246V|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A277V|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A312V|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A410V|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|8);CSQ=missense_variant|gCg/gTg|A/V|ENSG00000162572|SCNN1D|ENST00000338555|6/15|benign(0.005)|tolerated(0.29)|246/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|8/17|||-/328|nonsense_mediated_decay|1,missense_variant|gCg/gTg|A/V|ENSG00000162572|SCNN1D|ENST00000325425|6/15|benign(0.003)|tolerated(0.29)|312/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,missense_variant|Cgg/Tgg|R/W|ENSG00000162572|SCNN1D|ENST00000379099|1/7|unknown(0)|tolerated(0.05)|38/308|protein_coding|1,missense_variant|gCg/gTg|A/V|ENSG00000162572|SCNN1D|ENST00000400928|5/14|benign(0.005)|tolerated(0.29)|246/638|protein_coding|1,missense_variant|gCg/gTg|A/V|ENSG00000162572|SCNN1D|ENST00000379116|9/18|benign(0.003)|tolerated(0.28)|410/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:9.03:0,9,113 0/0:13,0:13:24.06:0,24,277 0/0:12,0:12:30.08:0,30,342 0/0:4,0:5:9.03:0,9,116 0/0:34,0:35:75.20:0,75,929 0/0:29,0:32:69.21:0,69,863 0/0:56,0:57:99:0,138,1781 0/0:32,0:32:69.20:0,69,867 0/0:53,0:55:99:0,129,1641 0/0:48,0:50:99:0,108,1268 0/0:33,0:36:81.24:0,81,1042 0/0:37,0:40:93.27:0,93,1130 0/0:57,0:58:99:0,135,1704 0/0:11,1:12:30.10:0,30,401 0/0:30,0:30:72.23:0,72,952 0/0:22,0:22:57.18:0,57,740 0/0:14,0:15:33.10:0,33,431 0/0:33,0:33:78.23:0,78,979 0/0:14,0:14:33.10:0,33,430 0/0:29,0:29:78.23:0,78,1008 0/0:24,0:24:54.14:0,54,666 0/0:19,0:19:48.14:0,48,614 0/0:18,0:18:45.14:0,45,605 0/0:10,0:10:27.09:0,27,363 0/0:23,1:24:48.15:0,48,632 0/0:16,0:16:42.11:0,42,555 0/0:16,0:16:45.15:0,45,610 0/0:16,0:16:39.10:0,39,486 0/0:23,0:23:63.19:0,63,816 0/0:31,0:31:78.23:0,78,1009 0/0:27,0:27:63.20:0,63,840 0/0:13,0:13:36.12:0,36,474 0/0:24,0:24:60.18:0,60,783 0/1:14,11:25:99:297,0,331 0/0:11,0:11:27.08:0,27,342 0/0:20,0:20:45.14:0,45,599 0/0:25,0:27:42.12:0,42,559 0/0:27,0:27:66.19:0,66,851 0/0:14,0:15:27.06:0,27,325 0/0:44,0:45:99:0,117,1472 0/0:36,0:36:87.28:0,87,1130 0/0:34,1:35:42.49:0,42,1017 0/0:26,0:26:63.19:0,63,811 0/0:22,0:22:63.20:0,63,806 0/0:29,0:29:69.22:0,69,902 0/0:48,0:49:99:0,129,1626 0/0:50,0:50:99:0,126,1578 0/0:10,0:10:24.08:0,24,322 0/0:29,0:29:69.20:0,69,845 0/0:46,0:46:99:0,102,1298 0/0:46,0:46:96.26:0,96,1176 0/0:49,0:51:99:0,105,1340 0/0:35,0:35:81.21:0,81,1001 0/0:47,0:47:99:0,108,1397 0/0:30,0:30:69.20:0,69,880 0/0:29,0:30:66.20:0,66,842 0/0:22,0:22:54.17:0,54,723 0/0:32,0:33:75.22:0,75,947 0/0:20,0:20:45.14:0,45,583 0/0:26,0:26:60.17:0,60,745 -chr1 1222690 . C T 972.9 . AC=5;AF=0.0417;AN=120;BaseQRankSum=-2.953;DP=1085;Dels=0.00;FS=4.145;HRun=0;HaplotypeScore=2.3729;InbreedingCoeff=-0.0488;MQ=53.44;MQ0=0;MQRankSum=5.040;QD=11.58;ReadPosRankSum=-1.089;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|6),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|5),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|11),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|6),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|9),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|8);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:9.03:0,9,117 0/0:8,0:8:21.04:0,21,248 0/0:10,0:10:21.06:0,21,245 0/0:11,0:11:18.03:0,18,207 0/0:27,0:27:63.18:0,63,766 0/0:24,0:24:63.17:0,63,764 0/0:42,0:42:99:0,102,1293 0/0:12,0:12:30.08:0,30,362 0/0:34,0:34:90.28:0,90,1160 0/1:18,28:46:99:759,0,520 0/0:15,0:15:39.12:0,39,481 0/0:19,0:19:54.15:0,54,658 0/0:35,0:35:81.25:0,81,1031 0/0:7,0:7:21.07:0,21,260 0/0:12,0:12:33.10:0,33,420 0/1:10,2:12:13.72:14,0,258 0/0:10,0:10:30.06:0,30,319 0/0:11,0:11:27.08:0,27,336 0/1:6,3:9:48.85:49,0,207 0/0:12,0:12:27.08:0,27,340 0/0:17,0:17:45.14:0,45,576 0/0:11,0:11:18.06:0,18,239 0/0:7,0:7:18.05:0,18,224 0/0:3,0:3:6.02:0,6,73 0/1:4,6:10:99:125,0,120 0/0:9,0:9:24.08:0,24,314 0/0:6,0:6:12.04:0,12,144 0/0:5,0:5:15.05:0,15,191 0/0:10,0:10:27.08:0,27,335 0/0:8,0:8:24.07:0,24,300 0/0:8,0:8:21.06:0,21,260 0/0:6,0:7:15.02:0,15,181 0/0:9,0:9:18.06:0,18,228 0/0:18,0:18:48.14:0,48,584 0/0:8,0:8:18.06:0,18,230 0/0:13,0:13:36.09:0,36,434 0/0:15,0:15:42.13:0,42,530 0/0:15,0:15:42.13:0,42,517 0/0:18,0:18:48.15:0,48,595 0/0:24,0:24:69.20:0,69,840 0/0:30,0:30:84.25:0,84,1024 0/0:17,0:17:36.11:0,36,449 0/0:19,0:19:48.14:0,48,596 0/0:17,0:17:36.11:0,36,459 0/0:18,1:19:14.18:0,14,576 0/0:23,0:23:66.18:0,66,799 0/0:50,0:50:99:0,126,1501 0/0:14,0:14:36.11:0,36,457 0/0:19,0:19:54.14:0,54,637 0/0:70,0:70:99:0,178,2199 0/0:45,0:45:99:0,111,1353 0/0:27,0:27:81.23:0,81,971 0/0:37,1:38:99:0,102,1252 0/0:27,0:27:69.20:0,69,866 0/0:28,0:28:75.23:0,75,922 0/0:13,0:14:36.10:0,36,454 0/1:3,4:7:57.50:130,0,57 0/0:16,0:16:42.11:0,42,537 0/0:15,0:15:36.11:0,36,464 0/0:7,0:7:15.02:0,15,176 -chr1 1222695 . G C 2613.18 . AC=15;AF=0.1250;AN=120;BaseQRankSum=-2.534;DP=1083;Dels=0.00;FS=12.740;HRun=1;HaplotypeScore=2.6047;InbreedingCoeff=0.2827;MQ=53.52;MQ0=0;MQRankSum=0.965;QD=13.75;ReadPosRankSum=2.874;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|6),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|5),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|11),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|6),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|9),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|8);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:6.02:0,6,73 0/0:6,0:6:12.03:0,12,143 0/0:7,0:7:15.05:0,15,185 0/0:8,0:8:18.06:0,18,221 0/0:23,0:23:48.13:0,48,590 0/0:24,0:24:54.17:0,54,694 0/0:38,0:38:81.26:0,81,1063 0/0:14,0:14:30.09:0,30,387 0/0:34,0:34:72.21:0,72,940 0/0:45,0:45:99:0,126,1619 0/1:7,10:17:99:305,0,117 0/0:17,0:17:48.15:0,48,606 0/0:31,0:31:69.21:0,69,895 0/0:7,0:7:18.05:0,18,218 0/0:13,0:13:30.09:0,30,384 0/0:8,0:8:18.04:0,18,220 0/0:10,0:10:21.05:0,21,247 0/0:13,0:13:30.09:0,30,380 0/0:9,0:9:21.07:0,21,281 0/0:12,0:12:18.06:0,18,246 0/0:14,1:16:30.09:0,30,387 0/0:9,0:9:12.04:0,12,165 0/0:8,0:8:12.04:0,12,146 0/1:2,2:4:22.53:60,0,23 0/0:7,0:8:15.05:0,15,188 0/0:8,0:8:21.07:0,21,273 1/1:1,5:6:12.03:146,12,0 0/0:4,0:4:12.04:0,12,147 0/0:10,0:10:24.08:0,24,308 0/0:8,0:8:15.05:0,15,189 0/0:8,0:8:18.05:0,18,221 0/1:3,3:6:66.20:90,0,66 0/0:9,0:9:18.06:0,18,228 1/1:2,14:16:30.09:370,30,0 0/1:3,6:9:66.66:67,0,88 0/0:12,0:12:24.06:0,24,305 0/1:7,7:14:99:157,0,128 0/0:16,0:16:36.10:0,36,450 0/0:21,0:21:45.13:0,45,558 0/0:24,0:24:33.07:0,33,400 0/0:29,0:29:60.14:0,60,689 0/0:18,0:18:30.08:0,30,351 0/0:25,0:25:60.13:0,60,708 0/0:15,1:16:24.08:0,24,315 0/1:10,11:21:99:224,0,248 0/0:22,0:22:48.12:0,48,567 0/0:50,0:50:93.28:0,93,1172 0/1:8,5:13:99:118,0,125 0/0:19,0:19:45.11:0,45,535 0/0:70,0:71:99:0,147,1744 0/0:51,0:51:87.23:0,87,1067 0/0:30,0:30:54.16:0,54,652 0/1:21,21:44:99:399,0,396 0/0:25,1:26:15.40:0,15,614 1/1:2,25:27:57.15:684,57,0 0/1:7,6:13:99:190,0,135 0/0:8,0:8:21.05:0,21,259 0/0:16,0:16:33.09:0,33,402 0/0:16,0:16:36.10:0,36,444 0/0:8,0:8:18.05:0,18,218 -chr1 1222739 . C G 156.37 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.552;DP=1353;Dels=0.00;FS=1.709;HRun=0;HaplotypeScore=1.1586;InbreedingCoeff=-0.0117;MQ=56.35;MQ0=0;MQRankSum=-0.469;QD=9.20;ReadPosRankSum=0.855;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|6),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|5),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|11),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|6),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|9),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|8);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:18.06:0,18,233 0/0:8,0:8:21.07:0,21,273 0/0:12,0:12:36.12:0,36,473 0/0:8,0:8:21.07:0,21,267 0/0:29,0:29:84.26:0,84,1099 0/0:21,0:21:60.20:0,60,797 0/0:43,0:43:99:0,129,1724 0/0:24,0:24:66.22:0,66,883 0/0:54,0:54:99:0,159,2095 0/0:55,0:55:99:0,160,2102 0/0:35,0:35:99:0,102,1331 0/0:16,0:16:45.13:0,45,579 0/0:29,0:29:87.28:0,87,1146 0/0:7,0:7:18.06:0,18,229 0/0:10,0:10:21.07:0,21,276 0/0:7,0:7:21.07:0,21,274 0/0:11,0:11:27.09:0,27,352 0/0:13,0:13:39.13:0,39,514 0/0:5,0:5:15.04:0,15,176 0/0:8,0:8:15.05:0,15,204 0/0:11,0:11:30.10:0,30,389 0/0:10,0:10:24.08:0,24,312 0/0:9,0:9:24.08:0,24,320 0/0:8,0:8:21.05:0,21,267 0/0:10,0:10:24.08:0,24,307 0/0:6,0:6:18.05:0,18,222 0/0:9,0:9:24.08:0,24,303 0/0:3,0:3:9.03:0,9,118 0/0:8,0:8:24.08:0,24,317 0/0:9,0:9:21.07:0,21,278 0/0:14,0:14:36.12:0,36,474 0/0:7,0:7:15.05:0,15,209 0/0:11,0:11:30.10:0,30,389 0/1:10,7:17:99:204,0,250 0/0:7,0:7:12.04:0,12,156 0/0:10,0:10:21.07:0,21,279 0/0:15,0:15:36.11:0,36,444 0/0:15,0:15:30.10:0,30,401 0/0:26,0:26:60.20:0,60,799 0/0:42,0:42:99:0,105,1386 0/0:43,0:43:96.30:0,96,1221 0/0:36,0:36:96.31:0,96,1253 0/0:27,0:27:63.20:0,63,806 0/0:23,0:23:54.18:0,54,725 0/0:35,0:35:93.28:0,93,1203 0/0:36,0:36:96.31:0,96,1233 0/0:51,0:51:99:0,120,1528 0/0:21,0:21:39.13:0,39,529 0/0:34,0:35:81.26:0,81,1057 0/0:72,0:72:99:0,150,1965 0/0:56,0:56:99:0,120,1556 0/0:44,0:44:96.30:0,96,1221 0/0:51,0:51:99:0,132,1714 0/0:22,0:23:51.16:0,51,639 0/0:37,0:37:90.28:0,90,1169 0/0:15,0:15:39.13:0,39,513 0/0:20,0:20:57.17:0,57,740 0/0:36,0:36:87.28:0,87,1152 0/0:22,0:22:48.15:0,48,634 0/0:21,0:21:57.19:0,57,754 -chr1 1222842 . C T 701.62 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-4.452;DP=3950;Dels=0.00;FS=3.995;HRun=0;HaplotypeScore=2.7986;InbreedingCoeff=-0.0085;MQ=57.76;MQ0=0;MQRankSum=2.038;QD=6.05;ReadPosRankSum=-0.162;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|6),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|5),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|11),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|6),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|9),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|8);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:9,0:9:24.04:0,24,262 0/0:15,0:15:33.07:0,33,358 0/0:19,0:19:48.09:0,48,545 0/0:13,0:13:27.08:0,27,325 0/0:37,0:38:99:0,102,1224 0/0:58,0:58:99:0,147,1807 0/0:70,0:71:99:0,193,2418 0/0:25,0:25:75.23:0,75,953 0/0:59,0:59:99:0,162,2023 0/0:67,0:68:99:0,178,2237 0/0:46,0:46:99:0,111,1342 0/0:52,0:53:99:0,147,1759 0/0:64,1:66:99:0,171,2071 0/0:18,0:18:36.11:0,36,463 0/0:29,0:29:75.19:0,75,907 0/0:30,0:30:66.19:0,66,851 0/0:19,0:19:51.15:0,51,647 0/0:33,0:33:69.20:0,69,892 0/0:28,0:28:63.17:0,63,766 0/0:35,0:36:84.23:0,84,1078 0/0:29,0:29:63.16:0,63,789 0/0:22,0:22:60.17:0,60,732 0/0:19,0:19:57.17:0,57,723 0/0:18,0:18:51.15:0,51,620 0/0:29,0:29:60.20:0,60,830 0/0:31,0:31:63.17:0,63,810 0/0:33,0:33:75.23:0,75,1008 0/0:25,0:25:66.19:0,66,861 0/0:47,0:47:99:0,111,1446 0/0:27,0:27:63.20:0,63,838 0/0:41,0:41:87.28:0,87,1164 0/0:30,0:30:63.20:0,63,827 0/0:26,0:26:60.19:0,60,787 0/0:25,0:26:63.18:0,63,787 0/0:20,0:20:48.14:0,48,615 0/0:28,0:28:63.18:0,63,820 0/0:44,0:45:99:0,114,1449 0/0:41,0:41:99:0,102,1345 0/0:85,0:86:99:0,193,2449 0/0:165,0:165:99:0,373,4857 0/0:142,0:149:99:0,319,4102 0/0:96,0:98:99:0,220,2810 0/0:94,0:95:99:0,211,2757 0/0:84,1:85:99:0,193,2467 0/0:96,0:98:99:0,232,2943 0/0:136,0:136:99:0,316,4072 0/0:198,1:200:99:0,426,5818 0/0:68,0:69:99:0,162,2035 0/0:140,0:142:99:0,289,3680 0/0:196,0:197:99:0,436,5585 0/0:161,0:161:99:0,373,4593 0/0:145,0:146:99:0,328,4081 0/0:151,1:153:99:0,322,4115 0/1:62,51:116:99:749,0,1637 0/0:83,0:84:99:0,184,2333 0/0:98,0:99:99:0,223,2848 0/0:63,0:65:99:0,141,1815 0/0:136,0:136:99:0,298,3804 0/0:83,0:84:99:0,181,2322 0/0:113,0:114:99:0,265,3433 -chr1 1222958 . C T 840.29 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.301;DP=3509;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.2081;InbreedingCoeff=-0.0084;MQ=58.04;MQ0=0;MQRankSum=0.486;QD=11.20;ReadPosRankSum=-3.869;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R297C|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R297C|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R328C|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R363C|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Tgc|R461C|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|9);CSQ=missense_variant|Cgc/Tgc|R/C|ENSG00000162572|SCNN1D|ENST00000338555|7/15|benign(0.037)|tolerated(0.18)|297/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|9/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|Cgc/Tgc|R/C|ENSG00000162572|SCNN1D|ENST00000325425|7/15|benign(0.075)|tolerated(0.15)|363/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,synonymous_variant|agC/agT|S|ENSG00000162572|SCNN1D|ENST00000379099|2/7|||88/308|protein_coding|1,missense_variant|Cgc/Tgc|R/C|ENSG00000162572|SCNN1D|ENST00000400928|6/14|benign(0.037)|tolerated(0.18)|297/638|protein_coding|1,missense_variant|Cgc/Tgc|R/C|ENSG00000162572|SCNN1D|ENST00000379116|10/18|benign(0.075)|tolerated(0.05)|461/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:17,0:17:42.12:0,42,500 0/0:17,0:17:42.13:0,42,533 0/0:20,0:20:48.15:0,48,601 0/0:17,0:17:45.11:0,45,538 0/0:61,0:61:99:0,141,1738 0/0:53,0:53:99:0,123,1488 0/0:105,0:105:99:0,238,3042 0/0:35,0:35:81.26:0,81,1063 0/0:105,0:105:99:0,268,3451 0/0:89,0:89:99:0,223,2880 0/1:40,32:75:99:888,0,1038 0/0:53,0:53:99:0,135,1689 0/0:67,0:68:99:0,153,1972 0/0:35,0:35:78.24:0,78,1008 0/0:45,0:45:99:0,111,1384 0/0:18,0:18:48.13:0,48,595 0/0:37,0:37:96.30:0,96,1245 0/0:46,0:46:99:0,126,1626 0/0:35,0:35:72.23:0,72,966 0/0:30,0:30:78.21:0,78,973 0/0:33,0:33:75.24:0,75,984 0/0:53,0:53:99:0,129,1697 0/0:44,0:44:99:0,108,1354 0/0:36,0:36:90.28:0,90,1165 0/0:30,0:30:75.23:0,75,977 0/0:29,0:29:78.24:0,78,1016 0/0:44,0:44:96.28:0,96,1246 0/0:32,0:32:69.20:0,69,898 0/0:47,0:47:99:0,120,1550 0/0:34,0:34:96.28:0,96,1184 0/0:45,0:45:99:0,123,1563 0/0:20,0:20:42.13:0,42,551 0/0:32,0:32:87.25:0,87,1080 0/0:39,0:39:99:0,99,1254 0/0:42,0:42:96.30:0,96,1233 0/0:23,0:23:57.17:0,57,725 0/0:60,1:61:99:0,104,1734 0/0:51,0:51:99:0,126,1652 0/0:60,0:60:99:0,144,1812 0/0:111,0:111:99:0,295,3732 0/0:97,0:97:99:0,247,3077 0/0:75,0:75:99:0,202,2570 0/0:78,0:78:99:0,193,2407 0/0:66,0:66:99:0,172,2142 0/0:67,0:67:99:0,172,2203 0/0:90,0:91:99:0,226,2850 0/0:142,0:143:99:0,358,4411 0/0:51,0:51:99:0,138,1759 0/0:88,0:88:99:0,199,2578 0/0:121,0:121:99:0,313,3997 0/0:132,0:133:99:0,343,4158 0/0:88,0:89:99:0,229,2859 0/0:94,0:94:99:0,235,2894 0/0:97,0:97:99:0,247,3092 0/0:72,0:72:99:0,184,2358 0/0:52,0:52:99:0,132,1673 0/0:40,0:40:99:0,102,1287 0/0:84,0:84:99:0,214,2683 0/0:75,0:75:99:0,172,2264 0/0:67,0:67:99:0,159,2025 -chr1 1222963 . C T 1912.86 . AC=2;AF=0.0167;AN=120;BaseQRankSum=0.048;DP=3402;DS;Dels=0.00;FS=5.465;HRun=0;HaplotypeScore=2.6679;InbreedingCoeff=-0.0170;MQ=58.00;MQ0=0;MQRankSum=-1.133;QD=11.45;ReadPosRankSum=1.587;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P298|638|SCNN1D|protein_coding|CODING|ENST00000338555|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P298|638|SCNN1D|protein_coding|CODING|ENST00000400928|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P329|669|SCNN1D|protein_coding|CODING|ENST00000379110|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P364|704|SCNN1D|protein_coding|CODING|ENST00000325425|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P462|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|9);CSQ=synonymous_variant|ccC/ccT|P|ENSG00000162572|SCNN1D|ENST00000338555|7/15|||298/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|9/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,synonymous_variant|ccC/ccT|P|ENSG00000162572|SCNN1D|ENST00000325425|7/15|||364/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,missense_variant|cCg/cTg|P/L|ENSG00000162572|SCNN1D|ENST00000379099|2/7|benign(0.04)|deleterious(0)|90/308|protein_coding|1,synonymous_variant|ccC/ccT|P|ENSG00000162572|SCNN1D|ENST00000400928|6/14|||298/638|protein_coding|1,synonymous_variant|ccC/ccT|P|ENSG00000162572|SCNN1D|ENST00000379116|10/18|||462/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:16,0:16:36.08:0,36,418 0/0:15,0:15:30.10:0,30,382 0/0:22,0:22:48.15:0,48,611 0/0:18,0:18:42.06:0,42,477 0/0:53,0:54:99:0,126,1587 0/0:51,0:51:99:0,114,1396 0/0:101,0:102:99:0,244,3052 0/0:38,0:39:90.25:0,90,1150 0/0:112,0:112:99:0,313,3951 0/0:80,0:83:99:0,217,2725 0/0:78,0:80:99:0,187,2398 0/0:52,0:53:99:0,135,1674 0/0:71,0:71:99:0,178,2221 0/0:34,0:34:81.26:0,81,1073 0/0:44,0:44:99:0,111,1418 0/0:19,0:19:42.13:0,42,539 0/0:35,0:35:93.30:0,93,1233 0/0:43,0:43:99:0,120,1558 0/0:34,0:34:69.22:0,69,919 0/0:32,0:32:87.21:0,87,1058 0/0:33,0:33:81.25:0,81,1069 0/0:52,0:52:99:0,129,1692 0/0:39,0:39:99:0,99,1265 0/0:35,0:35:87.28:0,87,1161 0/0:31,0:31:75.23:0,75,967 0/0:31,0:31:81.26:0,81,1076 0/0:43,0:44:96.30:0,96,1264 0/0:29,0:29:66.21:0,66,878 0/0:48,0:48:99:0,123,1596 0/0:32,0:32:93.29:0,93,1168 0/0:48,0:48:99:0,123,1605 0/0:20,0:20:45.14:0,45,584 0/0:31,0:31:87.28:0,87,1112 0/0:34,0:34:84.25:0,84,1087 0/0:40,0:41:99:0,99,1269 0/0:20,0:20:60.16:0,60,732 0/0:58,0:58:99:0,147,1882 0/0:50,0:50:99:0,126,1670 0/0:51,0:51:99:0,126,1583 0/0:102,1:104:99:0,254,3549 0/0:100,0:100:99:0,235,3008 0/0:78,0:78:99:0,205,2564 0/0:76,0:76:99:0,196,2427 0/0:63,0:63:99:0,147,1859 0/0:64,0:64:99:0,168,2155 0/0:86,0:86:99:0,214,2699 0/0:136,2:140:99:0,301,4076 0/0:50,0:50:99:0,135,1733 0/1:40,41:81:99:1102,0,1070 0/0:112,0:112:99:0,304,3845 0/0:128,1:130:99:0,285,3952 0/1:54,32:86:99:876,0,1402 0/0:85,4:89:99:0,121,2676 0/0:88,0:88:99:0,235,2959 0/0:69,0:70:99:0,172,2222 0/0:49,0:49:99:0,129,1659 0/0:37,0:37:96.28:0,96,1195 0/0:80,0:80:99:0,205,2567 0/0:69,0:69:99:0,150,1974 0/0:64,0:64:99:0,162,2053 -chr1 1223385 . G C 1473.29 . AC=14;AF=0.1250;AN=112;BaseQRankSum=0.369;DP=567;Dels=0.00;FS=6.998;HRun=0;HaplotypeScore=0.6667;InbreedingCoeff=0.0907;MQ=56.62;MQ0=0;MQRankSum=0.356;QD=13.15;ReadPosRankSum=0.501;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E380Q|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E380Q|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E411Q|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E446Q|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Cag|E544Q|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=missense_variant|Gag/Cag|E/Q|ENSG00000162572|SCNN1D|ENST00000338555|9/15|benign(0.006)|tolerated(0.57)|380/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|11/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|Gag/Cag|E/Q|ENSG00000162572|SCNN1D|ENST00000325425|9/15|benign(0.012)|tolerated(0.54)|446/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,missense_variant|Gag/Cag|E/Q|ENSG00000162572|SCNN1D|ENST00000379099|3/7|benign(0.047)|tolerated(0.87)|197/308|protein_coding|1,missense_variant|Gag/Cag|E/Q|ENSG00000162572|SCNN1D|ENST00000400928|8/14|benign(0.006)|tolerated(0.57)|380/638|protein_coding|1,missense_variant|Gag/Cag|E/Q|ENSG00000162572|SCNN1D|ENST00000379116|12/18|benign(0.012)|tolerated(0.47)|544/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,76 0/0:2,0:2:6.01:0,6,59 0/0:3,0:3:9.03:0,9,109 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:6.02:0,6,82 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.04:0,12,154 0/0:6,0:7:18.06:0,18,230 ./. ./. ./. 0/0:10,0:10:24.08:0,24,310 0/0:23,0:23:54.17:0,54,700 0/0:17,0:17:36.11:0,36,479 0/0:14,0:14:30.10:0,30,407 0/0:14,0:14:30.10:0,30,391 0/0:16,0:16:42.14:0,42,557 0/0:16,0:16:36.10:0,36,423 0/0:18,0:18:42.14:0,42,563 0/0:26,0:26:63.19:0,63,804 0/0:21,0:22:54.13:0,54,665 0/1:12,4:16:99:115,0,283 0/0:17,0:17:45.14:0,45,579 0/0:13,0:13:30.10:0,30,393 1/1:0,7:7:15.05:197,15,0 0/0:12,0:12:21.07:0,21,284 0/0:8,0:8:21.05:0,21,268 0/0:16,0:16:39.11:0,39,489 0/0:26,0:26:57.17:0,57,726 0/1:5,8:13:99:241,0,120 0/0:20,0:20:48.13:0,48,612 0/1:11,9:20:99:243,0,266 0/1:5,8:13:99:223,0,110 0/0:20,0:20:48.16:0,48,636 0/1:6,9:15:99:206,0,166 0/0:21,0:21:57.18:0,57,731 0/0:6,0:6:12.04:0,12,156 0/0:9,0:9:21.07:0,21,272 0/0:11,0:11:21.06:0,21,263 0/0:5,0:5:9.03:0,9,116 0/0:4,0:4:12.03:0,12,138 0/0:8,0:8:18.06:0,18,232 0/1:2,2:4:24.41:24,0,68 0/0:4,0:4:12.04:0,12,149 0/0:12,0:12:33.11:0,33,432 0/1:3,1:4:21.40:21,0,98 0/0:5,0:5:9.03:0,9,118 0/0:10,0:10:21.07:0,21,275 0/0:3,0:3:6.02:0,6,85 0/0:3,0:3:9.03:0,9,117 0/1:2,2:4:55.64:59,0,56 0/1:3,1:4:32.20:32,0,72 1/1:0,6:6:18.06:234,18,0 0/1:4,2:6:55.73:56,0,131 0/0:2,0:2:6.02:0,6,71 0/0:2,0:2:3.01:0,3,37 0/0:8,0:8:21.06:0,21,267 0/0:8,0:8:18.06:0,18,228 -chr1 1223465 . GC G 883.64 . AC=11;AF=0.110;AN=100;BaseQRankSum=3.043;DP=292;FS=1.960;HRun=2;HaplotypeScore=26.6146;InbreedingCoeff=0.0959;MQ=54.67;MQ0=0;MQRankSum=1.559;QD=15.24;ReadPosRankSum=1.688;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,45 ./. 0/1:2,0:2:32.95:33,0,39 0/0:2,0:2:6.02:0,6,90 ./. 0/0:2,0:2:3.01:0,3,45 ./. 0/0:1,0:1:3.01:0,3,45 ./. ./. 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,45 0/0:7,0:7:18.05:0,18,251 0/1:4,7:11:75.90:243,0,76 0/1:2,5:7:67.93:174,0,68 0/0:3,0:3:9.03:0,9,135 0/0:12,0:12:33.11:0,33,493 0/0:10,0:10:27.09:0,27,388 0/1:6,4:10:99:171,0,111 0/0:11,0:11:30.08:0,30,426 0/0:12,0:12:33.11:0,33,479 0/0:11,0:11:24.03:0,24,332 0/0:4,0:4:12.04:0,12,179 0/0:13,0:13:33.11:0,33,485 0/0:7,0:7:18.06:0,18,269 0/0:3,0:3:9.03:0,9,135 0/0:5,0:5:15.05:0,15,224 0/0:4,0:4:9.03:0,9,125 0/0:10,0:10:27.09:0,27,387 0/0:12,0:12:24.08:0,24,358 0/0:9,0:9:21.07:0,21,295 0/0:13,0:13:27.09:0,27,392 0/0:10,0:10:24.08:0,24,360 0/0:4,0:4:12.04:0,12,179 1/1:3,6:9:18.06:233,18,0 0/0:4,0:4:12.04:0,12,180 0/1:9,1:10:11.93:12,0,333 0/0:3,0:3:9.03:0,9,126 0/0:1,0:1:3.01:0,3,45 0/0:7,0:7:18.06:0,18,261 0/0:4,0:4:12.04:0,12,179 1/1:2,1:3:6.02:71,6,0 0/0:5,0:5:9.03:0,9,135 0/1:2,1:3:32.96:33,0,39 ./. 0/0:5,0:5:12.04:0,12,180 0/0:3,0:3:3.01:0,3,42 0/0:4,0:4:12.04:0,12,168 0/0:7,0:7:12.04:0,12,180 ./. 0/0:3,0:3:6.02:0,6,90 ./. ./. 0/0:3,0:3:9.03:0,9,135 0/0:3,0:3:6.02:0,6,90 0/0:1,0:1:3.01:0,3,45 0/0:3,0:3:9.03:0,9,135 0/1:1,2:3:35.95:69,0,36 0/0:4,0:4:9.03:0,9,135 -chr1 1223570 . C T 69.93 . AC=6;AF=0.065;AN=92;BaseQRankSum=0.235;DP=128;Dels=0.00;FS=2.433;HRun=0;HaplotypeScore=0.0933;InbreedingCoeff=0.2052;MQ=53.21;MQ0=0;MQRankSum=0.920;QD=17.48;ReadPosRankSum=-0.706;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:9.03:0,9,113 ./. 0/0:2,0:2:6.02:0,6,76 0/0:2,0:2:6.02:0,6,75 ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:1,0:1:3.01:0,3,40 0/0:5,0:5:15.04:0,15,181 0/0:4,0:4:12.04:0,12,151 0/0:1,0:1:3.01:0,3,33 0/0:7,0:7:15.03:0,15,187 0/0:4,0:4:12.02:0,12,145 0/0:3,0:3:9.03:0,9,108 0/0:5,0:5:12.04:0,12,153 0/0:1,0:1:3.01:0,3,42 0/0:4,0:4:12.04:0,12,156 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,73 0/0:6,0:6:18.06:0,18,234 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 ./. 0/0:4,0:4:12.04:0,12,152 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:9.03:0,9,115 0/0:3,0:3:9.03:0,9,116 0/0:5,0:5:15.05:0,15,201 1/1:0,2:2:6.02:78,6,0 ./. 0/0:6,0:6:18.06:0,18,243 ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,37 0/0:5,0:5:12.04:0,12,154 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:9.03:0,9,113 0/0:1,0:1:3.01:0,3,39 ./. 0/0:2,0:2:6.01:0,6,64 0/0:7,0:7:12.04:0,12,165 1/1:0,1:1:3.01:42,3,0 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:6.02:0,6,76 0/0:6,0:6:12.04:0,12,163 0/0:3,0:3:6.02:0,6,80 0/0:4,0:4:9.02:0,9,112 ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,72 ./. 0/0:2,0:2:3.01:0,3,45 ./. 0/0:1,0:1:3.01:0,3,30 -chr1 1223572 . C T 52.77 . AC=4;AF=0.044;AN=90;BaseQRankSum=1.225;DP=128;Dels=0.00;FS=2.461;HRun=0;HaplotypeScore=0.0513;InbreedingCoeff=0.1293;MQ=53.41;MQ0=0;MQRankSum=1.609;QD=17.59;ReadPosRankSum=-0.758;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:9.03:0,9,113 ./. 0/0:2,0:2:6.02:0,6,76 0/0:2,0:2:6.02:0,6,79 ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:1,0:1:3.01:0,3,40 0/0:5,0:5:15.02:0,15,183 0/0:4,0:4:12.04:0,12,151 0/0:1,0:1:3.01:0,3,33 0/0:7,0:7:15.05:0,15,198 0/0:4,0:4:12.03:0,12,146 0/0:2,0:2:6.02:0,6,75 0/0:5,0:5:12.03:0,12,144 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:12.04:0,12,151 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,70 0/0:6,0:6:18.06:0,18,228 0/0:1,0:1:3:0,3,29 ./. ./. 0/0:4,0:4:6.02:0,6,80 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:6.02:0,6,82 0/0:3,0:3:9.03:0,9,116 0/0:5,0:5:15.05:0,15,201 1/1:0,2:2:6.02:80,6,0 ./. 0/0:6,0:6:18.05:0,18,230 ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,39 0/0:5,0:5:12.04:0,12,154 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:9.03:0,9,114 0/0:1,0:1:3.01:0,3,39 ./. 0/0:2,0:2:6.02:0,6,66 0/0:7,0:7:12.04:0,12,165 1/1:0,1:1:3.01:42,3,0 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:6.01:0,6,65 0/0:6,0:6:12.04:0,12,161 0/0:3,0:3:6.02:0,6,80 0/0:4,0:4:9.02:0,9,113 ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,72 ./. 0/0:2,0:2:3.01:0,3,45 ./. 0/0:1,0:1:3.01:0,3,33 -chr1 1223584 . T C 172.88 . AC=12;AF=0.128;AN=94;BaseQRankSum=-0.765;DP=109;Dels=0.00;FS=5.887;HRun=3;HaplotypeScore=0.0818;InbreedingCoeff=0.1717;MQ=52.94;MQ0=0;MQRankSum=-1.734;QD=15.72;ReadPosRankSum=0.356;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:9.01:0,9,98 ./. 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,40 ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 0/0:5,0:5:15.05:0,15,195 0/0:3,0:3:9.03:0,9,115 0/0:1,0:1:3.01:0,3,33 0/0:6,0:6:12.04:0,12,169 0/1:1,2:3:32.74:51,0,33 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.04:0,12,145 0/0:2,0:2:3.01:0,3,42 0/0:2,0:2:6.02:0,6,81 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,73 0/0:3,0:3:9.03:0,9,113 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 ./. 0/0:3,0:3:9:0,9,96 0/0:2,0:2:3.01:0,3,33 0/0:3,0:3:9.03:0,9,120 0/0:1,0:1:3.01:0,3,40 0/0:3,0:3:9.03:0,9,122 0/0:1,0:1:3.01:0,3,41 ./. 0/0:4,0:4:12.04:0,12,161 0/0:1,0:1:3.01:0,3,32 1/1:0,1:1:3.01:41,3,0 0/0:1,0:1:3.01:0,3,39 0/0:9,0:9:21.06:0,21,262 0/0:2,0:2:6.02:0,6,67 ./. 0/1:1,2:3:28.77:66,0,29 0/0:1,0:1:3.01:0,3,39 1/1:0,1:1:3:28,3,0 0/0:2,0:2:3.01:0,3,33 0/0:6,0:6:12.04:0,12,154 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,30 0/0:5,0:5:12.04:0,12,161 0/0:2,0:2:6.02:0,6,77 0/0:4,0:4:9.03:0,9,114 ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,72 ./. 0/0:2,0:2:3.01:0,3,45 ./. 1/1:0,1:1:3.01:33,3,0 -chr1 1223608 . T C 97.92 . AC=5;AF=0.060;AN=84;BaseQRankSum=0.588;DP=98;Dels=0.00;FS=1.905;HRun=1;HaplotypeScore=0.1871;InbreedingCoeff=0.0757;MQ=49.92;MQ0=0;MQRankSum=0.349;QD=13.99;ReadPosRankSum=1.013;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9:0,9,89 0/0:1,0:1:3.01:0,3,32 ./. ./. ./. 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,71 ./. 0/0:1,0:1:3.01:0,3,33 0/0:5,0:5:12.04:0,12,157 0/0:2,0:2:6.02:0,6,66 0/0:1,0:1:3.01:0,3,38 0/0:2,0:2:3.01:0,3,39 0/0:1,0:1:3.01:0,3,32 0/0:3,0:3:6.02:0,6,82 0/0:1,0:1:3.01:0,3,40 1/1:0,1:1:3.01:33,3,0 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 ./. 0/0:3,0:3:9.03:0,9,109 0/0:5,0:5:15.04:0,15,161 0/0:1,0:1:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. 0/0:3,0:3:9.03:0,9,115 0/1:1,1:2:32.56:33,0,35 0/0:2,0:2:6.02:0,6,75 0/0:2,0:2:6.02:0,6,76 0/0:11,0:11:24.07:0,24,310 0/0:3,0:3:6.02:0,6,67 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,72 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3:0,3,28 0/0:3,0:3:6.02:0,6,67 0/0:3,0:3:9.03:0,9,116 ./. 0/0:2,0:2:6.02:0,6,65 ./. 0/0:8,0:8:21.06:0,21,252 0/0:2,0:2:6.02:0,6,77 1/1:1,3:4:9.03:113,9,0 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3:0,3,25 0/0:1,0:1:3.01:0,3,42 ./. 0/0:4,0:4:9.03:0,9,121 ./. ./. -chr1 1223626 . T C 50.01 . AC=6;AF=0.081;AN=74;BaseQRankSum=-0.295;DP=80;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.4822;InbreedingCoeff=0.0222;MQ=49.62;MQ0=0;MQRankSum=0.318;QD=7.14;ReadPosRankSum=-0.200;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3.01:0,3,36 ./. ./. 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3.01:0,3,33 ./. 0/0:3,0:3:9.03:0,9,115 ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,42 ./. ./. 0/0:3,0:3:9.03:0,9,108 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6.02:0,6,67 0/0:2,0:2:6.02:0,6,78 0/0:2,0:2:6.02:0,6,68 0/0:2,0:2:3.01:0,3,42 ./. 1/1:0,1:1:3.01:31,3,0 0/0:3,0:3:9.03:0,9,121 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:2,0:2:6.01:0,6,64 0/0:4,0:4:9:0,9,90 0/0:2,0:2:6.02:0,6,74 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 0/1:1,1:2:34.63:35,0,35 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,76 0/0:10,0:10:21.05:0,21,263 0/0:1,1:2:3.01:0,3,33 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,40 ./. 0/0:1,0:1:3:0,3,28 0/0:3,0:3:9.03:0,9,108 0/0:2,0:2:6.02:0,6,73 ./. 0/1:1,1:2:25.53:26,0,32 ./. 0/0:8,0:8:21.06:0,21,247 0/0:1,0:1:3.01:0,3,40 1/1:1,1:2:3.01:42,3,0 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3:0,3,25 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,38 0/0:3,0:3:9.03:0,9,120 ./. ./. -chr1 1223660 . A T 124.16 . AC=11;AF=0.183;AN=60;BaseQRankSum=-2.177;DP=70;Dels=0.00;FS=6.078;HRun=0;HaplotypeScore=0.4653;InbreedingCoeff=0.0992;MQ=47.05;MQ0=0;MQRankSum=-3.819;QD=6.21;ReadPosRankSum=-0.646;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3.01:33,3,0 ./. 0/0:2,0:2:3:0,3,27 ./. ./. ./. 0/0:1,0:1:3.01:0,3,36 ./. 0/0:3,0:3:9.02:0,9,96 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,30 ./. ./. 0/0:3,0:3:6:0,6,64 ./. 0/0:2,0:2:3.01:0,3,30 0/0:1,0:1:3.01:0,3,40 0/0:3,0:3:9.01:0,9,93 0/0:1,0:1:3.01:0,3,33 ./. 0/1:2,1:3:22.52:23,0,67 0/0:5,0:5:6:0,6,67 ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:9.03:0,9,108 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. 0/0:1,0:1:2.99:0,3,23 ./. 0/0:2,0:2:6.02:0,6,83 0/1:6,1:7:15.56:16,0,141 0/0:2,0:2:6.02:0,6,65 0/0:1,0:1:3.01:0,3,31 0/0:1,0:1:3.01:0,3,32 0/0:2,0:2:6.01:0,6,63 1/1:0,1:1:3:28,3,0 0/0:3,0:4:6.02:0,6,74 ./. ./. 0/0:1,1:2:3.01:0,3,42 ./. 0/1:3,3:6:56.54:69,0,57 ./. 1/1:0,1:1:3.01:33,3,0 ./. 1/1:0,1:1:2.99:23,3,0 ./. 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:3.01:0,3,42 ./. ./. -chr1 1223669 . T C 30.84 . AC=2;AF=0.037;AN=54;BaseQRankSum=-0.298;DP=66;Dels=0.00;FS=2.157;HRun=2;HaplotypeScore=0.3049;InbreedingCoeff=-0.1912;MQ=46.88;MQ0=0;MQRankSum=-2.343;QD=3.85;ReadPosRankSum=-1.235;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.01:0,6,60 ./. 0/1:1,1:2:25.53:27,0,26 ./. ./. ./. 0/0:1,0:1:3.01:0,3,37 ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:1,0:1:3:0,3,25 ./. 0/0:2,0:2:3:0,3,25 ./. 0/0:4,0:4:6.02:0,6,83 ./. ./. 0/0:2,0:2:6.02:0,6,76 0/0:4,1:5:6.02:0,6,89 ./. ./. ./. ./. 0/0:4,0:4:9.03:0,9,107 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. 0/0:2,0:2:2.99:0,3,23 ./. 0/0:1,0:1:3.01:0,3,41 0/0:7,0:7:12.04:0,12,159 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:9.02:0,9,100 0/0:1,0:1:3:0,3,28 0/0:3,0:3:3.01:0,3,45 ./. ./. 0/0:1,0:2:3.01:0,3,42 ./. 0/1:3,3:6:28.77:58,0,29 ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3:0,3,25 ./. 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6.02:0,6,79 ./. ./. -chr1 1223721 . C T 44.82 . AC=6;AF=0.150;AN=40;BaseQRankSum=0.689;DP=40;Dels=0.00;FS=2.004;HRun=0;HaplotypeScore=0.3378;InbreedingCoeff=0.0355;MQ=46.71;MQ0=0;MQRankSum=-1.020;QD=4.07;ReadPosRankSum=-1.793;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 1/1:0,1:1:3.01:30,3,0 ./. 0/0:1,0:1:3.01:0,3,36 ./. ./. ./. 0/0:2,0:2:6.02:0,6,73 0/0:1,0:1:2.99:0,3,24 ./. ./. ./. 0/0:2,0:2:3:0,3,26 ./. ./. 0/0:1,0:1:3.01:0,3,36 ./. 0/0:1,0:1:3.01:0,3,41 ./. 0/0:2,0:2:3.01:0,3,35 ./. ./. 0/1:2,1:3:27.42:27,0,32 0/0:3,0:3:9.03:0,9,111 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,35 1/1:0,1:1:3.01:33,3,0 ./. 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.01:0,6,61 ./. 0/0:1,0:1:3.01:0,3,37 0/0:4,0:4:3.01:0,3,33 ./. 0/0:3,0:3:9.03:0,9,110 0/0:2,0:2:6.02:0,6,69 ./. ./. ./. 0/1:5,1:6:24.97:25,0,111 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,37 ./. ./. -chr1 1223741 . T C 53.75 . AC=4;AF=0.105;AN=38;BaseQRankSum=-0.303;DP=42;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.3143;InbreedingCoeff=-0.0438;MQ=43.53;MQ0=0;MQRankSum=1.186;QD=4.48;ReadPosRankSum=-0.745;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,28 ./. ./. ./. 0/0:1,0:1:3.01:0,3,36 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. 0/0:3,0:3:6:0,6,56 1/1:0,2:2:6.02:75,6,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1:3,1:4:24.41:24,0,65 ./. 0/0:2,0:2:3.01:0,3,33 0/0:2,0:2:3.01:0,3,41 ./. 0/0:1,0:1:3.01:0,3,31 0/0:3,0:3:3.01:0,3,33 ./. 0/0:3,0:3:6.02:0,6,82 0/0:2,0:2:6.02:0,6,70 ./. 0/0:3,0:3:3.01:0,3,39 ./. 0/1:5,1:6:17.47:17,0,116 ./. ./. 0/0:3,0:3:9.01:0,9,98 ./. ./. ./. 0/0:1,0:1:3.01:0,3,31 ./. 0/0:1,0:1:2.99:0,3,23 -chr1 1223754 . C T 577.41 . AC=26;AF=0.619;AN=42;BaseQRankSum=1.117;DP=42;Dels=0.00;FS=5.016;HRun=0;HaplotypeScore=0.4750;InbreedingCoeff=-0.0583;MQ=42.10;MQ0=0;MQRankSum=1.817;QD=16.04;ReadPosRankSum=-0.617;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,28 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. 1/1:0,1:1:3.01:34,3,0 ./. ./. 0/1:1,1:2:27.42:33,0,27 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:41,3,0 0/1:3,1:4:24.41:24,0,65 1/1:0,1:1:3.01:35,3,0 1/1:2,1:3:3.01:32,3,0 0/0:2,0:2:3.01:0,3,37 0/0:1,0:1:3:0,3,28 1/1:0,1:1:3.01:41,3,0 1/1:1,1:2:3.01:41,3,0 ./. 1/1:1,2:3:6.02:80,6,0 0/1:1,1:2:23.61:24,0,34 ./. 0/1:3,1:4:29.55:30,0,57 ./. 0/1:3,3:6:12.67:95,0,13 ./. ./. 0/1:1,2:3:24.41:61,0,24 ./. ./. ./. 0/0:1,0:1:3.01:0,3,32 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 -chr1 1223759 . T C 283.09 . AC=16;AF=0.400;AN=40;BaseQRankSum=0.405;DP=42;Dels=0.00;FS=20.948;HRun=2;HaplotypeScore=0.3988;InbreedingCoeff=0.0952;MQ=42.43;MQ0=0;MQRankSum=2.503;QD=12.31;ReadPosRankSum=-1.841;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,28 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 1/1:0,1:1:3.01:40,3,0 ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 0/1:3,1:4:24.41:24,0,65 0/0:1,0:1:3.01:0,3,31 0/1:2,1:3:18.68:27,0,19 0/0:1,1:2:3.01:0,3,35 0/0:1,0:1:3:0,3,28 1/1:0,1:1:3.01:41,3,0 1/1:0,2:2:3.01:42,3,0 ./. 0/1:2,1:3:29.23:29,0,39 0/0:2,0:2:6.02:0,6,70 ./. 0/0:5,0:5:6.02:0,6,83 ./. 0/1:4,2:6:40.33:58,0,40 ./. ./. 0/0:3,0:3:9.02:0,9,103 ./. ./. ./. 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 -chr1 1223772 . C T 118.73 . AC=8;AF=0.235;AN=34;BaseQRankSum=0.790;DP=42;Dels=0.02;FS=6.468;HRun=0;HaplotypeScore=0.2464;InbreedingCoeff=-0.0704;MQ=39.82;MQ0=0;MQRankSum=-1.874;QD=6.25;ReadPosRankSum=0.384;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1:2,2:4:35.74:54,0,36 0/1:2,1:3:21.65:22,0,31 0/1:1,2:3:21.65:22,0,31 ./. 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,40 ./. 1/1:0,2:2:3.01:45,3,0 0/0:3,0:3:9.01:0,9,94 ./. 0/0:5,0:5:9.03:0,9,112 ./. 0/1:5,1:6:18.66:19,0,53 ./. ./. 0/0:3,0:3:6.01:0,6,68 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 -chr1 1223790 . C T 300.88 . AC=13;AF=0.433;AN=30;BaseQRankSum=1.925;DP=47;Dels=0.04;FS=9.204;HRun=0;HaplotypeScore=0.6820;InbreedingCoeff=-0.0492;MQ=39.36;MQ0=0;MQRankSum=-0.298;QD=10.38;ReadPosRankSum=-3.275;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 ./. 1/1:1,1:2:3.01:38,3,0 ./. ./. ./. ./. ./. ./. 1/1:1,1:2:3.01:33,3,0 ./. ./. ./. ./. ./. ./. 0/1:2,3:5:17.66:69,0,18 0/0:3,0:3:6.01:0,6,66 0/1:1,2:3:21.65:25,0,22 0/0:1,0:1:2.99:0,3,23 0/0:1,0:2:3:0,3,28 ./. ./. ./. 0/0:2,1:3:4.83:0,5,45 0/1:1,2:3:20.61:53,0,21 ./. 0/1:5,1:6:24.41:24,0,53 ./. 0/1:3,1:4:18.69:22,0,19 ./. ./. 0/0:3,0:3:6.02:0,6,68 ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 ./. 1/1:0,2:2:6.02:77,6,0 -chr1 1223795 . T C 177.98 . AC=11;AF=0.324;AN=34;BaseQRankSum=1.748;DP=49;Dels=0.00;FS=11.458;HRun=2;HaplotypeScore=1.0405;InbreedingCoeff=0.1689;MQ=39.01;MQ0=0;MQRankSum=0.452;QD=10.47;ReadPosRankSum=-2.573;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,30 ./. ./. 1/1:0,1:1:3.01:41,3,0 1/1:0,1:1:3.01:34,3,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:33,3,0 ./. ./. ./. ./. ./. ./. 0/1:4,1:5:27.42:27,0,39 0/0:3,0:3:6.01:0,6,72 0/0:4,0:4:9.02:0,9,93 0/0:1,0:1:3.01:0,3,38 0/1:2,1:3:21.65:29,0,22 ./. ./. ./. 0/0:4,0:4:6.02:0,6,86 0/1:2,1:3:18.68:19,0,24 ./. 0/0:5,1:6:12.03:0,12,133 ./. 0/0:4,0:4:6:0,6,52 ./. ./. 0/0:3,0:3:6.02:0,6,73 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. 1/1:0,2:2:6.02:79,6,0 -chr1 1223808 . C T 254.07 . AC=14;AF=0.412;AN=34;BaseQRankSum=0.313;DP=55;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.8609;InbreedingCoeff=-0.0598;MQ=39.41;MQ0=0;MQRankSum=-2.458;QD=7.70;ReadPosRankSum=0.432;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,34 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,32 1/1:1,1:2:3.01:33,3,0 ./. ./. ./. ./. ./. ./. 0/1:3,2:5:27.42:39,0,27 0/0:4,0:4:9.02:0,9,102 0/0:3,0:3:9.02:0,9,98 0/0:1,0:2:3.01:0,3,33 0/1:2,1:4:21.65:22,0,33 ./. ./. ./. 0/0:5,0:5:9.03:0,9,125 1/1:0,3:3:6:54,6,0 ./. 0/1:4,2:6:29.55:30,0,58 ./. 0/1:1,3:4:15.68:52,0,16 ./. ./. 0/1:1,1:2:18.68:27,0,19 1/1:0,1:1:3:28,3,0 ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 0/1:4,1:5:24.41:24,0,80 -chr1 1223826 . T C 75.31 . AC=9;AF=0.188;AN=48;BaseQRankSum=-1.209;DP=64;Dels=0.00;FS=1.930;HRun=1;HaplotypeScore=0.5668;InbreedingCoeff=0.0706;MQ=39.48;MQ0=0;MQRankSum=-1.000;QD=4.71;ReadPosRankSum=0.045;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3:0,3,29 ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. ./. 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:3.01:0,3,33 ./. ./. ./. ./. ./. ./. 0/0:3,0:3:3.01:0,3,30 0/0:4,0:4:9.02:0,9,102 0/1:3,1:4:26.55:27,0,88 0/0:1,1:2:2.99:0,3,23 0/1:3,1:4:26.54:27,0,90 1/1:1,1:2:3:28,3,0 0/0:2,0:2:3.01:0,3,40 ./. 0/0:5,0:5:15.05:0,15,192 0/1:2,1:4:14.68:15,0,56 ./. 0/0:8,0:8:18.05:0,18,203 ./. 0/0:4,0:4:9.01:0,9,86 ./. 0/0:1,0:1:3.01:0,3,33 ./. 1/1:0,1:1:3.01:33,3,0 ./. 0/0:1,0:1:3.01:0,3,35 ./. 1/1:0,1:1:3.01:33,3,0 0/0:5,0:5:9.03:0,9,123 -chr1 1223831 . T C 93.99 . AC=8;AF=0.174;AN=46;BaseQRankSum=0.839;DP=67;Dels=0.00;FS=1.794;HRun=2;HaplotypeScore=0.6496;InbreedingCoeff=0.1389;MQ=39.56;MQ0=0;MQRankSum=-1.754;QD=7.23;ReadPosRankSum=-1.754;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,32 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. 0/0:2,0:2:3.01:0,3,30 ./. 1/1:0,1:1:3:28,3,0 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3:0,3,25 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:4,0:4:9.02:0,9,101 0/0:5,0:5:15.04:0,15,169 0/0:1,1:2:3:0,3,28 0/0:6,0:6:12.03:0,12,135 0/0:2,0:2:3:0,3,28 0/0:2,0:2:3.01:0,3,41 ./. 0/0:5,0:5:15.03:0,15,180 0/0:5,0:5:9.01:0,9,95 ./. 0/1:6,1:7:21.40:21,0,88 ./. 0/1:1,2:3:15.68:52,0,16 ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,33 0/0:5,0:5:9.03:0,9,123 -chr1 1223846 . T C 55.02 . AC=8;AF=0.143;AN=56;BaseQRankSum=2.634;DP=80;Dels=0.00;FS=6.864;HRun=1;HaplotypeScore=0.8057;InbreedingCoeff=-0.0215;MQ=39.58;MQ0=0;MQRankSum=-2.072;QD=2.50;ReadPosRankSum=-0.901;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3:0,3,28 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:3.01:0,3,34 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,30 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,37 ./. ./. ./. ./. 1/1:0,1:1:3:28,3,0 0/0:1,0:1:3.01:0,3,36 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,67 0/0:2,0:2:3.01:0,3,39 ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:30,3,0 0/1:4,1:5:20.60:21,0,63 0/0:5,0:5:12.03:0,12,131 0/0:2,0:2:6.02:0,6,67 0/1:5,1:6:12.64:13,0,113 0/0:2,0:2:5.99:0,6,50 0/0:5,0:5:3.01:0,3,45 ./. 0/0:9,0:9:18.05:0,18,218 0/0:6,0:6:12.02:0,12,126 ./. 0/1:3,1:4:27.42:35,0,27 ./. 0/1:4,1:5:18.40:18,0,114 0/0:1,0:1:3.01:0,3,40 0/0:2,0:2:6:0,6,58 ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. 0/0:2,0:2:6.01:0,6,58 0/0:5,0:5:9.03:0,9,123 -chr1 1223851 . T C 109.95 . AC=9;AF=0.161;AN=56;BaseQRankSum=-1.835;DP=80;Dels=0.00;FS=1.589;HRun=2;HaplotypeScore=0.5852;InbreedingCoeff=-0.0310;MQ=40.14;MQ0=0;MQRankSum=-1.699;QD=3.55;ReadPosRankSum=1.584;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:2,0:2:6.01:0,6,62 0/0:2,0:2:6.02:0,6,65 0/0:1,0:1:3.01:0,3,34 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,30 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. ./. 0/0:1,0:1:3:0,3,28 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,34 0/0:2,0:2:6.01:0,6,60 ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,67 0/0:2,0:2:3:0,3,29 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,30 0/0:5,0:5:9.02:0,9,102 0/1:2,2:4:24.43:53,0,24 0/0:2,0:2:6.02:0,6,67 0/0:6,0:6:15.04:0,15,167 0/0:2,0:2:6:0,6,51 0/0:4,1:5:3.01:0,3,45 ./. 0/1:8,1:9:9.61:10,0,177 0/1:4,1:5:15.67:16,0,63 ./. 0/0:4,0:4:9.03:0,9,112 ./. 0/1:4,1:5:7.66:8,0,121 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6:0,6,56 ./. ./. ./. 0/0:1,0:1:3.01:0,3,32 ./. 1/1:0,2:2:6.01:60,6,0 0/1:4,1:5:24.41:24,0,81 -chr1 1223864 . T C 42.18 . AC=6;AF=0.094;AN=64;BaseQRankSum=-0.935;DP=85;Dels=0.00;FS=8.168;HRun=1;HaplotypeScore=0.4761;InbreedingCoeff=-0.1023;MQ=39.89;MQ0=0;MQRankSum=-1.619;QD=3.52;ReadPosRankSum=0.274;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:5,0:5:9.02:0,9,92 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3.01:0,3,36 ./. ./. ./. 0/0:1,0:1:3:0,3,26 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,35 ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3.01:0,3,35 0/0:1,0:1:3.01:0,3,31 0/1:1,1:2:27.42:27,0,27 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 0/0:2,0:2:3.01:0,3,42 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,30 0/0:4,0:4:9.02:0,9,109 0/0:6,0:6:9.03:0,9,106 0/1:1,1:2:27.42:27,0,27 0/0:5,0:5:12.04:0,12,157 0/1:1,1:2:21.66:23,0,22 0/0:5,0:5:3.01:0,3,45 ./. 0/0:10,0:10:21.07:0,21,270 0/1:4,1:5:15.64:16,0,92 ./. 0/0:3,0:3:6.02:0,6,76 ./. 0/0:4,0:4:12.03:0,12,137 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6:0,6,58 0/0:1,0:1:3.01:0,3,32 ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. 0/0:2,0:2:5.99:0,6,53 0/0:5,0:5:9.03:0,9,123 -chr1 1223873 . T TCC 58.95 . AC=5;AF=0.076;AN=66;BaseQRankSum=2.703;DP=91;FS=1.912;HRun=3;HaplotypeScore=29.9562;InbreedingCoeff=-0.1751;MQ=40.59;MQ0=0;MQRankSum=-2.282;QD=3.27;ReadPosRankSum=-0.842;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:6,0:6:15.05:0,15,210 0/0:3,0:3:9.03:0,9,126 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,84 ./. 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,41 ./. 0/0:2,0:2:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 0/1:2,0:2:3.60:4,0,30 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,84 0/0:2,0:2:3.01:0,3,42 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:3.01:0,3,42 0/0:2,0:2:3.01:0,3,42 0/0:6,0:6:6.02:0,6,84 0/0:3,0:3:1.24:0,1,3 0/0:5,0:5:15.05:0,15,210 0/0:2,0:2:6.02:0,6,84 0/0:6,0:6:9.03:0,9,126 ./. 0/0:10,0:10:24.08:0,24,336 0/1:5,1:6:39.62:40,0,152 ./. 0/0:4,0:4:9.03:0,9,122 ./. 0/1:3,1:4:43.01:43,0,114 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,84 0/1:1,1:2:16.79:17,0,29 ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. 0/0:1,1:2:5.61:0,6,52 0/1:3,1:4:42.38:42,0,114 -chr1 1223887 . C T 208.26 . AC=15;AF=0.242;AN=62;BaseQRankSum=1.248;DP=86;Dels=0.00;FS=1.200;HRun=0;HaplotypeScore=0.4017;InbreedingCoeff=-0.1357;MQ=40.83;MQ0=0;MQRankSum=-2.152;QD=4.84;ReadPosRankSum=0.390;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:6,0:6:12.01:0,12,139 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3.01:0,3,36 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/1:1,1:2:18.68:36,0,19 ./. 0/0:1,0:1:3.01:0,3,34 0/0:1,0:1:3.01:0,3,33 ./. 0/0:2,0:2:3:0,3,28 ./. 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:32,3,0 0/0:1,0:1:3:0,3,25 ./. ./. ./. ./. 0/1:1,1:2:24.57:36,0,25 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 1/1:0,2:2:3:28,3,0 0/1:3,2:5:22.63:23,0,27 0/0:1,0:1:2.99:0,3,23 0/0:4,0:4:9.03:0,9,112 0/1:1,1:2:21.65:22,0,27 0/1:5,1:6:24.28:24,0,111 ./. 0/1:8,1:9:15.38:15,0,161 0/1:5,2:7:12.66:13,0,99 ./. 0/1:2,2:4:35.76:44,0,36 0/0:1,0:1:3.01:0,3,33 0/0:6,0:6:18.05:0,18,199 0/0:2,0:2:3.01:0,3,45 0/1:1,1:2:18.68:19,0,27 0/0:2,1:3:6.01:0,6,63 ./. ./. 0/0:1,0:1:3.01:0,3,31 ./. 0/0:2,0:2:3:0,3,25 0/0:4,0:4:6.02:0,6,85 -chr1 1223900 . C T 905.84 . AC=36;AF=0.643;AN=56;BaseQRankSum=0.938;DP=77;Dels=0.00;FS=0.998;HRun=0;HaplotypeScore=0.6461;InbreedingCoeff=0.0959;MQ=40.99;MQ0=0;MQRankSum=-1.278;QD=14.38;ReadPosRankSum=0.258;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:5,0:5:12.02:0,12,123 0/0:2,0:2:6.01:0,6,64 ./. 0/0:1,0:1:3.01:0,3,36 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:3.01:42,3,0 ./. 1/1:0,1:1:3.01:40,3,0 ./. ./. 1/1:1,1:2:3:28,3,0 ./. ./. 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. 1/1:0,2:2:6.02:75,6,0 ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 1/1:0,2:2:6.01:63,6,0 0/0:1,1:2:3:0,3,28 0/1:2,2:4:27.42:27,0,27 0/0:1,0:2:3.01:0,3,33 1/1:0,3:3:9.03:108,9,0 1/1:0,2:2:6.01:61,6,0 0/1:5,1:6:24.28:24,0,115 ./. 0/1:4,4:8:59.31:59,0,95 0/1:3,4:7:14.60:100,0,15 ./. 0/1:2,3:5:35.75:48,0,36 ./. 0/1:5,2:7:48.20:48,0,118 1/1:0,2:2:3.01:45,3,0 1/1:0,2:2:6:53,6,0 1/1:1,2:3:3.01:38,3,0 ./. ./. 1/1:0,1:1:3.01:30,3,0 0/0:1,0:1:3.01:0,3,41 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:40,3,0 -chr1 1223905 . T C 98.29 . AC=9;AF=0.167;AN=54;BaseQRankSum=-1.946;DP=77;Dels=0.00;FS=3.277;HRun=2;HaplotypeScore=0.5934;InbreedingCoeff=0.1031;MQ=40.55;MQ0=0;MQRankSum=-0.402;QD=5.46;ReadPosRankSum=-2.098;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/1:3,2:5:20.60:21,0,64 0/0:2,0:2:6:0,6,57 ./. 0/0:1,0:1:3.01:0,3,36 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,73 ./. 0/0:1,0:1:3:0,3,29 ./. ./. 0/0:2,0:2:3:0,3,28 ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. 0/0:3,0:3:6:0,6,63 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:3.01:0,3,30 0/0:1,1:2:3:0,3,28 0/0:4,0:4:6.02:0,6,67 0/0:2,0:2:6.01:0,6,60 1/1:0,2:2:6.01:61,6,0 0/1:1,1:2:21.65:27,0,22 0/0:6,0:6:15.04:0,15,173 ./. 0/0:6,1:7:12.92:0,13,150 0/0:8,0:8:18.01:0,18,172 ./. 0/0:5,0:5:9.02:0,9,100 ./. 0/1:6,1:7:10.61:11,0,146 0/0:2,0:2:3.01:0,3,45 0/0:2,0:2:3:0,3,25 ./. ./. ./. 0/0:1,0:1:3.01:0,3,30 0/0:1,0:1:3.01:0,3,42 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:38,3,0 -chr1 1223963 . T C 128.73 . AC=10;AF=0.385;AN=26;BaseQRankSum=-0.635;DP=29;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.4996;InbreedingCoeff=-0.0973;MQ=39.99;MQ0=0;MQRankSum=1.102;QD=6.78;ReadPosRankSum=0.301;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,28 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,45 ./. ./. ./. ./. ./. ./. ./. 0/1:3,1:4:24.41:24,0,69 ./. ./. 0/1:1,1:2:27.42:34,0,27 ./. ./. 0/0:1,0:1:3.01:0,3,35 ./. ./. 0/1:2,2:4:21.65:22,0,27 ./. 0/1:4,1:5:15.67:16,0,70 ./. 1/1:0,2:2:3.01:33,3,0 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. 0/0:1,0:1:3:0,3,25 ./. 1/1:0,1:1:3.01:35,3,0 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,33 -chr1 1225096 . C T 123.66 . AC=9;AF=0.563;AN=16;BaseQRankSum=0.278;DP=16;Dels=0.00;FS=6.990;HRun=0;HaplotypeScore=0.8108;MQ=33.81;MQ0=0;MQRankSum=-1.246;QD=13.74;ReadPosRankSum=1.769;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:32,3,0 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. 1/1:0,1:1:3.01:32,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. 0/1:1,1:2:18.68:19,0,35 ./. ./. ./. 1/1:0,4:4:6.01:65,6,0 -chr1 1225121 . T C 79.61 . AC=9;AF=0.300;AN=30;BaseQRankSum=-0.698;DP=26;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=1.1615;InbreedingCoeff=0.2471;MQ=30.87;MQ0=0;MQRankSum=-1.397;QD=11.37;ReadPosRankSum=-0.698;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,73 ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3:0,3,28 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. 1/1:0,1:1:3:25,3,0 ./. 0/0:1,0:1:3:0,3,25 1/1:0,1:1:3.01:33,3,0 ./. 1/1:1,1:2:3.01:33,3,0 ./. 0/0:1,0:1:3.01:0,3,37 ./. ./. ./. ./. 0/0:2,0:2:6.01:0,6,64 ./. 0/1:1,1:2:27.42:27,0,29 ./. 0/0:3,1:4:6.01:0,6,62 -chr1 1225125 . TCC T 136.07 . AC=9;AF=0.281;AN=32;BaseQRankSum=0.701;DP=25;FS=18.560;HRun=5;HaplotypeScore=19.9646;InbreedingCoeff=-0.0780;MQ=30.60;MQ0=0;MQRankSum=2.186;QD=11.34;ReadPosRankSum=1.196;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,110 ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,55 ./. ./. ./. 0/0:1,0:1:3.01:0,3,55 ./. ./. ./. ./. ./. ./. ./. 0/1:0,1:1:0:0,0,0 ./. ./. ./. 0/0:1,0:1:3.01:0,3,55 ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 0/1:1,1:2:35.20:35,0,48 0/0:1,0:1:3.01:0,3,55 ./. ./. ./. 0/0:1,0:1:3.01:0,3,55 ./. 0/0:1,0:1:3.01:0,3,55 0/0:1,0:1:2.84:0,3,14 ./. 0/0:2,0:2:3:0,3,27 ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. ./. 0/1:1,1:2:24.59:25,0,49 ./. 0/1:1,1:2:35.99:36,0,46 ./. 0/1:2,1:3:35.98:36,0,48 -chr1 1225141 . T C 32.44 . AC=5;AF=0.147;AN=34;BaseQRankSum=-0.213;DP=26;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.3484;InbreedingCoeff=0.0778;MQ=30.54;MQ0=0;MQRankSum=-1.319;QD=8.11;ReadPosRankSum=-1.149;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3:0,3,28 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 0/0:1,0:1:2.99:0,3,23 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. 0/0:1,0:1:3:0,3,25 ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 ./. 0/0:2,0:2:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,41 ./. ./. ./. ./. 0/0:2,0:2:6:0,6,60 ./. 0/1:1,1:2:27.42:27,0,33 ./. 0/0:2,1:3:6.01:0,6,61 -chr1 1225163 . TCC T 121.19 . AC=12;AF=0.353;AN=34;BaseQRankSum=0.452;DP=22;FS=9.260;HRun=5;HaplotypeScore=17.1552;InbreedingCoeff=0.3248;MQ=32.45;MQ0=0;MQRankSum=-1.759;QD=17.31;ReadPosRankSum=0.050;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,55 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,55 ./. ./. ./. 0/0:1,0:1:3.01:0,3,55 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 0/0:1,0:1:2.74:0,3,12 ./. ./. ./. 1/1:1,0:1:0.89:2,1,0 1/1:1,1:2:3.01:34,3,0 0/0:1,0:1:3.01:0,3,55 ./. ./. ./. 1/1:0,1:1:3.01:42,3,0 ./. 0/0:1,0:1:3.01:0,3,55 1/1:0,1:1:3.01:42,3,0 ./. 0/0:1,0:1:0:0,0,0 ./. 0/0:1,0:1:3.01:0,3,52 ./. ./. ./. 0/0:1,0:1:3.01:0,3,45 ./. ./. 0/0:2,0:2:6.02:0,6,98 ./. 0/0:1,0:1:3.01:0,3,37 -chr1 1225174 . C T 237.41 . AC=18;AF=0.643;AN=28;BaseQRankSum=0.648;DP=22;Dels=0.00;FS=2.363;HRun=0;HaplotypeScore=1.0277;InbreedingCoeff=0.3305;MQ=32.25;MQ0=0;MQRankSum=-0.648;QD=26.38;ReadPosRankSum=-0.059;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,82 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3:28,3,0 ./. ./. 0/0:1,0:1:3.01:0,3,32 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 0/0:3,0:3:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. 1/1:0,1:1:3.01:38,3,0 ./. 1/1:0,1:1:3.01:39,3,0 -chr1 1225239 . A T 100.39 . AC=6;AF=0.500;AN=12;BaseQRankSum=0.550;DP=8;Dels=0.00;FS=3.680;HRun=0;HaplotypeScore=0.0000;MQ=42.45;MQ0=0;MQRankSum=0.550;QD=25.10;ReadPosRankSum=0.550;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,35 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:40,3,0 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. ./. ./. ./. 1/1:0,1:1:3.01:32,3,0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1/1:0,2:2:6.02:77,6,0 -chr1 1225261 . T C 133.06 . AC=10;AF=0.200;AN=50;BaseQRankSum=0.107;DP=45;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.3102;InbreedingCoeff=0.1724;MQ=37.78;MQ0=0;MQRankSum=-0.997;QD=14.78;ReadPosRankSum=-0.534;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,36 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:2,0:2:6.01:0,6,63 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:2.99:0,3,23 ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. 1/1:0,2:2:6.02:70,6,0 ./. ./. 0/0:3,0:3:9.02:0,9,102 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,38 ./. ./. ./. ./. 0/0:3,0:3:6.02:0,6,73 0/0:3,0:3:9.03:0,9,114 ./. ./. 0/1:1,1:2:27.42:27,0,27 ./. 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:33,3,0 ./. 0/0:4,0:4:12.03:0,12,140 ./. ./. ./. 0/1:1,1:2:27.42:27,0,27 ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/0:4,0:4:9.02:0,9,112 -chr1 1225279 . T C 111.05 . AC=13;AF=0.210;AN=62;BaseQRankSum=0.114;DP=66;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.5124;InbreedingCoeff=0.2853;MQ=35.30;MQ0=0;MQRankSum=-1.427;QD=11.10;ReadPosRankSum=-1.376;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,25 ./. 0/0:1,0:1:3:0,3,25 ./. ./. ./. ./. ./. ./. ./. 0/0:3,0:3:6.02:0,6,71 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,34 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 0/1:1,1:2:17.68:18,0,27 ./. ./. ./. 0/0:2,0:2:6.02:0,6,73 ./. ./. 0/0:4,1:5:12.03:0,12,136 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. 0/0:3,0:3:6.02:0,6,74 0/0:5,0:5:12.04:0,12,144 ./. 1/1:0,1:1:3.01:33,3,0 1/1:1,1:2:3.01:33,3,0 1/1:0,1:1:3.01:33,3,0 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,33 ./. 0/0:3,1:4:9.02:0,9,104 0/0:3,0:3:9.02:0,9,100 1/1:1,1:2:3.01:33,3,0 0/0:2,0:2:3:0,3,28 0/0:4,0:4:12.03:0,12,140 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:9.01:0,9,89 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:4,0:4:9:0,9,99 -chr1 1225284 . T C 256.36 . AC=13;AF=0.210;AN=62;BaseQRankSum=0.970;DP=68;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.5134;InbreedingCoeff=0.1617;MQ=35.13;MQ0=0;MQRankSum=-1.184;QD=12.82;ReadPosRankSum=0.233;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,27 ./. 0/0:1,0:1:3:0,3,25 ./. ./. ./. ./. ./. ./. ./. 0/0:3,0:3:6.02:0,6,71 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,31 ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,41 0/0:2,0:2:6.02:0,6,67 ./. ./. ./. 1/1:0,2:2:6.02:73,6,0 ./. ./. 0/1:2,3:5:54.84:55,0,57 0/0:2,0:2:3.01:0,3,33 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. 1/1:0,3:3:6.02:78,6,0 0/0:5,0:5:12.04:0,12,147 ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,1:2:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:3.01:0,3,33 ./. 0/0:4,0:4:9.02:0,9,106 0/1:2,1:3:24.41:24,0,58 0/0:2,0:2:3.01:0,3,33 1/1:1,1:2:3:25,3,0 0/0:4,0:4:12.03:0,12,136 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 0/1:1,2:3:24.42:46,0,24 1/1:0,1:1:3.01:33,3,0 0/0:2,0:2:6.02:0,6,67 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:4,0:4:9.02:0,9,112 -chr1 1225302 . C T 193.86 . AC=15;AF=0.242;AN=62;BaseQRankSum=-1.436;DP=91;Dels=0.00;FS=1.834;HRun=0;HaplotypeScore=1.1816;InbreedingCoeff=0.2195;MQ=33.76;MQ0=0;MQRankSum=0.576;QD=8.43;ReadPosRankSum=1.178;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. 0/0:1,0:1:3:0,3,25 ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:4,0:4:9.02:0,9,96 0/0:4,0:4:9.03:0,9,103 ./. ./. ./. 1/1:0,1:1:2.99:24,3,0 0/0:1,0:1:3.01:0,3,40 1/1:0,1:1:3.01:32,3,0 ./. ./. ./. ./. ./. ./. 0/0:3,0:3:6.02:0,6,67 ./. ./. ./. 1/1:0,3:3:6.02:66,6,0 ./. ./. 0/0:6,0:6:12.04:0,12,152 1/1:1,1:2:3.01:33,3,0 0/0:2,0:2:6.02:0,6,77 ./. 1/1:0,1:1:3.01:33,3,0 ./. ./. 0/0:3,0:3:6.01:0,6,71 0/0:5,0:5:9.02:0,9,102 ./. 0/1:2,1:3:30.29:30,0,56 0/0:3,0:3:6.02:0,6,67 0/0:1,0:1:2.99:0,3,23 1/1:1,1:2:3.01:33,3,0 ./. ./. 0/0:4,0:4:3.01:0,3,33 0/0:3,0:3:3.01:0,3,33 0/0:3,0:3:6.01:0,6,60 0/0:2,0:2:3.01:0,3,33 0/1:4,1:5:21.43:21,0,73 0/0:1,0:1:3.01:0,3,33 ./. 0/0:5,0:5:12.03:0,12,128 ./. 0/0:3,0:3:9:0,9,90 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:3.01:0,3,33 0/0:2,0:2:3.01:0,3,33 0/1:3,2:5:27.42:38,0,27 -chr1 1225312 . G A 158.46 . AC=11;AF=0.172;AN=64;BaseQRankSum=-0.966;DP=93;Dels=0.02;FS=7.390;HRun=0;HaplotypeScore=1.6923;InbreedingCoeff=-0.0065;MQ=33.88;MQ0=0;MQRankSum=-1.247;QD=6.09;ReadPosRankSum=0.910;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6:0,6,58 ./. ./. 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:3,0:4:6.01:0,6,62 0/0:3,0:3:9.03:0,9,101 ./. 0/0:1,0:1:3:0,3,28 ./. ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,39 ./. ./. ./. ./. ./. ./. 0/1:2,2:4:24.41:24,0,61 ./. ./. ./. 0/0:3,0:3:9.02:0,9,98 ./. ./. 0/1:3,2:6:54.83:55,0,66 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:3.01:0,3,39 ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:2,0:3:3.01:0,3,38 0/0:5,0:5:9.02:0,9,97 ./. 0/1:1,2:3:27.42:27,0,33 1/1:1,1:3:3:26,3,0 0/0:1,0:2:2.99:0,3,24 0/0:3,0:3:6.02:0,6,69 ./. ./. 0/0:4,0:4:6.02:0,6,67 ./. 0/0:3,0:3:6.01:0,6,60 0/0:1,0:1:3.01:0,3,33 0/0:4,0:4:9.02:0,9,103 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3.01:0,3,33 0/1:3,2:5:42.21:42,0,74 ./. 0/0:2,0:3:3.01:0,3,33 0/1:1,1:2:22.63:23,0,27 1/1:1,1:2:3.01:33,3,0 ./. 0/0:4,0:5:6.01:0,6,65 -chr1 1225319 . T C 311.15 . AC=16;AF=0.229;AN=70;BaseQRankSum=0.007;DP=97;Dels=0.00;FS=12.678;HRun=1;HaplotypeScore=0.6200;InbreedingCoeff=0.0685;MQ=35.32;MQ0=0;MQRankSum=-2.217;QD=9.15;ReadPosRankSum=2.287;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,39 0/0:2,0:2:6:0,6,58 ./. ./. 0/0:3,0:3:9.03:0,9,112 0/0:3,0:3:9.03:0,9,112 ./. ./. 0/0:3,0:3:9.03:0,9,102 0/0:2,0:2:6.02:0,6,65 ./. 0/0:2,0:2:5.99:0,6,54 ./. ./. 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,39 1/1:0,1:1:3.01:33,3,0 ./. ./. ./. ./. 0/0:2,0:2:3:0,3,28 0/1:1,3:4:27.42:27,0,33 ./. ./. ./. 0/0:3,0:3:9.03:0,9,102 ./. ./. 0/1:4,2:6:54.85:55,0,55 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.01:0,6,65 ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:4,0:4:3.01:0,3,45 0/0:1,3:4:3.01:0,3,33 ./. 0/1:1,2:3:30.29:55,0,30 1/1:1,2:3:6.02:67,6,0 ./. 0/0:2,0:2:6.02:0,6,73 ./. 0/0:1,0:1:3.01:0,3,40 0/0:4,0:4:6.02:0,6,67 ./. 0/0:4,0:4:9.02:0,9,91 0/0:1,0:1:3.01:0,3,33 0/0:4,0:4:6.01:0,6,63 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:2.99:0,3,24 0/1:3,2:5:51.84:52,0,74 1/1:0,1:1:3.01:33,3,0 0/0:2,1:3:3.01:0,3,31 0/1:1,1:2:23.61:27,0,24 1/1:1,1:2:3.01:33,3,0 ./. 0/1:5,1:6:21.41:21,0,78 -chr1 1225325 . G A 205.95 . AC=12;AF=0.176;AN=68;BaseQRankSum=-2.064;DP=103;Dels=0.00;FS=4.701;HRun=0;HaplotypeScore=0.5398;InbreedingCoeff=-0.0183;MQ=36.25;MQ0=0;MQRankSum=-2.585;QD=6.86;ReadPosRankSum=1.419;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:4,0:4:12.04:0,12,151 0/0:3,0:3:9.03:0,9,112 ./. ./. 0/0:4,0:4:9.03:0,9,103 0/0:2,0:2:6.02:0,6,67 ./. 0/0:2,0:2:3:0,3,28 ./. ./. ./. 0/0:1,0:1:3.01:0,3,39 1/1:0,1:1:2.99:23,3,0 ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,32 0/1:2,1:4:27.42:27,0,33 ./. 0/0:2,0:2:6.02:0,6,75 ./. 0/0:3,0:3:9.02:0,9,96 ./. ./. 0/1:3,2:6:35.39:58,0,35 0/0:1,0:1:3:0,3,29 0/0:2,0:2:6.01:0,6,68 ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:4,0:4:3.01:0,3,39 0/0:4,0:4:3.01:0,3,33 ./. 0/1:1,2:3:30.29:58,0,30 0/1:4,1:6:16.68:17,0,27 ./. 0/0:3,0:3:9.03:0,9,112 ./. 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:6.02:0,6,67 ./. 0/0:5,0:5:12.03:0,12,134 0/0:1,0:1:3.01:0,3,33 0/0:4,0:4:6.01:0,6,63 1/1:0,1:1:3.01:32,3,0 0/0:1,0:1:3.01:0,3,33 0/1:3,2:5:43.11:43,0,68 ./. 0/0:3,1:4:3.01:0,3,37 0/1:1,1:2:27.42:27,0,27 1/1:0,1:2:3.01:33,3,0 ./. 0/0:4,0:6:9.01:0,9,91 -chr1 1225330 . G A 109.49 . AC=8;AF=0.129;AN=62;BaseQRankSum=-2.003;DP=109;Dels=0.00;FS=4.693;HRun=0;HaplotypeScore=0.7228;InbreedingCoeff=-0.1427;MQ=36.47;MQ0=0;MQRankSum=-2.668;QD=3.78;ReadPosRankSum=0.963;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:4,0:4:12.04:0,12,151 0/0:3,0:3:9.03:0,9,112 ./. ./. 0/0:4,0:4:9.03:0,9,103 0/0:2,0:2:3.01:0,3,33 ./. 0/0:2,0:2:6.01:0,6,63 ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. 0/0:1,0:1:3:0,3,28 ./. 0/0:2,0:2:3.01:0,3,38 0/1:2,1:4:23.61:27,0,24 ./. 0/0:2,0:2:6.02:0,6,79 ./. 0/0:3,0:3:6.02:0,6,67 ./. ./. 0/1:3,2:6:54.85:55,0,57 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:3.01:0,3,39 ./. ./. ./. ./. 0/0:3,0:4:3.01:0,3,42 0/0:4,0:5:3.01:0,3,33 ./. 0/1:1,2:3:17.68:18,0,33 0/1:4,1:6:27.42:27,0,27 ./. 0/0:4,0:4:12.03:0,12,146 ./. 0/0:1,0:1:3.01:0,3,42 0/0:3,0:3:6.02:0,6,67 ./. 0/0:7,0:7:15.04:0,15,174 0/0:3,0:3:6.02:0,6,67 0/0:4,0:4:6.01:0,6,63 ./. ./. 0/1:3,1:5:21.41:21,0,77 ./. 0/0:3,0:4:3.01:0,3,40 0/1:1,1:3:23.61:24,0,27 1/1:1,1:2:3.01:33,3,0 ./. 0/0:4,1:6:12.03:0,12,134 -chr1 1225335 . T C 238.86 . AC=13;AF=0.191;AN=68;BaseQRankSum=-1.449;DP=110;Dels=0.00;FS=7.186;HRun=1;HaplotypeScore=0.5462;InbreedingCoeff=-0.0481;MQ=36.64;MQ0=0;MQRankSum=-2.715;QD=6.46;ReadPosRankSum=-1.710;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:9.02:0,9,105 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:4,0:4:12.03:0,12,143 0/0:3,0:3:9.03:0,9,112 ./. ./. 0/0:4,0:4:9.03:0,9,103 1/1:0,2:2:3.01:33,3,0 ./. 0/0:2,0:2:6.01:0,6,60 ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. 0/0:1,0:1:3:0,3,28 ./. 0/0:1,0:1:3.01:0,3,38 0/1:2,2:4:22.63:27,0,23 ./. 0/0:2,0:2:6.02:0,6,76 ./. 0/0:3,0:3:6.02:0,6,69 ./. ./. 0/1:4,2:6:54.85:55,0,55 0/0:1,0:1:3:0,3,28 0/0:2,0:2:3.01:0,3,32 ./. 0/0:1,0:1:3.01:0,3,31 ./. ./. 0/0:2,0:3:3.01:0,3,42 0/0:4,0:4:3.01:0,3,33 ./. 0/1:1,2:3:30.30:48,0,30 1/1:3,3:6:3.01:33,3,0 0/0:3,0:3:3.01:0,3,30 0/0:4,0:4:12.04:0,12,146 ./. 0/0:1,0:1:3.01:0,3,42 0/0:3,0:3:3.01:0,3,33 ./. 0/0:9,0:10:18.05:0,18,226 0/0:3,0:3:6.02:0,6,67 0/0:4,0:4:6.01:0,6,63 1/1:0,1:1:3.01:33,3,0 ./. 0/1:3,2:5:51.84:52,0,74 ./. 0/0:3,0:3:3.01:0,3,39 0/1:2,1:3:27.42:27,0,27 0/1:1,1:2:27.42:27,0,32 ./. 0/1:4,1:5:18.40:18,0,121 -chr1 1225340 . TC T 227.19 . AC=9;AF=0.132;AN=68;BaseQRankSum=5.045;DP=112;FS=7.004;HRun=2;HaplotypeScore=30.7520;InbreedingCoeff=-0.0950;MQ=37.06;MQ0=0;MQRankSum=-2.051;QD=7.33;ReadPosRankSum=-0.410;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:4,0:4:12.04:0,12,180 0/0:1,0:1:3.01:0,3,45 ./. ./. 0/0:4,0:4:12.04:0,12,180 0/0:2,0:2:6.02:0,6,90 ./. ./. 0/0:3,0:3:9.03:0,9,135 ./. ./. 0/0:2,0:2:6.02:0,6,90 ./. ./. ./. 0/0:1,0:1:3.01:0,3,45 ./. ./. ./. 0/0:1,0:1:3.01:0,3,45 0/0:1,0:1:3.01:0,3,45 0/0:1,0:1:3.01:0,3,45 0/1:2,2:4:29.67:30,0,39 ./. 0/0:3,0:3:9.03:0,9,135 ./. 0/0:3,0:3:6.02:0,6,73 ./. ./. 0/1:4,2:6:62.38:62,0,76 0/0:1,0:1:0.47:0,0,1 0/0:2,0:2:3.01:0,3,45 ./. 0/0:1,0:1:3.01:0,3,44 ./. ./. 0/0:3,0:3:3.01:0,3,45 0/0:4,0:4:3.01:0,3,45 ./. 0/1:1,2:3:35.97:65,0,36 1/1:4,1:5:3.01:37,3,0 ./. 0/0:5,0:5:11.94:0,12,180 ./. 0/0:1,0:1:3.01:0,3,45 0/0:4,0:4:3.01:0,3,45 ./. 0/0:10,0:10:21.07:0,21,311 0/0:3,0:3:6.02:0,6,87 0/0:5,0:4:9.03:0,9,135 0/1:2,1:3:25.17:25,0,81 ./. 0/1:3,2:5:59.33:59,0,120 0/0:1,0:1:0:0,0,0 0/0:2,0:2:3.01:0,3,45 0/1:2,1:3:29.13:29,0,41 0/1:1,1:2:31.19:31,0,39 ./. 0/0:4,0:4:8.90:0,9,135 -chr1 1225343 . G A 137.99 . AC=9;AF=0.141;AN=64;BaseQRankSum=-2.584;DP=116;Dels=0.01;FS=2.292;HRun=0;HaplotypeScore=0.6542;InbreedingCoeff=-0.1498;MQ=37.81;MQ0=0;MQRankSum=-2.776;QD=4.45;ReadPosRankSum=-2.598;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:4,0:4:12.03:0,12,139 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:4,0:4:12.04:0,12,148 0/0:2,0:2:6.02:0,6,79 ./. ./. 0/0:4,0:4:12.03:0,12,136 ./. ./. 0/0:2,0:2:6.01:0,6,59 ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3:0,3,25 0/1:2,2:4:27.42:27,0,33 0/0:1,0:1:3.01:0,3,35 0/0:3,0:3:6.02:0,6,79 ./. 0/0:3,0:3:3.01:0,3,33 ./. ./. 0/1:2,2:5:18.67:47,0,19 ./. 0/0:2,0:3:6.02:0,6,76 ./. 0/0:1,0:1:3:0,3,25 ./. ./. 0/0:3,0:3:6.02:0,6,73 0/0:3,0:4:3.01:0,3,33 ./. 0/1:1,2:3:30.29:52,0,30 1/1:2,1:5:3:27,3,0 ./. 0/0:5,0:5:12.03:0,12,147 ./. 0/0:1,0:1:3.01:0,3,42 0/0:4,1:5:6.02:0,6,67 ./. 0/0:10,0:10:18.06:0,18,227 0/0:3,0:3:6.02:0,6,67 0/0:4,0:5:9.02:0,9,95 0/1:3,1:4:21.40:21,0,90 ./. 0/1:3,2:5:21.42:21,0,69 ./. 0/0:2,0:2:3.01:0,3,34 0/1:2,1:3:17.68:18,0,27 0/1:1,1:2:27.42:27,0,35 ./. 0/0:3,0:4:9.02:0,9,104 -chr1 1225350 . G C 61.74 . AC=4;AF=0.065;AN=62;BaseQRankSum=-1.443;DP=105;Dels=0.00;FS=2.393;HRun=5;HaplotypeScore=0.7473;InbreedingCoeff=-0.1912;MQ=39.32;MQ0=0;MQRankSum=-2.240;QD=4.75;ReadPosRankSum=-3.424;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:4,0:4:12.03:0,12,140 0/0:1,0:1:3.01:0,3,33 ./. ./. 0/0:6,0:6:18.06:0,18,222 0/0:2,0:2:6.02:0,6,75 0/0:1,0:1:3.01:0,3,33 ./. 0/0:4,0:4:12.03:0,12,136 ./. ./. 0/0:2,0:2:6.01:0,6,59 ./. ./. ./. 0/0:1,0:1:3.01:0,3,40 ./. ./. ./. 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,38 0/1:2,1:3:27.42:27,0,31 0/0:2,0:2:6.02:0,6,80 0/0:3,0:3:9.03:0,9,114 ./. ./. ./. ./. 0/1:4,2:6:54.84:55,0,56 ./. 0/0:4,0:4:6.02:0,6,84 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,38 0/0:3,0:3:3.01:0,3,33 ./. 0/1:1,1:2:27.42:27,0,33 ./. ./. 0/0:5,0:5:12.04:0,12,146 ./. 0/0:2,0:2:3.01:0,3,45 0/0:4,0:4:6.02:0,6,67 ./. 0/0:10,0:10:15.04:0,15,182 0/0:2,0:2:3.01:0,3,33 0/0:4,0:4:3.01:0,3,33 0/0:3,0:3:9.03:0,9,107 ./. 0/0:3,0:3:9.01:0,9,88 ./. 0/0:2,0:2:3.01:0,3,39 0/0:2,0:2:3.01:0,3,33 0/1:1,1:2:27.42:27,0,36 ./. 0/0:3,0:3:9.02:0,9,109 -chr1 1225371 . C T 52.17 . AC=8;AF=0.114;AN=70;BaseQRankSum=0.850;DP=87;Dels=0.00;FS=2.411;HRun=0;HaplotypeScore=0.1882;InbreedingCoeff=0.0721;MQ=42.92;MQ0=0;MQRankSum=-1.185;QD=3.07;ReadPosRankSum=-0.451;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:3,0:3:6.02:0,6,66 ./. ./. ./. 0/1:2,1:3:24.41:24,0,66 ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. 0/0:2,0:2:6.02:0,6,74 ./. 0/0:1,0:1:3.01:0,3,30 ./. ./. ./. 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3:0,3,29 0/0:1,0:1:3.01:0,3,32 ./. 0/0:3,0:3:9.03:0,9,122 0/0:2,1:3:6.02:0,6,77 ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3.01:0,3,35 0/0:2,0:2:6.01:0,6,67 ./. 0/0:3,0:3:6.02:0,6,83 ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,32 0/0:2,0:2:3.01:0,3,33 0/0:2,0:2:6.01:0,6,61 0/0:3,0:3:6.02:0,6,81 0/0:4,0:4:9.01:0,9,89 0/0:3,0:3:3:0,3,28 0/0:7,0:7:12.04:0,12,143 ./. 0/0:2,0:2:3.01:0,3,45 0/0:3,0:3:3.01:0,3,33 ./. 0/1:8,2:10:18.39:18,0,152 0/0:2,0:2:3.01:0,3,33 0/0:2,1:3:3.01:0,3,33 0/0:6,0:6:18.06:0,18,231 ./. 0/0:1,0:1:3.01:0,3,33 1/1:0,1:1:3.01:33,3,0 0/0:1,0:1:3:0,3,27 1/1:1,1:2:3.01:33,3,0 0/0:1,0:1:3.01:0,3,42 ./. 0/0:2,0:2:6.01:0,6,63 -chr1 1225389 . C T 253.01 . AC=13;AF=0.167;AN=78;BaseQRankSum=1.797;DP=127;Dels=0.00;FS=3.410;HRun=0;HaplotypeScore=0.3513;InbreedingCoeff=0.1116;MQ=41.93;MQ0=0;MQRankSum=-1.326;QD=9.04;ReadPosRankSum=-2.083;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. ./. ./. 0/1:1,1:2:27.42:27,0,33 ./. 0/0:3,0:3:6.02:0,6,82 ./. 0/0:1,0:1:3.01:0,3,31 ./. ./. ./. 1/1:0,2:2:6.02:75,6,0 ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:1,0:1:3:0,3,26 0/0:2,0:2:6.02:0,6,67 0/1:1,1:2:27.42:27,0,27 0/0:3,0:3:9.02:0,9,95 0/0:1,0:1:3:0,3,29 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:3.01:0,3,33 0/0:3,0:3:9.03:0,9,126 0/0:3,0:3:6.01:0,6,66 ./. ./. 0/1:1,1:2:23.61:24,0,34 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,35 ./. 0/0:3,0:3:6.02:0,6,81 0/0:1,0:1:3.01:0,3,33 ./. ./. 1/1:0,1:1:3.01:41,3,0 0/0:1,0:1:3.01:0,3,42 0/0:5,0:5:15.02:0,15,153 0/0:4,0:4:9.02:0,9,95 0/0:3,0:3:6.02:0,6,82 0/1:5,3:8:45.82:46,0,141 0/1:3,4:7:73.58:74,0,74 0/0:12,0:12:27.06:0,27,316 ./. 0/0:2,0:2:3.01:0,3,45 0/0:9,0:9:24.05:0,24,246 ./. 0/0:9,2:11:18.05:0,18,218 0/0:2,0:2:3.01:0,3,33 0/0:4,0:4:6.02:0,6,67 0/0:6,0:6:18.05:0,18,224 1/1:0,1:1:3.01:33,3,0 1/1:1,2:3:3.01:30,3,0 0/0:3,0:3:9.02:0,9,100 ./. 0/0:1,0:1:3.01:0,3,31 0/0:3,0:3:9.03:0,9,116 ./. 0/0:2,1:3:0.89:0,1,2 -chr1 1225407 . T C 47.15 . AC=5;AF=0.054;AN=92;BaseQRankSum=-1.004;DP=162;Dels=0.00;FS=2.276;HRun=1;HaplotypeScore=0.5729;InbreedingCoeff=-0.1734;MQ=42.85;MQ0=0;MQRankSum=-1.615;QD=1.68;ReadPosRankSum=2.014;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. ./. ./. 0/0:1,0:1:3.01:0,3,33 ./. 0/0:2,0:2:3.01:0,3,33 ./. 0/0:2,0:2:6.02:0,6,74 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. ./. 0/0:5,0:5:15.05:0,15,193 0/0:3,0:3:3.01:0,3,45 0/0:2,0:2:3.01:0,3,41 ./. 0/0:1,0:1:3:0,3,26 0/1:1,1:2:27.42:27,0,27 0/0:4,0:4:9.03:0,9,111 0/0:5,0:5:15.04:0,15,169 0/0:2,0:2:3.01:0,3,33 0/0:1,0:1:3.01:0,3,40 0/0:1,0:1:3.01:0,3,33 0/0:3,0:3:9.03:0,9,119 0/0:3,0:3:6.02:0,6,72 0/0:2,0:2:6.01:0,6,61 ./. 0/0:2,0:2:6.02:0,6,79 0/0:1,0:1:3.01:0,3,37 0/0:1,0:1:3.01:0,3,39 ./. 0/0:2,0:2:3.01:0,3,45 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,38 0/0:1,0:1:3.01:0,3,33 0/0:2,0:2:6.02:0,6,82 0/0:4,0:4:12.03:0,12,150 0/1:4,1:5:18.41:18,0,104 0/1:3,3:6:53.90:54,0,59 0/0:3,0:3:9.03:0,9,120 0/0:10,0:10:24.05:0,24,259 0/0:9,0:9:24.03:0,24,241 0/0:13,0:13:27.07:0,27,321 ./. 0/0:4,0:4:9.03:0,9,119 0/0:10,0:10:24.05:0,24,267 0/0:1,0:1:3.01:0,3,33 0/1:10,1:11:12.38:12,0,180 0/0:2,0:2:3.01:0,3,33 0/0:2,1:3:3.01:0,3,35 0/0:6,0:6:18.06:0,18,226 0/0:3,0:3:9.03:0,9,109 0/0:2,0:2:6:0,6,54 ./. 0/0:5,0:5:9.02:0,9,100 0/0:1,0:1:3.01:0,3,33 0/1:3,1:4:24.41:24,0,77 0/0:1,0:1:3.01:0,3,42 0/0:5,0:5:12.01:0,12,125 -chr1 1225425 . C T 793.83 . AC=31;AF=0.337;AN=92;BaseQRankSum=1.412;DP=187;Dels=0.02;FS=6.178;HRun=0;HaplotypeScore=0.4105;InbreedingCoeff=-0.0399;MQ=43.23;MQ0=0;MQRankSum=-4.142;QD=6.56;ReadPosRankSum=0.059;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,53 ./. ./. ./. ./. ./. ./. 0/0:2,0:2:6.02:0,6,68 0/0:1,0:1:3.01:0,3,33 0/0:1,0:1:3.01:0,3,33 ./. ./. ./. 0/0:5,0:5:15.05:0,15,192 1/1:0,2:3:3.01:45,3,0 0/0:1,1:2:3.01:0,3,41 ./. 0/1:1,2:3:19.67:20,0,32 0/0:2,0:2:6.02:0,6,67 0/1:4,2:6:57.71:58,0,86 0/1:2,2:4:54.83:55,0,67 1/1:0,1:1:3.01:33,3,0 ./. 1/1:0,1:1:3.01:33,3,0 0/0:3,0:3:9.03:0,9,116 0/0:1,0:1:3.01:0,3,33 1/1:0,2:2:6.01:61,6,0 ./. 0/0:2,1:3:3.01:0,3,37 0/0:2,0:2:6:0,6,64 0/0:3,0:3:6.02:0,6,78 ./. 0/0:2,0:2:3.01:0,3,45 1/1:0,1:1:3:27,3,0 0/0:1,0:1:3.01:0,3,42 1/1:0,1:1:3.01:33,3,0 0/1:1,1:2:35.21:36,0,35 0/1:4,1:5:12.62:13,0,138 0/1:4,1:5:12.67:13,0,83 0/0:5,1:6:3.01:0,3,31 0/1:4,2:6:45.44:45,0,123 0/1:8,1:9:9.37:9,0,213 0/1:9,5:14:66.01:66,0,196 0/1:9,2:11:12.37:12,0,194 ./. 0/0:4,0:4:12.04:0,12,154 0/1:8,3:11:79.97:80,0,157 0/0:1,0:1:3.01:0,3,33 0/1:8,1:9:16.51:17,0,131 0/1:2,1:3:18.64:19,0,64 0/0:3,0:3:3.01:0,3,33 0/0:7,0:7:18.05:0,18,220 0/1:2,3:5:43:106,0,43 0/0:3,0:3:9.01:0,9,94 1/1:3,1:4:3.01:33,3,0 1/1:1,4:5:12.03:132,12,0 0/0:3,0:3:6.02:0,6,75 0/0:5,0:5:12.03:0,12,146 0/0:1,0:1:3.01:0,3,41 0/1:7,2:9:31.28:31,0,187 -chr1 1225443 . T C 468.02 . AC=15;AF=0.163;AN=92;BaseQRankSum=-2.292;DP=235;Dels=0.00;FS=6.953;HRun=1;HaplotypeScore=0.6031;InbreedingCoeff=-0.1815;MQ=43.46;MQ0=0;MQRankSum=-0.753;QD=4.78;ReadPosRankSum=-1.745;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.01:0,6,55 ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,32 ./. ./. ./. ./. 0/0:5,0:5:12.04:0,12,154 0/0:3,0:3:6.01:0,6,69 0/0:2,1:3:6.01:0,6,65 ./. 0/0:4,0:4:9.02:0,9,107 0/0:1,1:2:3.01:0,3,33 0/0:9,0:9:24.07:0,24,290 0/0:5,0:5:15.04:0,15,177 0/0:4,0:4:12.03:0,12,134 0/0:2,0:2:6.02:0,6,73 0/0:1,0:1:3.01:0,3,33 0/1:1,2:3:28.77:66,0,29 ./. 0/0:2,0:2:6.01:0,6,61 ./. 0/0:2,1:3:3.01:0,3,38 0/0:2,0:2:6.02:0,6,80 0/0:5,0:5:12.04:0,12,160 0/0:3,0:3:3.01:0,3,32 1/1:0,1:1:3.01:38,3,0 0/0:3,0:3:6.02:0,6,67 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,108 0/0:3,0:3:9.03:0,9,120 0/0:8,0:8:24.06:0,24,284 0/1:5,1:6:26.21:26,0,104 0/0:9,0:9:18.04:0,18,204 0/0:7,0:7:21.05:0,21,254 0/1:8,3:11:63.42:63,0,230 0/1:11,2:13:19.30:19,0,276 0/1:7,2:9:9.65:10,0,129 0/1:3,1:4:20.61:21,0,49 0/0:4,0:4:12.04:0,12,153 0/0:15,0:15:24.08:0,24,314 0/0:3,0:3:9.02:0,9,100 0/1:2,2:4:20.66:36,0,21 0/1:2,2:4:49.07:61,0,49 0/1:5,3:8:60.54:91,0,61 0/1:3,3:6:84.62:85,0,95 0/1:4,2:6:19.31:19,0,139 0/0:6,1:7:12.02:0,12,133 0/0:3,0:3:3.01:0,3,33 0/1:5,2:7:21.40:21,0,92 0/0:3,0:3:9.03:0,9,116 0/0:7,0:7:18.03:0,18,209 0/0:1,0:1:3.01:0,3,42 0/1:10,6:16:62.24:62,0,294 -chr1 1225452 . T TCC 330.82 . AC=10;AF=0.104;AN=96;BaseQRankSum=1.749;DP=270;FS=4.169;HRun=3;HaplotypeScore=57.3296;InbreedingCoeff=-0.1229;MQ=43.34;MQ0=0;MQRankSum=-2.041;QD=5.09;ReadPosRankSum=-2.421;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.03:0,9,126 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:2,0:2:3.01:0,3,41 ./. 0/0:3,0:3:3.01:0,3,42 ./. 0/0:4,0:4:8.76:0,9,96 0/0:3,0:3:9.03:0,9,126 0/0:3,0:3:6.02:0,6,84 0/0:2,0:2:5.49:0,5,24 0/0:4,0:4:12.04:0,12,156 0/0:2,0:2:3.01:0,3,42 0/0:10,0:10:22.79:0,23,298 0/0:6,0:6:15.52:0,16,210 0/1:6,1:7:97.91:192,0,98 0/1:2,1:3:41.21:41,0,75 0/0:1,0:1:3.01:0,3,41 0/0:4,0:4:12.04:0,12,156 ./. 0/0:3,0:3:8.90:0,9,99 0/0:1,0:1:1.25:0,1,3 0/0:4,0:4:5.99:0,6,64 0/0:2,0:2:3.01:0,3,42 0/0:7,0:7:18.06:0,18,252 0/0:3,0:3:0.89:0,1,2 ./. 0/1:1,1:3:30.58:49,0,31 0/0:2,0:2:6.02:0,6,84 0/1:4,0:4:35.98:36,0,115 0/0:3,0:3:9.03:0,9,126 0/0:10,0:10:24.08:0,24,336 0/0:6,0:6:10.39:0,10,128 0/1:12,1:13:34:34,0,304 0/0:9,0:9:22.30:0,22,279 0/0:12,0:12:29.79:0,30,384 0/0:12,0:12:27.54:0,28,360 0/0:9,0:9:15.05:0,15,202 0/1:5,1:6:18.19:18,0,84 0/1:3,0:3:8.19:8,0,75 0/1:14,1:15:14.18:14,0,397 0/1:3,1:4:40:40,0,105 0/0:6,0:6:11.22:0,11,131 0/0:4,0:4:12.04:0,12,166 0/0:8,0:8:14.41:0,14,176 0/0:7,0:7:12.03:0,12,156 0/0:7,0:7:18.02:0,18,227 0/1:7,0:7:36.78:37,0,115 0/0:2,0:2:3.01:0,3,42 0/0:9,0:9:24.07:0,24,308 0/0:3,0:3:9.03:0,9,126 0/0:9,0:9:18.06:0,18,252 0/0:1,0:1:3.01:0,3,42 0/0:18,0:18:47.83:0,48,640 -chr1 1225461 . T C 238.55 . AC=14;AF=0.1273;AN=110;BaseQRankSum=-0.273;DP=319;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.9594;InbreedingCoeff=-0.1003;MQ=43.75;MQ0=0;MQRankSum=-1.815;QD=2.41;ReadPosRankSum=0.946;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9.01:0,9,83 ./. ./. 0/0:1,0:1:3:0,3,28 ./. ./. 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3:0,3,28 0/0:3,0:3:9.01:0,9,88 0/0:6,0:6:15.03:0,15,153 0/0:1,0:1:3:0,3,28 0/0:3,0:3:9.01:0,9,88 0/0:2,0:2:6.01:0,6,62 0/0:4,0:4:9.03:0,9,108 0/0:6,0:6:15.03:0,15,173 0/1:1,1:2:18.68:19,0,32 0/0:3,0:3:9.01:0,9,91 0/1:2,2:4:13.67:61,0,14 0/0:2,0:2:3.01:0,3,33 0/0:10,0:10:24.07:0,24,295 0/0:6,0:6:18.05:0,18,207 0/1:7,1:8:17.51:18,0,195 0/1:2,1:3:32.73:33,0,59 0/0:3,0:3:9.03:0,9,107 0/0:4,0:4:12.04:0,12,154 ./. 0/0:3,0:3:6.01:0,6,62 0/0:1,0:1:3.01:0,3,33 0/0:7,0:7:12.04:0,12,152 0/1:3,1:4:24.41:24,0,71 0/0:8,0:8:24.08:0,24,326 0/0:3,0:3:3:0,3,29 1/1:0,1:1:3.01:33,3,0 0/0:3,0:3:9.02:0,9,96 0/0:3,0:3:6.02:0,6,77 0/0:4,0:4:12.04:0,12,143 0/0:6,0:6:18.06:0,18,230 0/0:11,0:11:27.07:0,27,334 0/0:7,0:7:15.02:0,15,158 0/1:10,4:14:76.81:77,0,197 0/0:8,0:8:24.05:0,24,271 0/1:11,1:12:3.36:3,0,282 0/1:12,2:14:27.11:27,0,268 0/1:7,2:9:51.83:52,0,87 0/0:7,0:7:15.03:0,15,164 0/0:4,0:4:9.03:0,9,116 0/1:14,2:16:0.59:1,0,271 0/0:6,0:6:18.05:0,18,217 0/0:7,0:8:12.04:0,12,159 0/1:3,1:4:15.63:16,0,95 0/1:6,2:8:24.18:24,0,162 0/0:6,0:6:12.04:0,12,154 0/0:10,0:10:24.07:0,24,290 0/0:9,0:9:21.05:0,21,241 0/0:1,0:1:3.01:0,3,33 0/0:9,0:9:21.06:0,21,253 0/0:3,0:4:9.03:0,9,114 0/0:10,0:10:21.07:0,21,275 0/0:1,0:1:3.01:0,3,39 0/0:21,1:22:48.14:0,48,623 -chr1 1225466 . T C 184.63 . AC=11;AF=0.0948;AN=116;BaseQRankSum=-1.477;DP=342;Dels=0.00;FS=1.813;HRun=2;HaplotypeScore=0.9329;InbreedingCoeff=-0.1688;MQ=44.09;MQ0=0;MQRankSum=-2.845;QD=1.85;ReadPosRankSum=-1.214;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:9:0,9,78 ./. ./. 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,41 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3:0,3,28 0/0:5,0:5:15.03:0,15,171 0/0:8,0:9:24.06:0,24,282 0/0:1,0:1:3:0,3,28 0/0:4,0:4:12.02:0,12,131 0/0:3,0:3:9.02:0,9,96 0/0:3,0:3:9.03:0,9,112 0/1:6,1:7:17.21:17,0,163 0/0:2,0:2:6.01:0,6,62 0/0:5,0:5:15.04:0,15,168 0/0:6,0:6:15.03:0,15,178 0/0:1,0:2:3.01:0,3,33 0/0:9,0:9:24.06:0,24,275 0/1:3,3:6:80.37:80,0,81 0/0:8,0:8:24.07:0,24,287 0/0:3,0:3:9.03:0,9,106 0/0:4,0:4:9.03:0,9,108 0/0:3,0:3:9.03:0,9,108 0/0:1,0:1:3.01:0,3,33 0/1:3,1:4:24.41:24,0,53 0/0:1,0:1:3.01:0,3,33 0/0:6,1:7:12.02:0,12,143 0/0:5,0:5:12.04:0,12,153 0/1:8,1:9:14.67:15,0,296 0/0:1,2:3:3.01:0,3,41 0/0:1,0:1:3.01:0,3,33 0/0:5,0:5:12.03:0,12,128 0/0:2,1:3:6.02:0,6,77 0/1:3,1:4:21.40:21,0,97 0/1:5,1:6:19.74:20,0,176 0/0:11,1:12:27.04:0,27,312 0/1:5,2:7:12.67:13,0,94 0/1:11,2:13:42.67:43,0,245 0/0:7,0:7:21.05:0,21,247 0/1:10,2:12:36.81:37,0,245 0/1:11,3:15:51.91:52,0,250 0/0:8,0:8:15.04:0,15,169 0/0:7,0:7:12.02:0,12,121 0/0:4,0:4:9.03:0,9,111 0/1:16,1:17:3.35:3,0,304 0/0:6,0:6:15.05:0,15,190 0/0:8,0:9:15.05:0,15,196 0/0:4,0:4:12.03:0,12,132 0/0:8,0:8:15.05:0,15,189 0/0:5,1:6:12.04:0,12,154 0/0:10,0:10:24.07:0,24,301 0/0:8,1:9:15.02:0,15,170 0/0:1,0:1:3.01:0,3,32 0/0:12,0:13:33.08:0,33,380 0/0:4,0:4:12.04:0,12,147 0/0:8,2:10:21.06:0,21,262 0/0:1,0:1:3.01:0,3,30 0/0:22,0:22:51.15:0,51,654 -chr1 1225470 . T TCC 366.85 . AC=11;AF=0.0948;AN=116;BaseQRankSum=3.645;DP=363;FS=6.315;HRun=3;HaplotypeScore=61.2598;InbreedingCoeff=-0.1667;MQ=44.55;MQ0=0;MQRankSum=-2.973;QD=4.32;ReadPosRankSum=-1.690;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3.01:0,3,42 ./. ./. 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 0/0:6,0:6:18.06:0,18,240 0/0:10,0:10:30.10:0,30,419 0/0:1,0:1:3.01:0,3,42 0/0:4,0:4:12.04:0,12,168 0/0:4,0:4:12.04:0,12,167 0/0:3,0:3:6.02:0,6,84 0/1:6,1:7:30.95:31,0,231 0/0:3,0:3:9.03:0,9,126 0/1:1,4:5:26.97:155,0,27 0/0:6,0:6:15.05:0,15,210 0/0:3,0:3:6.02:0,6,84 0/0:10,0:10:24.08:0,24,336 0/0:6,0:6:11.11:0,11,165 0/0:9,0:9:25.90:0,26,332 0/1:3,0:3:41.21:41,0,75 0/1:5,0:5:35.19:35,0,109 0/0:3,0:3:9.03:0,9,126 0/0:1,0:1:3.01:0,3,42 0/0:5,0:5:13.07:0,13,142 0/0:1,0:1:3.01:0,3,40 0/0:7,0:7:12.04:0,12,168 0/0:4,0:4:12.04:0,12,168 0/0:10,0:10:30.10:0,30,420 0/1:5,0:5:26.57:27,0,36 0/0:2,0:2:6.02:0,6,84 0/1:4,1:5:46.02:46,0,66 0/0:3,0:3:9.03:0,9,126 0/0:5,0:5:15.05:0,15,194 0/0:6,0:6:15.05:0,15,210 0/0:13,0:13:33.10:0,33,438 0/0:7,0:7:12.93:0,13,170 0/0:13,0:13:33.11:0,33,441 0/0:8,0:8:23.97:0,24,301 0/0:13,0:13:24.96:0,25,328 0/0:14,0:14:33.10:0,33,442 0/0:6,0:6:12.04:0,12,168 0/1:7,1:8:87.71:88,0,184 0/0:4,0:4:6.02:0,6,84 0/1:18,0:18:11.41:11,0,415 0/1:9,0:9:27.97:28,0,236 0/0:9,0:8:21.06:0,21,279 0/0:4,0:4:9.03:0,9,123 0/0:8,0:8:18.03:0,18,228 0/0:7,0:7:14.98:0,15,185 0/1:9,1:10:30.97:31,0,270 0/1:10,0:10:30.28:30,0,193 0/0:1,0:1:3.01:0,3,41 0/0:13,0:13:27.09:0,27,375 0/0:4,0:4:9.03:0,9,120 0/0:11,0:11:18.94:0,19,253 0/0:1,0:1:3.01:0,3,42 0/0:23,0:23:65.95:0,66,875 -chr1 1225479 . T C 216.38 . AC=8;AF=0.0690;AN=116;BaseQRankSum=-0.622;DP=392;Dels=0.00;FS=4.070;HRun=1;HaplotypeScore=1.0837;InbreedingCoeff=0.0601;MQ=45.51;MQ0=0;MQRankSum=-3.522;QD=3.73;ReadPosRankSum=-0.410;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3:0,3,28 ./. 0/0:1,0:1:3:0,3,28 0/0:3,0:3:9.02:0,9,103 0/0:3,0:3:9.02:0,9,95 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3:0,3,28 0/1:7,1:8:2.62:3,0,220 0/0:10,0:11:30.07:0,30,348 0/0:1,0:1:3:0,3,28 0/0:5,0:5:15.03:0,15,156 0/0:5,0:5:15.02:0,15,148 0/0:3,0:3:6.02:0,6,71 0/0:9,0:9:24.06:0,24,293 0/0:2,1:3:6.02:0,6,79 0/1:2,3:5:51.82:91,0,52 0/0:7,0:7:18.05:0,18,225 0/0:2,0:2:6.02:0,6,75 0/0:9,0:9:27.07:0,27,313 0/0:4,0:4:9.01:0,9,97 0/0:11,0:11:30.08:0,30,356 0/0:4,0:4:9.03:0,9,109 0/0:5,0:5:15.05:0,15,184 0/0:3,0:3:9.02:0,9,108 0/0:1,0:1:3.01:0,3,33 0/0:6,0:6:15.04:0,15,184 0/0:1,0:1:3.01:0,3,33 0/0:6,0:6:12.04:0,12,160 0/0:5,0:5:15.05:0,15,185 0/0:11,0:11:33.11:0,33,439 0/0:5,0:5:9.01:0,9,98 1/1:0,4:4:12.03:134,12,0 0/0:4,0:4:12.03:0,12,132 0/0:4,0:4:9.03:0,9,112 0/0:4,1:5:12.03:0,12,141 0/0:7,0:7:18.06:0,18,235 0/0:13,1:14:5.39:0,5,321 0/0:7,0:7:12:0,12,122 0/0:15,1:16:39.10:0,39,453 0/0:9,0:9:27.07:0,27,310 0/1:9,2:11:3.60:4,0,247 0/1:8,4:12:68.42:68,0,165 0/1:3,1:4:21.40:21,0,95 0/0:9,0:9:24.05:0,24,277 0/0:6,0:6:12.04:0,12,158 0/0:20,0:20:39.08:0,39,460 0/0:9,0:9:24.06:0,24,289 0/0:8,0:8:18.05:0,18,226 0/0:6,0:6:15.04:0,15,172 0/0:7,0:7:18.05:0,18,224 0/0:6,1:7:15.05:0,15,193 0/0:11,0:11:27.07:0,27,324 0/0:7,1:10:18.04:0,18,212 0/0:3,0:3:9.03:0,9,105 0/1:13,1:14:3.35:3,0,294 0/0:5,0:5:12.03:0,12,141 0/0:10,0:10:21.04:0,21,252 0/0:1,0:1:3.01:0,3,36 0/0:27,1:28:63.17:0,63,785 -chr1 1225484 . T C 214.92 . AC=16;AF=0.1379;AN=116;BaseQRankSum=-1.446;DP=412;Dels=0.00;FS=17.524;HRun=2;HaplotypeScore=1.1210;InbreedingCoeff=-0.1039;MQ=45.67;MQ0=0;MQRankSum=-3.630;QD=1.52;ReadPosRankSum=1.200;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.01:0,6,55 0/0:1,0:1:3:0,3,28 ./. 0/0:1,0:1:3:0,3,28 0/0:4,0:4:12.02:0,12,130 0/0:3,0:3:9.01:0,9,85 0/0:2,0:2:6.01:0,6,55 0/0:1,0:1:3:0,3,28 0/0:8,0:8:24.02:0,24,249 0/0:12,0:12:36.08:0,36,394 0/0:2,0:2:6.01:0,6,62 0/0:5,0:5:15.03:0,15,154 0/0:6,0:6:18.03:0,18,183 0/0:3,0:3:6.02:0,6,76 0/0:8,1:9:20.52:0,21,249 0/0:3,0:3:9.01:0,9,100 0/1:4,2:6:47.88:48,0,123 0/0:8,0:8:21.06:0,21,255 0/0:1,0:1:3.01:0,3,42 0/1:8,2:10:39.48:39,0,244 0/0:5,0:5:12.04:0,12,145 0/0:12,0:12:33.10:0,33,395 0/0:4,0:4:9.03:0,9,112 0/0:4,0:5:12.04:0,12,153 0/0:3,0:3:9.02:0,9,106 1/1:0,1:1:3.01:33,3,0 0/0:6,0:6:15.04:0,15,183 ./. 0/0:6,0:6:12.04:0,12,159 0/0:6,0:6:18.05:0,18,220 0/0:11,0:11:33.10:0,33,423 0/0:5,0:5:6.02:0,6,74 0/0:4,0:4:12.03:0,12,134 0/1:3,1:4:24.41:24,0,58 0/0:3,1:4:5.94:0,6,57 0/1:4,1:5:21.40:21,0,95 0/0:6,0:6:18.06:0,18,237 0/0:14,0:15:30.08:0,30,379 0/1:5,3:8:40.34:40,0,57 0/1:16,2:18:18.75:19,0,441 0/1:9,2:11:26.03:26,0,290 0/0:10,1:11:27.07:0,27,329 0/1:9,1:11:11.53:12,0,218 0/0:4,0:4:9.01:0,9,96 0/1:8,1:9:5.64:6,0,184 0/0:6,0:6:12.03:0,12,150 0/1:15,2:17:5.66:6,0,388 0/1:7,1:8:9.36:9,0,241 0/0:8,0:8:18.04:0,18,216 0/1:4,3:7:73.66:80,0,74 0/0:8,1:9:23.91:0,24,246 0/0:8,0:8:15.05:0,15,201 0/1:10,1:11:10.71:11,0,273 0/0:9,0:9:15.04:0,15,181 0/0:6,0:6:18.05:0,18,216 0/1:13,2:15:0.35:0,0,317 0/0:7,0:7:18.05:0,18,220 0/0:8,1:9:21.04:0,21,242 0/0:1,0:1:3.01:0,3,30 0/0:25,2:29:32.48:0,32,685 -chr1 1225488 . T TCC 73.7 . AC=6;AF=0.0517;AN=116;BaseQRankSum=3.896;DP=442;FS=2.167;HRun=3;HaplotypeScore=66.4298;InbreedingCoeff=-0.0944;MQ=46.00;MQ0=0;MQRankSum=-2.159;QD=1.23;ReadPosRankSum=-2.147;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:3.01:0,3,42 0/0:1,0:1:3.01:0,3,42 ./. 0/0:1,0:1:3.01:0,3,42 0/0:5,0:5:12.04:0,12,168 0/0:5,0:5:12.04:0,12,168 0/0:6,0:6:9.03:0,9,126 0/0:1,0:1:3.01:0,3,42 0/0:12,0:12:33.11:0,33,461 0/0:13,0:13:36.12:0,36,493 0/0:2,0:2:6.02:0,6,84 0/0:6,0:6:18.06:0,18,252 0/0:7,0:7:21.07:0,21,293 0/0:4,0:4:2.99:0,3,24 0/0:9,0:9:23.85:0,24,321 0/0:3,0:3:6.02:0,6,84 0/0:8,0:8:23.81:0,24,307 0/0:8,0:8:24.08:0,24,325 0/0:1,0:1:3.01:0,3,42 0/0:10,0:10:25.33:0,25,338 0/0:5,0:5:6.49:0,6,85 0/0:15,0:15:36.12:0,36,500 0/1:5,0:5:38.20:38,0,114 0/0:6,0:6:18.06:0,18,248 0/0:3,0:3:9.03:0,9,126 0/0:1,0:1:3.01:0,3,42 0/1:5,1:6:39.97:40,0,114 0/0:2,0:2:4.26:0,4,45 0/0:9,0:9:24.07:0,24,320 0/0:7,0:7:18.06:0,18,252 0/0:13,0:13:39.13:0,39,532 0/0:5,0:5:12.92:0,13,148 0/0:4,0:4:12.04:0,12,168 0/0:3,1:4:9.03:0,9,126 0/0:4,0:4:9.03:0,9,126 0/0:5,0:5:12.51:0,13,166 0/0:6,0:6:18.06:0,18,248 0/0:16,0:16:31.34:0,31,422 0/0:6,0:6:12.93:0,13,165 0/0:18,0:18:40.57:0,41,577 0/0:12,0:12:31.35:0,31,422 0/0:13,0:13:34:0,34,457 0/0:11,0:11:25.32:0,25,325 0/0:4,0:4:6.02:0,6,84 0/1:9,1:10:46.89:47,0,255 0/0:6,0:6:9.03:0,9,126 0/1:16,0:17:16.66:17,0,492 0/0:8,0:8:22.31:0,22,286 0/0:7,0:6:16.02:0,16,212 0/0:7,0:7:15.04:0,15,194 0/0:9,0:9:24.08:0,24,335 0/0:8,1:9:18.06:0,18,240 0/0:11,0:11:23.97:0,24,310 0/1:7,1:8:40.94:41,0,153 0/0:6,0:6:16.30:0,16,213 0/1:13,1:14:0.98:1,0,447 0/0:7,0:7:15.05:0,15,205 0/0:9,0:9:15.94:0,16,212 ./. 0/0:29,0:29:76.06:0,76,976 -chr1 1225497 . T C 35.56 . AC=5;AF=0.0439;AN=114;BaseQRankSum=-3.665;DP=477;Dels=0.00;FS=3.756;HRun=1;HaplotypeScore=1.4250;InbreedingCoeff=-0.0704;MQ=45.97;MQ0=0;MQRankSum=-2.358;QD=0.73;ReadPosRankSum=0.893;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3:0,3,28 ./. ./. 0/0:6,0:6:18.03:0,18,184 0/0:6,0:6:18.02:0,18,169 0/0:10,0:10:27.04:0,27,269 0/0:1,0:1:3:0,3,28 0/0:15,0:15:42.06:0,42,434 0/0:19,0:19:51.10:0,51,545 0/0:2,0:2:6.01:0,6,59 0/0:7,0:7:21.03:0,21,200 0/0:8,0:8:24.03:0,24,235 0/0:3,0:3:6.02:0,6,76 0/0:11,0:11:30.10:0,30,390 0/1:1,1:2:18.68:33,0,19 0/0:9,0:9:27.05:0,27,318 0/0:8,0:8:21.06:0,21,268 0/0:2,0:2:6.02:0,6,82 0/0:10,0:10:24.07:0,24,291 0/0:4,0:4:6.02:0,6,72 0/0:17,0:17:45.12:0,45,534 0/0:8,0:8:21.07:0,21,274 0/0:8,1:9:24.08:0,24,312 0/0:3,0:3:6.02:0,6,78 0/0:1,0:1:3.01:0,3,33 0/0:5,0:5:15.05:0,15,194 0/0:2,0:2:3.01:0,3,41 0/0:11,0:11:33.10:0,33,418 0/0:7,0:7:15.05:0,15,199 0/0:13,0:13:39.13:0,39,510 0/0:6,0:6:15.02:0,15,148 0/0:4,0:4:12.03:0,12,134 0/0:4,0:4:9.02:0,9,96 0/0:3,1:4:6.02:0,6,82 0/0:7,0:7:18.04:0,18,191 0/0:7,0:7:21.07:0,21,263 0/0:16,0:16:36.08:0,36,435 0/0:6,0:6:9.01:0,9,97 0/1:17,2:19:5.20:5,0,474 0/0:12,0:12:27.07:0,27,336 0/0:11,0:11:30.09:0,30,373 0/1:5,4:10:64.75:65,0,106 0/0:3,0:3:6.02:0,6,75 0/1:10,1:11:3.40:3,0,271 0/0:7,0:7:15.05:0,15,198 0/0:16,2:18:36.11:0,36,455 0/0:8,0:8:21.05:0,21,253 0/0:7,0:8:18.05:0,18,212 0/1:6,1:7:6.65:7,0,122 0/0:9,0:9:21.06:0,21,257 0/0:8,1:9:18.06:0,18,238 0/0:10,0:10:24.07:0,24,302 0/0:10,0:10:21.06:0,21,248 0/0:8,0:8:24.07:0,24,302 0/0:16,0:16:39.09:0,39,456 0/0:7,0:7:18.03:0,18,202 0/0:9,0:9:18.04:0,18,220 ./. 0/0:29,0:29:57.17:0,57,724 -chr1 1225502 . T C 688.93 . AC=16;AF=0.1404;AN=114;BaseQRankSum=0.243;DP=497;Dels=0.00;FS=19.856;HRun=2;HaplotypeScore=1.6402;InbreedingCoeff=-0.0754;MQ=46.34;MQ0=0;MQRankSum=-4.470;QD=5.22;ReadPosRankSum=0.940;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3:0,3,28 ./. ./. 0/0:6,0:6:18.02:0,18,168 0/0:6,0:6:15.01:0,15,135 0/0:11,0:11:33.05:0,33,331 0/0:1,0:1:3:0,3,28 0/0:17,0:17:45.06:0,45,455 0/0:21,0:21:54.10:0,54,574 0/0:2,0:2:6.01:0,6,61 0/0:7,0:7:21.02:0,21,198 0/0:9,0:9:27.04:0,27,269 0/0:3,1:4:9.03:0,9,123 0/0:10,0:10:30.08:0,30,362 0/0:2,0:2:6:0,6,64 0/0:9,0:9:24.06:0,24,287 0/0:8,0:8:24.07:0,24,288 0/0:3,0:3:9.03:0,9,121 0/1:5,2:8:45.93:46,0,125 0/0:3,1:4:6.02:0,6,71 0/0:15,1:16:45.11:0,45,551 0/0:7,0:8:18.06:0,18,235 0/0:10,0:10:24.08:0,24,325 0/0:4,0:4:9.02:0,9,100 0/0:1,0:1:3.01:0,3,33 0/0:5,0:5:12.04:0,12,157 0/0:1,0:1:3.01:0,3,39 0/1:10,1:11:10.58:11,0,311 0/0:8,0:8:21.07:0,21,273 0/0:17,0:17:48.14:0,48,602 0/1:5,2:7:43.08:43,0,109 1/1:0,4:4:12.03:134,12,0 0/1:3,1:4:20.60:21,0,58 0/0:4,0:4:6.02:0,6,82 0/1:1,5:6:19.78:127,0,20 0/0:8,0:8:21.07:0,21,260 0/0:14,0:15:36.10:0,36,456 0/0:7,0:7:9.02:0,9,116 0/0:18,2:20:25.44:0,25,536 0/1:10,3:13:29.06:29,0,265 0/0:11,0:11:27.09:0,27,349 0/1:5,4:10:72.35:72,0,98 0/1:2,1:3:27.42:27,0,36 0/1:8,4:12:87.32:87,0,193 0/0:8,0:8:21.07:0,21,277 0/0:16,1:18:36.09:0,36,437 0/0:7,1:8:18.06:0,18,232 0/0:8,0:8:18.05:0,18,220 0/1:2,5:7:54.86:85,0,55 0/1:9,1:10:9.36:9,0,233 0/0:7,2:9:15.05:0,15,195 0/1:3,7:11:52.40:154,0,52 0/1:9,2:11:9.39:9,0,210 0/0:8,0:8:24.07:0,24,295 0/1:13,2:15:11.67:12,0,339 0/0:7,0:7:15.04:0,15,172 0/0:12,0:12:27.08:0,27,335 ./. 0/0:28,0:28:54.13:0,54,642 -chr1 1225504 . C T 33.71 . AC=3;AF=0.0263;AN=114;BaseQRankSum=-2.542;DP=505;Dels=0.00;FS=4.534;HRun=0;HaplotypeScore=1.6971;InbreedingCoeff=-0.0570;MQ=46.78;MQ0=0;MQRankSum=1.064;QD=1.16;ReadPosRankSum=2.168;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3:0,3,28 ./. ./. 0/0:6,0:6:18.03:0,18,180 0/0:7,0:7:21.02:0,21,205 0/0:10,0:10:30.04:0,30,299 0/0:1,0:1:3:0,3,28 0/0:17,0:17:48.08:0,48,500 0/0:22,0:22:60.14:0,60,671 0/0:3,0:3:9:0,9,92 0/0:5,0:5:15.02:0,15,148 0/0:9,0:9:27.04:0,27,270 0/0:4,0:4:9.03:0,9,119 0/1:6,3:9:78.68:79,0,206 0/0:2,0:2:6.01:0,6,66 0/0:10,0:10:27.08:0,27,324 0/0:10,0:10:30.08:0,30,359 0/0:3,0:3:9.03:0,9,121 0/0:8,0:8:18.05:0,18,212 0/0:6,0:6:9.03:0,9,110 0/0:16,0:16:39.12:0,39,496 0/0:8,0:8:21.07:0,21,279 0/0:10,0:10:27.09:0,27,357 0/0:5,0:5:15.05:0,15,181 0/0:1,0:1:3.01:0,3,33 0/0:5,0:5:15.05:0,15,198 0/0:2,0:2:3.01:0,3,42 0/0:11,0:11:33.09:0,33,426 0/0:8,0:8:21.07:0,21,276 0/0:17,0:17:48.12:0,48,591 0/0:7,0:7:15.03:0,15,167 0/0:4,0:4:12.03:0,12,134 0/0:4,0:4:9.01:0,9,92 0/0:4,0:4:6.02:0,6,87 0/0:6,0:6:18.04:0,18,194 0/0:8,0:8:24.08:0,24,310 0/0:15,0:15:39.10:0,39,486 0/0:7,0:7:9.02:0,9,116 0/0:20,0:20:51.15:0,51,639 0/0:13,0:13:27.07:0,27,324 0/1:10,1:11:9.89:10,0,283 0/0:10,0:10:21.04:0,21,230 0/0:3,0:3:6.02:0,6,76 0/0:12,0:12:30.07:0,30,348 0/0:8,0:8:21.07:0,21,279 0/0:19,0:19:42.12:0,42,518 0/0:8,0:8:18.06:0,18,231 0/0:9,0:9:21.06:0,21,260 0/0:7,0:7:12.03:0,12,134 0/0:10,0:10:24.07:0,24,288 0/1:8,1:9:12.54:13,0,178 0/0:11,0:11:21.06:0,21,263 0/0:11,0:11:24.07:0,24,278 0/0:8,0:8:21.07:0,21,271 0/0:13,2:15:12.41:0,12,379 0/0:7,0:7:15.04:0,15,171 0/0:12,0:12:24.08:0,24,310 ./. 0/0:29,0:29:60.15:0,60,711 -chr1 1225505 . G A 87.65 . AC=6;AF=0.0526;AN=114;BaseQRankSum=0.061;DP=508;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=1.7900;InbreedingCoeff=-0.0837;MQ=47.10;MQ0=0;MQRankSum=-0.730;QD=1.65;ReadPosRankSum=0.134;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,28 0/0:1,0:1:3:0,3,25 ./. ./. 0/0:7,0:7:21.04:0,21,225 0/0:7,0:7:18.02:0,18,179 0/0:10,0:10:27.05:0,27,272 0/0:1,0:1:3:0,3,28 0/0:16,0:16:42.07:0,42,432 0/0:21,0:21:57.13:0,57,638 0/0:3,0:3:9:0,9,92 0/0:6,0:6:18.03:0,18,191 0/1:8,1:9:3.63:4,0,181 0/0:3,0:3:9.03:0,9,116 0/0:9,0:9:27.08:0,27,326 0/0:2,0:2:6.01:0,6,66 0/0:10,0:10:24.07:0,24,300 0/0:10,0:10:24.06:0,24,290 0/0:3,0:3:9.03:0,9,123 0/0:8,0:8:15.05:0,15,183 0/0:6,0:6:9.03:0,9,114 0/0:16,0:16:36.11:0,36,452 0/0:7,0:7:21.07:0,21,273 0/0:9,0:10:27.09:0,27,362 0/0:5,0:5:15.04:0,15,175 0/0:1,0:1:3.01:0,3,30 0/0:5,0:5:15.04:0,15,191 0/0:1,0:1:3.01:0,3,42 0/0:12,0:12:36.10:0,36,463 0/0:8,0:8:21.07:0,21,272 0/0:17,0:17:45.14:0,45,574 0/0:7,0:7:15.03:0,15,162 0/0:4,0:4:12.03:0,12,134 0/0:4,0:4:6:0,6,58 0/1:3,1:4:33.29:36,0,33 0/1:5,1:6:18.09:18,0,134 0/0:9,0:9:24.06:0,24,301 0/0:15,0:15:33.09:0,33,415 0/0:7,0:7:9.02:0,9,116 0/0:18,0:21:48.12:0,48,580 0/0:12,0:13:21.06:0,21,265 0/1:9,1:10:9.36:9,0,251 0/0:9,0:10:18.03:0,18,189 0/0:2,0:3:6.02:0,6,74 0/1:9,3:12:85.04:85,0,149 0/0:8,0:8:21.07:0,21,279 0/0:18,0:18:36.11:0,36,454 0/0:6,0:8:15.05:0,15,195 0/0:10,0:10:21.06:0,21,258 0/0:7,0:7:9.02:0,9,103 0/0:9,0:10:21.06:0,21,249 0/0:8,0:9:15.05:0,15,194 0/1:9,2:11:35.07:35,0,165 0/0:8,0:11:18.05:0,18,206 0/0:8,0:8:21.06:0,21,267 0/0:15,0:15:30.08:0,30,363 0/0:7,0:7:15.02:0,15,165 0/0:11,0:13:24.08:0,24,308 ./. 0/0:27,1:30:32.72:0,33,697 -chr1 1225506 . TCC T 120.88 . AC=8;AF=0.0702;AN=114;BaseQRankSum=7.487;DP=525;FS=3.030;HRun=5;HaplotypeScore=77.2182;InbreedingCoeff=-0.0982;MQ=47.37;MQ0=0;MQRankSum=-3.071;QD=1.92;ReadPosRankSum=-7.075;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_truncation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,103 0/0:1,0:1:3.01:0,3,55 ./. ./. 0/0:9,0:9:27.09:0,27,481 0/0:7,0:7:21.07:0,21,385 0/0:10,0:10:30.10:0,30,550 0/0:2,0:2:6.02:0,6,103 0/0:16,0:16:42.12:0,42,739 0/0:21,0:21:51.15:0,51,903 0/0:3,0:3:6.02:0,6,110 0/0:6,0:6:18.06:0,18,330 0/0:8,0:8:21.06:0,21,335 0/0:3,0:3:9.03:0,9,165 0/1:8,1:9:14.60:15,0,412 0/0:2,0:2:6.02:0,6,110 0/0:10,0:10:30.08:0,30,505 0/0:10,0:10:30.10:0,30,542 0/0:3,0:3:9.03:0,9,165 0/0:8,0:8:12.35:0,12,234 0/0:7,0:7:16.30:0,16,264 0/0:16,0:16:38.59:0,39,719 0/0:8,0:8:21.07:0,21,366 0/0:10,0:10:24.14:0,24,485 0/0:5,0:5:14.98:0,15,235 0/0:2,0:2:6.02:0,6,99 0/0:5,0:5:15.05:0,15,273 0/0:2,0:2:1.62:0,2,53 0/0:12,0:12:36.12:0,36,655 0/0:9,0:9:24.08:0,24,429 0/0:18,1:19:16.62:0,17,847 0/1:8,0:8:21.61:22,0,243 0/0:4,0:4:12.04:0,12,220 0/1:3,1:4:29.97:30,0,121 0/1:3,0:3:3.67:4,0,101 0/1:6,0:6:7.90:8,0,131 0/0:10,0:10:27.08:0,27,458 0/0:16,0:16:42.13:0,42,764 0/0:7,0:7:17.34:0,17,305 0/0:21,0:21:55.43:0,55,1032 0/0:13,0:13:17.61:0,18,396 0/1:11,1:12:45.58:46,0,326 0/0:9,0:9:14.23:0,14,314 0/0:3,0:3:6.02:0,6,107 0/1:12,0:12:45.63:46,0,422 0/0:8,0:8:21.07:0,21,382 0/0:19,0:19:42.10:0,42,723 0/0:8,0:8:14.97:0,15,305 0/0:12,0:11:28.39:0,28,530 0/1:9,0:9:79.82:80,0,102 0/0:11,0:11:30.06:0,30,504 0/0:9,0:9:15.11:0,15,325 0/0:11,0:11:21.07:0,21,310 0/0:11,0:11:23.75:0,24,424 0/0:8,0:8:17.18:0,17,329 0/0:16,0:16:34.14:0,34,626 0/0:6,1:7:12.09:0,12,261 0/0:13,0:13:26.35:0,26,494 ./. 0/0:30,0:30:59.63:0,60,1247 -chr1 1225507 . C T 63.16 . AC=5;AF=0.0439;AN=114;BaseQRankSum=0.195;DP=525;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=2.6528;InbreedingCoeff=-0.0729;MQ=47.37;MQ0=0;MQRankSum=-0.118;QD=1.58;ReadPosRankSum=1.001;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.01:0,6,68 0/0:1,0:1:3:0,3,28 ./. ./. 0/0:9,0:9:27.06:0,27,305 0/0:7,0:7:21.01:0,21,201 0/0:10,0:10:30.03:0,30,297 0/0:2,0:2:6.01:0,6,68 0/0:16,0:16:45.08:0,45,467 0/0:21,0:21:57.13:0,57,648 0/0:3,0:3:9.02:0,9,103 0/0:6,0:6:18.03:0,18,191 0/1:7,1:8:6.63:7,0,158 0/0:3,0:3:9.03:0,9,114 0/0:8,0:8:18.06:0,18,244 0/0:2,0:2:6.01:0,6,66 0/0:10,0:10:27.05:0,27,325 0/0:10,0:10:24.04:0,24,271 0/0:3,0:3:9.03:0,9,126 0/0:8,0:8:18.05:0,18,208 0/0:7,0:7:15.05:0,15,187 0/0:16,0:16:39.09:0,39,485 0/0:8,0:8:21.07:0,21,277 0/0:9,0:10:27.09:0,27,360 0/0:5,0:5:12.04:0,12,154 0/0:2,0:2:3.01:0,3,35 0/0:5,0:5:15.05:0,15,196 0/0:2,0:2:3.01:0,3,42 0/0:12,0:12:36.11:0,36,465 0/0:9,0:9:24.05:0,24,294 0/0:18,0:18:51.16:0,51,655 0/0:7,0:8:15.04:0,15,170 0/0:4,0:4:12.03:0,12,134 0/0:3,0:3:5.99:0,6,53 0/1:2,1:3:36.21:36,0,39 0/1:5,1:6:18.94:19,0,138 0/0:10,0:10:24.07:0,24,304 0/0:16,0:16:42.12:0,42,525 0/0:7,0:7:9.02:0,9,116 0/0:21,0:21:54.16:0,54,664 0/0:12,0:13:27.07:0,27,333 0/0:10,0:11:24.05:0,24,298 0/0:9,0:9:18.03:0,18,190 0/0:2,1:3:6.02:0,6,75 0/1:10,2:12:45.13:45,0,235 0/0:8,0:8:21.07:0,21,281 0/0:18,0:18:39.12:0,39,503 0/0:8,0:8:15.05:0,15,196 0/0:11,0:12:27.08:0,27,332 0/0:7,0:9:9.02:0,9,103 0/0:11,0:11:27.08:0,27,324 0/0:9,0:9:18.06:0,18,223 0/1:9,2:11:51.69:52,0,175 0/0:11,0:11:24.07:0,24,272 0/0:8,0:8:18.06:0,18,242 0/0:16,0:16:36.11:0,36,441 0/0:6,0:6:15.04:0,15,175 0/0:12,0:13:27.08:0,27,341 ./. 0/0:30,0:30:63.17:0,63,773 -chr1 1225512 . G A 59.61 . AC=5;AF=0.0431;AN=116;BaseQRankSum=0.671;DP=562;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=2.9722;InbreedingCoeff=-0.0588;MQ=48.31;MQ0=0;MQRankSum=-3.136;QD=1.24;ReadPosRankSum=-1.130;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.01:0,6,68 0/0:2,0:2:6.01:0,6,55 ./. ./. 0/0:9,0:9:27.05:0,27,290 0/0:11,0:11:27.04:0,27,269 0/0:11,0:11:33.03:0,33,325 0/0:1,0:1:3.01:0,3,41 0/0:16,0:16:48.08:0,48,487 0/0:20,0:20:57.12:0,57,622 0/0:3,0:3:6.01:0,6,67 0/0:6,0:6:18.03:0,18,192 0/0:7,0:7:18.02:0,18,173 0/0:3,0:3:9.02:0,9,112 0/0:10,0:10:27.08:0,27,335 0/0:2,0:2:6.01:0,6,66 0/0:10,0:10:24.07:0,24,302 0/0:10,0:10:30.09:0,30,369 0/0:3,0:3:9.03:0,9,122 0/0:6,0:6:12.03:0,12,139 0/0:9,0:9:21.06:0,21,257 0/0:14,0:14:39.09:0,39,469 0/0:8,0:9:21.07:0,21,277 0/0:10,0:10:27.08:0,27,352 0/0:7,0:7:21.04:0,21,252 0/0:6,0:6:18.05:0,18,214 0/0:5,0:5:15.05:0,15,194 0/0:2,0:2:3.01:0,3,42 0/0:12,0:12:36.10:0,36,453 0/0:9,0:9:21.07:0,21,280 0/0:19,0:19:48.14:0,48,618 0/0:9,0:10:24.05:0,24,271 0/0:4,0:4:12.03:0,12,134 0/0:5,0:5:9.03:0,9,107 0/0:5,0:5:12.04:0,12,155 0/1:2,5:7:57.52:98,0,58 0/0:11,0:11:27.08:0,27,342 0/0:18,0:18:45.14:0,45,582 0/0:7,0:7:9.02:0,9,116 0/0:18,0:19:45.14:0,45,572 0/1:12,1:13:0.62:1,0,264 0/0:13,0:13:33.10:0,33,410 0/0:8,1:9:15.01:0,15,152 0/1:2,1:3:24.41:24,0,68 0/1:11,1:12:3.37:3,0,272 0/0:9,0:9:21.07:0,21,283 0/0:18,0:19:42.12:0,42,524 0/0:6,1:8:15.04:0,15,172 0/0:13,1:15:33.10:0,33,419 0/0:7,1:10:15.04:0,15,175 0/1:11,1:13:0.34:0,0,331 0/0:11,0:11:24.07:0,24,297 0/0:9,0:10:18.05:0,18,218 0/0:10,0:10:30.07:0,30,337 0/0:8,0:8:18.06:0,18,233 0/0:16,0:17:36.10:0,36,426 0/0:8,0:8:15.04:0,15,167 0/0:17,0:17:42.13:0,42,540 0/0:1,0:1:3.01:0,3,34 0/0:29,0:29:66.12:0,66,769 -chr1 1225517 . T C 31.29 . AC=10;AF=0.0862;AN=116;BaseQRankSum=-0.543;DP=597;Dels=0.00;FS=8.293;HRun=1;HaplotypeScore=2.0472;InbreedingCoeff=0.0340;MQ=48.76;MQ0=0;MQRankSum=-2.154;QD=0.33;ReadPosRankSum=-1.343;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.01:0,6,64 0/0:3,0:3:9.01:0,9,83 ./. ./. 0/1:7,1:8:17.19:17,0,198 0/0:11,0:11:33.04:0,33,323 0/0:12,1:13:11.39:0,11,329 1/1:0,1:1:3.01:41,3,0 0/0:18,0:18:51.07:0,51,507 0/1:16,2:18:10.96:11,0,413 0/0:3,0:3:9.02:0,9,101 0/0:5,0:5:15.02:0,15,152 0/1:6,2:8:6.63:7,0,158 0/0:5,0:5:15.03:0,15,176 0/0:11,0:11:33.11:0,33,426 0/0:3,0:3:9.01:0,9,101 0/0:10,1:11:27.08:0,27,342 0/0:11,0:11:30.06:0,30,351 0/0:4,0:4:12.04:0,12,165 0/0:6,0:6:12.03:0,12,135 0/0:8,1:9:21.07:0,21,278 0/0:17,1:18:36.11:0,36,449 0/0:11,0:11:27.08:0,27,336 0/0:10,0:10:24.08:0,24,317 0/1:6,1:7:23.17:23,0,182 0/0:10,0:10:30.10:0,30,384 0/0:6,0:6:15.05:0,15,194 0/0:2,0:2:3.01:0,3,42 0/0:12,0:12:36.11:0,36,434 0/0:8,0:8:24.05:0,24,297 0/0:20,0:20:57.16:0,57,722 0/0:11,0:11:27.06:0,27,303 0/1:6,1:7:16.74:17,0,179 0/0:7,0:7:15.04:0,15,183 0/0:5,0:5:12.04:0,12,160 0/0:8,0:8:21.03:0,21,226 0/0:13,0:13:30.09:0,30,387 0/0:19,0:19:51.15:0,51,649 0/0:8,0:8:9.03:0,9,133 0/0:20,1:21:51.12:0,51,632 0/0:10,0:10:21.07:0,21,294 0/0:15,0:15:42.13:0,42,534 0/0:8,0:8:15.03:0,15,166 0/1:3,1:4:26.54:27,0,103 0/0:12,0:12:27.07:0,27,320 0/0:9,0:9:21.07:0,21,277 0/0:21,1:22:20.74:0,21,624 0/0:7,1:8:15.04:0,15,175 0/0:17,0:17:42.13:0,42,528 0/0:9,1:10:18.05:0,18,209 0/0:13,0:13:33.10:0,33,405 0/1:11,1:13:12.92:13,0,273 0/0:10,0:10:18.06:0,18,233 0/0:12,0:12:33.06:0,33,370 0/0:7,1:8:21.07:0,21,276 0/0:17,0:17:36.11:0,36,446 0/0:8,0:8:21.06:0,21,251 0/0:18,0:18:42.12:0,42,521 0/0:1,0:1:3.01:0,3,39 0/1:25,3:28:1.99:2,0,709 -chr1 1225522 . T C 265.0 . AC=14;AF=0.1207;AN=116;BaseQRankSum=-0.678;DP=629;Dels=0.00;FS=97.747;HRun=2;HaplotypeScore=1.7833;InbreedingCoeff=-0.1442;MQ=49.06;MQ0=0;MQRankSum=-5.490;QD=1.44;ReadPosRankSum=-0.496;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.01:0,6,64 0/0:3,0:3:9.01:0,9,83 ./. ./. 0/0:8,0:8:18.04:0,18,202 0/0:11,0:11:30.04:0,30,291 0/0:14,0:14:39.05:0,39,390 0/0:2,0:2:6.02:0,6,81 0/0:17,1:18:20.40:0,20,414 0/0:18,0:18:51.09:0,51,531 0/0:4,0:4:9.01:0,9,93 0/0:6,0:6:18.02:0,18,177 0/0:8,0:8:21.02:0,21,202 0/0:6,0:6:18.06:0,18,243 0/0:12,0:12:36.10:0,36,446 0/1:2,1:3:15.67:16,0,64 0/1:10,1:11:12.37:12,0,223 0/1:10,1:11:0.59:1,0,274 0/0:7,0:7:21.07:0,21,283 0/0:5,1:6:12.04:0,12,145 0/0:9,0:9:21.06:0,21,268 0/0:18,1:20:12.50:0,13,459 0/0:11,0:11:27.07:0,27,348 0/0:11,0:11:27.09:0,27,355 0/0:7,0:7:15.05:0,15,206 0/0:9,1:10:27.09:0,27,366 0/0:8,0:8:18.06:0,18,228 0/0:2,0:2:3.01:0,3,38 0/1:10,1:11:0.33:0,0,344 0/0:9,0:9:27.09:0,27,345 0/0:20,0:20:48.16:0,48,633 0/1:9,2:11:30.12:30,0,231 0/1:6,3:9:73.22:73,0,184 0/0:7,1:8:18.06:0,18,230 0/0:7,1:8:18.53:0,19,225 0/0:10,0:10:27.05:0,27,304 0/0:14,0:14:33.10:0,33,422 0/1:18,2:20:19.28:19,0,575 0/1:3,4:8:35.39:79,0,35 0/1:19,3:22:15.50:16,0,522 0/0:12,0:12:27.09:0,27,355 0/0:16,0:16:39.12:0,39,498 0/0:8,1:10:17.99:0,18,177 0/0:4,0:4:12.04:0,12,161 0/1:8,3:11:69.42:69,0,184 0/0:9,0:9:24.07:0,24,311 0/1:24,3:27:18.02:18,0,632 0/0:6,3:9:15.05:0,15,187 0/0:17,0:17:39.10:0,39,485 0/1:8,3:11:42.80:43,0,185 0/1:10,3:13:32.59:33,0,311 0/0:13,0:13:30.08:0,30,370 0/0:10,0:10:18.06:0,18,228 0/0:11,0:11:27.08:0,27,329 0/0:8,0:8:21.07:0,21,282 0/1:13,3:16:11.67:12,0,317 0/0:8,0:8:12.04:0,12,160 0/0:17,0:17:39.12:0,39,495 0/0:1,0:1:3.01:0,3,41 0/0:26,2:28:19.79:0,20,720 -chr1 1225526 . T TCC 411.2 . AC=10;AF=0.0862;AN=116;BaseQRankSum=4.261;DP=667;FS=14.873;HRun=3;HaplotypeScore=89.4036;InbreedingCoeff=-0.1134;MQ=49.86;MQ0=0;MQRankSum=-3.366;QD=3.29;ReadPosRankSum=-3.904;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,74 0/0:2,0:2:6.02:0,6,84 ./. ./. 0/1:8,0:8:36.68:37,0,191 0/0:10,0:10:30.10:0,30,420 0/0:16,0:16:45.15:0,45,630 0/0:2,0:2:6.02:0,6,84 0/0:22,0:22:55.42:0,55,781 0/0:18,0:18:51.17:0,51,702 0/0:6,0:6:15.05:0,15,210 0/0:6,0:6:15.05:0,15,210 0/0:7,0:7:21.07:0,21,294 0/0:7,0:7:21.06:0,21,271 0/0:13,0:13:37.37:0,37,507 0/1:5,0:5:35.98:36,0,103 0/0:11,0:11:33.08:0,33,419 0/0:9,0:9:24.08:0,24,323 0/0:8,0:8:23.67:0,24,304 0/0:6,0:6:9.03:0,9,126 0/0:10,0:10:21.07:0,21,283 0/1:19,0:21:5.97:6,0,530 0/0:12,0:12:33.11:0,33,446 0/0:13,0:13:33.11:0,33,455 0/0:10,0:10:24.07:0,24,319 0/0:13,0:13:27.09:0,27,378 0/1:7,1:8:82.98:83,0,227 0/0:2,0:2:3.01:0,3,42 0/0:12,0:12:36.12:0,36,484 0/0:9,0:9:24.08:0,24,321 0/0:20,0:20:54.18:0,54,755 0/0:11,0:11:27.09:0,27,364 0/1:8,3:11:99:132,0,263 0/0:8,0:8:21.07:0,21,291 0/0:9,0:10:7.08:0,7,346 0/0:9,0:9:21.07:0,21,294 0/0:15,0:15:36.12:0,36,488 0/0:19,0:19:51.17:0,51,706 0/0:8,0:8:15.05:0,15,210 0/0:25,0:25:58.43:0,58,786 0/0:12,0:12:27.09:0,27,378 0/1:17,0:17:49.29:49,0,442 0/0:7,0:7:10.27:0,10,129 0/0:4,0:4:12.04:0,12,168 0/0:11,0:11:24.07:0,24,336 0/0:12,0:12:25.32:0,25,363 0/0:29,0:29:75.19:0,75,1006 0/1:9,0:9:19:19,0,153 0/0:17,0:17:48.16:0,48,671 0/1:8,2:10:81.39:81,0,267 0/0:18,0:18:44.36:0,44,578 0/0:13,0:13:30.10:0,30,412 0/0:10,0:10:17.73:0,18,215 0/0:10,0:10:22.52:0,23,241 0/0:9,0:9:25.32:0,25,321 0/1:19,0:19:55.86:56,0,420 0/0:7,1:8:7.26:0,7,123 0/1:15,2:17:64.07:64,0,480 0/0:1,0:1:3.01:0,3,42 0/0:29,0:29:38.63:0,39,885 -chr1 1225535 . T C 848.26 . AC=10;AF=0.0862;AN=116;BaseQRankSum=-1.442;DP=750;Dels=0.00;FS=4.302;HRun=1;HaplotypeScore=1.3486;InbreedingCoeff=-0.1129;MQ=50.86;MQ0=0;MQRankSum=1.251;QD=5.89;ReadPosRankSum=-1.457;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,29 0/0:3,0:3:6.01:0,6,62 ./. ./. 0/0:7,0:7:21.02:0,21,214 0/0:10,1:11:5.39:0,5,272 0/0:20,0:20:60.08:0,60,593 0/0:5,0:5:15.05:0,15,184 0/0:21,0:21:60.09:0,60,614 0/0:21,0:21:57.08:0,57,594 0/0:6,0:6:18.03:0,18,202 0/0:6,0:6:18.02:0,18,175 0/0:7,0:7:21.01:0,21,199 0/0:9,0:9:27.09:0,27,356 0/0:17,0:17:48.12:0,48,564 0/0:5,0:5:15.02:0,15,172 0/0:12,0:12:30.09:0,30,375 0/1:12,2:14:43.11:43,0,374 0/0:10,0:10:30.10:0,30,400 0/0:4,0:4:12.04:0,12,144 0/0:11,0:11:30.09:0,30,368 0/0:21,0:21:45.13:0,45,564 0/0:12,0:12:33.11:0,33,435 0/0:13,0:14:36.12:0,36,476 0/0:11,1:12:30.08:0,30,385 0/0:14,0:14:39.13:0,39,523 0/1:10,2:12:42.11:42,0,303 0/0:2,0:2:3.01:0,3,42 0/0:14,0:14:39.09:0,39,464 0/0:12,1:13:11.42:0,11,393 0/0:21,0:21:57.16:0,57,736 0/0:10,0:10:24.06:0,24,299 0/0:12,0:12:36.10:0,36,432 0/0:8,0:8:21.07:0,21,280 0/1:4,9:13:80.66:327,0,81 0/0:10,0:10:27.07:0,27,329 0/1:14,2:16:39.90:40,0,392 0/0:21,0:21:60.17:0,60,774 0/0:9,0:9:15.05:0,15,201 0/0:29,0:29:69.19:0,69,848 0/0:15,0:15:33.10:0,33,429 0/1:10,7:17:99:132,0,296 0/0:9,1:10:15.05:0,15,182 0/0:7,0:7:15.04:0,15,187 0/0:10,0:10:27.08:0,27,319 0/0:13,1:14:33.10:0,33,419 0/0:33,0:33:84.24:0,84,1056 0/1:4,4:8:40.77:41,0,125 0/0:20,0:20:48.15:0,48,620 0/1:8,3:11:9.36:9,0,223 0/0:16,2:18:12.58:0,13,560 0/0:16,0:16:39.12:0,39,502 0/1:11,3:14:83.29:83,0,254 0/0:13,0:13:27.08:0,27,335 0/1:6,6:12:99:192,0,198 0/0:19,1:20:36.11:0,36,446 0/0:9,0:9:12.04:0,12,164 0/0:21,0:21:48.15:0,48,617 0/0:2,0:2:3.01:0,3,35 0/1:20,6:26:83.46:83,0,524 -chr1 1225540 . T C 45.1 . AC=3;AF=0.0259;AN=116;BaseQRankSum=-1.838;DP=782;Dels=0.00;FS=14.682;HRun=2;HaplotypeScore=1.0795;InbreedingCoeff=-0.0391;MQ=51.27;MQ0=0;MQRankSum=-3.072;QD=2.37;ReadPosRankSum=-2.538;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,39 0/0:4,0:4:12.02:0,12,117 ./. ./. 0/0:6,0:6:18.03:0,18,198 0/0:10,0:10:30.04:0,30,294 0/0:17,0:17:48.05:0,48,465 0/0:6,0:6:18.05:0,18,211 0/0:17,1:18:23.42:0,23,483 0/0:19,0:19:57.08:0,57,580 0/0:6,0:6:18.03:0,18,201 0/1:4,1:5:15.65:16,0,80 0/0:7,0:7:21.03:0,21,205 0/0:11,0:11:33.10:0,33,431 0/0:18,0:18:51.15:0,51,643 0/1:3,2:5:51.83:52,0,89 0/0:13,0:13:33.08:0,33,400 0/0:14,0:14:42.13:0,42,530 0/0:11,0:11:33.11:0,33,445 0/0:6,0:6:18.04:0,18,199 0/0:10,2:12:24.07:0,24,309 0/0:19,1:20:45.12:0,45,559 0/0:11,0:11:30.10:0,30,408 0/0:13,0:14:36.12:0,36,480 0/0:11,1:13:30.10:0,30,410 0/0:13,1:14:39.13:0,39,533 0/0:14,1:15:42.13:0,42,536 0/0:3,0:3:6.02:0,6,75 0/0:13,2:15:8.70:0,9,467 0/0:12,0:13:36.12:0,36,467 0/0:23,0:23:63.20:0,63,830 0/0:10,0:10:24.06:0,24,304 0/0:13,0:13:39.10:0,39,469 0/0:8,0:8:21.07:0,21,282 0/0:15,1:16:38.01:0,38,503 0/0:12,0:12:33.09:0,33,407 0/0:17,0:17:42.12:0,42,516 0/0:22,0:22:63.20:0,63,827 0/0:9,0:9:15.03:0,15,177 0/0:29,1:30:63.18:0,63,804 0/0:15,0:15:33.11:0,33,432 0/0:19,0:19:48.15:0,48,607 0/0:8,2:10:12.04:0,12,149 0/0:9,0:9:18.06:0,18,235 0/0:10,0:10:27.08:0,27,326 0/0:13,1:14:33.11:0,33,436 0/0:32,1:33:40.38:0,40,883 0/1:6,3:9:54.53:55,0,151 0/0:21,1:22:42.13:0,42,554 0/0:11,0:11:24.07:0,24,282 0/0:22,0:22:51.16:0,51,646 0/0:15,0:15:39.12:0,39,481 0/0:16,2:18:5.69:0,6,413 0/0:15,1:16:42.12:0,42,515 0/0:13,0:13:39.12:0,39,500 0/0:20,1:21:39.12:0,39,486 0/0:9,0:9:12.04:0,12,165 0/0:20,0:21:48.14:0,48,620 0/0:3,0:3:6.02:0,6,83 0/0:24,0:24:54.13:0,54,645 -chr1 1225543 . G C 72.05 . AC=1;AF=0.0086;AN=116;BaseQRankSum=1.703;DP=821;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=1.7205;InbreedingCoeff=-0.0188;MQ=51.72;MQ0=0;MQRankSum=1.023;QD=3.79;ReadPosRankSum=-1.656;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,32 0/0:5,0:5:15.02:0,15,149 ./. ./. 0/0:6,0:6:15.02:0,15,157 0/0:10,0:10:30.05:0,30,308 0/0:17,0:17:51.06:0,51,497 0/0:8,0:8:24.05:0,24,265 0/0:17,0:17:48.09:0,48,519 0/0:15,0:15:45.08:0,45,483 0/0:10,0:10:30.04:0,30,307 0/0:4,0:4:9.01:0,9,92 0/0:7,0:7:21.03:0,21,205 0/0:12,0:12:36.11:0,36,468 0/0:20,0:20:51.13:0,51,607 0/0:5,0:5:12.03:0,12,143 0/0:13,0:13:30.08:0,30,369 0/0:16,0:16:45.11:0,45,565 0/0:11,0:11:33.10:0,33,426 0/0:7,0:7:18.05:0,18,216 0/0:14,0:14:39.10:0,39,476 0/0:20,1:22:48.12:0,48,582 0/0:12,0:12:33.10:0,33,426 0/0:13,1:14:33.10:0,33,426 0/0:12,0:12:33.09:0,33,430 0/0:16,0:17:42.13:0,42,546 0/0:14,1:16:39.12:0,39,486 0/0:3,0:3:6.02:0,6,70 0/0:16,0:16:42.13:0,42,527 0/0:12,1:13:33.10:0,33,424 0/0:23,0:23:60.18:0,60,778 0/0:10,0:10:24.07:0,24,307 0/0:14,0:14:39.09:0,39,468 0/0:8,0:8:21.07:0,21,285 0/0:16,0:16:42.14:0,42,557 0/0:12,0:12:30.08:0,30,374 0/0:18,0:18:45.14:0,45,582 0/0:21,0:21:63.19:0,63,812 0/0:9,0:9:15.03:0,15,179 0/0:31,0:31:69.18:0,69,839 0/0:18,0:18:42.13:0,42,546 0/0:20,0:20:45.11:0,45,542 0/0:10,0:10:15.03:0,15,184 0/0:9,0:9:18.06:0,18,236 0/0:10,0:10:27.07:0,27,314 0/0:17,0:17:42.13:0,42,534 0/0:34,0:34:78.23:0,78,964 0/0:7,1:8:15.04:0,15,177 0/0:24,0:25:45.12:0,45,575 0/0:13,0:13:30.07:0,30,342 0/0:19,0:19:45.13:0,45,563 0/0:16,0:16:45.13:0,45,540 0/1:14,5:19:99:120,0,271 0/0:18,0:18:42.12:0,42,508 0/0:15,1:16:33.10:0,33,414 0/0:21,2:24:36.11:0,36,441 0/0:9,0:9:12.04:0,12,164 0/0:22,0:22:51.12:0,51,609 0/0:3,0:3:6.02:0,6,83 0/0:26,0:26:57.15:0,57,700 -chr1 1225544 . T TCC 104.04 . AC=3;AF=0.0263;AN=114;BaseQRankSum=5.030;DP=839;FS=11.849;HRun=3;HaplotypeScore=111.7887;InbreedingCoeff=-0.0353;MQ=51.88;MQ0=0;MQRankSum=-4.162;QD=3.15;ReadPosRankSum=-3.869;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:6,0:6:18.06:0,18,246 ./. ./. 0/0:7,0:7:15.05:0,15,210 0/0:10,0:10:27.09:0,27,367 0/0:15,0:15:45.15:0,45,630 0/0:8,0:8:24.08:0,24,336 0/0:16,0:16:45.13:0,45,611 0/0:15,0:15:42.14:0,42,576 0/0:11,0:11:30.10:0,30,420 0/0:4,0:4:9.03:0,9,126 0/0:7,0:7:18.06:0,18,252 0/0:13,0:13:33.11:0,33,462 0/0:21,0:21:54.18:0,54,754 0/1:3,2:5:71.98:96,0,72 0/0:13,1:14:33.11:0,33,460 0/0:16,0:16:42.14:0,42,587 0/0:11,0:11:33.11:0,33,462 0/0:8,0:8:15.05:0,15,209 0/0:13,0:13:39.13:0,39,545 0/0:22,0:22:45.15:0,45,629 0/0:12,0:12:33.11:0,33,461 0/0:14,0:14:34.35:0,34,501 0/0:12,0:12:30.10:0,30,420 0/0:17,0:17:48.16:0,48,671 0/0:16,0:16:45.11:0,45,608 0/0:2,0:2:6.02:0,6,84 0/0:17,0:17:42.14:0,42,588 0/0:13,0:14:33.11:0,33,450 0/0:24,0:24:60.20:0,60,837 0/0:10,0:10:22.32:0,22,333 0/0:14,0:14:39.13:0,39,546 0/0:9,0:9:24.07:0,24,316 0/0:16,0:16:45.15:0,45,627 0/0:13,0:13:33.11:0,33,453 0/0:18,0:18:48.16:0,48,671 0/0:21,0:21:60.20:0,60,840 0/0:10,0:10:5.93:0,6,198 0/0:30,0:30:63.29:0,63,995 0/0:21,0:21:45.14:0,45,618 0/0:21,0:21:48.16:0,48,672 0/0:10,0:10:15.05:0,15,210 0/0:9,0:9:18.06:0,18,252 0/0:10,0:10:24.08:0,24,334 0/0:17,0:17:45.15:0,45,629 0/0:37,0:37:90.03:0,90,1249 0/1:7,1:8:36.99:37,0,172 0/0:25,0:24:42.14:0,42,579 0/0:13,0:13:28.47:0,28,417 0/0:19,0:19:42.14:0,42,587 0/0:16,0:16:45.15:0,45,621 0/0:18,0:18:35.78:0,36,452 0/1:19,1:20:59.26:59,0,534 0/0:16,0:16:39.13:0,39,546 0/0:25,0:25:45.14:0,45,613 0/0:10,0:10:12.04:0,12,168 0/0:23,0:23:57.19:0,57,790 0/0:3,0:3:9.03:0,9,126 0/0:26,0:26:14.48:0,14,696 -chr1 1225553 . C T 5273.44 . AC=32;AF=0.2807;AN=114;BaseQRankSum=1.380;DP=911;Dels=0.00;FS=0.497;HRun=0;HaplotypeScore=1.8119;InbreedingCoeff=-0.1881;MQ=52.16;MQ0=0;MQRankSum=2.230;QD=11.39;ReadPosRankSum=-0.044;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:8,0:8:24.04:0,24,257 ./. ./. 0/1:8,1:9:10.31:10,0,208 0/0:9,0:9:24.04:0,24,239 0/0:15,0:15:45.05:0,45,433 0/0:10,0:10:27.06:0,27,302 0/0:17,0:17:48.09:0,48,515 0/0:17,0:17:45.09:0,45,484 0/0:12,0:12:36.06:0,36,384 0/0:5,0:5:15.01:0,15,145 0/0:8,0:8:24.04:0,24,253 0/1:11,4:15:99:121,0,357 0/1:16,8:24:99:179,0,436 0/0:4,0:4:6.02:0,6,84 0/0:14,1:15:5.69:0,6,441 0/1:15,3:18:75.54:76,0,454 0/1:10,3:13:82.91:83,0,354 0/1:3,4:7:61.77:124,0,62 0/1:6,8:14:99:272,0,175 0/0:24,1:25:66.20:0,66,816 0/0:13,0:13:39.12:0,39,493 0/0:15,0:15:39.10:0,39,478 0/0:12,0:13:30.10:0,30,407 0/1:12,8:20:99:205,0,395 0/1:3,15:18:62.22:456,0,62 0/1:1,1:2:27.42:27,0,29 0/0:16,0:16:42.12:0,42,516 0/0:18,0:18:45.15:0,45,590 0/1:14,10:24:99:311,0,460 0/1:10,1:11:0.58:1,0,291 0/1:10,5:15:99:111,0,304 0/1:1,11:12:0.33:370,0,0 0/1:7,11:18:99:358,0,220 1/1:0,13:13:36.10:461,36,0 0/1:15,4:19:99:103,0,418 0/0:22,0:22:63.19:0,63,832 0/1:2,9:11:6.60:214,0,7 0/1:19,9:28:99:188,0,516 0/1:17,5:22:99:130,0,392 0/0:25,0:25:54.16:0,54,675 0/1:11,2:13:17.51:18,0,204 0/0:16,0:16:42.13:0,42,523 0/1:8,6:14:99:101,0,233 0/0:16,1:17:8.69:0,9,455 0/0:39,0:39:90.29:0,90,1173 0/1:5,2:7:56.18:56,0,96 0/0:25,1:26:45.15:0,45,603 0/1:5,10:15:99:208,0,110 0/1:15,7:22:99:151,0,317 0/1:13,2:15:30.06:30,0,440 0/1:6,11:17:99:224,0,178 0/0:18,1:19:12.47:0,12,453 0/1:6,12:19:99:353,0,102 0/1:11,14:25:99:266,0,157 0/0:10,1:11:15.05:0,15,194 0/0:23,0:23:45.12:0,45,563 1/1:0,3:3:5.99:66,6,0 0/0:23,1:25:26.48:0,26,630 -chr1 1225558 . T C 207.02 . AC=1;AF=0.0086;AN=116;BaseQRankSum=0.020;DP=961;Dels=0.00;FS=8.305;HRun=2;HaplotypeScore=1.2090;InbreedingCoeff=-0.0183;MQ=52.59;MQ0=0;MQRankSum=-0.514;QD=12.94;ReadPosRankSum=1.515;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL ./. 0/0:8,0:8:24.04:0,24,257 0/0:1,0:1:3:0,3,28 ./. 0/0:7,0:7:21.04:0,21,229 0/0:9,0:9:24.04:0,24,250 0/0:19,0:19:54.07:0,54,560 0/0:9,0:9:27.06:0,27,299 0/0:19,0:19:57.10:0,57,621 0/0:18,0:18:51.08:0,51,559 0/0:12,0:12:36.06:0,36,388 0/0:5,0:5:12.02:0,12,124 0/0:10,0:10:30.06:0,30,321 0/0:17,0:17:42.14:0,42,563 0/0:24,0:24:63.18:0,63,807 0/0:7,0:7:15.04:0,15,179 0/0:16,0:16:42.13:0,42,553 0/0:20,0:20:54.13:0,54,672 0/0:13,0:13:39.12:0,39,502 0/0:8,0:8:21.05:0,21,267 0/0:15,0:15:45.13:0,45,573 0/0:25,0:25:66.20:0,66,841 0/0:15,0:15:42.13:0,42,537 0/0:15,0:15:39.12:0,39,488 0/0:14,0:14:42.14:0,42,564 0/0:19,0:20:54.17:0,54,723 0/0:19,0:19:51.16:0,51,665 0/0:4,0:4:9.03:0,9,102 0/0:14,0:14:36.09:0,36,427 0/0:18,0:18:48.16:0,48,629 0/0:24,1:25:27.45:0,27,809 0/0:13,0:13:33.10:0,33,422 0/0:14,0:14:39.10:0,39,482 0/0:14,0:14:39.12:0,39,497 0/0:20,0:20:57.18:0,57,752 0/0:14,0:14:39.11:0,39,498 0/0:19,0:19:54.17:0,54,695 0/0:23,0:23:63.21:0,63,846 0/0:8,2:10:15.05:0,15,197 0/0:29,1:30:69.21:0,69,868 0/0:23,0:23:54.14:0,54,673 0/0:30,0:31:72.19:0,72,883 0/0:12,2:14:27.05:0,27,317 0/0:16,0:16:42.12:0,42,515 0/0:12,1:13:33.10:0,33,427 0/0:19,0:19:48.14:0,48,584 0/0:41,1:42:99:0,102,1247 0/0:6,1:7:15.02:0,15,161 0/0:28,0:28:51.16:0,51,668 0/1:6,10:16:99:255,0,108 0/0:22,1:23:48.15:0,48,614 0/0:15,2:17:1.49:0,1,466 0/0:16,2:18:36.09:0,36,430 0/0:19,3:22:11.70:0,12,506 0/0:21,0:21:45.14:0,45,572 0/0:24,1:25:39.12:0,39,512 0/0:8,1:9:15.05:0,15,196 0/0:23,0:23:48.15:0,48,611 0/0:5,0:5:12.04:0,12,152 0/0:25,1:26:38.49:0,38,749 -chr1 1225562 . T TCC 147.67 . AC=5;AF=0.0417;AN=120;BaseQRankSum=3.446;DP=1028;FS=15.375;HRun=3;HaplotypeScore=125.4377;InbreedingCoeff=0.2845;MQ=53.39;MQ0=0;MQRankSum=-2.465;QD=3.14;ReadPosRankSum=-3.790;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,42 0/0:8,0:8:24.08:0,24,330 0/0:2,0:2:6.01:0,6,67 0/0:2,0:2:3.01:0,3,42 0/0:8,0:8:24.08:0,24,331 0/0:8,0:8:12.04:0,12,162 0/0:20,0:20:51.16:0,51,699 0/0:10,0:10:30.10:0,30,420 0/0:20,0:20:51.17:0,51,702 0/0:20,0:20:54.18:0,54,756 0/0:14,0:14:42.14:0,42,582 0/0:5,0:5:15.05:0,15,210 0/0:13,0:13:30.10:0,30,420 0/0:19,0:19:51.17:0,51,714 0/0:22,0:22:60.20:0,60,840 0/0:9,0:9:18.06:0,18,252 0/0:18,0:18:48.16:0,48,672 0/0:20,0:20:48.16:0,48,671 0/0:13,0:13:39.12:0,39,531 0/0:11,0:11:24.07:0,24,323 0/0:18,0:18:48.16:0,48,659 0/0:27,0:27:75.25:0,75,1031 0/0:19,0:19:51.17:0,51,713 0/0:16,0:16:39.13:0,39,546 0/0:14,0:14:42.14:0,42,588 0/0:20,0:20:57.19:0,57,785 0/0:21,0:21:60.19:0,60,816 1/1:1,3:4:9.03:165,9,0 0/0:13,0:13:36.12:0,36,503 0/0:16,0:16:45.15:0,45,629 0/0:27,0:27:68.43:0,68,919 0/0:14,0:14:36.12:0,36,504 0/0:15,0:15:39.13:0,39,537 0/0:15,0:15:42.14:0,42,587 0/0:22,0:22:63.21:0,63,881 0/0:15,0:15:39.13:0,39,546 0/0:20,0:20:51.17:0,51,707 0/0:22,0:22:60.20:0,60,840 0/0:13,0:13:27:0,27,491 0/0:31,0:31:84.25:0,84,1156 0/0:24,0:24:57.19:0,57,798 0/0:35,0:35:84.28:0,84,1171 0/0:15,0:15:30.10:0,30,420 0/0:19,0:19:57.18:0,57,765 0/1:14,0:14:18.93:19,0,423 0/1:18,1:19:3.87:4,0,621 0/0:44,0:44:99:0,111,1552 0/0:11,0:11:27.09:0,27,368 0/0:27,0:27:63.21:0,63,882 0/0:16,0:17:31.21:0,31,606 0/0:23,0:23:54.18:0,54,756 0/0:20,0:20:48.16:0,48,671 0/0:20,0:20:32.94:0,33,576 0/0:22,0:22:45.15:0,45,630 0/0:21,0:21:51.16:0,51,699 0/0:24,0:24:48.16:0,48,668 0/1:9,1:10:59.47:59,0,189 0/0:25,0:25:66.22:0,66,913 0/0:6,0:6:18.06:0,18,240 0/0:27,0:27:69.21:0,69,941 -chr1 1225571 . C T 5357.09 . AC=38;AF=0.3167;AN=120;BaseQRankSum=-0.715;DP=1167;Dels=0.00;FS=5.301;HRun=0;HaplotypeScore=2.7736;InbreedingCoeff=0.0326;MQ=54.57;MQ0=0;MQRankSum=-3.297;QD=10.50;ReadPosRankSum=-0.766;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3.01:41,3,0 0/1:8,2:10:46.60:47,0,218 1/1:1,2:3:6:53,6,0 1/1:0,3:3:9.03:115,9,0 0/0:13,0:13:39.10:0,39,477 0/0:11,0:11:27.08:0,27,353 0/0:25,0:25:75.17:0,75,882 0/0:12,0:12:36.09:0,36,419 0/0:24,0:24:69.19:0,69,860 0/0:21,0:21:63.16:0,63,755 0/0:15,0:15:45.10:0,45,519 0/1:6,2:8:58.40:58,0,179 0/1:12,1:13:0.90:1,0,390 0/1:14,8:22:99:218,0,453 0/0:21,2:23:54.17:0,54,706 0/1:5,3:8:45.80:46,0,176 0/0:21,1:22:60.19:0,60,792 0/1:14,8:22:99:198,0,429 0/1:11,3:14:65.56:66,0,388 0/1:6,8:14:99:229,0,155 0/1:10,11:21:99:376,0,257 0/0:26,2:28:75.22:0,75,935 0/0:25,0:25:63.20:0,63,827 0/0:18,0:18:45.14:0,45,592 0/0:18,0:18:51.17:0,51,679 0/1:15,7:22:99:191,0,464 0/1:20,2:22:11.51:12,0,680 1/1:0,4:4:9.03:109,9,0 0/0:17,0:17:45.14:0,45,554 0/0:19,0:19:45.14:0,45,599 0/1:15,12:27:99:333,0,469 0/0:12,0:12:33.10:0,33,424 0/1:14,2:16:18.75:19,0,482 0/1:7,10:17:99:320,0,229 0/0:25,1:26:37.44:0,37,897 0/1:8,9:17:99:248,0,273 0/0:19,2:21:54.14:0,54,690 0/0:25,0:25:75.24:0,75,990 1/1:1,16:17:11.45:438,11,0 1/1:4,29:33:12.17:769,12,0 0/1:16,11:28:99:241,0,507 0/0:37,2:39:35.73:0,36,1151 0/1:17,3:20:74.68:75,0,400 0/0:22,0:22:60.18:0,60,746 0/0:15,1:16:8.70:0,9,485 0/0:26,1:27:40.50:0,41,763 0/0:45,1:46:79.76:0,80,1311 0/1:5,6:11:99:181,0,139 0/0:27,0:27:63.19:0,63,813 0/1:20,2:22:14.06:14,0,563 0/0:28,1:29:69.22:0,69,878 0/0:23,0:23:54.17:0,54,708 0/1:9,13:22:99:293,0,228 0/1:20,5:25:99:115,0,479 0/1:18,5:23:92.74:93,0,468 0/1:17,7:24:99:100,0,304 0/1:8,5:13:99:122,0,199 0/0:24,1:25:54.16:0,54,672 1/1:0,7:7:18.06:236,18,0 0/0:25,3:28:4.01:0,4,756 -chr1 1225576 . T C 4461.84 . AC=22;AF=0.1833;AN=120;BaseQRankSum=2.082;DP=1262;Dels=0.00;FS=21.631;HRun=2;HaplotypeScore=2.8144;InbreedingCoeff=0.1776;MQ=54.78;MQ0=0;MQRankSum=0.294;QD=13.48;ReadPosRankSum=0.090;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,41 0/1:8,2:10:50.83:51,0,207 1/1:0,5:5:15.03:157,15,0 1/1:0,6:6:18.06:237,18,0 0/0:13,0:13:39.10:0,39,476 0/0:10,1:11:30.09:0,30,398 0/0:23,0:23:69.14:0,69,804 0/0:11,0:11:33.07:0,33,360 0/0:23,0:23:69.20:0,69,859 0/0:21,0:21:63.16:0,63,760 0/0:14,0:14:42.09:0,42,479 0/1:6,2:8:58.40:58,0,180 0/0:15,0:15:45.10:0,45,532 0/1:14,9:23:99:223,0,425 0/0:23,1:24:60.19:0,60,793 0/0:8,0:8:21.06:0,21,260 0/0:24,0:24:63.18:0,63,819 0/0:24,0:24:66.21:0,66,852 0/1:16,4:20:99:104,0,413 0/1:7,7:14:99:243,0,169 0/1:10,13:23:99:462,0,216 0/0:31,0:31:78.23:0,78,979 0/0:24,0:24:57.19:0,57,758 0/0:19,0:19:45.15:0,45,608 0/0:23,0:23:63.20:0,63,838 0/1:15,9:24:99:236,0,454 0/0:24,0:24:69.22:0,69,905 0/0:4,0:4:9.03:0,9,108 0/0:18,1:19:51.16:0,51,641 0/0:19,0:19:48.14:0,48,617 0/1:16,15:31:99:434,0,497 0/0:13,0:13:39.12:0,39,496 0/0:16,0:16:48.15:0,48,623 0/0:20,0:20:54.17:0,54,715 0/0:27,1:28:46:0,46,965 0/1:10,7:17:99:194,0,332 0/0:22,0:23:54.18:0,54,717 0/0:26,0:26:75.22:0,75,978 1/1:3,14:17:11.42:409,11,0 1/1:4,29:33:5.32:751,5,0 0/1:20,12:32:99:300,0,535 0/0:44,1:45:82.57:0,83,1422 0/1:20,3:23:67.29:67,0,514 0/0:27,0:27:69.19:0,69,871 0/0:16,2:18:11.70:0,12,513 0/0:30,1:31:72.23:0,72,950 0/0:45,1:46:99:0,114,1426 0/1:7,7:14:99:218,0,141 0/0:30,0:30:72.19:0,72,916 0/0:22,0:22:57.17:0,57,697 0/0:33,0:33:81.22:0,81,1005 0/0:22,1:23:17.20:0,17,638 0/1:13,11:24:99:251,0,347 0/0:25,2:27:57.16:0,57,724 0/0:30,0:30:60.17:0,60,766 0/0:26,0:26:54.14:0,54,651 0/0:14,0:14:27.09:0,27,356 0/0:27,0:27:57.14:0,57,716 0/1:4,3:7:65.29:65,0,138 0/0:29,2:31:53.53:0,54,923 -chr1 1225579 . G C 1702.39 . AC=10;AF=0.0833;AN=120;BaseQRankSum=1.093;DP=1332;Dels=0.00;FS=11.111;HRun=2;HaplotypeScore=2.9711;InbreedingCoeff=0.0608;MQ=55.00;MQ0=0;MQRankSum=0.576;QD=11.74;ReadPosRankSum=0.329;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,1:1:3.01:41,3,0 0/0:9,0:9:24.05:0,24,273 0/0:6,0:6:18.04:0,18,204 0/0:8,0:8:24.06:0,24,301 0/0:12,0:12:36.11:0,36,465 0/0:11,0:11:30.09:0,30,398 0/0:23,0:23:63.15:0,63,764 0/0:13,0:13:39.10:0,39,451 0/0:23,0:23:69.20:0,69,858 0/0:23,0:23:66.17:0,66,788 0/0:16,0:16:48.11:0,48,557 0/0:9,0:9:27.07:0,27,326 0/1:14,3:17:72.57:73,0,457 0/0:23,0:23:60.19:0,60,780 0/0:24,0:24:63.20:0,63,831 0/0:7,0:7:18.05:0,18,218 0/0:24,0:25:60.19:0,60,795 0/1:17,9:26:99:246,0,466 0/0:24,0:24:57.18:0,57,742 0/0:15,0:15:39.13:0,39,525 0/0:25,0:25:66.20:0,66,856 0/0:29,0:29:75.20:0,75,942 0/0:25,0:25:63.20:0,63,817 0/0:17,1:18:48.13:0,48,605 0/0:24,1:25:35.61:0,36,793 0/0:24,0:25:63.19:0,63,794 0/0:25,0:25:72.20:0,72,913 0/0:6,0:6:15.04:0,15,173 0/0:22,0:23:60.17:0,60,738 0/0:23,0:23:57.18:0,57,730 0/0:33,0:33:84.26:0,84,1101 0/1:9,5:14:99:138,0,283 0/1:8,8:16:99:257,0,259 0/1:14,8:22:99:244,0,394 0/0:28,1:29:78.24:0,78,1010 0/0:16,1:17:48.14:0,48,617 0/0:25,0:25:60.19:0,60,792 0/0:26,0:26:75.24:0,75,984 0/0:18,0:18:39.10:0,39,484 0/0:34,2:36:81.23:0,81,991 0/0:31,0:32:66.21:0,66,862 0/0:46,1:47:99:0,117,1451 0/0:26,0:26:66.20:0,66,836 0/0:28,0:28:69.19:0,69,861 0/1:3,14:17:31.71:439,0,32 0/0:28,1:31:72.22:0,72,938 0/0:46,0:48:99:0,108,1315 0/0:15,0:15:39.11:0,39,474 0/0:31,0:31:75.21:0,75,943 0/0:22,0:22:57.17:0,57,707 0/0:36,1:37:93.28:0,93,1158 0/0:24,0:24:57.18:0,57,743 0/1:15,10:25:99:276,0,389 0/0:27,2:29:54.17:0,54,726 0/0:30,0:30:60.17:0,60,768 0/0:28,0:28:57.16:0,57,717 0/0:17,0:17:39.12:0,39,494 0/0:29,0:29:63.20:0,63,812 0/1:3,4:7:66.72:133,0,67 0/0:31,0:31:81.23:0,81,1019 -chr1 1225597 . G A 764.88 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.619;DP=1769;Dels=0.00;FS=3.258;HRun=0;HaplotypeScore=1.9881;InbreedingCoeff=-0.0171;MQ=55.96;MQ0=0;MQRankSum=3.394;QD=15.61;ReadPosRankSum=2.984;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:21.06:0,21,247 0/0:12,0:12:33.09:0,33,396 0/0:10,0:10:27.07:0,27,327 0/0:11,0:11:33.10:0,33,406 0/0:21,0:21:63.21:0,63,840 0/0:15,0:15:45.14:0,45,597 0/0:26,0:26:75.25:0,75,1006 0/0:20,0:20:57.19:0,57,755 0/0:32,0:32:93.28:0,93,1200 0/0:37,0:37:99:0,105,1364 0/0:16,0:16:48.14:0,48,592 0/0:16,0:16:48.14:0,48,614 0/0:25,0:25:75.24:0,75,975 0/0:27,0:27:66.20:0,66,816 0/0:27,0:29:66.19:0,66,840 0/0:13,0:13:36.11:0,36,447 0/0:29,0:30:78.24:0,78,1014 0/0:36,0:36:90.28:0,90,1179 0/0:32,0:32:78.25:0,78,1025 0/0:19,0:19:48.14:0,48,609 0/0:33,0:33:87.25:0,87,1113 0/0:39,1:40:99:0,99,1247 0/0:35,0:35:99:0,102,1307 0/0:21,0:22:54.14:0,54,680 0/0:28,0:28:72.23:0,72,953 0/0:32,1:33:44.27:0,44,970 0/0:34,0:35:84.26:0,84,1081 0/0:8,0:8:24.07:0,24,284 0/0:23,0:23:60.19:0,60,775 0/0:29,0:29:69.22:0,69,922 0/0:40,0:41:96.28:0,96,1255 0/0:27,0:27:66.20:0,66,838 0/0:28,0:28:75.22:0,75,953 0/0:33,0:33:84.24:0,84,1081 0/0:35,0:37:90.25:0,90,1135 0/0:27,0:28:72.19:0,72,902 0/0:32,0:33:69.19:0,69,888 0/0:39,0:39:99:0,102,1332 0/0:20,0:20:48.14:0,48,610 0/0:46,0:46:99:0,108,1388 0/0:38,1:41:96.29:0,96,1211 0/0:52,1:53:99:0,144,1803 0/0:34,1:35:60.56:0,61,1055 0/0:35,0:35:78.24:0,78,997 0/1:3,14:20:57.29:469,0,57 0/0:32,0:33:81.25:0,81,1047 0/0:64,0:66:99:0,147,1779 0/0:22,0:22:60.16:0,60,721 0/0:43,0:44:99:0,99,1240 0/0:35,0:35:93.26:0,93,1136 0/0:47,0:49:99:0,123,1541 0/0:31,0:31:78.21:0,78,968 0/0:33,0:35:87.24:0,87,1088 0/0:38,0:38:87.27:0,87,1121 0/0:34,0:35:84.21:0,84,1044 0/1:11,16:28:99:361,0,250 0/0:22,0:22:51.16:0,51,659 0/0:42,0:43:99:0,99,1214 0/0:13,0:13:33.10:0,33,422 0/0:37,0:37:93.28:0,93,1199 -chr1 1225604 . A G 288.23 . AC=1;AF=0.0083;AN=120;BaseQRankSum=1.165;DP=1945;Dels=0.00;FS=50.790;HRun=0;HaplotypeScore=2.6125;InbreedingCoeff=-0.0085;MQ=56.12;MQ0=0;MQRankSum=-4.687;QD=13.10;ReadPosRankSum=-3.197;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:8,0:8:24.07:0,24,279 0/0:12,0:12:36.11:0,36,446 0/0:15,0:15:36.10:0,36,429 0/0:12,0:12:36.11:0,36,435 0/0:23,0:23:69.22:0,69,916 0/0:17,0:17:51.16:0,51,668 0/0:32,0:32:96.28:0,96,1258 0/0:25,0:25:75.24:0,75,990 0/0:35,0:35:96.31:0,96,1273 0/0:46,0:46:99:0,135,1796 0/1:10,12:22:99:336,0,340 0/0:17,0:17:51.16:0,51,668 0/0:25,0:26:75.24:0,75,984 0/0:34,0:34:84.27:0,84,1084 0/0:31,0:32:72.18:0,72,908 0/0:14,0:14:36.11:0,36,444 0/0:34,0:34:93.30:0,93,1244 0/0:40,0:41:99:0,105,1337 0/0:32,0:32:84.26:0,84,1091 0/0:23,0:23:63.17:0,63,761 0/0:36,0:37:96.28:0,96,1230 0/0:46,0:46:99:0,123,1561 0/0:36,0:36:99:0,102,1347 0/0:24,0:24:60.19:0,60,795 0/0:30,0:31:78.25:0,78,1042 0/0:38,0:39:90.26:0,90,1158 0/0:39,0:39:99:0,105,1317 0/0:10,0:10:27.08:0,27,338 0/0:31,0:32:75.22:0,75,964 0/0:32,0:32:72.23:0,72,975 0/0:39,0:39:99:0,105,1354 0/0:30,0:31:69.21:0,69,885 0/0:32,0:32:84.25:0,84,1063 0/0:36,0:36:99:0,102,1317 0/0:42,0:42:90.27:0,90,1165 0/0:32,0:32:81.26:0,81,1054 0/0:39,0:39:81.25:0,81,1067 0/0:42,0:42:99:0,114,1498 0/0:22,1:23:26.59:0,27,676 0/0:46,2:48:56.49:0,56,1438 0/0:40,1:41:93.29:0,93,1197 0/0:54,0:56:99:0,141,1767 0/0:35,0:35:87.28:0,87,1133 0/0:38,0:39:90.27:0,90,1144 0/0:22,0:22:54.16:0,54,693 0/0:34,0:34:81.24:0,81,1039 0/0:67,0:68:99:0,150,1784 0/0:22,0:24:60.18:0,60,749 0/0:45,0:45:96.29:0,96,1230 0/0:37,0:39:93.29:0,93,1169 0/0:52,0:54:99:0,129,1619 0/0:33,1:35:44.26:0,44,995 0/0:34,1:37:56.85:0,57,1090 0/0:38,0:40:90.28:0,90,1184 0/0:37,0:37:90.21:0,90,1110 0/0:28,1:30:41.77:0,42,862 0/0:24,0:24:51.15:0,51,639 0/0:40,0:41:93.26:0,93,1164 0/0:15,0:15:39.12:0,39,490 0/0:35,1:37:59.85:0,60,1131 -chr1 1225612 . G A 8878.59 . AC=25;AF=0.2083;AN=120;BaseQRankSum=-2.436;DP=2093;Dels=0.00;FS=21.815;HRun=0;HaplotypeScore=1.7123;InbreedingCoeff=0.1407;MQ=56.18;MQ0=0;MQRankSum=1.022;QD=13.60;ReadPosRankSum=-1.768;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:9,0:9:27.05:0,27,288 0/1:5,7:12:99:212,0,161 1/1:0,14:15:39.11:473,39,0 1/1:0,13:13:33.10:412,33,0 0/0:27,0:27:81.26:0,81,1082 0/0:19,0:19:54.17:0,54,696 0/0:37,0:37:99:0,111,1477 0/0:28,0:28:84.26:0,84,1097 0/0:41,0:41:99:0,114,1498 0/0:47,0:47:99:0,138,1817 0/1:9,12:21:99:314,0,293 0/1:10,7:17:99:221,0,337 0/0:30,0:30:90.29:0,90,1179 0/0:40,0:40:87.26:0,87,1108 0/0:33,0:33:81.23:0,81,1019 0/1:14,7:21:99:192,0,421 0/0:38,1:40:51.07:0,51,1173 0/0:47,0:47:99:0,117,1532 0/1:27,8:35:99:193,0,748 0/1:14,14:30:99:341,0,415 0/1:17,16:34:99:468,0,487 0/0:49,0:49:99:0,123,1613 0/0:40,0:40:96.32:0,96,1309 0/0:27,1:28:69.21:0,69,891 0/0:34,0:34:84.26:0,84,1096 0/1:17,18:36:99:508,0,441 0/0:41,0:41:99:0,108,1329 0/0:11,0:11:27.06:0,27,323 0/0:36,0:36:90.26:0,90,1142 0/0:36,0:36:87.28:0,87,1161 0/1:19,26:45:99:722,0,450 0/0:34,0:34:66.19:0,66,878 0/0:35,0:35:96.27:0,96,1207 0/1:16,24:42:99:702,0,461 0/0:43,0:44:90.26:0,90,1148 0/1:17,26:44:99:688,0,355 0/0:41,0:42:87.28:0,87,1175 0/0:48,0:48:99:0,129,1709 1/1:1,22:23:26.73:696,27,0 0/1:31,20:51:99:558,0,968 0/1:31,12:43:99:246,0,793 0/0:56,0:57:99:0,156,1947 0/1:29,6:35:99:153,0,816 0/0:40,0:40:93.26:0,93,1163 0/0:23,0:23:54.17:0,54,712 0/0:34,0:34:84.26:0,84,1090 0/0:70,0:72:99:0,150,1861 1/1:0,26:26:57.15:692,57,0 0/0:44,0:44:99:0,105,1358 0/0:43,0:43:99:0,108,1368 0/1:29,27:56:99:686,0,789 0/0:34,0:34:84.26:0,84,1063 0/0:37,0:39:96.26:0,96,1230 0/1:29,11:40:99:243,0,802 0/0:39,0:39:87.26:0,87,1132 0/0:30,0:31:78.23:0,78,964 0/0:26,0:26:54.16:0,54,666 0/0:39,0:40:99:0,99,1244 0/1:8,6:14:99:160,0,219 0/0:39,0:40:99:0,99,1273 -chr1 1225641 . C A 16235.21 . AC=27;AF=0.2250;AN=120;BaseQRankSum=-0.237;DP=2629;Dels=0.00;FS=1.703;HRun=0;HaplotypeScore=1.7639;InbreedingCoeff=0.3777;MQ=56.48;MQ0=0;MQRankSum=2.792;QD=20.32;ReadPosRankSum=2.777;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|9),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|8),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|14),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|9),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|12),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|11);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:15.03:0,15,162 0/0:15,0:15:42.12:0,42,502 0/1:6,5:11:99:167,0,154 0/1:4,4:8:92.35:105,0,92 0/0:29,0:29:87.28:0,87,1164 0/0:22,0:22:63.21:0,63,839 0/0:41,0:41:99:0,123,1647 0/0:26,0:26:78.26:0,78,1039 0/0:41,0:41:99:0,120,1578 0/0:58,0:58:99:0,169,2226 0/1:11,13:24:99:386,0,356 0/1:8,9:17:99:301,0,261 0/0:31,1:32:53.29:0,53,1151 0/0:48,0:48:99:0,105,1405 0/1:32,22:54:99:617,0,976 1/1:0,30:30:72.23:961,72,0 0/0:63,0:63:99:0,141,1838 0/0:66,0:66:99:0,153,2069 0/0:44,0:44:99:0,117,1558 0/0:45,1:46:99:0,123,1605 0/0:45,0:45:99:0,105,1441 0/0:79,0:80:99:0,184,2450 0/0:54,0:54:99:0,129,1731 0/0:47,0:47:99:0,117,1508 0/0:46,0:47:99:0,117,1540 0/0:45,0:45:99:0,105,1421 0/1:22,30:52:99:730,0,546 0/0:24,0:24:60.19:0,60,770 0/0:55,0:55:99:0,135,1777 0/0:54,0:54:99:0,126,1684 0/0:69,0:69:99:0,181,2377 0/1:36,15:51:99:272,0,988 0/0:56,0:56:99:0,141,1867 1/1:0,60:60:99:1896,144,0 0/0:46,0:46:99:0,108,1405 0/1:25,33:58:99:853,0,650 0/0:54,0:54:99:0,126,1688 0/0:67,0:67:99:0,178,2369 0/0:28,1:29:30:0,30,856 0/0:77,0:77:99:0,193,2486 0/0:48,0:48:99:0,123,1587 0/1:34,36:70:99:1015,0,879 1/1:1,40:41:77.91:1365,78,0 0/0:38,1:39:56.28:0,56,1143 1/1:0,37:37:93.25:1171,93,0 0/0:42,0:42:99:0,102,1325 0/0:69,0:69:99:0,163,2096 1/1:1,34:35:87.25:1089,87,0 0/0:53,1:54:95.98:0,96,1627 1/1:0,52:52:99:1634,126,0 1/1:2,60:62:99:2010,123,0 0/0:34,1:35:55.03:0,55,1114 0/1:19,15:34:99:369,0,569 0/1:28,17:45:99:466,0,663 0/0:41,0:41:99:0,105,1376 0/1:16,20:36:99:518,0,419 0/0:30,0:30:69.22:0,69,872 0/0:44,0:44:93.29:0,93,1228 0/1:11,11:22:99:310,0,321 0/0:42,0:42:99:0,102,1358 -chr1 1225804 . A G 641.95 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.178;DP=3135;Dels=0.00;FS=4.019;HRun=0;HaplotypeScore=3.7390;InbreedingCoeff=-0.0085;MQ=57.48;MQ0=0;MQRankSum=2.112;QD=13.10;ReadPosRankSum=1.189;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|10),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|9),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|15),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|10),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|13),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|12);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:9,0:9:24.07:0,24,296 0/0:10,0:10:24.07:0,24,283 0/0:12,0:12:33.11:0,33,430 0/0:8,0:8:21.06:0,21,259 0/0:28,0:28:84.26:0,84,1076 0/0:25,0:25:72.22:0,72,925 0/0:42,0:42:99:0,126,1605 0/0:27,0:27:75.24:0,75,974 0/0:41,0:41:99:0,123,1617 0/0:60,0:60:99:0,175,2243 0/0:20,0:20:60.20:0,60,788 0/0:18,0:18:51.16:0,51,655 0/0:33,0:33:99:0,99,1295 0/0:29,0:29:87.28:0,87,1133 0/0:45,0:45:99:0,105,1363 0/0:18,0:18:54.17:0,54,686 0/0:38,0:38:99:0,102,1329 0/0:27,0:29:69.22:0,69,886 0/0:46,0:46:99:0,123,1613 0/0:41,0:41:99:0,102,1307 0/0:37,0:37:93.28:0,93,1244 0/0:39,0:40:99:0,111,1425 0/0:46,0:46:99:0,123,1602 0/0:26,0:26:75.24:0,75,978 0/0:42,0:42:99:0,117,1511 0/0:30,0:31:78.24:0,78,998 0/0:39,0:39:99:0,108,1425 0/0:31,0:31:87.27:0,87,1125 0/0:44,0:44:99:0,117,1543 0/0:43,0:44:99:0,114,1465 0/0:50,1:51:99:0,135,1774 0/0:24,0:24:72.23:0,72,931 0/0:40,0:40:99:0,108,1370 0/1:26,23:49:99:690,0,758 0/0:29,0:29:78.23:0,78,1006 0/0:40,0:40:99:0,99,1281 0/0:29,0:29:81.23:0,81,1037 0/0:55,0:56:99:0,141,1794 0/0:78,0:79:99:0,202,2611 0/0:123,0:126:99:0,319,4013 0/0:82,0:84:99:0,190,2448 0/0:104,0:104:99:0,259,3279 0/0:73,1:75:99:0,187,2371 0/0:70,0:70:99:0,163,2129 0/0:52,0:53:99:0,129,1597 0/0:82,0:84:99:0,196,2515 0/0:119,1:121:99:0,289,3621 0/0:48,0:49:99:0,117,1486 0/0:123,0:123:99:0,289,3732 0/0:91,0:94:99:0,220,2690 0/0:135,0:135:99:0,340,4243 0/0:77,0:77:99:0,187,2376 0/0:74,0:74:99:0,178,2264 0/0:107,0:107:99:0,253,3185 0/0:84,1:85:99:0,205,2564 0/0:66,0:66:99:0,156,2051 0/0:49,0:49:99:0,129,1628 0/0:74,0:77:99:0,184,2337 0/0:60,0:60:99:0,144,1869 0/0:65,0:65:99:0,150,1959 -chr1 1225810 . C CGG 5006.7 . AC=3;AF=0.0250;AN=120;BaseQRankSum=1.861;DP=3131;FS=0.360;HRun=6;HaplotypeScore=237.1014;InbreedingCoeff=0.6361;MQ=57.43;MQ0=0;MQRankSum=-0.361;QD=33.60;ReadPosRankSum=-1.506;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|10),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|9),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|15),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|10),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|13),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|12);CSQ=intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant&feature_elongation|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:9,0:9:15.04:0,15,183 0/0:9,0:9:24.07:0,24,290 0/0:9,0:9:24.07:0,24,292 0/0:8,0:8:12.03:0,12,144 0/0:33,0:33:87.26:0,87,1051 0/0:24,0:24:66.20:0,66,802 0/0:37,0:37:84.24:0,84,1025 0/0:24,0:24:57.17:0,57,695 0/0:32,0:32:87.27:0,87,1056 0/0:60,0:60:99:0,150,1826 0/0:17,0:17:45.14:0,45,548 0/0:15,0:15:30.09:0,30,364 0/0:24,0:24:66.20:0,66,803 0/0:36,0:36:99:0,102,1220 0/0:41,0:40:99:0,105,1278 0/0:18,0:18:48.15:0,48,586 0/0:40,0:40:99:0,105,1281 0/0:27,0:27:60.18:0,60,732 0/0:40,0:40:99:0,102,1238 0/0:40,0:40:96.25:0,96,1146 0/0:39,0:39:59.32:0,59,1030 0/0:36,0:38:99:0,105,1230 0/0:41,0:41:99:0,111,1343 0/0:21,0:21:63.19:0,63,754 0/0:40,0:40:99:0,105,1275 0/0:33,0:33:81.23:0,81,973 0/0:40,0:40:99:0,108,1313 0/0:31,0:31:84.26:0,84,1024 0/0:40,0:40:99:0,108,1317 0/0:42,0:42:99:0,120,1458 0/0:50,0:50:99:0,129,1557 0/0:27,0:27:78.24:0,78,944 0/0:40,0:40:99:0,102,1230 0/1:26,20:47:99:840,0,681 0/0:26,0:26:75.24:0,75,915 0/0:42,0:42:99:0,108,1316 0/0:34,0:34:96.29:0,96,1164 0/0:57,0:57:99:0,144,1756 0/0:80,0:80:99:0,208,2518 0/0:127,0:127:99:0,328,3955 0/0:91,0:91:99:0,222,2664 0/0:110,0:110:99:0,280,3395 0/0:73,1:74:99:0,190,2303 0/0:71,0:72:99:0,187,2265 0/0:55,0:56:99:0,126,1600 0/0:84,0:85:99:0,207,2507 0/0:122,0:124:99:0,283,3424 0/0:49,0:49:99:0,120,1463 0/0:127,0:127:99:0,319,3864 1/1:21,78:102:99:4167,222,0 0/0:132,0:133:99:0,318,3803 0/0:82,0:82:99:0,205,2475 0/0:72,0:74:99:0,171,2084 0/0:106,0:106:99:0,252,3026 0/0:89,0:89:99:0,244,2947 0/0:64,0:65:99:0,156,1966 0/0:48,0:48:99:0,112,1346 0/0:81,0:81:99:0,178,2147 0/0:59,0:59:99:0,159,1932 0/0:63,0:64:99:0,165,1968 -chr1 1225824 . G A 1475.6 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.326;DP=3390;Dels=0.00;FS=1.074;HRun=1;HaplotypeScore=2.3868;InbreedingCoeff=-0.0086;MQ=57.43;MQ0=0;MQRankSum=2.353;QD=12.20;ReadPosRankSum=-2.766;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|10),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|9),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|15),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|10),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|13),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|12);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:8,0:8:24.05:0,24,280 0/0:10,0:10:24.07:0,24,285 0/0:8,0:8:24.08:0,24,315 0/0:7,0:7:18.06:0,18,225 0/0:36,0:36:99:0,105,1389 0/0:29,0:29:84.22:0,84,1057 0/0:36,0:36:99:0,108,1412 0/0:22,0:22:60.16:0,60,735 0/0:32,0:32:96.31:0,96,1277 0/0:62,0:62:99:0,187,2418 0/0:16,0:16:48.16:0,48,639 0/0:17,0:17:48.15:0,48,612 0/0:24,0:24:66.21:0,66,873 0/0:36,0:36:99:0,99,1272 0/0:45,0:45:99:0,99,1264 0/0:16,0:16:48.15:0,48,601 0/0:40,0:40:96.29:0,96,1214 0/0:27,0:27:72.23:0,72,921 0/0:40,0:41:99:0,105,1286 0/0:40,0:40:99:0,105,1327 0/0:36,0:37:96.30:0,96,1250 0/0:44,0:44:99:0,111,1417 0/0:41,0:41:99:0,102,1330 0/0:25,0:25:69.20:0,69,863 0/0:35,0:35:96.27:0,96,1231 0/0:37,0:37:99:0,102,1320 0/0:45,0:45:99:0,105,1377 0/0:31,0:31:75.23:0,75,975 0/0:43,0:43:99:0,105,1332 0/0:44,0:44:99:0,111,1400 0/0:55,0:55:99:0,147,1882 0/0:31,0:31:81.25:0,81,1041 0/0:44,0:44:99:0,102,1317 0/0:48,1:49:99:0,114,1465 0/0:27,0:27:69.21:0,69,886 0/0:43,0:43:99:0,105,1331 0/0:41,0:41:99:0,108,1371 0/0:63,1:64:99:0,153,1958 0/0:88,0:88:99:0,199,2547 0/0:141,0:141:99:0,337,4220 0/0:99,0:99:99:0,241,2987 0/0:110,0:111:99:0,283,3555 0/0:83,0:83:99:0,217,2669 0/0:74,0:74:99:0,178,2295 0/0:62,0:62:99:0,144,1777 0/0:94,0:94:99:0,220,2747 0/0:135,0:135:99:0,331,4041 0/0:52,0:52:99:0,117,1474 0/0:136,0:136:99:0,313,3982 0/1:61,59:121:99:1523,0,1620 0/0:149,0:150:99:0,349,4317 0/0:93,0:93:99:0,217,2764 0/0:89,0:90:99:0,202,2544 0/0:113,0:114:99:0,247,3042 0/0:111,0:111:99:0,253,3156 0/0:71,0:71:99:0,172,2182 0/0:52,0:52:99:0,138,1706 0/0:84,0:84:99:0,193,2429 0/0:70,0:70:99:0,159,2007 0/0:68,1:71:99:0,150,1899 -chr1 1225945 . G C 3949.71 . AC=3;AF=0.0250;AN=120;BaseQRankSum=-1.101;DP=3777;Dels=0.00;FS=22.292;HRun=0;HaplotypeScore=4.0017;InbreedingCoeff=0.6569;MQ=57.83;MQ0=0;MQRankSum=-0.665;QD=25.32;ReadPosRankSum=2.508;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|11),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|10),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|16),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|11),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|14),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|13);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:12,0:12:33.10:0,33,408 0/0:15,0:15:42.10:0,42,518 0/0:13,0:13:30.10:0,30,387 0/0:8,0:8:24.06:0,24,297 0/0:42,0:42:99:0,123,1602 0/0:34,0:34:99:0,102,1360 0/0:39,0:39:99:0,114,1498 0/0:23,0:23:57.16:0,57,725 0/0:57,0:57:99:0,166,2193 0/0:59,0:59:99:0,178,2283 0/0:27,0:27:78.26:0,78,1049 0/0:29,0:29:84.27:0,84,1084 0/0:45,0:45:99:0,123,1609 0/0:67,0:70:99:0,166,2149 0/0:73,0:73:99:0,184,2429 0/0:42,0:42:99:0,99,1328 0/0:51,0:51:99:0,114,1470 0/0:52,1:53:99:0,132,1762 0/0:64,0:64:99:0,169,2190 0/0:58,0:59:99:0,141,1832 0/0:45,0:45:99:0,120,1555 0/0:69,0:69:99:0,168,2182 0/0:55,0:55:99:0,126,1724 0/0:33,0:34:78.25:0,78,1025 0/0:54,0:54:99:0,141,1860 0/0:43,0:43:99:0,102,1351 0/1:25,11:36:99:297,0,649 0/0:40,0:40:87.26:0,87,1162 0/0:69,0:69:99:0,163,2153 0/0:51,0:52:99:0,120,1573 0/0:58,0:58:99:0,147,1950 0/0:40,0:40:99:0,99,1280 0/0:51,0:51:99:0,114,1528 0/0:50,0:50:99:0,126,1648 0/0:36,0:37:90.28:0,90,1176 0/0:43,0:43:99:0,102,1376 0/0:55,0:55:99:0,141,1845 0/0:91,0:91:99:0,211,2794 0/0:91,0:91:99:0,217,2827 0/0:141,0:141:99:0,340,4311 0/0:124,0:125:99:0,307,3819 0/0:92,1:93:99:0,238,3051 0/0:93,0:93:99:0,241,3014 0/0:73,0:73:99:0,187,2389 0/0:63,1:64:99:0,122,1787 0/0:78,0:78:99:0,190,2428 0/0:169,0:170:99:0,409,5169 0/0:64,0:64:99:0,159,2016 0/0:120,0:120:99:0,292,3691 1/1:5,114:120:99:3653,224,0 0/0:132,0:133:99:0,316,4017 0/0:74,0:75:99:0,178,2255 0/0:69,0:70:99:0,184,2367 0/0:106,0:106:99:0,253,3193 0/0:67,0:67:99:0,175,2252 0/0:67,0:67:99:0,172,2205 0/0:57,0:57:99:0,138,1764 0/0:82,0:82:99:0,193,2528 0/0:59,0:59:99:0,135,1722 0/0:92,0:92:99:0,196,2586 -chr1 1225959 . C G 25993.98 . AC=36;AF=0.3000;AN=120;BaseQRankSum=1.580;DP=3659;Dels=0.00;FS=21.530;HRun=2;HaplotypeScore=2.4662;InbreedingCoeff=0.2055;MQ=57.98;MQ0=0;MQRankSum=1.714;QD=17.82;ReadPosRankSum=0.723;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|11),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|10),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|16),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|11),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|14),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|13);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000467651|||||processed_transcript|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 1/1:0,8:8:18.06:225,18,0 0/1:2,8:10:43.35:260,0,43 0/1:12,5:17:99:143,0,278 0/1:3,2:5:62.86:63,0,87 0/0:38,0:38:99:0,114,1497 0/0:35,0:35:99:0,105,1398 0/0:34,0:34:99:0,102,1340 0/0:21,0:21:60.17:0,60,748 0/0:57,0:57:99:0,172,2295 0/0:64,0:64:99:0,184,2416 0/1:10,8:18:99:271,0,335 0/1:9,16:25:99:540,0,276 0/1:19,16:35:99:486,0,627 0/0:67,0:67:99:0,153,2019 0/0:68,0:69:99:0,169,2188 0/0:42,0:42:99:0,99,1282 0/0:56,0:56:99:0,138,1735 0/1:36,17:53:99:420,0,1052 0/1:52,11:63:99:191,0,1614 0/0:59,0:59:99:0,135,1776 0/0:49,0:49:99:0,123,1544 0/1:36,31:67:99:874,0,938 0/0:49,0:49:99:0,114,1534 0/1:21,14:36:99:365,0,672 0/0:52,0:52:99:0,132,1727 0/0:40,0:41:96.29:0,96,1260 1/1:0,37:37:96.30:1241,96,0 0/0:39,0:39:84.27:0,84,1129 0/0:73,0:73:99:0,169,2203 0/0:57,0:57:99:0,135,1749 0/0:61,0:61:99:0,147,1951 0/1:22,18:40:99:460,0,622 0/0:51,0:51:99:0,111,1456 0/1:24,26:50:99:729,0,637 0/1:18,19:37:99:479,0,535 1/1:0,50:50:99:1536,114,0 0/1:31,31:62:99:882,0,891 0/0:89,1:90:99:0,211,2838 0/1:53,27:80:99:711,0,1505 0/0:130,0:130:99:0,322,4113 0/0:127,0:127:99:0,310,3937 0/0:91,0:91:99:0,223,2882 0/0:95,0:95:99:0,244,3143 0/0:73,1:74:99:0,181,2338 1/1:1,59:60:99:1775,106,0 0/0:79,0:79:99:0,190,2508 0/0:160,2:162:99:0,348,4793 0/1:33,29:62:99:736,0,866 0/1:55,50:105:99:1423,0,1219 1/1:0,112:113:99:3780,298,0 0/1:71,52:123:99:1448,0,1884 0/0:75,1:76:99:0,132,2077 1/1:2,57:59:99:1918,116,0 0/0:100,0:100:99:0,244,3082 1/1:1,68:69:99:2150,166,0 0/1:39,25:64:99:689,0,1069 0/1:35,18:53:99:474,0,1074 0/0:79,1:80:99:0,151,2394 1/1:0,57:57:99:1723,135,0 0/0:81,1:82:99:0,129,2117 -chr1 1226063 . G A 1804.82 . AC=5;AF=0.0417;AN=120;BaseQRankSum=-2.166;DP=2009;Dels=0.00;FS=1.053;HRun=0;HaplotypeScore=1.1275;InbreedingCoeff=-0.0436;MQ=58.53;MQ0=0;MQRankSum=0.440;QD=9.35;ReadPosRankSum=-0.405;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A472T|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A472T|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A503T|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A538T|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A636T|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=missense_variant|Gcc/Acc|A/T|ENSG00000162572|SCNN1D|ENST00000338555|12/15|benign(0.168)|tolerated(0.19)|472/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|14/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|Gcc/Acc|A/T|ENSG00000162572|SCNN1D|ENST00000325425|12/15|benign(0.109)|tolerated(0.39)|538/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,missense_variant|Gcc/Acc|A/T|ENSG00000162572|SCNN1D|ENST00000379099|6/7|benign(0.297)|tolerated(0.13)|289/308|protein_coding|1,missense_variant|Gcc/Acc|A/T|ENSG00000162572|SCNN1D|ENST00000400928|11/14|benign(0.168)|tolerated(0.19)|472/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,missense_variant|Gcc/Acc|A/T|ENSG00000162572|SCNN1D|ENST00000379116|15/18|benign(0.109)|tolerated(0.29)|636/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:9,0:9:24.08:0,24,318 0/0:15,0:15:42.13:0,42,522 0/0:12,0:12:36.11:0,36,465 0/0:7,0:7:21.07:0,21,275 0/0:27,0:27:81.26:0,81,1053 0/0:32,0:32:93.31:0,93,1253 0/0:50,0:50:99:0,144,1897 0/0:23,0:23:69.20:0,69,878 0/0:54,0:54:99:0,163,2164 0/0:59,0:59:99:0,178,2328 0/0:31,0:31:93.28:0,93,1200 0/0:26,0:26:75.24:0,75,984 0/0:38,0:38:99:0,111,1416 0/0:35,0:35:96.29:0,96,1256 0/0:46,0:46:99:0,120,1618 0/1:17,12:29:99:324,0,563 0/0:41,0:41:99:0,102,1368 0/0:42,0:42:99:0,111,1504 0/1:47,6:54:99:109,0,1318 0/0:43,0:43:99:0,108,1426 0/0:29,0:29:75.25:0,75,1011 0/0:42,0:42:99:0,111,1474 0/0:30,0:30:69.23:0,69,935 0/0:26,1:27:35.92:0,36,898 0/0:47,0:47:99:0,123,1673 0/0:43,0:43:99:0,114,1487 0/0:29,0:29:75.23:0,75,1000 0/0:24,0:24:48.16:0,48,655 0/0:40,0:40:99:0,111,1496 0/0:41,0:41:96.32:0,96,1306 0/0:38,0:38:96.28:0,96,1237 0/0:36,0:36:93.27:0,93,1221 0/0:41,0:41:99:0,105,1387 0/0:55,0:55:99:0,144,1922 0/0:25,0:25:69.23:0,69,929 0/0:48,0:48:99:0,117,1549 0/0:49,0:49:99:0,114,1546 0/0:51,0:52:99:0,126,1712 0/0:23,0:23:63.21:0,63,839 0/0:50,0:50:99:0,129,1677 0/1:21,22:44:99:635,0,519 0/1:15,20:35:99:579,0,459 0/1:21,10:31:99:262,0,645 0/0:18,0:20:45.12:0,45,554 0/0:15,0:15:30.10:0,30,391 0/0:28,0:28:72.23:0,72,947 0/0:58,0:58:99:0,156,2030 0/0:12,0:12:33.10:0,33,415 0/0:30,0:30:84.26:0,84,1080 0/0:47,0:47:99:0,129,1665 0/0:43,0:44:99:0,117,1468 0/0:32,0:32:87.22:0,87,1060 0/0:16,0:16:45.14:0,45,559 0/0:33,0:33:75.24:0,75,975 0/0:23,0:23:66.21:0,66,861 0/0:18,0:18:51.16:0,51,668 0/0:21,0:21:57.17:0,57,718 0/0:21,0:21:51.16:0,51,666 0/0:18,0:18:51.16:0,51,674 0/0:21,0:21:48.12:0,48,572 -chr1 1226102 . G A 4016.45 . AC=11;AF=0.0917;AN=120;BaseQRankSum=-1.245;DP=1541;Dels=0.00;FS=2.281;HRun=0;HaplotypeScore=1.2555;InbreedingCoeff=0.2951;MQ=58.35;MQ0=0;MQRankSum=0.176;QD=16.67;ReadPosRankSum=2.379;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:8,0:8:21.07:0,21,267 0/0:7,0:7:15.05:0,15,188 0/0:12,0:12:27.08:0,27,341 0/0:7,0:7:15.05:0,15,201 0/0:20,0:20:54.17:0,54,712 0/0:30,0:30:90.26:0,90,1186 0/0:32,0:32:93.28:0,93,1214 0/0:19,0:19:54.17:0,54,706 0/0:47,0:47:99:0,141,1860 0/0:57,0:57:99:0,163,2149 0/1:15,5:20:99:129,0,488 0/0:18,0:18:54.18:0,54,713 0/0:30,0:30:90.29:0,90,1173 0/0:26,0:26:69.22:0,69,908 0/0:34,0:34:90.29:0,90,1199 0/0:22,0:22:48.16:0,48,656 0/0:33,0:33:87.28:0,87,1147 0/0:32,0:32:90.29:0,90,1177 0/0:41,0:41:99:0,108,1432 0/0:28,0:28:75.24:0,75,966 0/0:28,0:28:72.22:0,72,918 0/0:27,0:27:72.20:0,72,936 0/0:25,0:26:51.17:0,51,702 0/0:27,0:27:81.26:0,81,1055 0/0:31,0:31:87.25:0,87,1119 0/0:27,0:28:75.24:0,75,974 0/1:12,15:27:99:286,0,309 0/0:16,0:17:30.10:0,30,413 0/0:25,0:25:63.21:0,63,857 0/0:29,0:29:69.21:0,69,907 0/0:32,0:32:87.27:0,87,1138 0/1:9,17:26:99:449,0,283 0/0:28,0:28:66.21:0,66,883 1/1:0,40:41:99:1380,105,0 0/0:18,0:18:48.16:0,48,643 0/1:27,12:39:99:343,0,818 0/0:33,0:33:78.26:0,78,1068 0/0:49,0:49:99:0,117,1579 0/0:16,0:16:45.15:0,45,614 0/0:38,0:38:99:0,102,1326 0/0:34,0:34:87.28:0,87,1130 0/0:23,0:23:69.21:0,69,885 0/0:19,0:19:54.17:0,54,714 0/0:21,0:21:57.14:0,57,716 1/1:1,13:14:39.11:481,39,0 0/0:21,0:21:60.19:0,60,763 0/0:46,0:47:99:0,129,1663 0/0:9,0:9:24.08:0,24,304 0/0:25,0:25:72.22:0,72,932 0/0:36,0:36:99:0,99,1263 0/1:21,13:34:99:397,0,577 0/0:21,1:22:15.95:0,16,645 0/1:8,8:16:99:187,0,223 0/1:13,11:24:99:364,0,330 0/0:12,0:12:33.10:0,33,410 0/0:11,0:11:30.10:0,30,395 0/0:17,0:17:45.15:0,45,597 0/0:15,0:15:45.11:0,45,569 0/0:16,0:16:39.09:0,39,498 0/0:17,0:17:51.13:0,51,633 -chr1 1226139 . G A 53.13 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.435;DP=1276;Dels=0.00;FS=8.998;HRun=1;HaplotypeScore=0.7541;InbreedingCoeff=-0.0093;MQ=58.09;MQ0=0;MQRankSum=-1.197;QD=2.95;ReadPosRankSum=-0.731;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.04:0,15,169 0/0:9,0:9:27.04:0,27,302 0/0:13,0:13:39.11:0,39,466 0/0:5,0:5:12.03:0,12,138 0/0:19,0:19:51.16:0,51,657 0/0:19,0:19:51.15:0,51,640 0/0:31,0:31:75.19:0,75,920 0/0:18,0:18:51.12:0,51,628 0/0:29,0:31:81.26:0,81,1062 0/0:55,0:55:99:0,153,1957 0/0:20,0:20:45.13:0,45,569 0/0:10,0:11:21.06:0,21,262 0/0:27,0:27:60.16:0,60,741 0/0:26,1:28:63.19:0,63,799 0/0:30,0:30:81.25:0,81,1038 0/0:14,0:14:42.10:0,42,518 0/0:26,0:26:69.20:0,69,865 0/0:26,0:27:69.21:0,69,870 0/0:27,0:27:69.20:0,69,902 0/0:24,0:24:57.18:0,57,719 0/0:15,0:15:42.11:0,42,511 0/0:17,0:17:48.14:0,48,592 0/0:16,0:16:42.14:0,42,563 0/0:25,0:25:66.18:0,66,823 0/0:16,0:17:45.14:0,45,581 0/0:15,0:15:42.13:0,42,535 0/0:20,1:21:48.15:0,48,633 0/0:13,0:13:33.10:0,33,429 0/0:20,0:20:51.16:0,51,664 0/0:22,0:22:60.19:0,60,790 0/0:28,0:28:78.20:0,78,971 0/0:19,0:19:42.13:0,42,543 0/0:23,0:23:60.16:0,60,742 0/0:26,0:26:63.20:0,63,837 0/0:14,0:14:36.10:0,36,460 0/0:25,0:25:72.22:0,72,912 0/0:20,0:20:57.18:0,57,746 0/0:40,0:41:96.31:0,96,1272 0/0:14,0:14:33.11:0,33,433 0/0:35,0:35:96.27:0,96,1211 0/0:31,0:31:87.27:0,87,1111 0/0:20,0:20:60.19:0,60,789 0/0:17,0:17:42.14:0,42,541 0/0:18,0:18:54.17:0,54,698 0/1:11,7:18:99:101,0,342 0/0:14,0:14:39.12:0,39,499 0/0:43,0:44:99:0,114,1441 0/0:11,0:12:30.09:0,30,378 0/0:22,0:22:48.15:0,48,634 0/0:31,0:31:75.19:0,75,915 0/0:29,0:30:81.21:0,81,1005 0/0:20,0:20:57.18:0,57,723 0/0:19,0:19:51.14:0,51,632 0/0:21,0:21:57.16:0,57,736 0/0:14,0:14:33.10:0,33,430 0/0:16,0:16:48.15:0,48,615 0/0:10,0:10:27.08:0,27,342 0/0:17,0:18:48.15:0,48,608 0/0:13,0:13:36.11:0,36,469 0/0:23,0:23:51.14:0,51,641 -chr1 1226217 . A G 385.18 . AC=1;AF=0.0083;AN=120;BaseQRankSum=1.713;DP=1445;Dels=0.00;FS=1.054;HRun=0;HaplotypeScore=1.4065;InbreedingCoeff=-0.0114;MQ=58.08;MQ0=0;MQRankSum=0.322;QD=12.84;ReadPosRankSum=0.561;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:21.04:0,21,228 0/0:4,0:5:9.01:0,9,88 0/0:8,0:8:18.05:0,18,222 0/0:3,0:3:6.02:0,6,74 0/0:11,0:11:33.07:0,33,395 0/0:16,0:16:42.13:0,42,528 0/0:17,0:18:39.11:0,39,485 0/0:7,0:8:18.06:0,18,234 0/0:24,0:24:60.17:0,60,774 0/0:23,0:24:60.16:0,60,751 0/0:8,1:9:24.08:0,24,316 0/0:12,0:12:30.08:0,30,361 0/0:17,0:18:45.11:0,45,564 0/0:20,0:20:48.11:0,48,585 0/0:33,0:33:87.26:0,87,1085 0/0:18,0:19:48.14:0,48,598 0/0:24,0:24:66.20:0,66,820 0/0:32,0:32:78.24:0,78,996 0/0:29,0:29:75.15:0,75,899 0/0:22,0:22:60.17:0,60,731 0/0:22,0:22:60.19:0,60,760 0/0:38,0:41:81.26:0,81,1066 0/0:28,0:29:66.15:0,66,818 0/0:25,0:26:66.20:0,66,832 0/0:25,0:25:69.20:0,69,857 0/0:22,0:22:51.16:0,51,630 0/0:21,0:21:48.14:0,48,607 0/0:17,0:17:39.07:0,39,432 0/0:30,0:30:84.25:0,84,1062 0/0:31,0:31:78.19:0,78,951 0/0:37,0:37:90.25:0,90,1106 0/0:29,0:29:75.22:0,75,907 0/0:30,0:30:75.23:0,75,952 0/0:29,0:29:72.23:0,72,937 0/0:22,0:22:51.16:0,51,658 0/0:21,0:21:48.13:0,48,577 0/0:27,0:27:69.22:0,69,903 0/0:25,0:25:66.20:0,66,831 0/0:27,0:27:78.16:0,78,936 0/0:43,0:45:99:0,108,1332 0/0:24,0:26:63.16:0,63,755 0/0:24,0:24:57.16:0,57,728 0/0:30,0:31:84.19:0,84,983 0/0:17,0:18:42.09:0,42,496 0/1:14,16:30:99:433,0,360 0/0:17,0:17:39.10:0,39,489 0/0:53,0:54:99:0,135,1607 0/0:17,0:18:45.14:0,45,586 0/0:33,0:35:90.25:0,90,1116 0/0:42,0:42:99:0,105,1247 0/0:42,0:43:99:0,105,1317 0/0:26,0:28:75.22:0,75,928 0/0:25,0:27:66.17:0,66,790 0/0:30,1:34:63.15:0,63,724 0/0:20,0:21:48.13:0,48,594 0/0:20,0:21:51.13:0,51,615 0/0:16,0:16:36.10:0,36,447 0/0:22,0:23:57.17:0,57,716 0/0:14,0:15:39.12:0,39,496 0/0:22,1:23:60.17:0,60,725 -chr1 1226221 . A G 12961.74 . AC=36;AF=0.3000;AN=120;BaseQRankSum=0.407;DP=1473;Dels=0.00;FS=8.750;HRun=2;HaplotypeScore=1.9078;InbreedingCoeff=0.3380;MQ=58.10;MQ0=0;MQRankSum=0.672;QD=20.00;ReadPosRankSum=-0.137;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/1:5,1:6:15.38:15,0,158 0/0:5,0:5:9.03:0,9,110 0/0:8,0:8:18.06:0,18,225 0/0:1,0:1:3.01:0,3,31 0/1:5,8:13:99:257,0,122 0/1:8,7:15:99:238,0,263 0/0:17,0:17:39.12:0,39,483 0/0:8,1:9:21.06:0,21,268 0/0:23,1:24:66.21:0,66,849 0/0:26,1:27:69.21:0,69,882 1/1:0,10:10:30.10:405,30,0 0/0:12,0:12:33.10:0,33,410 0/0:18,0:18:48.15:0,48,620 0/0:18,0:18:45.14:0,45,581 0/1:24,9:33:99:229,0,793 0/1:10,10:20:99:233,0,302 0/0:23,0:23:63.20:0,63,832 0/0:31,0:31:87.28:0,87,1138 0/0:28,0:28:78.25:0,78,1022 0/0:23,0:23:63.20:0,63,825 0/0:23,0:23:66.20:0,66,838 0/1:29,15:44:99:287,0,899 0/0:28,0:28:66.22:0,66,890 0/1:15,10:25:99:247,0,460 0/0:27,0:27:66.21:0,66,876 0/0:22,0:22:48.16:0,48,640 1/1:0,20:20:51.16:670,51,0 0/0:18,0:18:48.15:0,48,590 0/0:30,0:30:81.26:0,81,1071 0/0:30,0:30:75.24:0,75,991 0/0:38,1:39:99:0,99,1298 0/1:17,11:28:99:314,0,451 0/0:30,0:30:78.24:0,78,1032 0/1:13,15:28:99:384,0,437 0/1:11,11:23:99:294,0,307 0/1:13,8:21:99:210,0,423 0/1:15,12:27:99:357,0,448 1/1:0,26:26:78.25:1015,78,0 0/0:30,0:30:87.27:0,87,1126 0/0:44,0:44:99:0,108,1403 0/0:25,1:26:63.19:0,63,800 0/0:26,0:26:66.21:0,66,869 0/0:32,0:32:87.28:0,87,1126 0/0:16,1:17:0.37:0,0,464 1/1:1,30:31:47.82:970,48,0 0/0:17,1:18:42.14:0,42,555 0/0:55,0:55:99:0,138,1788 0/1:8,8:16:99:273,0,251 0/0:38,0:38:99:0,102,1337 1/1:0,46:46:99:1449,114,0 0/1:25,18:43:99:462,0,768 0/0:29,0:29:75.24:0,75,980 1/1:0,31:31:84.25:1045,84,0 1/1:0,32:32:75.22:924,75,0 1/1:0,24:24:54.17:717,54,0 1/1:0,19:20:51.16:668,51,0 0/0:18,0:18:45.12:0,45,584 0/1:15,8:24:99:199,0,447 0/1:7,10:17:99:301,0,228 1/1:1,24:25:29.21:801,29,0 -chr1 1226231 . G A 1060.58 . AC=4;AF=0.0333;AN=120;BaseQRankSum=0.134;DP=1522;Dels=0.00;FS=3.076;HRun=0;HaplotypeScore=2.2801;InbreedingCoeff=-0.0375;MQ=58.05;MQ0=0;MQRankSum=1.141;QD=13.26;ReadPosRankSum=0.602;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:15.03:0,15,164 0/0:5,0:5:12.04:0,12,144 0/0:8,0:8:15.04:0,15,185 0/0:2,0:2:6.02:0,6,68 0/0:15,0:15:33.10:0,33,423 0/0:15,0:15:42.14:0,42,560 0/0:15,0:15:33.10:0,33,408 0/0:8,0:8:18.06:0,18,237 0/0:21,0:21:60.19:0,60,789 0/0:21,0:21:54.16:0,54,667 0/1:4,5:9:91.51:177,0,92 0/0:11,0:11:33.10:0,33,412 0/0:16,0:17:48.15:0,48,613 0/0:18,0:18:45.13:0,45,577 0/0:33,0:33:87.27:0,87,1142 0/0:20,0:20:45.14:0,45,595 0/0:25,0:25:69.21:0,69,898 0/0:27,0:27:75.24:0,75,990 0/0:29,0:29:75.25:0,75,1015 0/0:25,0:25:60.19:0,60,773 0/0:26,0:26:72.22:0,72,933 0/0:43,0:43:99:0,111,1477 0/0:30,0:30:75.24:0,75,1006 0/0:25,0:25:66.20:0,66,852 0/0:29,0:29:75.23:0,75,984 0/0:23,0:23:57.18:0,57,740 0/0:22,0:22:57.18:0,57,750 0/0:21,0:21:57.16:0,57,697 0/0:33,0:33:84.26:0,84,1101 0/0:33,0:33:81.25:0,81,1054 0/0:37,0:37:93.28:0,93,1208 0/0:30,0:30:72.18:0,72,932 0/0:30,0:30:69.22:0,69,935 0/1:12,16:28:99:390,0,371 0/0:24,0:24:57.18:0,57,755 0/1:14,9:23:99:283,0,445 0/0:30,0:30:81.24:0,81,1051 0/0:26,0:26:75.24:0,75,996 0/0:29,0:29:81.26:0,81,1076 0/0:51,0:51:99:0,105,1386 0/0:26,0:26:69.21:0,69,867 0/0:25,0:25:63.20:0,63,840 0/0:33,0:33:90.28:0,90,1166 0/0:15,0:17:36.09:0,36,451 0/0:33,0:33:84.25:0,84,1071 0/0:21,0:21:45.15:0,45,613 0/0:57,0:57:99:0,135,1721 0/1:11,9:20:99:303,0,299 0/0:41,0:41:99:0,99,1313 0/0:49,0:49:99:0,123,1555 0/0:47,0:47:99:0,120,1540 0/0:33,0:33:90.28:0,90,1147 0/0:34,0:34:81.24:0,81,1022 0/0:32,0:32:72.21:0,72,879 0/0:28,0:28:66.21:0,66,853 0/0:22,0:22:54.15:0,54,681 0/0:18,0:18:42.13:0,42,554 0/0:22,0:22:66.17:0,66,805 0/0:16,0:16:45.15:0,45,600 0/0:26,0:26:66.19:0,66,845 -chr1 1226233 . G A 432.75 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.014;DP=1544;Dels=0.00;FS=11.621;HRun=0;HaplotypeScore=1.7754;InbreedingCoeff=-0.0115;MQ=58.14;MQ0=0;MQRankSum=1.437;QD=9.21;ReadPosRankSum=-0.335;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.02:0,12,138 0/0:5,0:5:12.03:0,12,134 0/0:8,0:8:15.05:0,15,195 0/0:2,0:2:6.01:0,6,66 0/0:16,0:16:33.10:0,33,411 0/0:15,0:15:42.14:0,42,558 0/0:16,0:16:33.09:0,33,399 0/0:8,0:8:18.04:0,18,209 0/0:21,0:21:60.16:0,60,739 0/0:23,0:23:60.16:0,60,729 0/0:10,0:10:27.08:0,27,343 0/0:11,0:11:33.10:0,33,408 0/0:15,0:15:45.14:0,45,570 0/0:17,0:17:42.13:0,42,546 0/0:34,0:34:90.29:0,90,1185 0/0:20,0:20:45.14:0,45,595 0/0:28,0:28:72.22:0,72,954 0/0:25,0:25:72.23:0,72,942 0/0:28,0:28:72.24:0,72,964 0/0:25,0:25:63.18:0,63,802 0/0:26,0:26:72.22:0,72,929 0/0:43,0:44:99:0,111,1459 0/0:30,0:30:75.24:0,75,1012 0/0:26,0:26:69.22:0,69,897 0/0:29,0:29:75.23:0,75,971 0/0:23,0:23:57.17:0,57,726 0/0:24,0:24:63.19:0,63,811 0/0:22,0:22:54.16:0,54,666 0/0:33,0:33:84.27:0,84,1107 0/0:34,0:34:84.26:0,84,1097 0/0:37,0:37:96.27:0,96,1224 0/0:29,0:30:72.21:0,72,920 0/0:31,0:31:72.22:0,72,948 0/0:29,0:29:66.20:0,66,860 0/0:22,0:22:51.16:0,51,685 0/0:22,0:23:63.20:0,63,816 0/0:33,0:33:87.28:0,87,1144 0/0:27,0:27:75.24:0,75,989 0/0:31,0:31:81.26:0,81,1073 0/0:54,0:54:99:0,108,1389 0/0:27,0:27:66.20:0,66,818 0/0:25,0:25:63.20:0,63,831 0/0:33,0:33:93.29:0,93,1208 0/0:17,0:17:42.12:0,42,526 0/0:32,0:32:84.25:0,84,1078 0/0:22,0:22:51.16:0,51,682 0/0:60,0:60:99:0,141,1830 0/0:20,0:20:54.15:0,54,699 0/0:41,0:41:99:0,105,1376 0/1:23,24:47:99:480,0,700 0/0:47,0:47:99:0,120,1540 0/0:33,0:33:90.28:0,90,1140 0/0:35,0:35:90.24:0,90,1098 0/0:33,0:33:75.20:0,75,914 0/0:27,0:27:66.21:0,66,856 0/0:21,0:21:54.17:0,54,691 0/0:20,0:20:51.16:0,51,665 0/0:22,0:22:66.20:0,66,829 0/0:17,0:17:48.15:0,48,626 0/0:26,0:26:63.20:0,63,826 -chr1 1226246 . C T 658.46 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.957;DP=1671;Dels=0.00;FS=1.750;HRun=0;HaplotypeScore=1.4315;InbreedingCoeff=-0.0192;MQ=58.19;MQ0=0;MQRankSum=1.240;QD=9.98;ReadPosRankSum=-0.155;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,75 0/0:7,0:7:9.02:0,9,96 0/0:8,0:8:15.05:0,15,189 0/0:5,0:5:9.02:0,9,105 0/0:15,0:15:42.12:0,42,515 0/0:10,0:10:30.10:0,30,400 0/0:17,0:17:45.14:0,45,580 0/0:7,0:7:18.06:0,18,229 0/0:20,0:20:60.18:0,60,753 0/0:21,0:21:54.17:0,54,690 0/0:10,0:10:30.10:0,30,393 0/0:10,0:10:27.09:0,27,348 0/0:15,0:15:45.14:0,45,574 0/1:14,1:15:5.67:6,0,377 0/0:37,0:37:99:0,102,1304 0/0:24,0:24:63.18:0,63,783 0/0:28,0:28:72.21:0,72,931 0/0:27,0:27:78.24:0,78,998 0/0:27,0:27:69.22:0,69,894 0/0:23,0:25:54.16:0,54,699 0/0:27,1:28:69.17:0,69,860 0/0:49,0:49:99:0,114,1486 0/0:29,0:29:69.22:0,69,911 0/0:26,0:26:63.20:0,63,816 0/0:32,0:32:75.19:0,75,939 0/0:28,0:28:72.20:0,72,878 0/0:25,0:25:66.19:0,66,854 0/0:21,0:22:48.14:0,48,602 0/0:34,0:34:81.25:0,81,1046 0/0:30,0:30:75.21:0,75,940 0/0:36,0:36:90.24:0,90,1115 0/0:31,0:31:75.19:0,75,911 0/0:31,0:31:75.24:0,75,980 0/0:28,0:28:66.20:0,66,842 0/0:22,0:23:54.17:0,54,710 0/0:24,0:24:60.19:0,60,782 0/0:35,1:36:87.22:0,87,1106 0/0:34,0:34:90.28:0,90,1166 0/0:36,0:36:96.28:0,96,1204 0/0:64,0:65:99:0,150,1904 0/0:30,0:30:81.22:0,81,973 0/0:28,0:28:72.22:0,72,922 0/0:41,0:41:99:0,108,1375 0/0:20,0:20:42.12:0,42,524 0/0:36,0:36:87.25:0,87,1124 0/0:25,0:25:63.20:0,63,827 0/0:69,0:69:99:0,159,1997 0/0:19,0:19:51.13:0,51,623 0/0:45,0:45:99:0,105,1359 0/1:27,24:51:99:706,0,646 0/0:61,0:62:99:0,141,1776 0/0:39,0:39:99:0,108,1311 0/0:41,0:42:99:0,108,1351 0/0:38,0:38:75.22:0,75,926 0/0:31,0:31:81.19:0,81,997 0/0:23,0:23:51.16:0,51,651 0/0:22,0:22:54.16:0,54,688 0/0:23,0:23:69.21:0,69,846 0/0:20,0:20:54.15:0,54,664 0/0:30,0:30:72.22:0,72,918 -chr1 1226267 . G A 198.26 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.326;DP=1848;Dels=0.00;FS=1.356;HRun=0;HaplotypeScore=0.8439;InbreedingCoeff=-0.0108;MQ=58.43;MQ0=0;MQRankSum=-0.958;QD=8.62;ReadPosRankSum=1.398;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|12),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|11),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|17),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|12),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|15),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|14);CSQ=splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,splice_region_variant&intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,splice_region_variant&intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:2,0:2:6.02:0,6,81 0/0:4,0:4:12.03:0,12,137 0/0:8,0:8:24.08:0,24,300 0/0:8,0:8:21.06:0,21,252 0/0:13,0:13:33.11:0,33,439 0/0:12,0:12:36.10:0,36,467 0/0:19,0:19:57.17:0,57,744 0/0:8,0:8:24.08:0,24,330 0/0:23,0:23:69.22:0,69,913 0/0:28,0:28:81.26:0,81,1067 0/0:11,0:11:30.10:0,30,401 0/0:9,0:9:27.09:0,27,366 0/0:10,0:10:30.10:0,30,391 0/0:21,0:21:48.15:0,48,643 0/0:47,0:47:99:0,123,1628 0/0:27,0:27:63.20:0,63,829 0/0:29,0:29:75.23:0,75,962 0/0:30,0:30:78.25:0,78,1051 0/0:31,0:31:72.23:0,72,953 0/0:25,0:26:66.18:0,66,848 0/0:38,0:38:96.29:0,96,1247 0/0:50,0:50:99:0,126,1630 0/0:28,0:29:78.25:0,78,1025 0/0:23,0:23:60.18:0,60,773 0/0:31,0:31:72.23:0,72,958 0/0:35,0:35:75.24:0,75,987 0/0:30,0:30:84.26:0,84,1090 0/0:22,0:22:57.17:0,57,739 0/0:37,0:37:96.25:0,96,1209 0/0:35,0:35:90.29:0,90,1187 0/0:39,0:39:93.30:0,93,1230 0/0:32,0:32:75.24:0,75,976 0/0:41,0:41:87.27:0,87,1159 0/0:30,0:30:72.21:0,72,917 0/0:25,0:25:63.21:0,63,844 0/0:21,0:21:57.17:0,57,725 0/0:35,0:35:87.28:0,87,1144 0/0:39,0:39:99:0,105,1402 0/0:39,0:39:99:0,102,1297 0/0:70,0:70:99:0,175,2231 0/0:40,0:40:99:0,102,1304 0/0:28,0:28:75.24:0,75,992 0/0:37,0:37:93.30:0,93,1220 0/0:27,0:27:69.22:0,69,932 0/0:39,0:39:96.30:0,96,1242 0/0:31,0:31:90.28:0,90,1169 0/0:88,0:89:99:0,208,2688 0/1:13,10:23:99:246,0,391 0/0:55,0:55:99:0,132,1695 0/0:53,0:53:99:0,144,1840 0/0:59,0:59:99:0,153,1997 0/0:36,0:37:87.26:0,87,1127 0/0:40,0:40:99:0,108,1377 0/0:39,0:39:84.25:0,84,1063 0/0:35,0:36:90.26:0,90,1172 0/0:31,0:31:66.21:0,66,880 0/0:26,0:26:69.22:0,69,893 0/0:32,0:32:78.24:0,78,990 0/0:26,0:26:69.22:0,69,895 0/0:33,0:33:87.24:0,87,1104 -chr1 1226292 . G A 2311.15 . AC=4;AF=0.0333;AN=120;BaseQRankSum=-0.197;DP=2007;Dels=0.00;FS=0.860;HRun=0;HaplotypeScore=1.1337;InbreedingCoeff=-0.0381;MQ=58.08;MQ0=0;MQRankSum=0.237;QD=11.79;ReadPosRankSum=1.765;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T481|638|SCNN1D|protein_coding|CODING|ENST00000338555|),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T481|638|SCNN1D|protein_coding|CODING|ENST00000400928|),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T512|669|SCNN1D|protein_coding|CODING|ENST00000379110|),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T547|704|SCNN1D|protein_coding|CODING|ENST00000325425|),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T645|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|15);CSQ=synonymous_variant|acG/acA|T|ENSG00000162572|SCNN1D|ENST00000338555|13/15|||481/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|15/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,synonymous_variant|acG/acA|T|ENSG00000162572|SCNN1D|ENST00000325425|13/15|||547/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,synonymous_variant|acG/acA|T|ENSG00000162572|SCNN1D|ENST00000379099|7/7|||298/308|protein_coding|1,synonymous_variant|acG/acA|T|ENSG00000162572|SCNN1D|ENST00000400928|12/14|||481/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,synonymous_variant|acG/acA|T|ENSG00000162572|SCNN1D|ENST00000379116|16/18|||645/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12.02:0,12,136 0/0:2,0:2:6.02:0,6,75 0/0:4,0:4:12.04:0,12,155 0/0:9,0:9:18.05:0,18,218 0/0:13,0:13:30.10:0,30,394 0/0:12,0:12:21.07:0,21,277 0/0:18,0:18:54.16:0,54,674 0/0:9,0:9:27.08:0,27,344 0/0:28,0:28:75.24:0,75,972 0/0:22,0:22:63.18:0,63,809 0/0:11,0:11:30.10:0,30,394 0/0:9,0:9:21.07:0,21,274 0/0:9,0:10:21.07:0,21,268 0/0:23,1:24:13.51:0,14,610 0/0:47,0:47:99:0,117,1501 0/0:33,0:33:75.24:0,75,988 0/0:26,0:26:66.18:0,66,814 0/0:35,0:35:90.28:0,90,1169 0/0:37,0:37:87.28:0,87,1128 0/0:33,0:34:75.24:0,75,977 0/0:42,0:44:93.28:0,93,1192 0/0:42,0:42:99:0,102,1344 0/0:31,0:31:75.24:0,75,982 0/0:27,0:27:66.20:0,66,836 0/0:25,0:26:63.16:0,63,780 0/0:37,0:39:87.22:0,87,1051 0/0:30,0:30:81.25:0,81,1030 0/0:18,0:18:45.12:0,45,577 0/0:44,0:44:99:0,99,1262 0/0:42,0:42:99:0,102,1265 0/0:37,0:37:99:0,102,1252 0/1:13,20:33:99:492,0,240 0/0:47,0:47:99:0,108,1372 0/0:28,0:28:72.22:0,72,894 0/0:24,0:24:63.19:0,63,825 0/0:23,0:23:54.17:0,54,705 0/0:39,0:39:90.27:0,90,1138 0/0:47,0:47:99:0,108,1418 0/0:36,0:36:96.29:0,96,1202 0/0:82,0:82:99:0,196,2392 0/0:40,0:40:99:0,99,1266 0/0:27,0:27:60.19:0,60,786 0/0:45,0:45:99:0,111,1386 0/0:23,0:24:57.17:0,57,738 0/1:24,24:48:99:534,0,554 0/0:40,0:41:99:0,105,1319 0/0:88,0:89:99:0,205,2555 0/0:28,0:28:63.19:0,63,799 0/0:67,0:68:99:0,141,1800 0/0:62,0:62:99:0,156,1906 0/1:38,29:67:99:816,0,976 0/0:45,1:46:66.70:0,67,1193 0/1:27,21:48:99:562,0,721 0/0:40,0:40:93.26:0,93,1146 0/0:41,0:41:99:0,99,1253 0/0:29,0:29:69.20:0,69,868 0/0:33,1:34:87.22:0,87,1013 0/0:32,0:32:69.21:0,69,863 0/0:31,0:31:75.21:0,75,944 0/0:40,0:40:99:0,105,1331 -chr1 1226348 . C G 14565.59 . AC=27;AF=0.2250;AN=120;BaseQRankSum=-4.148;DP=2185;Dels=0.00;FS=12.103;HRun=0;HaplotypeScore=3.8823;InbreedingCoeff=0.3031;MQ=57.72;MQ0=0;MQRankSum=-0.548;QD=19.76;ReadPosRankSum=2.686;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|13),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|12),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|18),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|13),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|16),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|15);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,1:6:9.03:0,9,107 0/0:2,0:2:6.01:0,6,66 0/1:1,1:2:30.11:30,0,33 0/1:1,3:4:27.10:67,0,27 0/0:11,0:11:24.08:0,24,326 0/0:14,0:14:30.09:0,30,372 0/0:21,0:21:57.19:0,57,753 0/0:17,0:17:48.16:0,48,645 0/0:30,0:30:81.24:0,81,1056 0/0:29,0:29:78.24:0,78,1011 1/1:0,16:16:42.12:529,42,0 0/1:1,5:6:21.26:171,0,21 0/0:22,0:22:54.18:0,54,712 0/0:32,0:32:72.22:0,72,925 0/1:27,11:38:99:276,0,771 0/0:30,0:30:63.17:0,63,813 0/0:28,0:28:66.21:0,66,862 0/0:44,0:44:96.31:0,96,1304 0/0:45,0:45:99:0,114,1447 0/1:16,25:41:99:665,0,394 0/0:41,0:41:96.28:0,96,1228 0/1:15,15:30:99:425,0,404 0/0:37,0:37:96.30:0,96,1263 0/0:30,0:30:75.24:0,75,989 0/0:30,0:30:69.22:0,69,918 0/0:35,1:36:78.24:0,78,996 0/1:17,14:31:99:358,0,446 0/0:18,0:18:39.13:0,39,511 0/0:48,0:49:99:0,99,1326 0/0:39,0:39:87.28:0,87,1138 0/0:45,0:45:99:0,117,1528 0/1:13,17:30:99:531,0,361 0/0:50,0:50:99:0,117,1530 1/1:0,28:31:75.21:929,75,0 0/0:21,0:21:48.14:0,48,606 0/1:15,13:28:99:367,0,368 0/0:43,0:46:99:0,120,1552 1/1:1,50:51:99:1651,126,0 0/0:33,0:33:78.24:0,78,977 0/0:93,0:93:99:0,220,2837 0/0:41,0:41:99:0,105,1323 0/0:37,0:37:96.29:0,96,1203 0/0:34,0:34:87.25:0,87,1131 0/0:30,1:31:32.99:0,33,843 1/1:0,41:41:90.27:1180,90,0 0/0:46,0:46:99:0,99,1277 0/0:93,0:93:99:0,211,2700 0/1:7,19:27:99:499,0,208 0/0:73,0:73:99:0,166,2110 1/1:1,73:76:99:2306,178,0 0/1:38,36:74:99:760,0,1045 0/0:53,0:53:99:0,129,1637 1/1:0,54:54:99:1573,123,0 0/1:24,20:44:99:399,0,688 0/0:52,0:52:99:0,126,1640 0/1:17,16:33:99:399,0,371 0/0:38,0:38:96.29:0,96,1198 0/0:50,0:50:99:0,126,1581 0/1:19,17:36:99:375,0,566 0/1:3,41:44:1.12:1076,0,1 -chr1 1226350 . C T 913.84 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.958;DP=2174;Dels=0.00;FS=1.375;HRun=0;HaplotypeScore=3.4324;InbreedingCoeff=-0.0112;MQ=57.70;MQ0=0;MQRankSum=0.687;QD=12.52;ReadPosRankSum=2.553;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|13),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|12),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|18),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|13),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|16),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|15);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:12.03:0,12,139 0/0:2,0:2:6.02:0,6,71 0/0:5,0:5:15.05:0,15,189 0/0:5,0:5:15.03:0,15,166 0/0:11,0:11:24.08:0,24,321 0/0:14,0:14:30.10:0,30,384 0/0:20,0:20:57.18:0,57,742 0/0:17,0:17:48.16:0,48,644 0/0:35,0:35:96.31:0,96,1283 0/0:34,0:34:93.30:0,93,1220 0/0:16,0:16:48.14:0,48,621 0/0:7,0:7:21.07:0,21,275 0/0:22,0:22:57.16:0,57,721 0/0:33,0:33:72.23:0,72,944 0/0:38,0:38:96.31:0,96,1243 0/0:29,0:29:63.20:0,63,827 0/0:27,0:27:66.21:0,66,864 0/0:42,1:43:96.30:0,96,1289 0/0:44,0:44:99:0,114,1470 0/0:43,0:43:99:0,105,1365 0/0:39,0:39:99:0,99,1286 0/0:30,0:30:72.23:0,72,944 0/0:38,0:38:96.30:0,96,1265 0/0:32,0:32:81.22:0,81,1039 0/0:29,0:29:66.21:0,66,894 0/0:34,0:34:75.23:0,75,972 0/0:31,0:31:72.22:0,72,944 0/0:19,0:19:51.14:0,51,637 0/0:47,0:47:99:0,99,1328 0/0:39,0:39:84.27:0,84,1104 0/0:44,0:44:99:0,114,1481 0/0:29,0:29:78.25:0,78,1026 0/0:48,0:48:99:0,111,1485 0/0:29,0:30:78.22:0,78,976 0/0:22,0:22:51.16:0,51,661 0/0:30,0:30:69.22:0,69,906 0/0:48,0:48:99:0,129,1680 0/0:50,0:50:99:0,138,1834 0/0:33,0:33:84.26:0,84,1059 0/0:92,0:92:99:0,217,2825 0/0:39,0:39:99:0,99,1260 0/0:37,0:37:96.30:0,96,1219 0/0:34,0:34:87.28:0,87,1140 0/0:28,0:28:60.19:0,60,766 0/0:42,0:42:96.29:0,96,1241 0/0:45,0:45:99:0,105,1358 0/0:90,0:90:99:0,202,2634 0/0:26,0:26:63.20:0,63,828 0/0:73,0:73:99:0,169,2137 0/1:38,35:73:99:962,0,931 0/0:75,0:75:99:0,175,2234 0/0:50,0:50:99:0,123,1555 0/0:53,0:53:99:0,129,1625 0/0:46,0:46:99:0,105,1335 0/0:51,0:51:99:0,120,1594 0/0:33,0:34:81.25:0,81,1028 0/0:36,0:36:90.28:0,90,1152 0/0:48,0:48:99:0,117,1513 0/0:36,0:36:87.26:0,87,1121 0/0:43,0:43:99:0,105,1321 -chr1 1226418 . C T 612.71 . AC=1;AF=0.0083;AN=120;BaseQRankSum=0.522;DP=1764;Dels=0.00;FS=13.559;HRun=0;HaplotypeScore=1.3627;InbreedingCoeff=-0.0097;MQ=57.73;MQ0=0;MQRankSum=0.737;QD=13.93;ReadPosRankSum=-1.089;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|13),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|12),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|18),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|13),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|16),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|15);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:18.04:0,18,207 0/0:5,0:5:15.05:0,15,190 0/0:10,0:10:30.10:0,30,387 0/0:3,0:3:9.03:0,9,120 0/0:24,0:24:63.19:0,63,780 0/0:18,0:18:54.17:0,54,699 0/0:36,0:36:99:0,102,1325 0/0:15,0:15:45.11:0,45,543 0/0:38,0:38:99:0,111,1432 0/0:29,1:30:44.26:0,44,1021 0/0:20,0:20:60.18:0,60,786 0/0:17,0:17:45.15:0,45,596 0/0:24,0:25:66.17:0,66,807 0/0:41,0:41:99:0,105,1355 0/0:43,0:44:99:0,120,1562 0/0:19,0:19:51.16:0,51,659 0/0:30,0:30:75.24:0,75,1003 0/0:33,0:33:84.26:0,84,1101 0/0:30,0:30:75.22:0,75,955 0/0:35,0:35:87.27:0,87,1120 0/0:29,0:29:78.23:0,78,992 0/0:31,0:31:78.25:0,78,1048 0/0:30,0:30:75.24:0,75,988 0/0:29,0:31:75.24:0,75,978 0/0:32,0:32:75.20:0,75,967 0/0:33,0:33:84.24:0,84,1068 0/0:39,0:39:99:0,99,1289 0/0:26,0:26:69.22:0,69,910 0/0:36,0:36:96.31:0,96,1251 0/0:28,0:28:75.23:0,75,992 0/1:21,23:44:99:660,0,583 0/0:30,0:30:69.22:0,69,924 0/0:36,0:36:96.28:0,96,1187 0/0:40,0:40:99:0,99,1226 0/0:28,0:28:69.21:0,69,906 0/0:27,0:27:75.23:0,75,987 0/0:38,0:38:99:0,99,1290 0/0:46,0:46:99:0,114,1467 0/0:27,0:27:72.21:0,72,904 0/0:60,0:60:99:0,144,1846 0/0:35,0:35:93.29:0,93,1182 0/0:26,0:27:66.20:0,66,839 0/0:19,0:19:42.14:0,42,557 0/0:26,0:26:75.24:0,75,966 0/0:26,0:26:60.18:0,60,743 0/0:23,0:23:57.17:0,57,708 0/0:48,0:48:99:0,117,1490 0/0:15,0:15:39.12:0,39,495 0/0:44,0:44:99:0,99,1226 0/0:49,0:49:99:0,123,1539 0/0:50,0:50:99:0,117,1443 0/0:34,0:34:84.26:0,84,1051 0/0:40,0:40:99:0,102,1307 0/0:19,0:19:36.09:0,36,430 0/0:29,0:29:72.22:0,72,908 0/0:23,0:23:54.14:0,54,643 0/0:17,0:18:48.13:0,48,600 0/0:27,0:27:63.19:0,63,798 0/0:20,0:20:51.15:0,51,662 0/0:21,0:21:54.17:0,54,685 -chr1 1226419 . G A 122.55 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-2.320;DP=1752;Dels=0.00;FS=6.374;HRun=0;HaplotypeScore=1.2212;InbreedingCoeff=-0.0099;MQ=57.75;MQ0=0;MQRankSum=0.393;QD=5.33;ReadPosRankSum=0.165;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|13),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|12),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|18),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|13),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|16),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|15);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:15.03:0,15,172 0/0:5,0:5:15.04:0,15,178 0/0:11,0:11:33.10:0,33,422 0/0:3,0:3:9.03:0,9,121 0/0:22,0:22:57.18:0,57,753 0/0:20,0:20:60.19:0,60,774 0/0:35,0:35:99:0,99,1279 0/0:16,0:16:48.10:0,48,584 0/0:34,0:34:99:0,99,1262 0/0:30,0:30:84.27:0,84,1121 0/0:21,0:21:63.20:0,63,823 0/0:18,0:18:54.17:0,54,701 0/0:22,0:24:63.18:0,63,810 0/0:41,0:41:99:0,99,1298 0/0:44,0:44:99:0,117,1531 0/0:19,0:19:48.13:0,48,622 0/0:30,0:30:72.23:0,72,970 0/0:33,0:33:84.27:0,84,1102 0/0:31,0:31:69.22:0,69,893 0/0:34,0:34:87.26:0,87,1124 0/0:30,0:30:81.25:0,81,1040 0/0:32,0:32:78.24:0,78,1035 0/0:30,0:30:81.24:0,81,1038 0/0:33,0:33:75.22:0,75,974 0/0:31,0:31:78.24:0,78,1005 0/0:34,0:35:81.25:0,81,1043 0/0:41,0:41:99:0,105,1359 0/0:26,0:26:66.21:0,66,869 0/0:34,0:35:90.28:0,90,1154 0/0:28,0:28:75.22:0,75,974 0/0:45,0:46:99:0,114,1493 0/0:29,0:29:72.21:0,72,952 0/0:37,0:37:96.28:0,96,1198 0/0:40,0:41:99:0,99,1240 0/0:28,0:28:69.22:0,69,912 0/0:30,0:30:81.27:0,81,1085 0/0:38,0:38:99:0,105,1350 0/0:47,0:47:99:0,114,1463 0/0:26,0:26:63.20:0,63,815 0/0:57,0:60:99:0,138,1735 0/0:32,0:32:84.26:0,84,1066 0/0:23,0:23:63.18:0,63,780 0/0:18,0:19:39.13:0,39,517 0/0:26,0:26:75.24:0,75,958 0/0:26,0:26:57.15:0,57,715 0/0:22,0:23:60.17:0,60,721 0/0:47,0:48:99:0,108,1384 0/0:15,0:15:36.12:0,36,475 0/0:43,0:43:93.25:0,93,1155 0/0:46,0:46:99:0,114,1409 0/0:50,0:50:99:0,117,1416 0/0:29,0:30:69.21:0,69,872 0/0:36,0:38:93.28:0,93,1185 0/0:18,0:18:39.09:0,39,449 0/0:24,0:26:63.17:0,63,793 0/1:13,8:23:99:170,0,309 0/0:18,0:18:48.15:0,48,605 0/0:27,0:27:63.19:0,63,782 0/0:19,0:19:45.14:0,45,598 0/0:21,0:21:54.17:0,54,689 -chr1 1226423 . T C 2109.1 . AC=4;AF=0.0333;AN=120;BaseQRankSum=1.172;DP=1776;Dels=0.00;FS=0.924;HRun=3;HaplotypeScore=1.1033;InbreedingCoeff=0.4687;MQ=57.78;MQ0=0;MQRankSum=3.304;QD=24.24;ReadPosRankSum=0.918;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|13),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|12),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|18),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|13),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|16),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|15);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:6,0:6:15.02:0,15,169 0/0:6,0:6:18.05:0,18,222 0/0:12,0:12:36.09:0,36,435 0/0:5,0:5:12.04:0,12,157 0/0:18,1:19:51.16:0,51,653 0/0:20,0:20:57.18:0,57,747 0/0:35,0:35:99:0,99,1288 0/0:17,0:17:48.14:0,48,615 0/0:38,0:38:99:0,105,1382 0/0:32,0:32:93.29:0,93,1209 0/1:15,7:22:99:221,0,524 0/0:16,0:16:48.16:0,48,637 0/0:23,0:23:63.19:0,63,827 0/0:40,2:42:61.09:0,61,1245 0/0:45,0:45:99:0,120,1564 0/0:21,0:21:51.15:0,51,661 0/0:32,1:33:81.25:0,81,1071 0/0:36,0:36:90.29:0,90,1188 0/0:34,1:35:87.25:0,87,1116 0/0:34,0:34:84.27:0,84,1099 0/0:30,0:30:81.24:0,81,1048 0/0:35,0:35:93.30:0,93,1231 0/0:32,0:32:90.24:0,90,1120 0/0:35,0:35:87.27:0,87,1111 0/0:28,2:30:78.22:0,78,977 0/0:36,0:36:96.29:0,96,1211 0/0:42,0:42:99:0,108,1391 0/0:27,0:27:72.22:0,72,930 0/0:34,1:35:57.71:0,58,1144 0/0:33,0:33:90.27:0,90,1151 0/0:44,1:45:99:0,117,1528 0/0:26,2:28:30.47:0,30,908 0/0:39,2:41:99:0,108,1368 0/0:41,1:42:99:0,102,1288 0/0:30,0:30:75.23:0,75,963 0/0:30,0:30:90.28:0,90,1191 0/0:39,0:39:99:0,99,1300 1/1:0,46:46:99:1499,114,0 0/0:25,0:26:69.17:0,69,848 0/0:59,0:60:99:0,141,1791 0/0:31,0:31:75.22:0,75,938 0/0:23,0:23:63.20:0,63,811 0/0:19,1:20:48.15:0,48,620 0/0:26,0:27:69.21:0,69,882 0/0:22,2:25:27.92:0,28,716 0/0:21,1:23:57.16:0,57,701 0/0:47,0:47:99:0,120,1508 0/0:15,0:15:36.12:0,36,483 0/0:40,1:41:84.23:0,84,1043 0/0:46,0:47:99:0,126,1551 0/0:47,1:48:99:0,114,1447 0/0:28,0:28:72.22:0,72,890 0/0:34,1:36:84.27:0,84,1100 0/0:16,0:16:39.12:0,39,486 0/0:24,1:25:63.18:0,63,792 0/0:22,0:22:54.17:0,54,686 0/0:19,0:19:51.16:0,51,655 0/0:27,1:28:66.20:0,66,836 0/0:17,0:17:42.13:0,42,539 0/1:3,16:19:38.85:488,0,39 -chr1 1226512 . G A 620.19 . AC=1;AF=0.0083;AN=120;BaseQRankSum=1.007;DP=1562;Dels=0.00;FS=9.380;HRun=0;HaplotypeScore=0.9448;InbreedingCoeff=-0.0116;MQ=58.77;MQ0=0;MQRankSum=0.069;QD=24.81;ReadPosRankSum=-2.040;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V518M|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V518M|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V549M|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V584M|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V682M|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|16);CSQ=missense_variant|Gtg/Atg|V/M|ENSG00000162572|SCNN1D|ENST00000338555|14/15|benign(0.109)|tolerated(0.11)|518/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|16/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|Gtg/Atg|V/M|ENSG00000162572|SCNN1D|ENST00000325425|14/15|benign(0.036)|tolerated(0.12)|584/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,missense_variant|Gtg/Atg|V/M|ENSG00000162572|SCNN1D|ENST00000400928|13/14|benign(0.109)|tolerated(0.11)|518/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,missense_variant|Gtg/Atg|V/M|ENSG00000162572|SCNN1D|ENST00000379116|17/18|benign(0.036)|tolerated(0.1)|682/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:12.02:0,12,138 0/0:4,0:4:9.03:0,9,115 0/0:8,0:8:24.08:0,24,309 0/0:6,0:6:15.05:0,15,189 0/0:19,0:19:54.17:0,54,689 0/1:6,19:25:99:668,0,156 0/0:32,0:32:96.27:0,96,1237 0/0:20,0:20:57.19:0,57,755 0/0:63,0:63:99:0,187,2453 0/0:35,0:35:99:0,99,1308 0/0:20,0:20:60.19:0,60,782 0/0:12,0:12:36.12:0,36,471 0/0:27,0:27:81.26:0,81,1048 0/0:37,0:37:90.25:0,90,1153 0/0:40,0:40:96.31:0,96,1282 0/0:25,0:25:63.19:0,63,799 0/0:45,2:47:28.46:0,28,1321 0/0:36,0:36:90.27:0,90,1191 0/0:43,0:43:99:0,108,1421 0/0:41,0:41:99:0,105,1378 0/0:39,0:39:87.25:0,87,1161 0/0:44,0:44:99:0,111,1465 0/0:50,0:51:99:0,114,1533 0/0:47,0:47:99:0,105,1404 0/0:32,0:32:78.25:0,78,1027 0/0:45,0:45:99:0,102,1391 0/0:33,0:35:78.22:0,78,1018 0/0:32,0:32:81.24:0,81,1043 0/0:50,0:50:99:0,117,1559 0/0:41,1:42:77.63:0,78,1287 0/0:51,0:52:99:0,123,1623 0/0:32,0:32:84.27:0,84,1098 0/0:39,0:39:96.30:0,96,1276 0/0:51,0:51:99:0,132,1726 0/0:35,0:35:81.26:0,81,1091 0/0:61,0:61:99:0,132,1808 0/0:47,0:47:99:0,117,1585 0/0:47,0:47:99:0,123,1597 0/0:4,0:4:12.04:0,12,153 0/0:13,0:13:33.10:0,33,427 0/0:15,0:15:45.14:0,45,574 0/0:7,0:7:18.06:0,18,229 0/0:12,0:12:33.11:0,33,429 0/0:8,0:8:24.07:0,24,298 0/0:9,0:9:24.08:0,24,317 0/0:10,0:10:27.09:0,27,351 0/0:19,0:19:54.17:0,54,687 0/0:5,0:5:15.05:0,15,199 0/0:13,0:13:39.12:0,39,493 0/0:18,0:18:54.17:0,54,684 0/0:15,0:15:42.13:0,42,519 0/0:6,0:7:18.05:0,18,224 0/0:22,0:22:63.20:0,63,824 0/0:10,0:10:27.09:0,27,362 0/0:8,0:8:24.08:0,24,320 0/0:8,0:8:18.06:0,18,237 0/0:7,0:7:18.05:0,18,231 0/0:8,0:8:24.08:0,24,308 0/0:10,0:10:30.05:0,30,363 0/0:9,0:9:27.09:0,27,345 -chr1 1226539 . C T 817.48 . AC=5;AF=0.0417;AN=120;BaseQRankSum=-2.085;DP=1317;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.6593;InbreedingCoeff=-0.0489;MQ=58.71;MQ0=0;MQRankSum=0.576;QD=13.62;ReadPosRankSum=0.439;EFF=DOWNSTREAM(MODIFIER||||138|SCNN1D|protein_coding|CODING|ENST00000470022|),DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|14),INTRON(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|13),INTRON(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|19),INTRON(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|14),INTRON(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|17),INTRON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|16);CSQ=intron_variant|||ENSG00000162572|SCNN1D|ENST00000338555||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,intron_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000325425||||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000470022||||-/139|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000400928||||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,intron_variant|||ENSG00000162572|SCNN1D|ENST00000379116||||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:5,0:5:12.02:0,12,139 0/0:2,0:2:6.02:0,6,70 0/0:7,0:7:21.06:0,21,263 0/0:8,0:8:21.07:0,21,263 0/0:19,0:19:54.18:0,54,728 0/0:17,0:17:51.16:0,51,661 0/0:37,0:37:99:0,108,1414 0/1:5,8:13:99:256,0,149 0/0:50,0:50:99:0,144,1890 0/0:33,0:33:99:0,99,1274 0/0:25,0:25:72.23:0,72,940 0/0:14,0:14:42.13:0,42,529 0/0:28,0:28:81.23:0,81,1031 0/0:24,0:24:63.20:0,63,829 0/0:31,0:31:81.26:0,81,1077 0/0:25,0:26:54.18:0,54,734 0/0:39,0:39:90.29:0,90,1212 0/0:30,0:30:69.22:0,69,937 0/0:38,0:38:93.28:0,93,1241 0/0:32,0:32:72.22:0,72,964 0/0:31,0:31:69.21:0,69,907 0/0:43,0:43:99:0,102,1345 0/0:46,0:46:99:0,105,1413 0/0:37,0:37:90.29:0,90,1193 0/1:13,15:28:99:371,0,408 0/0:36,0:36:84.27:0,84,1130 0/0:25,0:25:60.19:0,60,795 0/0:29,0:29:72.22:0,72,917 0/0:40,0:40:93.30:0,93,1243 0/0:27,0:27:78.20:0,78,981 0/0:37,2:40:48.53:0,49,1131 0/0:24,0:24:63.20:0,63,828 0/0:30,0:30:81.24:0,81,1046 0/0:40,0:40:99:0,111,1409 0/0:26,0:26:60.19:0,60,801 0/0:52,0:52:99:0,108,1486 0/0:39,0:39:99:0,105,1375 0/0:45,0:45:99:0,114,1483 0/0:5,0:5:12.04:0,12,158 0/0:11,0:11:27.07:0,27,321 0/0:13,0:13:39.12:0,39,511 0/0:5,0:5:15.05:0,15,187 0/1:3,4:7:86.87:131,0,87 0/1:1,3:5:27.95:65,0,28 0/0:5,0:5:12.04:0,12,149 0/0:8,0:8:21.07:0,21,271 0/0:19,0:19:51.14:0,51,632 0/0:5,0:5:12.04:0,12,146 0/0:6,0:6:18.06:0,18,225 0/0:14,0:14:36.09:0,36,463 0/0:14,0:14:36.11:0,36,450 0/1:3,4:7:51.82:99,0,52 0/0:19,0:19:54.17:0,54,696 0/0:8,0:8:21.07:0,21,277 0/0:8,0:8:24.08:0,24,315 0/0:7,0:7:18.06:0,18,226 0/0:4,0:4:9.02:0,9,106 0/0:10,0:10:24.08:0,24,314 0/0:9,0:9:27.09:0,27,355 0/0:11,0:11:30.09:0,30,377 -chr1 1226651 . G C 418.81 . AC=5;AF=0.0417;AN=120;BaseQRankSum=2.115;DP=667;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.3223;InbreedingCoeff=-0.0562;MQ=58.20;MQ0=0;MQRankSum=0.758;QD=9.74;ReadPosRankSum=-0.561;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcC|S526|638|SCNN1D|protein_coding|CODING|ENST00000338555|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcC|S526|638|SCNN1D|protein_coding|CODING|ENST00000400928|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcC|S557|669|SCNN1D|protein_coding|CODING|ENST00000379110|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcC|S592|704|SCNN1D|protein_coding|CODING|ENST00000325425|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcC|S690|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|17);CSQ=synonymous_variant|tcG/tcC|S|ENSG00000162572|SCNN1D|ENST00000338555|15/15|||526/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|17/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,synonymous_variant|tcG/tcC|S|ENSG00000162572|SCNN1D|ENST00000325425|15/15|||592/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,synonymous_variant|tcG/tcC|S|ENSG00000162572|SCNN1D|ENST00000400928|14/14|||526/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,synonymous_variant|tcG/tcC|S|ENSG00000162572|SCNN1D|ENST00000379116|18/18|||690/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:5:6:0,6,59 0/0:7,0:7:15.05:0,15,184 0/0:6,0:6:9.03:0,9,107 0/0:3,0:3:2.99:0,3,23 0/0:13,0:13:24.05:0,24,295 0/0:15,0:15:39.12:0,39,494 0/0:31,0:31:81.22:0,81,993 0/0:10,0:10:27.09:0,27,350 0/0:28,0:28:69.20:0,69,848 0/0:36,0:36:87.24:0,87,1086 0/0:15,0:15:33.11:0,33,431 0/0:14,0:14:33.11:0,33,432 0/1:12,8:20:99:225,0,300 0/0:8,0:8:18.06:0,18,230 0/0:13,0:13:36.12:0,36,466 0/1:3,2:5:67.94:68,0,97 0/0:13,0:13:36.11:0,36,460 0/1:6,3:9:97.16:97,0,173 0/0:10,0:10:27.09:0,27,345 0/0:20,0:20:54.17:0,54,694 0/0:11,0:11:30.10:0,30,393 0/0:10,0:11:24.08:0,24,317 0/0:14,2:16:39.10:0,39,505 0/0:14,0:14:39.12:0,39,496 0/0:17,0:17:48.15:0,48,615 0/0:11,0:11:33.09:0,33,415 0/0:11,0:11:30.08:0,30,367 0/0:8,0:8:21.06:0,21,273 0/0:7,0:7:21.05:0,21,264 0/0:18,0:18:45.13:0,45,567 0/0:11,0:11:30.08:0,30,368 0/0:15,0:15:42.12:0,42,520 0/0:7,0:7:21.06:0,21,269 0/0:9,0:9:18.06:0,18,233 0/0:7,0:7:21.07:0,21,278 0/0:10,0:10:30.10:0,30,387 0/0:17,0:17:48.16:0,48,649 0/0:13,0:13:33.09:0,33,423 0/0:6,0:6:15.03:0,15,182 0/0:11,0:11:33.09:0,33,397 0/0:10,0:10:30.08:0,30,375 0/0:2,0:2:3.01:0,3,33 0/1:4,2:6:57.70:58,0,108 0/0:4,0:4:9.02:0,9,112 0/1:1,2:3:25.32:75,0,25 0/0:4,0:4:9.02:0,9,102 0/0:18,0:18:45.14:0,45,553 0/0:5,0:5:12.04:0,12,150 0/0:7,0:7:21.05:0,21,263 0/0:13,0:13:36.10:0,36,435 0/0:12,0:12:30.08:0,30,391 0/0:7,0:7:15.05:0,15,188 0/0:14,0:14:33.10:0,33,427 0/0:5,0:5:12.04:0,12,150 0/0:7,1:8:18.06:0,18,243 0/0:5,0:5:12.04:0,12,162 0/0:9,0:9:24.06:0,24,293 0/0:6,0:6:18.06:0,18,233 0/0:9,0:9:21.06:0,21,264 0/0:9,0:9:21.05:0,21,260 -chr1 1226690 . C T 282.98 . AC=2;AF=0.0167;AN=120;BaseQRankSum=-0.735;DP=758;Dels=0.00;FS=19.978;HRun=0;HaplotypeScore=0.3775;InbreedingCoeff=-0.0239;MQ=58.31;MQ0=0;MQRankSum=0.192;QD=12.30;ReadPosRankSum=0.815;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S539|638|SCNN1D|protein_coding|CODING|ENST00000338555|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S539|638|SCNN1D|protein_coding|CODING|ENST00000400928|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S570|669|SCNN1D|protein_coding|CODING|ENST00000379110|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S605|704|SCNN1D|protein_coding|CODING|ENST00000325425|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S703|802|SCNN1D|protein_coding|CODING|ENST00000379116|),UTR_3_PRIME(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|17);CSQ=synonymous_variant|tcC/tcT|S|ENSG00000162572|SCNN1D|ENST00000338555|15/15|||539/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000162572|SCNN1D|ENST00000379101|17/17|||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,synonymous_variant|tcC/tcT|S|ENSG00000162572|SCNN1D|ENST00000325425|15/15|||605/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,synonymous_variant|tcC/tcT|S|ENSG00000162572|SCNN1D|ENST00000400928|14/14|||539/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,synonymous_variant|tcC/tcT|S|ENSG00000162572|SCNN1D|ENST00000379116|18/18|||703/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:4,0:4:6.02:0,6,79 0/0:6,0:6:18.05:0,18,210 0/0:9,0:9:24.08:0,24,311 0/0:3,0:3:9.03:0,9,115 0/0:13,0:13:33.10:0,33,423 0/0:10,0:10:27.09:0,27,360 0/0:25,0:25:72.23:0,72,947 0/0:13,0:13:36.12:0,36,470 0/0:26,0:26:78.26:0,78,1044 0/0:30,0:30:90.29:0,90,1188 0/0:14,0:14:42.14:0,42,555 0/0:19,0:19:54.17:0,54,687 0/0:28,0:28:84.27:0,84,1092 0/0:9,0:9:21.07:0,21,283 0/1:9,8:17:99:213,0,314 0/0:7,0:7:18.06:0,18,250 0/0:14,0:14:33.11:0,33,440 0/0:15,0:15:39.12:0,39,496 0/0:12,0:12:33.10:0,33,427 0/0:20,0:20:42.13:0,42,549 0/0:15,0:15:36.12:0,36,475 0/0:9,0:9:27.09:0,27,358 0/0:16,0:16:39.13:0,39,514 0/0:12,0:13:33.10:0,33,436 0/0:13,0:13:36.10:0,36,469 0/0:14,0:14:39.13:0,39,512 0/0:9,0:9:21.07:0,21,279 0/0:10,0:10:21.06:0,21,267 0/0:6,0:6:12.04:0,12,159 0/0:23,0:23:51.16:0,51,691 0/0:7,0:7:15.05:0,15,208 0/0:22,0:22:48.15:0,48,626 0/0:9,0:9:24.07:0,24,301 0/0:12,0:12:33.10:0,33,417 0/0:5,0:5:15.04:0,15,192 0/0:14,0:14:36.12:0,36,489 0/0:24,0:24:63.20:0,63,852 0/0:16,0:16:33.11:0,33,450 0/0:9,0:9:21.07:0,21,270 0/0:17,0:17:45.14:0,45,594 0/0:15,0:15:36.11:0,36,489 0/0:7,0:7:18.06:0,18,232 0/0:7,0:7:15.05:0,15,205 0/0:5,0:5:12.04:0,12,161 0/0:4,0:4:12.04:0,12,157 0/0:6,0:6:15.05:0,15,188 0/0:23,0:23:45.14:0,45,601 0/0:6,0:6:15.05:0,15,184 0/0:8,0:8:21.07:0,21,278 0/0:15,0:16:39.12:0,39,499 0/0:14,0:14:30.10:0,30,404 0/0:15,0:15:33.11:0,33,442 0/0:9,0:9:24.08:0,24,328 0/0:6,0:6:15.05:0,15,190 0/0:10,0:10:30.09:0,30,382 0/1:2,4:6:62.75:135,0,63 0/0:7,0:8:18.06:0,18,238 0/0:9,0:9:27.09:0,27,356 0/0:12,0:12:30.09:0,30,383 0/0:15,0:15:36.12:0,36,468 -chr1 1226757 . G A 1577.2 . AC=12;AF=0.1000;AN=120;BaseQRankSum=-2.078;DP=939;Dels=0.00;FS=1.648;HRun=0;HaplotypeScore=0.5032;InbreedingCoeff=-0.1091;MQ=57.89;MQ0=0;MQRankSum=0.038;QD=8.76;ReadPosRankSum=0.677;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G562S|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G562S|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G593S|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G628S|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G726S|802|SCNN1D|protein_coding|CODING|ENST00000379116|);CSQ=missense_variant|Ggc/Agc|G/S|ENSG00000162572|SCNN1D|ENST00000338555|15/15|benign(0.125)|tolerated(0.39)|562/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|Ggc/Agc|G/S|ENSG00000162572|SCNN1D|ENST00000325425|15/15|benign(0.276)|tolerated(0.4)|628/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,missense_variant|Ggc/Agc|G/S|ENSG00000162572|SCNN1D|ENST00000400928|14/14|benign(0.125)|tolerated(0.39)|562/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,missense_variant|Ggc/Agc|G/S|ENSG00000162572|SCNN1D|ENST00000379116|18/18|benign(0.276)|tolerated(0.4)|726/802|protein_coding|1 GT:AD:DP:GQ:PL 0/1:3,3:6:27.42:27,0,33 0/0:9,0:9:24.07:0,24,280 0/1:2,3:5:51.98:62,0,52 0/0:3,1:4:9.03:0,9,107 0/0:17,0:17:48.14:0,48,612 0/0:21,0:21:63.19:0,63,811 0/0:30,0:30:81.23:0,81,1040 0/0:20,0:20:57.17:0,57,706 0/0:36,0:36:99:0,108,1383 0/0:36,0:36:99:0,102,1329 0/1:17,3:20:25.83:26,0,523 0/1:14,10:24:99:283,0,413 0/0:21,0:21:54.17:0,54,701 0/0:17,0:17:48.16:0,48,637 0/0:21,0:22:57.17:0,57,746 0/0:6,0:6:15.05:0,15,203 0/0:14,0:14:30.10:0,30,389 0/0:17,0:17:42.13:0,42,528 0/0:16,0:16:39.10:0,39,470 0/1:10,8:19:99:200,0,295 0/0:13,0:13:33.09:0,33,424 0/0:17,0:17:45.15:0,45,600 0/0:16,0:16:36.11:0,36,472 0/0:17,0:17:45.14:0,45,594 0/0:13,0:13:33.11:0,33,455 0/0:14,0:14:39.12:0,39,512 0/0:13,0:13:33.11:0,33,430 0/1:13,1:14:1.25:1,0,354 0/0:12,0:12:33.11:0,33,436 0/0:21,0:21:48.12:0,48,618 0/0:14,0:14:36.10:0,36,477 0/0:21,0:21:48.16:0,48,642 0/0:11,0:11:33.09:0,33,400 0/1:10,9:19:99:230,0,254 0/0:8,0:8:24.08:0,24,303 0/1:5,12:17:99:372,0,154 0/0:20,0:20:48.15:0,48,612 0/0:16,0:16:42.14:0,42,554 0/0:11,0:11:30.08:0,30,359 0/0:26,0:26:66.18:0,66,817 0/0:17,0:17:42.13:0,42,558 0/0:13,0:13:30.09:0,30,394 0/0:13,0:13:33.08:0,33,367 0/0:7,0:7:21.07:0,21,285 0/0:8,0:8:21.07:0,21,284 0/0:5,0:5:12.04:0,12,153 0/0:22,0:22:57.16:0,57,716 0/1:5,1:6:23.70:24,0,176 0/0:9,0:9:21.07:0,21,274 0/0:24,0:24:48.13:0,48,617 0/1:11,10:21:99:243,0,299 0/0:21,0:21:51.16:0,51,667 0/1:8,3:11:90.45:90,0,195 0/0:12,0:12:27.09:0,27,354 0/0:10,0:10:27.09:0,27,353 0/0:9,0:9:24.07:0,24,309 0/0:11,0:11:30.05:0,30,358 0/0:17,0:17:42.14:0,42,547 0/1:10,7:18:99:177,0,275 0/0:12,0:12:33.09:0,33,411 -chr1 1226851 . C T 188.21 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-1.990;DP=1115;Dels=0.00;FS=5.214;HRun=0;HaplotypeScore=0.5651;InbreedingCoeff=-0.0104;MQ=58.68;MQ0=0;MQRankSum=-1.264;QD=9.41;ReadPosRankSum=-0.899;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|processed_transcript|CODING|ENST00000379037|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000476572|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P593L|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P593L|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P624L|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P659L|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P757L|802|SCNN1D|protein_coding|CODING|ENST00000379116|);CSQ=missense_variant|cCg/cTg|P/L|ENSG00000162572|SCNN1D|ENST00000338555|15/15|benign(0.007)|deleterious(0.05)|593/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000476572|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000379037|||||processed_transcript|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|cCg/cTg|P/L|ENSG00000162572|SCNN1D|ENST00000325425|15/15|benign(0.005)|tolerated(0.09)|659/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,missense_variant|cCg/cTg|P/L|ENSG00000162572|SCNN1D|ENST00000400928|14/14|benign(0.007)|deleterious(0.05)|593/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,missense_variant|cCg/cTg|P/L|ENSG00000162572|SCNN1D|ENST00000379116|18/18|benign(0.005)|deleterious(0.02)|757/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:18.04:0,18,210 0/0:14,0:14:36.12:0,36,463 0/0:13,0:13:33.10:0,33,426 0/0:8,0:8:18.06:0,18,228 0/0:29,0:29:87.29:0,87,1168 0/0:25,0:25:75.24:0,75,998 0/0:51,0:51:99:0,150,2015 0/0:34,0:34:99:0,99,1330 0/0:73,0:73:99:0,217,2821 0/0:69,0:70:99:0,208,2789 0/0:33,0:33:93.30:0,93,1242 0/0:28,0:28:84.28:0,84,1121 0/0:40,0:40:99:0,117,1510 0/0:25,0:25:63.20:0,63,843 0/0:22,0:22:54.17:0,54,710 0/0:15,0:15:33.10:0,33,442 0/0:26,0:26:57.18:0,57,746 0/0:21,0:21:48.15:0,48,645 0/0:26,0:26:63.17:0,63,813 0/0:11,0:11:24.08:0,24,314 0/0:22,0:22:57.18:0,57,752 0/0:12,1:13:30.09:0,30,392 0/0:15,0:15:36.11:0,36,465 0/0:19,0:19:51.16:0,51,669 0/0:28,0:28:63.20:0,63,835 0/0:16,0:16:33.10:0,33,445 0/0:13,0:13:30.09:0,30,404 0/0:13,0:13:36.11:0,36,470 0/0:15,0:15:39.13:0,39,511 0/0:15,0:15:42.11:0,42,520 0/0:20,0:20:51.16:0,51,658 0/0:22,0:22:54.15:0,54,701 0/0:13,0:13:36.10:0,36,444 0/0:24,0:24:60.18:0,60,786 0/0:11,0:11:24.08:0,24,334 0/0:23,0:23:54.18:0,54,736 0/0:24,0:24:63.20:0,63,831 0/0:18,0:18:33.10:0,33,456 0/0:9,0:9:27.09:0,27,348 0/0:17,0:17:45.14:0,45,587 0/0:11,0:11:33.11:0,33,445 0/0:11,0:11:30.09:0,30,374 0/0:11,0:11:30.09:0,30,374 0/0:7,0:7:21.07:0,21,267 0/0:5,0:5:15.05:0,15,202 0/0:7,0:7:18.06:0,18,229 0/0:15,0:15:39.11:0,39,488 0/0:10,0:10:30.09:0,30,378 0/0:5,0:5:15.04:0,15,182 0/1:11,9:20:99:236,0,327 0/0:15,0:15:45.14:0,45,590 0/0:15,0:15:36.12:0,36,479 0/0:12,0:12:36.11:0,36,468 0/0:8,0:8:24.08:0,24,307 0/0:10,0:10:27.09:0,27,363 0/0:5,0:5:15.05:0,15,189 0/0:6,0:6:18.06:0,18,232 0/0:7,0:7:21.07:0,21,272 0/0:6,0:6:15.05:0,15,194 0/0:7,0:7:18.06:0,18,229 -chr1 1226889 . G A 2836.8 . AC=12;AF=0.1000;AN=120;BaseQRankSum=-2.929;DP=1114;Dels=0.00;FS=6.315;HRun=0;HaplotypeScore=0.3672;InbreedingCoeff=-0.1141;MQ=58.73;MQ0=0;MQRankSum=0.148;QD=15.76;ReadPosRankSum=0.535;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|processed_transcript|CODING|ENST00000379037|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000476572|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G606R|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G606R|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G637R|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G672R|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G770R|802|SCNN1D|protein_coding|CODING|ENST00000379116|);CSQ=missense_variant|Ggg/Agg|G/R|ENSG00000162572|SCNN1D|ENST00000338555|15/15|benign(0.159)|tolerated(0.42)|606/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000476572|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000379037|||||processed_transcript|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|Ggg/Agg|G/R|ENSG00000162572|SCNN1D|ENST00000325425|15/15|benign(0.001)|tolerated(0.38)|672/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,missense_variant|Ggg/Agg|G/R|ENSG00000162572|SCNN1D|ENST00000400928|14/14|benign(0.159)|tolerated(0.42)|606/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,missense_variant|Ggg/Agg|G/R|ENSG00000162572|SCNN1D|ENST00000379116|18/18|benign(0.001)|tolerated(0.08)|770/802|protein_coding|1 GT:AD:DP:GQ:PL 0/1:6,4:10:99:109,0,133 0/0:15,0:15:39.13:0,39,511 0/1:5,2:7:63.23:63,0,137 0/1:5,5:10:99:155,0,166 0/0:29,0:29:87.27:0,87,1146 0/0:34,0:34:99:0,99,1240 0/0:49,0:49:99:0,144,1914 0/0:27,0:27:78.25:0,78,1014 0/0:68,0:68:99:0,202,2629 0/0:85,0:85:99:0,250,3244 0/1:15,19:34:99:632,0,463 0/1:14,17:31:99:555,0,421 0/0:55,0:55:99:0,163,2122 0/0:20,0:20:42.14:0,42,571 0/0:24,0:24:66.19:0,66,859 0/0:12,0:12:27.09:0,27,380 0/0:20,0:21:48.14:0,48,629 0/0:18,0:18:42.14:0,42,577 0/0:23,0:23:51.14:0,51,666 0/1:3,6:9:62.28:168,0,62 0/0:23,0:23:57.17:0,57,739 0/0:11,0:11:30.08:0,30,384 0/0:16,0:16:36.12:0,36,486 0/0:18,0:18:51.16:0,51,649 0/0:26,0:26:69.22:0,69,922 0/0:13,0:13:27.09:0,27,366 0/0:7,0:8:18.06:0,18,238 0/0:10,0:10:27.08:0,27,344 0/0:13,0:13:30.10:0,30,416 0/0:11,0:11:30.10:0,30,395 0/0:23,0:23:60.18:0,60,785 0/0:22,0:22:48.15:0,48,639 0/0:19,0:19:42.14:0,42,558 0/1:4,14:18:89.94:410,0,90 0/0:3,0:3:9.03:0,9,118 0/1:4,15:19:38.22:461,0,38 0/0:24,0:24:60.19:0,60,797 0/0:18,0:18:45.14:0,45,603 0/0:8,0:8:24.08:0,24,312 0/0:21,0:21:54.14:0,54,670 0/0:16,0:16:45.13:0,45,551 0/0:9,0:9:27.07:0,27,317 0/0:9,0:9:21.06:0,21,261 0/0:5,0:5:15.05:0,15,198 0/0:8,0:8:15.05:0,15,203 0/0:9,0:9:21.07:0,21,277 0/0:17,0:17:48.12:0,48,578 0/1:7,2:9:47.15:47,0,211 0/0:8,0:8:24.08:0,24,312 0/0:19,0:20:57.18:0,57,729 0/1:11,6:17:99:184,0,318 0/0:14,0:14:36.11:0,36,459 0/1:6,5:11:94.46:164,0,94 0/0:11,0:11:33.09:0,33,405 0/0:5,0:5:15.04:0,15,181 0/0:6,0:6:18.04:0,18,218 0/0:8,0:8:24.07:0,24,289 0/0:16,0:16:42.14:0,42,557 0/1:3,2:5:52.74:53,0,105 0/0:6,0:6:18.06:0,18,232 -chr1 1226971 . T C 63.36 . AC=1;AF=0.0085;AN=118;BaseQRankSum=-1.160;DP=1268;Dels=0.00;FS=4.729;HRun=4;HaplotypeScore=0.4672;InbreedingCoeff=-0.0189;MQ=58.51;MQ0=0;MQRankSum=1.085;QD=3.73;ReadPosRankSum=-0.628;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|processed_transcript|CODING|ENST00000379037|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000476572|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L633P|638|SCNN1D|protein_coding|CODING|ENST00000338555|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L633P|638|SCNN1D|protein_coding|CODING|ENST00000400928|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L664P|669|SCNN1D|protein_coding|CODING|ENST00000379110|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L699P|704|SCNN1D|protein_coding|CODING|ENST00000325425|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L797P|802|SCNN1D|protein_coding|CODING|ENST00000379116|);CSQ=missense_variant|cTt/cCt|L/P|ENSG00000162572|SCNN1D|ENST00000338555|15/15|benign(0.02)|tolerated(0.18)|633/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000476572|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000379037|||||processed_transcript|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,missense_variant|cTt/cCt|L/P|ENSG00000162572|SCNN1D|ENST00000325425|15/15|benign(0.189)|tolerated(0.21)|699/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,missense_variant|cTt/cCt|L/P|ENSG00000162572|SCNN1D|ENST00000400928|14/14|benign(0.02)|tolerated(0.18)|633/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,missense_variant|cTt/cCt|L/P|ENSG00000162572|SCNN1D|ENST00000379116|18/18|benign(0.189)|deleterious(0.04)|797/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:7,0:7:15.04:0,15,180 0/0:17,0:17:42.11:0,42,497 0/0:15,0:15:45.14:0,45,564 0/0:13,0:13:30.09:0,30,370 0/0:37,2:39:99:0,99,1309 0/0:46,0:46:99:0,126,1646 0/0:75,0:75:99:0,208,2722 0/0:34,2:36:99:0,102,1346 0/0:86,0:86:99:0,250,3243 0/0:118,1:119:99:0,340,4412 0/0:37,0:38:99:0,108,1419 0/0:27,0:27:81.26:0,81,1062 0/0:63,1:64:99:0,178,2232 0/0:6,0:6:12.04:0,12,158 0/0:16,0:16:39.13:0,39,541 0/0:3,0:3:9.03:0,9,114 0/0:3,0:3:9.03:0,9,115 0/0:10,0:10:27.08:0,27,336 0/0:15,0:15:36.12:0,36,496 0/0:1,0:1:3.01:0,3,39 0/0:11,0:11:33.11:0,33,432 0/0:13,0:13:36.10:0,36,461 0/0:8,0:8:21.07:0,21,279 0/0:9,0:9:27.09:0,27,345 0/0:10,1:11:21.07:0,21,293 0/0:6,0:6:15.05:0,15,209 0/0:4,0:4:12.04:0,12,156 0/0:5,0:5:15.05:0,15,191 0/0:4,0:4:12.04:0,12,161 0/0:2,0:2:6.02:0,6,78 0/0:10,0:10:30.10:0,30,400 0/0:5,1:6:15.05:0,15,206 0/0:6,0:6:12.04:0,12,162 0/0:5,0:5:15.05:0,15,203 ./. 0/0:6,1:7:18.06:0,18,233 0/0:9,0:9:24.08:0,24,323 0/0:9,0:9:18.05:0,18,232 0/0:17,0:17:45.13:0,45,569 0/0:38,0:38:87.26:0,87,1104 0/0:17,0:17:48.13:0,48,590 0/0:22,2:24:48.14:0,48,612 0/0:17,0:17:42.13:0,42,548 0/0:18,0:18:36.08:0,36,449 0/0:25,1:26:60.20:0,60,816 0/0:17,0:17:45.14:0,45,586 0/0:37,0:37:93.28:0,93,1188 0/1:12,5:17:99:111,0,365 0/0:20,1:21:45.13:0,45,568 0/0:28,0:28:66.19:0,66,872 0/0:45,0:45:99:0,99,1277 0/0:30,1:31:78.23:0,78,981 0/0:20,1:21:51.16:0,51,670 0/0:22,0:22:48.12:0,48,608 0/0:20,0:20:51.15:0,51,661 0/0:12,1:13:30.09:0,30,374 0/0:13,0:14:33.11:0,33,436 0/0:32,0:32:72.22:0,72,932 0/0:13,0:13:30.10:0,30,391 0/0:19,0:19:45.14:0,45,583 -chr1 1227042 . G A 57.76 . AC=1;AF=0.0083;AN=120;BaseQRankSum=-0.393;DP=957;Dels=0.00;FS=2.494;HRun=0;HaplotypeScore=0.5259;InbreedingCoeff=-0.0359;MQ=58.61;MQ0=0;MQRankSum=0.096;QD=14.44;ReadPosRankSum=2.314;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|processed_transcript|CODING|ENST00000379037|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000476572|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|),UTR_3_PRIME(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|15),UTR_3_PRIME(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|14),UTR_3_PRIME(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|20),UTR_3_PRIME(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|15),UTR_3_PRIME(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|18);CSQ=3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000338555|15/15|||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000476572|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000379037|||||processed_transcript|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000325425|15/15|||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000400928|14/14|||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000379116|18/18|||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:8,0:8:18.05:0,18,220 0/0:12,0:12:33.10:0,33,416 0/0:13,0:13:36.11:0,36,459 0/0:7,0:7:21.06:0,21,258 0/0:18,0:18:48.16:0,48,641 0/0:23,0:24:69.20:0,69,880 0/0:49,0:49:99:0,141,1875 0/0:24,0:24:69.22:0,69,910 0/0:64,0:64:99:0,193,2560 0/0:54,0:54:99:0,159,2066 0/0:32,0:32:90.29:0,90,1188 0/0:18,0:18:45.13:0,45,576 0/0:40,0:40:99:0,117,1501 0/0:4,0:4:12.04:0,12,152 0/0:4,0:4:12.04:0,12,165 0/0:1,0:1:3.01:0,3,42 0/0:3,0:3:9.03:0,9,116 0/0:5,0:5:15.05:0,15,196 0/0:7,0:7:21.07:0,21,284 0/0:5,0:5:15.05:0,15,199 0/0:3,0:3:9.03:0,9,113 0/0:8,0:8:21.07:0,21,284 0/0:4,0:4:9.03:0,9,129 0/0:8,0:8:24.07:0,24,302 0/0:3,0:3:9.03:0,9,111 0/0:3,0:3:9.03:0,9,127 0/0:3,0:3:6.02:0,6,87 0/0:2,0:2:3.01:0,3,45 0/0:1,0:1:3.01:0,3,41 0/0:3,0:3:9.03:0,9,110 0/0:1,0:1:3.01:0,3,39 0/0:1,0:1:3.01:0,3,34 0/0:3,0:3:9.02:0,9,105 0/1:1,3:4:24.09:105,0,24 0/0:2,0:2:6.02:0,6,82 0/0:4,0:4:9.03:0,9,126 0/0:8,0:8:21.07:0,21,286 0/0:2,0:2:6.02:0,6,79 0/0:18,0:18:45.14:0,45,578 0/0:35,0:35:72.23:0,72,981 0/0:27,0:27:60.19:0,60,800 0/0:22,0:22:63.18:0,63,786 0/0:17,0:17:39.13:0,39,528 0/0:15,0:15:36.12:0,36,484 0/0:21,0:21:57.18:0,57,756 0/0:19,0:19:48.15:0,48,642 0/0:41,0:41:99:0,99,1307 0/0:13,0:13:33.10:0,33,440 0/0:21,0:21:42.14:0,42,563 0/0:21,0:21:51.16:0,51,666 0/0:34,0:34:84.26:0,84,1092 0/0:19,0:19:48.15:0,48,613 0/0:22,0:22:54.15:0,54,701 0/0:25,0:25:57.18:0,57,740 0/0:26,0:26:60.16:0,60,772 0/0:14,0:14:33.08:0,33,409 0/0:20,0:20:45.15:0,45,628 0/0:30,0:30:66.21:0,66,889 0/0:21,0:21:48.15:0,48,650 0/0:21,0:21:42.13:0,42,562 -chr1 1227196 . A G 1166.6 . AC=2;AF=0.024;AN=82;BaseQRankSum=1.195;DP=1062;Dels=0.00;FS=10.378;HRun=6;HaplotypeScore=1.5050;InbreedingCoeff=-0.0572;MQ=57.57;MQ0=0;MQRankSum=-0.308;QD=10.42;ReadPosRankSum=0.286;EFF=DOWNSTREAM(MODIFIER||||759|ACAP3|protein_coding|CODING|ENST00000353662|),DOWNSTREAM(MODIFIER||||834|ACAP3|protein_coding|CODING|ENST00000354700|),DOWNSTREAM(MODIFIER|||||ACAP3|processed_transcript|CODING|ENST00000379037|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000467278|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000470659|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000476572|),DOWNSTREAM(MODIFIER|||||ACAP3|retained_intron|CODING|ENST00000492936|),DOWNSTREAM(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|),UTR_3_PRIME(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000338555|15),UTR_3_PRIME(MODIFIER||||638|SCNN1D|protein_coding|CODING|ENST00000400928|14),UTR_3_PRIME(MODIFIER||||669|SCNN1D|protein_coding|CODING|ENST00000379110|20),UTR_3_PRIME(MODIFIER||||704|SCNN1D|protein_coding|CODING|ENST00000325425|15),UTR_3_PRIME(MODIFIER||||802|SCNN1D|protein_coding|CODING|ENST00000379116|18);CSQ=3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000338555|15/15|||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000467278|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000492936|||||retained_intron|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379101||||-/328|nonsense_mediated_decay|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000476572|||||retained_intron|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000379037|||||processed_transcript|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000354700||||-/834|protein_coding|1,3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000325425|15/15|||-/704|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000353662||||-/759|protein_coding|1,downstream_gene_variant|||ENSG00000162572|SCNN1D|ENST00000379099||||-/308|protein_coding|1,3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000400928|14/14|||-/638|protein_coding|1,downstream_gene_variant|||ENSG00000131584|ACAP3|ENST00000470659|||||retained_intron|1,3_prime_UTR_variant|||ENSG00000162572|SCNN1D|ENST00000379116|18/18|||-/802|protein_coding|1 GT:AD:DP:GQ:PL 0/0:3,0:3:6.02:0,6,74 0/0:4,0:4:12.03:0,12,141 0/0:6,0:6:18.05:0,18,215 0/0:2,0:2:6.01:0,6,64 0/0:9,0:9:21.07:0,21,271 0/0:9,0:9:24.05:0,24,282 0/0:11,1:12:27.09:0,27,358 0/0:7,0:7:21.04:0,21,263 0/0:8,0:8:24.08:0,24,306 0/0:18,0:18:54.17:0,54,689 0/0:7,0:7:18.05:0,18,220 0/0:3,0:3:6.02:0,6,82 0/0:11,0:11:30.10:0,30,388 ./. 0/0:1,0:1:3.01:0,3,39 ./. ./. 0/0:1,0:1:3.01:0,3,42 ./. ./. ./. ./. ./. ./. 0/0:3,0:3:6.02:0,6,83 ./. 0/0:1,0:1:3.01:0,3,37 ./. ./. ./. ./. ./. ./. ./. ./. 0/0:1,0:1:3.01:0,3,42 0/0:2,0:2:6.02:0,6,79 ./. 0/0:36,2:38:87.25:0,87,1078 0/0:51,1:52:99:0,132,1603 0/0:39,3:42:99:0,105,1277 0/0:38,0:38:96.25:0,96,1169 0/0:41,1:42:76.09:0,76,1336 0/0:30,1:31:78.19:0,78,922 0/1:20,21:41:99:439,0,477 0/0:31,1:32:75.14:0,75,872 0/0:69,1:70:99:0,168,2082 0/0:16,0:16:39.10:0,39,449 0/0:42,2:44:99:0,114,1425 0/1:33,37:70:99:789,0,893 0/0:94,4:98:99:0,229,2713 0/0:45,0:46:99:0,120,1463 0/0:54,3:57:99:0,141,1753 0/0:35,0:35:78.25:0,78,1018 0/0:33,3:36:93.23:0,93,1084 0/0:33,0:33:81.22:0,81,987 0/0:22,2:24:63.15:0,63,717 0/0:49,1:50:99:0,135,1607 0/0:27,0:27:66.20:0,66,832 0/0:31,0:31:81.24:0,81,1017 diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/.gitignore golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/.gitignore --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/.gitignore 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/.gitignore 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -t.sh -cov.out -cover.out -*.swp diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/header.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/header.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/header.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/header.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,301 +0,0 @@ -package vcfgo - -import ( - "encoding/csv" - "errors" - "fmt" - "math" - "regexp" - "strconv" - "strings" - "sync" -) - -var typeRe = `String|Integer|Float|Flag|Character|Unknown` -var infoRegexp = regexp.MustCompile(fmt.Sprintf(`##INFO=`, typeRe)) -var formatRegexp = regexp.MustCompile(fmt.Sprintf(`##FORMAT=`, typeRe)) -var filterRegexp = regexp.MustCompile(`##FILTER=`) -var contigRegexp = regexp.MustCompile(`contig=<.*((\w+)=([^,>]+))`) -var sampleRegexp = regexp.MustCompile(`SAMPLE=]+)`) -var pedRegexp = regexp.MustCompile(`PEDIGREE=<=([^,>]+)`) - -//var headerIdRegexp = regexp.MustCompile(`##([^=]+)=", i.Id, i.Number, i.Type, i.Description) -} - -// String returns a string representation. -func (i *SampleFormat) String() string { - return fmt.Sprintf("##FORMAT=", i.Id, i.Number, i.Type, i.Description) -} - -/* -func (h *Header) Validate(verr *VCFError) []error { - var errs []error - return errs -}*/ - -func (h *Header) parseSample(format []string, s string) (*SampleGenotype, []error) { - values := strings.Split(s, ":") - if len(format) != len(values) { - return NewSampleGenotype(), []error{fmt.Errorf("bad sample string: %s", s)} - } - //if geno == nil { - var value string - var geno = NewSampleGenotype() - var errs []error - //} - var e error - - for i, field := range format { - value = values[i] - switch field { - case "GT": - e = h.setSampleGT(geno, value) - case "DP": - e = h.setSampleDP(geno, value) - case "GL": - e = h.setSampleGL(geno, value, false) - case "PL": - e = h.setSampleGL(geno, value, true) - case "GQ": - if format, ok := h.SampleFormats[field]; ok { - e = h.setSampleGQ(geno, value, format.Type) - } - } - geno.Fields[field] = value - if e != nil { - errs = append(errs, e) - } - } - return geno, errs -} - -func (h *Header) setSampleDP(geno *SampleGenotype, value string) error { - var err error - geno.DP, err = strconv.Atoi(value) - if err != nil && (value == "" || value == ".") { - return nil - } - return err -} - -func (h *Header) setSampleGQ(geno *SampleGenotype, value string, Type string) error { - var err error - if Type == "Integer" { - geno.GQ, err = strconv.Atoi(value) - } else if Type == "Float" { - var v float64 - v, err = strconv.ParseFloat(value, 32) - if err == nil { - err = errors.New("setSampleGQ: GQ reported as float. rounding to int") - geno.GQ = int(math.Floor(v + 0.5)) - } - } - - if err != nil && (value == "" || value == ".") { - return nil - } - return err -} - -func (h *Header) setSampleGL(geno *SampleGenotype, value string, isPL bool) error { - var err error - if len(geno.GL) != 0 { - geno.GL = geno.GL[:0] - } - if value == "." || value == "" { - return nil - } - vals := strings.Split(value, ",") - var v float64 - for _, val := range vals { - v, err = strconv.ParseFloat(val, 64) - if isPL { - v /= -10.0 - } - geno.GL = append(geno.GL, v) - } - return err -} - -func (h *Header) setSampleGT(geno *SampleGenotype, value string) error { - geno.Phased = strings.Contains(value, "|") - splitString := "/" - if geno.Phased { - splitString = "|" - } - - alleles := strings.Split(value, splitString) - for _, allele := range alleles { - switch allele { - case ".": - geno.GT = append(geno.GT, -1) - case "1": - geno.GT = append(geno.GT, 1) - case "0": - geno.GT = append(geno.GT, 0) - default: - v, err := strconv.Atoi(allele) - if err != nil { - return err - } - geno.GT = append(geno.GT, v) - } - } - - return nil -} - -// NewHeader returns a Header with the requisite allocations. -func NewHeader() *Header { - var h Header - h.Filters = make(map[string]string) - h.Infos = make(map[string]*Info) - h.SampleFormats = make(map[string]*SampleFormat) - h.SampleNames = make([]string, 0) - h.Pedigrees = make([]string, 0) - h.Samples = make(map[string]string) - h.Extras = make([]string, 0) - h.Contigs = make([]map[string]string, 0, 64) - return &h -} - -func parseHeaderInfo(info string) (*Info, error) { - res := infoRegexp.FindStringSubmatch(info) - if len(res) != 5 { - return nil, fmt.Errorf("INFO error: %s, %v", info, res) - } - var i Info - i.Id = res[1] - i.Number = res[2] - i.Type = res[3] - i.Description = res[4] - return &i, nil -} - -func parseHeaderContig(contig string) (map[string]string, error) { - vmap := make(map[string]string) - contig = strings.TrimSuffix(strings.TrimPrefix(contig, "##contig=<"), ">") - rdr := csv.NewReader(strings.NewReader(contig)) - rdr.LazyQuotes = true - rdr.TrimLeadingSpace = true - contigs, err := rdr.Read() - - for _, pair := range contigs { - kv := strings.SplitN(pair, "=", 2) - vmap[kv[0]] = kv[1] - } - return vmap, err -} - -func parseHeaderExtraKV(kv string) ([]string, error) { - kv = strings.TrimLeft(kv, "##") - kv = strings.TrimLeft(kv, " ") - kvpair := strings.SplitN(kv, "=", 2) - - if len(kvpair) != 2 { - return nil, fmt.Errorf("header error in extra field: %s", kv) - } - return kvpair, nil -} - -func parseHeaderFormat(info string) (*SampleFormat, error) { - res := formatRegexp.FindStringSubmatch(info) - if len(res) != 5 { - return nil, fmt.Errorf("FORMAT error: %s", info) - } - var i SampleFormat - i.Id = res[1] - i.Number = res[2] - i.Type = res[3] - i.Description = res[4] - return &i, nil -} - -func parseHeaderFilter(info string) ([]string, error) { - res := filterRegexp.FindStringSubmatch(info) - if len(res) != 3 { - return nil, fmt.Errorf("FILTER error: %s", info) - } - return res[1:3], nil -} - -// return just the sample id. -func parseHeaderSample(line string) (string, error) { - res := sampleRegexp.FindStringSubmatch(line) - if len(res) != 2 { - return "", fmt.Errorf("error parsing ##SAMPLE") - } - return res[1], nil -} - -func parseHeaderFileVersion(format string) (string, error) { - res := fileVersionRegexp.FindStringSubmatch(format) - if len(res) != 2 { - return "-1", fmt.Errorf("file format error: %s", format) - } - - return res[1], nil -} - -func parseSampleLine(line string) ([]string, error) { - fields := strings.Split(line, "\t") - var samples []string - if len(fields) > 9 { - samples = fields[9:] - } else { - samples = []string{} - } - return samples, nil -} - -func parseOne(key, val, itype string) (interface{}, error) { - var v interface{} - var err error - switch itype { - case "Integer", "INTEGER": - v, err = strconv.Atoi(val) - case "Float", "FLOAT": - v, err = strconv.ParseFloat(val, 32) - case "Flag", "FLAG": - if val != "" { - err = fmt.Errorf("Info Error: flag field (%s) had value", key) - } - v = true - default: - v = val - } - return v, err -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/header_test.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/header_test.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/header_test.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/header_test.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,213 +0,0 @@ -package vcfgo_test - -import ( - "io" - "os" - "strings" - - "github.com/brentp/irelate/interfaces" - vcfgo "github.com/brentp/vcfgo" - - . "gopkg.in/check.v1" -) - -var vcfStr = `##fileformat=VCFv4.2 -##fileDate=20090805 -##source=myImputationProgramV3.1 -##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta -##contig= -##phasing=partial -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FILTER= -##FILTER= -##FILTER= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. -20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. -20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. -20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2:.,. -20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 -X 153171993 rs5201 A . . . . GT 0 1 . -TRIPLOID 153171993 rs5201 A . . . . GT 0|0|0 1/0/1 .` - -var bedStr = `1 0 10000 0.061011 -1 10000 10154 0.070013 -1 10154 10200 0.126639 -1 10400 10535 0.053691 -1 10535 10625 0.078448 -1 10625 11084 0.053691 -1 11084 11159 0.078448 -1 11159 11325 0.053691 -1 11325 11400 0.078448 -1 11400 11404 0.053691` - -// no fileformat -var badVcfStr = `##source=myImputationProgramV3.1 -##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta -##contig= -##phasing=partial -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.` - -type HeaderSuite struct { - reader io.Reader - vcfStr string -} - -type BadVcfSuite HeaderSuite - -var a = Suite(&HeaderSuite{vcfStr: vcfStr}) -var b = Suite(&BadVcfSuite{vcfStr: bedStr}) - -func (s *HeaderSuite) SetUpTest(c *C) { - s.reader = strings.NewReader(s.vcfStr) -} - -func (s *BadVcfSuite) SetUpTest(c *C) { - s.reader = strings.NewReader(s.vcfStr) -} - -func (s *HeaderSuite) TestReaderHeaderParseSample(c *C) { - r, err := vcfgo.NewReader(s.reader, false) - c.Assert(err, IsNil) - v := r.Read() - c.Assert(r.Error(), IsNil) - - fmt := v.Format - c.Assert(fmt, DeepEquals, []string{"GT", "GQ", "DP", "HQ"}) -} - -func (b *BadVcfSuite) TestReaderHeaderParseSample(c *C) { - r, err := vcfgo.NewReader(b.reader, false) - c.Assert(r, IsNil) - c.Assert(err, NotNil) -} - -func (s *HeaderSuite) TestSamples(c *C) { - r, err := vcfgo.NewReader(s.reader, false) - c.Assert(err, IsNil) - - v := r.Read() - samp := v.Samples[0] - - c.Assert(samp.DP, Equals, 1) - c.Assert(samp.GQ, Equals, 48) - - f, err := v.GetGenotypeField(samp, "HQ", -1) - c.Assert(err, IsNil) - c.Assert(f, DeepEquals, []int{51, 51}) - - samp2 := v.Samples[2] - f, err = v.GetGenotypeField(samp2, "HQ", -1) - c.Assert(err, IsNil) - c.Assert(f, DeepEquals, []int{-1, -1}) - - variants := make([]*vcfgo.Variant, 0) - chromCount := make(map[string]int) - var vv interfaces.IVariant - for vv = r.Read(); vv != nil; vv = r.Read() { - v := vv.(*vcfgo.Variant) - if v == nil { - break - } - - variants = append(variants, v) - chromCount[v.Chromosome]++ - } - - c.Assert(chromCount["20"], Equals, 4) - c.Assert(chromCount["X"], Equals, 1) - - c.Assert(int(variants[len(variants)-1].Pos), Equals, int(153171993)) - c.Assert(variants[3].Filter, Equals, "PASS") -} - -func (s *HeaderSuite) TestWeirdHeader(c *C) { - rr, err := os.Open("test-weird-header.vcf") - c.Assert(err, IsNil) - _, err = vcfgo.NewReader(rr, false) - c.Assert(err, IsNil) -} - -func (s *HeaderSuite) TestSampleGenotypes(c *C) { - r, err := vcfgo.NewReader(s.reader, false) - c.Assert(err, IsNil) - - variants := make([]*vcfgo.Variant, 0) - for { - v := r.Read() - if v == nil { - break - } - - variants = append(variants, v) - } - - // validate diploid parsing works - firstVariant := variants[0] - c.Assert(firstVariant.Samples[0].GT, DeepEquals, []int{0, 0}) - c.Assert(firstVariant.Samples[0].Phased, Equals, true) - - c.Assert(firstVariant.Samples[1].GT, DeepEquals, []int{1, 0}) - c.Assert(firstVariant.Samples[1].Phased, Equals, true) - - c.Assert(firstVariant.Samples[2].GT, DeepEquals, []int{1, 1}) - c.Assert(firstVariant.Samples[2].Phased, Equals, false) - - // validate haploid parsing works - hapVariant := variants[5] - c.Assert(hapVariant.Samples[0].GT, DeepEquals, []int{0}) - c.Assert(hapVariant.Samples[0].Phased, Equals, false) - - c.Assert(hapVariant.Samples[1].GT, DeepEquals, []int{1}) - c.Assert(hapVariant.Samples[1].Phased, Equals, false) - - c.Assert(hapVariant.Samples[2].GT, DeepEquals, []int{-1}) - c.Assert(hapVariant.Samples[2].Phased, Equals, false) - - // validate triploid parsing works - tripVariant := variants[6] - c.Assert(tripVariant.Samples[0].GT, DeepEquals, []int{0, 0, 0}) - c.Assert(tripVariant.Samples[0].Phased, Equals, true) - - c.Assert(tripVariant.Samples[1].GT, DeepEquals, []int{1, 0, 1}) - c.Assert(tripVariant.Samples[1].Phased, Equals, false) - - c.Assert(tripVariant.Samples[2].GT, DeepEquals, []int{-1}) - c.Assert(tripVariant.Samples[2].Phased, Equals, false) -} - -/* -func (s *VariantSuite) TestParseOne(c *C) { - - v, err := vcfgo.parseOne("key", "123", "Integer") - c.Assert(err, IsNil) - c.Assert(v, Equals, 123) - - v1, err := parseOne("key", "a123", "String") - c.Assert(err, IsNil) - c.Assert(v1, Equals, "a123") - - v2, err := parseOne("key", "asdf", "Flag") - c.Assert(err, ErrorMatches, ".*flag field .* had value") - c.Assert(v2, Equals, true) - - v3, err := parseOne("key", "", "Flag") - c.Assert(err, IsNil) - c.Assert(v3, Equals, true) - -} -*/ diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/info.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/info.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/info.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/info.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,402 +0,0 @@ -package vcfgo - -import ( - "bytes" - "fmt" - "strconv" - "strings" -) - -type InfoByte struct { - Info []byte - - header *Header -} - -func NewInfoByte(info []byte, h *Header) *InfoByte { - if len(info) == 1 && info[0] == '.' { - return &InfoByte{Info: []byte(""), header: h} - } - return &InfoByte{Info: info, header: h} -} - -/* -func bytesToString(b []byte) string { - bh := (*reflect.SliceHeader)(unsafe.Pointer(&b)) - sh := reflect.StringHeader{bh.Data, bh.Len} - return *(*string)(unsafe.Pointer(&sh)) -} -*/ - -// return the start and end positions of the value. -// for flag the value is the flag. -func getpositions(info []byte, key string) (start, end int) { - //if ipos := strings.LastIndex(bytesToString(info), ";"+key+"="); ipos != -1 { - if ipos := bytes.Index(info, []byte(";"+key+"=")); ipos != -1 { - start = ipos + 2 + len(key) - for end := start + 1; end < len(info)-1; end++ { - if info[end] == ';' { - return start, end - 1 - } - } - return start, len(info) - 1 - } - - bkey := []byte(key) - ipos, pos := 0, 0 - - for { - if pos >= len(info) { - return -1, -1 - } - if pos == 0 { - ipos = bytes.Index(info, bkey) - } else { - ipos = bytes.Index(info[pos:], bkey) - } - - if ipos == -1 { - return -1, -1 - } - pos += ipos - if pos != 0 && info[pos-1] != ';' { - pos += 1 - continue - } - eq := pos + bytes.IndexByte(info[pos:], '=') - // at end of field and we found an Flag - var semi int - if eq == -1 { - return pos, len(info) - } else if eq-pos != len(bkey) { - // found a longer key with same prefix. - semi = bytes.IndexByte(info[pos:], ';') - // flag field - if semi == -1 { - semi = len(info) - } else { - semi += pos - } - if semi-pos == len(bkey) { - return pos, semi - 1 - } - pos = semi + 1 - continue - } else { - semi = bytes.IndexByte(info[pos+1:], byte(';')) - } - if semi > -1 && eq > pos+semi { - // should be a flag. - return pos, pos + semi - } - - // not at end of info field - if semi != -1 { - semi += pos - } - return eq + 1, semi - } -} - -func (i InfoByte) Contains(key string) bool { - // short-circuit common case. - if !bytes.Contains(i.Info, []byte(key+"=")) { - return false - } - s, _ := getpositions(i.Info, key) - return s != -1 -} - -func (i InfoByte) Keys() []string { - sp := bytes.Split(i.Info, []byte{';'}) - keys := make([]string, 0, len(sp)) - for _, pair := range sp { - key := bytes.SplitN(pair, []byte{'='}, 2)[0] - keys = append(keys, string(key)) - } - return keys - -} - -func (i *InfoByte) Delete(key string) { - s, e := getpositions(i.Info, key) - if s == -1 { - return - } - // check if it's a flag - if s != 0 && i.Info[s-1] != ';' { - s -= (len(key) + 1) - } - if s < 0 { - s = 0 - } - if e == -1 { - e = len(i.Info) - } else { - e += 2 - } - if s == 0 && e == len(i.Info) { - i.Info = i.Info[:0] - } else if e < len(i.Info) { - i.Info = append(i.Info[:s], i.Info[e:]...) - } else { - i.Info = i.Info[:s-1] - } -} - -func ItoS(k string, v interface{}) string { - if _, ok := v.(bool); ok { - return k - } else if v == nil { - return "." - } else { - switch v.(type) { - case []interface{}: - vs := v.([]interface{}) - out := make([]string, len(vs)) - for i, vv := range vs { - out[i] = ItoS(k, vv) - } - return strings.Join(out, ",") - case float32: - return fmtFloat32(v.(float32)) - case float64: - return fmtFloat64(v.(float64)) - case int: - return fmt.Sprintf("%d", v.(int)) - case uint32: - return fmt.Sprintf("%d", v.(uint32)) - case []float64: - vals := v.([]float64) - svals := make([]string, len(vals)) - for i, val := range vals { - svals[i] = fmtFloat64(float64(val)) - } - return strings.Join(svals, ",") - case []float32: - vals := v.([]float32) - svals := make([]string, len(vals)) - for i, val := range vals { - svals[i] = fmtFloat32(float32(val)) - } - return strings.Join(svals, ",") - case []int: - vals := v.([]int) - svals := make([]string, len(vals)) - for i, val := range vals { - svals[i] = strconv.Itoa(int(val)) - } - return strings.Join(svals, ",") - case []int32: - vals := v.([]int32) - svals := make([]string, len(vals)) - for i, val := range vals { - svals[i] = strconv.Itoa(int(int32(val))) - } - return strings.Join(svals, ",") - case []string: - return strings.Join(v.([]string), ",") - - default: - return v.(string) - } - } -} - -func (i InfoByte) SGet(key string) []byte { - var sub []byte - if key == "" || len(i.Info) == 1 { - return sub - } - start, end := getpositions(i.Info, key) - if start == -1 { - return sub - } - if end == -1 { - end = len(i.Info) - 1 - } - val := i.Info[start : end+1] - return val -} - -// Get a value from the bytes typed according to the header. -func (i InfoByte) Get(key string) (interface{}, error) { - v := string(i.SGet(key)) - skey := string(key) - var ok bool - var hi *Info - if i.header == nil || i.header.Infos == nil { - ok = false - } else { - i.header.RLock() - hi, ok = i.header.Infos[key] - i.header.RUnlock() - } - if !ok { - err := fmt.Errorf("Info Error: %s not found in header", skey) - // flag - if skey == v { - return true, err - } - if v == "" { - return nil, err - } - return v, err - } - - if v == "" { - var err error - var val interface{} = nil - if hi.Type != "Flag" { - err = fmt.Errorf("Info Error: %s not found in INFO", skey) - } else { - val = false - } - return val, err - } - if v == key { - var err error - if hi.Type != "Flag" { - err = fmt.Errorf("Info Error: flag field (%s) should be specified as such in the header", skey) - } - return true, err - } - - var err error - var iv interface{} - if hi.Number == "1" || (hi.Number == "." && strings.IndexByte(v, ',') == -1) { - return parseOne(skey, v, hi.Type) - } - - switch hi.Number { - - case "0": - if hi.Type != "Flag" { - err = fmt.Errorf("Info Error: flag field (%s) should have Number=0", skey) - } - return true, err - - case "R", "A", "G", "2", "3", ".": - vals := strings.Split(v, ",") - var vi interface{} - switch hi.Type { - case "Integer": - vi = make([]int, len(vals)) - for j, val := range vals { - iv, err = parseOne(skey, val, hi.Type) - vi.([]int)[j] = iv.(int) - } - case "Float": - vi = make([]float32, len(vals)) - for j, val := range vals { - iv, err = parseOne(skey, val, hi.Type) - if o, ok := iv.(float32); ok { - vi.([]float32)[j] = o - } else { - vi.([]float32)[j] = float32(iv.(float64)) - } - - } - case "String": - vi = make([]string, len(vals)) - for j, val := range vals { - iv, err = parseOne(skey, val, hi.Type) - vi.([]string)[j] = iv.(string) - } - default: - vi = make([]interface{}, len(vals)) - for j, val := range vals { - iv, err = parseOne(skey, val, hi.Type) - vi.([]interface{})[j] = iv - } - } - return vi, nil - - default: - vals := strings.Split(v, ",") - var vi interface{} = make([]interface{}, len(vals)) - if _, err := strconv.Atoi(hi.Number); err == nil { - for j, val := range vals { - iv, err = parseOne(skey, val, hi.Type) - vi.([]interface{})[j] = iv - } - } - return vi, err - - } -} - -func (i InfoByte) String() string { - if len(i.Info) == 0 { - return "." - } - return string(i.Info) -} - -func (i InfoByte) Bytes() []byte { - return i.Info -} - -func (i *InfoByte) UpdateHeader(key string, value interface{}) { - i.header.Lock() - defer i.header.Unlock() - if i.header != nil { - switch value.(type) { - case bool: - i.header.Infos[key] = &Info{Id: key, Description: key, Number: "0", Type: "Flag"} - case string: - i.header.Infos[key] = &Info{Id: key, Description: key, Number: "1", Type: "Character"} - case int, int32, int64, uint32, uint64: - i.header.Infos[key] = &Info{Id: key, Description: key, Number: "1", Type: "Integer"} - case float32, float64: - i.header.Infos[key] = &Info{Id: key, Description: key, Number: "1", Type: "Float"} - case []interface{}: - v := value.([]interface{})[0] - i.UpdateHeader(key, v) - } - } -} - -func (i *InfoByte) Set(key string, value interface{}) error { - if len(i.Info) == 0 { - if v, ok := value.(bool); ok { - if v { - i.Info = []byte(key) - } - } else { - i.Info = []byte(fmt.Sprintf("%s=%s", key, ItoS(key, value))) - } - return nil - } - s, e := getpositions(i.Info, key) - if s == -1 || s == len(i.Info) { - if b, ok := value.(bool); ok { - if b { - i.Info = append(i.Info, ';') - i.Info = append(i.Info, key...) - } - return nil - } - slug := fmt.Sprintf(";%s=%s", key, ItoS(key, value)) - i.Info = append(i.Info, slug...) - //i.UpdateHeader(key, value) - return nil - } - if b, ok := value.(bool); ok { - if !b { - i.Delete(key) - } - return nil - } - slug := []byte(ItoS(key, value)) - if e == -1 { - i.Info = append(i.Info[:s], slug...) - } else { - i.Info = append(i.Info[:s], append(slug, i.Info[e+1:]...)...) - } - return nil -} - -func (i *InfoByte) Add(key string, value interface{}) { - i.Set(key, value) -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/info_test.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/info_test.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/info_test.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/info_test.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,123 +0,0 @@ -package vcfgo - -import ( - "io" - - . "gopkg.in/check.v1" -) - -type InfoSuite struct { - reader io.Reader -} - -var _ = Suite(&InfoSuite{}) - -func (s *InfoSuite) TestInfoGet(c *C) { - i := NewInfoByte([]byte("asdf=123;FLAG1;ddd=ddd;FLAG;dddd=dddd;as=22;FLAG2;other=as;FLAG3"), nil) - c.Assert(string(i.SGet("as")), Equals, "22") - c.Assert(string(i.SGet("asdf")), Equals, "123") - c.Assert(string(i.SGet("ddd")), Equals, "ddd") - c.Assert(string(i.SGet("dddd")), Equals, "dddd") - c.Assert(string(i.SGet("other")), Equals, "as") - c.Assert(string(i.SGet("FLAG1")), Equals, "FLAG1") - c.Assert(string(i.SGet("FLAG")), Equals, "FLAG") - c.Assert(string(i.SGet("FLAG2")), Equals, "FLAG2") - c.Assert(string(i.SGet("FLAG3")), Equals, "FLAG3") - c.Assert(string(i.SGet("FLAG4")), Equals, "") - c.Assert(string(i.SGet("dd")), Equals, "") - c.Assert(string(i.SGet("")), Equals, "") - c.Assert(string(i.SGet("ddddd")), Equals, "") - c.Assert(string(i.SGet("FLAG33")), Equals, "") - i = NewInfoByte([]byte("asdf=123;FLAG1;ddd=ddd;FLAG;dddd=dddd;as=22;FLAG2;other=as;FLAG3;asst=33,44"), nil) - c.Assert(string(i.SGet("t")), Equals, "") -} - -func (s *InfoSuite) TestEmptyInfo(c *C) { - i := NewInfoByte([]byte("."), nil) - c.Assert(i.String(), Equals, ".") -} - -func (s *InfoSuite) TestInfoSet(c *C) { - i := NewInfoByte([]byte("asdf=123;FLAG1;ddd=ddd;FLAG;dddd=dddd;as=22;FLAG2;other=as;FLAG3"), nil) - i.Set("as", "23") - c.Assert(string(i.SGet("as")), Equals, "23") - i.Set("asst", 24) - c.Assert(string(i.SGet("asst")), Equals, "24") - i.Set("t", 33) - a := string(i.SGet("t")) - c.Assert(a, Equals, "33") - i.Set("t", []int{93, 44, 55, 66}) - c.Assert(string(i.SGet("t")), Equals, "93,44,55,66") - i.Set("tt", "asdf") - c.Assert(string(i.SGet("t")), Equals, "93,44,55,66") - c.Assert(string(i.SGet("tt")), Equals, "asdf") - i.Set("ttt", "xxx") - c.Assert(string(i.SGet("t")), Equals, "93,44,55,66") - c.Assert(string(i.SGet("tt")), Equals, "asdf") - c.Assert(string(i.SGet("ttt")), Equals, "xxx") - - i.Set("zzz", "zzz") - i.Set("zz", "zz") - i.Set("z", "z") - c.Assert(string(i.SGet("zzz")), Equals, "zzz") - c.Assert(string(i.SGet("zz")), Equals, "zz") - c.Assert(string(i.SGet("z")), Equals, "z") - -} - -func (s *InfoSuite) TestInfoKeys(c *C) { - i := NewInfoByte([]byte("asdf=123;FLAG1;ddd=ddd;FLAG;dddd=dddd;as=22;FLAG2;other=as;FLAG3"), nil) - c.Assert(i.Keys(), DeepEquals, []string{"asdf", "FLAG1", "ddd", "FLAG", "dddd", "as", "FLAG2", "other", "FLAG3"}) -} - -func (s *InfoSuite) TestInfoDelete(c *C) { - i := NewInfoByte([]byte("asdf=123;FLAG1;ddd=ddd;FLAG;dddd=dddd;as=22;FLAG2;other=as;FLAG3"), nil) - i.Delete("asdf") - c.Assert(i.String(), Equals, "FLAG1;ddd=ddd;FLAG;dddd=dddd;as=22;FLAG2;other=as;FLAG3") - i.Delete("other") - c.Assert(i.String(), Equals, "FLAG1;ddd=ddd;FLAG;dddd=dddd;as=22;FLAG2;FLAG3") - - i.Delete("FLAG1") - c.Assert(i.String(), Equals, "ddd=ddd;FLAG;dddd=dddd;as=22;FLAG2;FLAG3") - - i.Delete("FLAG") - c.Assert(i.String(), Equals, "ddd=ddd;dddd=dddd;as=22;FLAG2;FLAG3") - - i.Delete("ddd") - c.Assert(i.String(), Equals, "dddd=dddd;as=22;FLAG2;FLAG3") - - i.Delete("FLAG3") - c.Assert(i.String(), Equals, "dddd=dddd;as=22;FLAG2") - - i.Delete("FLAG2") - c.Assert(i.String(), Equals, "dddd=dddd;as=22") - - i.Delete("dddd") - c.Assert(i.String(), Equals, "as=22") - - i.Delete("as") - c.Assert(i.String(), Equals, ".") - -} - -func (s *InfoSuite) TestInfoFlag(c *C) { - i := NewInfoByte([]byte("AAA;asdf=123;FLAG1;ddd=123"), nil) - i.Set("ggg", true) - c.Assert(i.String(), Equals, "AAA;asdf=123;FLAG1;ddd=123;ggg") - - i.Set("ggg", false) - c.Assert(i.String(), Equals, "AAA;asdf=123;FLAG1;ddd=123") - - i.Set("ggg", true) - c.Assert(i.String(), Equals, "AAA;asdf=123;FLAG1;ddd=123;ggg") - - i.Set("gga", true) - c.Assert(i.String(), Equals, "AAA;asdf=123;FLAG1;ddd=123;ggg;gga") - - i.Set("AAA", true) - c.Assert(i.String(), Equals, "AAA;asdf=123;FLAG1;ddd=123;ggg;gga") - - // NOTE: setting to false removes - i.Set("AAA", false) - c.Assert(i.String(), Equals, "asdf=123;FLAG1;ddd=123;ggg;gga") -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/internal_test.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/internal_test.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/internal_test.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/internal_test.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,24 +0,0 @@ -package vcfgo - -import . "gopkg.in/check.v1" - -type InternalSuite struct { -} - -var _ = Suite(&InternalSuite{}) - -func (s *InternalSuite) TestFloatFmt(c *C) { - - fmt := fmtFloat32(-0) - c.Assert(fmt, Equals, "0") - - fmt = fmtFloat32(-0.0) - c.Assert(fmt, Equals, "0") - - fmt = fmtFloat64(-0.0) - c.Assert(fmt, Equals, "0") - - fmt = fmtFloat64(-0) - c.Assert(fmt, Equals, "0") - -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/LICENSE golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/LICENSE --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/LICENSE 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/LICENSE 1970-01-01 00:00:00.000000000 +0000 @@ -1,21 +0,0 @@ -The MIT License (MIT) - -Copyright (c) 2015 Brent S. Pedersen. - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/normalize.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/normalize.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/normalize.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/normalize.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,52 +0,0 @@ -package vcfgo - -func leftalign(pos int, ref []byte, alt []byte, seq []byte) (int, []byte, []byte, error) { - /* actually this isn't necessary - if !bytes.HasSuffix(seq, ref) { - return 0, ref, alt, errors.New("leftalign: sequence should end with ref") - } - */ - subseq := seq[:len(seq)-len(ref)] - - quit := false - j := len(subseq) - - for j > 0 && !quit { - quit = true - if ref[len(ref)-1] == alt[len(alt)-1] { - ref = ref[:len(ref)-1] - alt = alt[:len(alt)-1] - quit = false - } - if len(ref) == 0 || len(alt) == 0 { - j-- - // use j + 1 to get a slice. - ref = append(subseq[j:j+1], ref...) - alt = append(subseq[j:j+1], alt...) - quit = false - - } - - } - return pos - (len(subseq) - j), ref, alt, nil -} - -func lefttrim(pos int, ref []byte, alt []byte) (int, []byte, []byte, error) { - if 1 == len(ref) && len(alt) == 1 { - return pos, ref, alt, nil - } - - n := 0 - minLen := len(ref) - if len(alt) < minLen { - minLen = len(alt) - } - - for n+1 < minLen && alt[n] == ref[n] { - n++ - } - - alt, ref = alt[n:], ref[n:] - pos += n - return pos, ref, alt, nil -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/normalize_test.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/normalize_test.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/normalize_test.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/normalize_test.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,77 +0,0 @@ -package vcfgo - -import ( - "testing" -) - -var leftaligntests = []struct { - pos int - ref []byte - alt []byte - seq []byte - - outPos int - outRef string - outAlt string -}{ - {123, []byte{'C', 'A', 'C'}, []byte{'C'}, []byte("GGGCACACAC"), 118, "GCA", "G"}, - {123, []byte{'C', 'A', 'C'}, []byte{'C'}, []byte("CACACAC"), 119, "CAC", "C"}, - {123, []byte{'C', 'C', 'A'}, []byte{'C', 'A', 'A'}, []byte("ACCCCCCA"), 123, "CC", "CA"}, - {123, []byte{'C'}, []byte{'A'}, []byte("ACCCCCC"), 123, "C", "A"}, -} - -var lefttrimtests = []struct { - pos int - ref []byte - alt []byte - - outPos int - outRef string - outAlt string -}{ - {123, []byte{'C', 'C'}, []byte{'C', 'A'}, 124, "C", "A"}, - {123, []byte{'C', 'C'}, []byte{'C', 'C', 'T'}, 124, "C", "CT"}, - {123, []byte{'C', 'C', 'C'}, []byte{'C', 'C', 'C', 'T'}, 125, "C", "CT"}, - {123, []byte{'C'}, []byte{'T'}, 123, "C", "T"}, -} - -func TestLeftAlign(t *testing.T) { - - for _, v := range leftaligntests { - p, r, a, err := leftalign(v.pos, v.ref, v.alt, v.seq) - - if p != v.outPos { - t.Errorf("position should be %d instead of %d\n", v.outPos, p) - } - if string(r) != v.outRef { - t.Errorf("ref should be %s instead of %s\n", v.outRef, string(r)) - } - if string(a) != v.outAlt { - t.Errorf("alt should be '%s' instead of %s", v.outAlt, a) - } - if err != nil { - t.Error(err) - } - } -} - -func TestLeftTrim(t *testing.T) { - - for _, v := range lefttrimtests { - p, r, a, err := lefttrim(v.pos, v.ref, v.alt) - - if p != v.outPos { - t.Errorf("position should be %d instead of %d\n", v.outPos, p) - } - if string(r) != v.outRef { - t.Errorf("ref should be %s instead of %s\n", v.outRef, string(r)) - } - if string(a) != v.outAlt { - t.Errorf("alt should be '%s' instead of %s", v.outAlt, a) - } - if err != nil { - t.Error(err) - } - - } -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/reader.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/reader.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/reader.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/reader.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,293 +0,0 @@ -// Package vcfgo implements a Reader and Writer for variant call format. -// It eases reading, filtering modifying VCF's even if they are not to spec. -// Example: -// f, _ := os.Open("examples/test.auto_dom.no_parents.vcf") -// rdr, err := vcfgo.NewReader(f) -// if err != nil { -// panic(err) -// } -// for { -// variant := rdr.Read() -// if variant == nil { -// break -// } -// fmt.Printf("%s\t%d\t%s\t%s\n", variant.Chromosome, variant.Pos, variant.Ref, variant.Alt) -// fmt.Printf("%s", variant.Info["DP"].(int) > 10) -// sample := variant.Samples[0] -// // we can get the PL field as a list (-1 is default in case of missing value) -// fmt.Println("%s", variant.GetGenotypeField(sample, "PL", -1)) -// _ = sample.DP -// } -// fmt.Fprintln(os.Stderr, rdr.Error()) -package vcfgo - -import ( - "bufio" - "bytes" - "fmt" - "io" - "log" - "os" - "strconv" - "strings" - "unsafe" -) - -// used for the quality score which is 0 to 255, but allows "." -const MISSING_VAL = 256 - -// Reader holds information about the current line number (for errors) and -// The VCF header that indicates the structure of records. -type Reader struct { - buf *bufio.Reader - Header *Header - verr *VCFError - LineNumber int64 - lazySamples bool - r io.Reader -} - -func NewWithHeader(r io.Reader, h *Header, lazySamples bool) (*Reader, error) { - buf := bufio.NewReaderSize(r, 32768*2) - var verr = NewVCFError() - return &Reader{buf, h, verr, 1, lazySamples, r}, nil -} - -// NewReader returns a Reader. -// If lazySamples is true, then the user will have to call Reader.ParseSamples() -// in order to access simple info. -func NewReader(r io.Reader, lazySamples bool) (*Reader, error) { - buffered := bufio.NewReaderSize(r, 32768*2) - - var verr = NewVCFError() - - var LineNumber int64 - h := NewHeader() - - for { - - LineNumber++ - line, err := buffered.ReadString('\n') - if err != nil && err != io.EOF { - verr.Add(err, LineNumber) - } - if len(line) > 1 && line[len(line)-1] == '\n' { - line = line[:len(line)-1] - } - - if LineNumber == 1 { - v, err := parseHeaderFileVersion(line) - verr.Add(err, LineNumber) - h.FileFormat = v - - } else if strings.HasPrefix(line, "##FORMAT") { - format, err := parseHeaderFormat(line) - verr.Add(err, LineNumber) - if format != nil { - h.SampleFormats[format.Id] = format - } - - } else if strings.HasPrefix(line, "##INFO") { - info, err := parseHeaderInfo(line) - verr.Add(err, LineNumber) - if info != nil { - h.Infos[info.Id] = info - } - - } else if strings.HasPrefix(line, "##FILTER") { - filter, err := parseHeaderFilter(line) - verr.Add(err, LineNumber) - if filter != nil && len(filter) == 2 { - h.Filters[filter[0]] = filter[1] - } - - } else if strings.HasPrefix(line, "##contig") { - contig, err := parseHeaderContig(line) - verr.Add(err, LineNumber) - if contig != nil { - if _, ok := contig["ID"]; ok { - h.Contigs = append(h.Contigs, contig) - } else { - verr.Add(fmt.Errorf("bad contig: %v", line), LineNumber) - } - } - } else if strings.HasPrefix(line, "##SAMPLE") { - sample, err := parseHeaderSample(line) - verr.Add(err, LineNumber) - if sample != "" { - h.Samples[sample] = line - } else { - verr.Add(fmt.Errorf("bad sample: %v", line), LineNumber) - } - } else if strings.HasPrefix(line, "##PEDIGREE") { - h.Pedigrees = append(h.Pedigrees, line) - } else if strings.HasPrefix(line, "##") { - kv, err := parseHeaderExtraKV(line) - verr.Add(err, LineNumber) - - if kv != nil && len(kv) == 2 { - h.Extras = append(h.Extras, line) - } - - } else if strings.HasPrefix(line, "#CHROM") { - var err error - h.SampleNames, err = parseSampleLine(line) - verr.Add(err, LineNumber) - //h.Validate(verr) - break - - } else { - e := fmt.Errorf("unexpected header line: %s", line) - return nil, e - } - } - reader := &Reader{buffered, h, verr, LineNumber, lazySamples, r} - return reader, reader.Error() -} - -func makeFields(line []byte) [][]byte { - fields := bytes.SplitN(line, []byte{'\t'}, 9) - s := 0 - for i, f := range fields { - if i == 7 { - break - } - s += len(f) + 1 - } - if s >= len(line) { - fmt.Fprintf(os.Stderr, "XXXXX: bad VCF line '%s'", line) - return fields - } - e := bytes.IndexByte(line[s:], '\t') - if e == -1 { - e = len(line) - } else { - e += s - } - - fields[7] = line[s:e] - return fields -} - -// Read returns a pointer to a Variant. Upon reading the caller is assumed -// to check Reader.Err() -func (vr *Reader) Read() *Variant { - - line, err := vr.buf.ReadBytes('\n') - if err != nil { - if len(line) == 0 && err == io.EOF { - return nil - } else if err != io.EOF { - vr.verr.Add(err, vr.LineNumber) - } - } - - vr.LineNumber++ - if line[len(line)-1] == '\n' { - line = line[:len(line)-1] - } - fields := makeFields(line) - return vr.Parse(fields) -} - -func unsafeString(b []byte) string { - return *(*string)(unsafe.Pointer(&b)) -} - -func (vr *Reader) Parse(fields [][]byte) *Variant { - if len(fields) < 7 { - s := make([]string, 0) - for _, b := range fields { - s = append(s, string(b)) - } - log.Printf("error at line %d: not enough fields for a VCF. Content was: '%s'\n", vr.LineNumber, strings.Join(s, "\t")) - } - - pos, err := strconv.ParseUint(unsafeString(fields[1]), 10, 64) - vr.verr.Add(err, vr.LineNumber) - - var qual float64 - if len(fields[5]) == 1 && fields[5][0] == '.' { - qual = MISSING_VAL - } else { - qual, err = strconv.ParseFloat(unsafeString(fields[5]), 32) - vr.verr.Add(err, vr.LineNumber) - } - - v := &Variant{Chromosome: string(fields[0]), Pos: pos, Id_: string(fields[2]), Reference: string(fields[3]), Alternate: strings.Split(string(fields[4]), ","), Quality: float32(qual), - Filter: string(fields[6]), Header: vr.Header} - - if len(fields) > 8 { - sample_fields := bytes.SplitN(fields[8], []byte{'\t'}, 2) - v.Format = strings.Split(string(sample_fields[0]), ":") - v.sampleString = string(sample_fields[1]) - if !vr.lazySamples { - err = vr.Header.ParseSamples(v) - vr.verr.Add(err, vr.LineNumber) - } - } - v.LineNumber = vr.LineNumber - - v.Info_ = NewInfoByte(fields[7], vr.Header) - return v -} - -// Force parsing of the sample fields. -func (h *Header) ParseSamples(v *Variant) error { - if v.Format == nil || v.sampleString == "" || v.Samples != nil { - return nil - } - var errors []error - v.Samples = make([]*SampleGenotype, len(h.SampleNames)) - - for i, sample := range strings.Split(v.sampleString, "\t") { - geno, moreErrors := h.parseSample(v.Format, sample) - errors = append(errors, moreErrors...) - - v.Samples[i] = geno - } - v.sampleString = "" - if len(errors) > 0 { - return errors[0] - } - return nil -} - -// AddInfoToHeader adds a INFO field to the header. -func (vr *Reader) AddInfoToHeader(id string, num string, stype string, desc string) { - h := vr.Header - h.Infos[id] = &Info{Id: id, Number: num, Type: stype, Description: desc} -} - -// AddFormatToHeader adds a FORMAT field to the header. -func (vr *Reader) AddFormatToHeader(id string, num string, stype string, desc string) { - h := vr.Header - h.SampleFormats[id] = &SampleFormat{Id: id, Number: num, Type: stype, Description: desc} -} - -func (vr *Reader) GetHeaderType(field string) string { - if h, ok := vr.Header.Infos[field]; ok { - return h.Type - } - return "" -} - -// Error() aggregates the multiple errors that can occur into a single object. -func (vr *Reader) Error() error { - if vr.verr.IsEmpty() { - return nil - } - return vr.verr -} - -// Clear empties the cache of errors. -func (vr *Reader) Clear() { - vr.verr.Clear() -} - -func (vr *Reader) Close() error { - if rc, ok := vr.r.(io.ReadCloser); ok { - return rc.Close() - } - return nil -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/reader_test.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/reader_test.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/reader_test.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/reader_test.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,140 +0,0 @@ -package vcfgo_test - -import ( - "io" - "os" - "strings" - - "github.com/brentp/vcfgo" - - . "gopkg.in/check.v1" -) - -type ReaderSuite struct { - reader io.Reader -} - -var _ = Suite(&ReaderSuite{}) - -func (s *ReaderSuite) SetUpTest(c *C) { - s.reader = strings.NewReader(vcfStr) - -} - -func (s *ReaderSuite) TestReaderHeaderSamples(c *C) { - v, err := vcfgo.NewReader(s.reader, false) - c.Assert(err, IsNil) - c.Assert(v.Header.SampleNames, DeepEquals, []string{"NA00001", "NA00002", "NA00003"}) - -} - -func (s *ReaderSuite) TestLazyReader(c *C) { - rdr, err := vcfgo.NewReader(s.reader, true) - c.Assert(err, IsNil) - rec := rdr.Read() //.(*vcfgo.Variant) - c.Assert(rec.String(), Equals, "20\t14370\trs6054257\tG\tA\t29.0\tPASS\tNS=3;DP=14;AF=0.5;DB;H2\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t1|0:48:8:51,51\t1/1:43:5:.,.") -} - -func (s *ReaderSuite) TestReaderHeaderInfos(c *C) { - v, err := vcfgo.NewReader(s.reader, false) - c.Assert(err, IsNil) - c.Assert(v.Header.Infos["NS"], DeepEquals, &vcfgo.Info{Id: "NS", Number: "1", Type: "Integer", Description: "Number of Samples With Data"}) - c.Assert(v.Header.Filters["q10"], Equals, "Quality below 10") - c.Assert(v.Header.SampleFormats["GT"], DeepEquals, &vcfgo.SampleFormat{Id: "GT", Number: "1", Type: "String", Description: "Genotype"}) -} - -func (s *ReaderSuite) TestReaderHeaderExtras(c *C) { - v, err := vcfgo.NewReader(s.reader, true) - c.Assert(err, IsNil) - c.Assert(len(v.Header.Extras), Equals, 4) - c.Assert(v.Header.Extras[0], Equals, "##fileDate=20090805") - -} - -func (s *ReaderSuite) TestReaderRead(c *C) { - rdr, err := vcfgo.NewReader(s.reader, false) - c.Assert(err, IsNil) - - rec := rdr.Read() //.(*vcfgo.Variant) - c.Assert(rec.Chromosome, Equals, "20") - c.Assert(rec.Pos, Equals, uint64(14370)) - c.Assert(rec.Id(), Equals, "rs6054257") - c.Assert(rec.Ref(), Equals, "G") - c.Assert(rec.Alt()[0], Equals, "A") - c.Assert(rec.Quality, Equals, float32(29.0)) - c.Assert(rec.Filter, Equals, "PASS") - - //20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 - rec0 := rdr.Read() //.(*vcfgo.Variant) - c.Assert(rec0.Chromosome, Equals, "20") - c.Assert(rec0.Pos, Equals, uint64(17330)) - c.Assert(rec0.Id(), Equals, ".") - c.Assert(rec0.Ref(), Equals, "T") - c.Assert(rec0.Alt()[0], Equals, "A") - c.Assert(rec0.Quality, Equals, float32(3)) - c.Assert(rec0.Filter, Equals, "q10") - - //20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 - rec = rdr.Read() //.(*vcfgo.Variant) - c.Assert(rec.Chromosome, Equals, "20") - c.Assert(int(rec.Pos), Equals, 1110696) - c.Assert(rec.Id(), Equals, "rs6040355") - c.Assert(rec.Ref(), Equals, "A") - c.Assert(rec.Alt(), DeepEquals, []string{"G", "T"}) - c.Assert(rec.Quality, Equals, float32(67)) - c.Assert(rec.Filter, Equals, "PASS") - - c.Assert(rec0.Chromosome, Equals, "20") - c.Assert(rec0.Pos, Equals, uint64(17330)) - c.Assert(rec0.Id(), Equals, ".") - c.Assert(rec0.Ref(), Equals, "T") - c.Assert(rec0.Alt()[0], Equals, "A") - c.Assert(rec0.Quality, Equals, float32(3)) - c.Assert(rec0.Filter, Equals, "q10") -} - -func (s *ReaderSuite) TestReaderRVGBug(c *C) { - v, err := os.Open("test-h.vcf") - if err != nil { - c.Fatalf("error opening test-h.vcf") - } - rdr, err := vcfgo.NewReader(v, false) - c.Assert(err, IsNil) - rec := rdr.Read() - _ = rec - -} - -func (s *ReaderSuite) TestSampleParsingErrors(c *C) { - sr := strings.NewReader(`##fileformat=VCFv4.0 -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S-1 S-2 S-3 -1 100000 . C G . . . GT 0|M 1/. 1/0 -2 200000 . C G . . . GT 0|0 0|1 1|E`) - - rdr, err := vcfgo.NewReader(sr, false) - - c.Assert(err, IsNil) - - c.Assert(rdr.Read(), NotNil) - c.Assert(rdr.Error(), ErrorMatches, ".*M.* invalid syntax.*") - - rdr.Clear() - - c.Assert(rdr.Read(), NotNil) - c.Assert(rdr.Error(), ErrorMatches, ".*E.* invalid syntax.*") -} - -func (s *ReaderSuite) TestSampleParsingErrors2(c *C) { - f, err := os.Open("test-dp.vcf") - c.Assert(err, IsNil) - - rdr, err := vcfgo.NewReader(f, false) - c.Assert(err, IsNil) - - variant := rdr.Read() - c.Assert(variant, NotNil) - - c.Assert(rdr.Error(), IsNil) - -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/README.md golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/README.md --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/README.md 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/README.md 1970-01-01 00:00:00.000000000 +0000 @@ -1,311 +0,0 @@ -[![GoDoc](https://godoc.org/github.com/brentp/vcfgo?status.svg)](https://godoc.org/github.com/brentp/vcfgo) -[![Build Status](https://travis-ci.org/brentp/vcfgo.svg)](https://travis-ci.org/brentp/vcfgo) -[![Coverage Status](https://coveralls.io/repos/brentp/vcfgo/badge.svg)](https://coveralls.io/r/brentp/vcfgo) - -vcfgo is a golang library to read, write and manipulate files in the variant call format. - -# vcfgo --- - import "github.com/brentp/vcfgo" - -Package vcfgo implements a Reader and Writer for variant call format. It eases -reading, filtering modifying VCF's even if they are not to spec. Example: - -## Usage - -```go -f, _ := os.Open("examples/test.auto_dom.no_parents.vcf") -rdr, err := vcfgo.NewReader(f, false) -if err != nil { - panic(err) -} -for { - variant := rdr.Read() - if variant == nil { - break - } - fmt.Printf("%s\t%d\t%s\t%v\n", variant.Chromosome, variant.Pos, variant.Ref(), variant.Alt()) - dp, err := variant.Info().Get("DP") - fmt.Printf("depth: %v\n", dp.(int)) - sample := variant.Samples[0] - // we can get the PL field as a list (-1 is default in case of missing value) - PL, err := variant.GetGenotypeField(sample, "PL", -1) - if err != nil { - panic(err) - } - fmt.Printf("%v\n", PL) - _ = sample.DP -} -fmt.Fprintln(os.Stderr, rdr.Error()) - -``` - -## Status - -`vcfgo` is well-tested, but still in development. It tries to tolerate, but report -errors; after every `rdr.Read()` call, the caller can check `rdr.Error()` -and get feedback on the errors without stopping execution unless it is explicitly -requested to do so. - -Info and sample fields are pre-parsed and stored as `map[string]interface{}` so -callers will have to cast to the appropriate type upon retrieval. - -#### type Header - -```go -type Header struct { - SampleNames []string - Infos map[string]*Info - SampleFormats map[string]*SampleFormat - Filters map[string]string - Extras map[string]string - FileFormat string - // contid id maps to a map of length, URL, etc. - Contigs map[string]map[string]string -} -``` - -Header holds all the type and format information for the variants. - -#### func NewHeader - -```go -func NewHeader() *Header -``` -NewHeader returns a Header with the requisite allocations. - -#### type Info - -```go -type Info struct { - Id string - Description string - Number string // A G R . '' - Type string // STRING INTEGER FLOAT FLAG CHARACTER UNKONWN -} -``` - -Info holds the Info and Format fields - -#### func (*Info) String - -```go -func (i *Info) String() string -``` -String returns a string representation. - -#### type InfoMap - -```go -type InfoMap map[string]interface{} -``` - -InfoMap holds the parsed Info field which can contain floats, ints and lists -thereof. - -#### func (InfoMap) String - -```go -func (m InfoMap) String() string -``` -String returns a string that matches the original info field. - -#### type Reader - -```go -type Reader struct { - Header *Header - - LineNumber int64 -} -``` - -Reader holds information about the current line number (for errors) and The VCF -header that indicates the structure of records. - -#### func NewReader - -```go -func NewReader(r io.Reader, lazySamples bool) (*Reader, error) -``` -NewReader returns a Reader. - -#### func (*Reader) Clear - -```go -func (vr *Reader) Clear() -``` -Clear empties the cache of errors. - -#### func (*Reader) Error - -```go -func (vr *Reader) Error() error -``` -Error() aggregates the multiple errors that can occur into a single object. - -#### func (*Reader) Read - -```go -func (vr *Reader) Read() *Variant -``` -Read returns a pointer to a Variant. Upon reading the caller is assumed to check -Reader.Err() - -#### type SampleFormat - -```go -type SampleFormat Info -``` - -SampleFormat holds the type info for Format fields. - -#### func (*SampleFormat) String - -```go -func (i *SampleFormat) String() string -``` -String returns a string representation. - -#### type SampleGenotype - -```go -type SampleGenotype struct { - Phased bool - GT []int - DP int - GL []float32 - GQ int - MQ int - Fields map[string]string -} -``` - -SampleGenotype holds the information about a sample. Several fields are -pre-parsed, but all fields are kept in Fields as well. - -#### func NewSampleGenotype - -```go -func NewSampleGenotype() *SampleGenotype -``` -NewSampleGenotype allocates the internals and returns a SampleGenotype - -#### func (*SampleGenotype) String - -```go -func (sg *SampleGenotype) String(fields []string) string -``` -String returns the string representation of the sample field. - -#### type VCFError - -```go -type VCFError struct { - Msgs []string - Lines []int64 -} -``` - -VCFError satisfies the error interface and allows multiple errors. This is -useful because, for example, on a single line, every sample may have a field -that doesn't match the description in the header. We want to keep parsing but -also let the caller know about the error. - -#### func NewVCFError - -```go -func NewVCFError() *VCFError -``` -NewVCFError allocates the needed ingredients. - -#### func (*VCFError) Add - -```go -func (e *VCFError) Add(err error, line int64) -``` -Add adds an error and the line number within the vcf where the error took place. - -#### func (*VCFError) Clear - -```go -func (e *VCFError) Clear() -``` -Clear empties the Messages - -#### func (*VCFError) Error - -```go -func (e *VCFError) Error() string -``` -Error returns a string with all errors delimited by newlines. - -#### func (*VCFError) IsEmpty - -```go -func (e *VCFError) IsEmpty() bool -``` -IsEmpty returns true if there no errors stored. - -#### type Variant - -```go -type Variant struct { - Chromosome string - Pos uint64 - Id string - Ref string - Alt []string - Quality float32 - Filter string - Info InfoMap - Format []string - Samples []*SampleGenotype - Header *Header - LineNumber int64 -} -``` - -Variant holds the information about a single site. It is analagous to a row in a -VCF file. - -#### func (*Variant) GetGenotypeField - -```go -func (v *Variant) GetGenotypeField(g *SampleGenotype, field string, missing interface{}) (interface{}, error) -``` -GetGenotypeField uses the information from the header to parse the correct time -from a genotype field. It returns an interface that can be asserted to the -expected type. - -#### func (*Variant) String - -```go -func (v *Variant) String() string -``` -String gives a string representation of a variant - -#### type Writer - -```go -type Writer struct { - io.Writer - Header *Header -} -``` - -Writer allows writing VCF files. - -#### func NewWriter - -```go -func NewWriter(w io.Writer, h *Header) (*Writer, error) -``` -NewWriter returns a writer after writing the header. - -#### func (*Writer) WriteVariant - -```go -func (w *Writer) WriteVariant(v *Variant) -``` -WriteVariant writes a single variant diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/regression_test.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/regression_test.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/regression_test.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/regression_test.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,65 +0,0 @@ -package vcfgo_test - -import ( - "fmt" - "io" - "strings" - - "github.com/brentp/vcfgo" - - . "gopkg.in/check.v1" -) - -var regr1 = `##fileformat=VCFv4.1 -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##INFO= -##INFO= -#CHROM POS ID REF ALT QUAL FILTER INFO -1 98683 . G A 610.487 . AB=0.282443;ABP=56.8661;AC=11;AF=0.34375;AN=32;AO=45;CIGAR=1X;TYPE=snp;XX=0.44,0.88 -1 98685 . G A 610.487 . AB=0;ABP=0` - -type RegressionSuite struct { - reader io.Reader - vcfStr string -} - -var _ = Suite(&RegressionSuite{vcfStr: regr1}) - -func (s *RegressionSuite) SetUpTest(c *C) { - s.reader = strings.NewReader(s.vcfStr) -} - -func (s *RegressionSuite) TestRegr1(c *C) { - rdr, err := vcfgo.NewReader(s.reader, false) - c.Assert(err, IsNil) - v := rdr.Read() //.(*vcfgo.Variant) - snp, err := v.Info().Get("TYPE") - c.Assert(err, IsNil) - c.Assert(snp, DeepEquals, []string{"snp"}) - - str := fmt.Sprintf("%s", v) - c.Assert(str, Equals, "1\t98683\t.\tG\tA\t610.5\t.\tAB=0.282443;ABP=56.8661;AC=11;AF=0.34375;AN=32;AO=45;CIGAR=1X;TYPE=snp;XX=0.44,0.88") -} - -func (s *RegressionSuite) TestRegr2(c *C) { - rdr, err := vcfgo.NewReader(s.reader, false) - c.Assert(err, IsNil) - v := rdr.Read() //.(*vcfgo.Variant) - v = rdr.Read() //.(*vcfgo.Variant) - - str := fmt.Sprintf("%s", v) - c.Assert(str, Equals, "1\t98685\t.\tG\tA\t610.5\t.\tAB=0;ABP=0") -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/sample_test.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/sample_test.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/sample_test.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/sample_test.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,137 +0,0 @@ -package vcfgo - -import ( - "bytes" - "io" - "strings" - - . "gopkg.in/check.v1" -) - -var sampleStr = `##fileformat=VCFv4.2 -##fileDate=20090805 -##source=myImputationProgramV3.1 -##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta -##contig= -##phasing=partial -##INFO= -##SAMPLE= -##SAMPLE= -##PEDIGREE= -##PEDIGREE= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BLOOD TISSUE` - -type SampleSuite struct { - reader io.Reader -} - -var _ = Suite(&SampleSuite{}) - -func (s *SampleSuite) SetUpTest(c *C) { - s.reader = strings.NewReader(sampleStr) - -} - -func (s *SampleSuite) TestReaderHeaderSamples(c *C) { - v, err := NewReader(s.reader, false) - c.Assert(err, IsNil) - c.Assert(v.Header.SampleNames, DeepEquals, []string{"BLOOD", "TISSUE"}) -} - -func (s *SampleSuite) TestReaderSamples(c *C) { - v, err := NewReader(s.reader, false) - c.Assert(err, IsNil) - samps := v.Header.Samples - c.Assert(len(samps), Equals, 2) - - for _, k := range []string{"Blood", "TissueSample"} { - _, ok := samps[k] - c.Assert(ok, Equals, true) - } - -} - -func (s *SampleSuite) TestWriterSamples(c *C) { - r, err := NewReader(s.reader, false) - c.Assert(err, IsNil) - - var wtr bytes.Buffer - _, err = NewWriter(&wtr, r.Header) - c.Assert(err, IsNil) - - str := wtr.String() - - c.Assert(strings.Contains(str, "\n##SAMPLE== len(ml) { - return nil, fmt.Errorf("requested bad alt in splitR: %v", m) - } - out := make([]interface{}, 2) - out[0] = ml[0] - out[1] = ml[i+1] - return out, nil -} - -// when we split on alt, it returns a single int since we are decomposing. -func splitA(m interface{}, i int, nAlts int) (interface{}, error) { - ml := m.([]interface{}) - if len(ml) != nAlts { - return nil, fmt.Errorf("incorrect number of alts in splitA: %v", m) - } - return ml[i], nil -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/splitalts_test.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/splitalts_test.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/splitalts_test.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/splitalts_test.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,81 +0,0 @@ -package vcfgo - -import . "gopkg.in/check.v1" - -type SplitAltSuite struct { -} - -var _ = Suite(&SplitAltSuite{}) - -func (s *SplitAltSuite) SetUpTest(c *C) { -} - -func (s *SplitAltSuite) TestSplitA(c *C) { - - in := []interface{}{"AA", "BB", "CC"} - out, err := splitA(in, 0, 3) - c.Assert(err, IsNil) - c.Assert(out, Equals, "AA") - - out, err = splitA(in, 0, 4) - c.Assert(err, Not(IsNil)) - - out, err = splitA(in, 2, 3) - c.Assert(err, IsNil) - c.Assert(out, Equals, "CC") - - in2 := []interface{}{} - out, err = splitA(in2, 0, 3) - c.Assert(err, Not(IsNil)) - -} - -func (s *SplitAltSuite) TestSplitR(c *C) { - - in := []interface{}{"ref", "alt1", "alt2"} - out, err := splitR(in, 0, 3) - c.Assert(err, Not(IsNil)) - c.Assert(out, IsNil) - - out, err = splitR(in, 0, 2) - c.Assert(err, IsNil) - c.Assert(out, DeepEquals, []interface{}{"ref", "alt1"}) - - out, err = splitR(in, 1, 2) - c.Assert(err, IsNil) - c.Assert(out, DeepEquals, []interface{}{"ref", "alt2"}) - - out, err = splitR(in, 2, 2) - c.Assert(err, Not(IsNil)) -} - -func (s *SplitAltSuite) TestSplitG(c *C) { - - in := []interface{}{281, 5, 9, 58, 0, 115, 338, 46, 116, 809} - out, err := splitG(in, 1, 3) - c.Assert(err, IsNil) - c.Assert(out, DeepEquals, []interface{}{281, 5, 9}) - - out, err = splitG(in, 2, 3) - c.Assert(err, IsNil) - c.Assert(out, DeepEquals, []interface{}{281, 58, 115}) - - in = []interface{}{0, 30, 323, 31, 365, 483, 38, 291, 325, 567} - out, err = splitG(in, 3, 3) - c.Assert(err, IsNil) - c.Assert(out, DeepEquals, []interface{}{0, 38, 567}) - -} -func (s *SplitAltSuite) TestSplitGT(c *C) { - - in := []interface{}{"1", "2"} - out, err := splitGT(in, 3) - c.Assert(err, IsNil) - c.Assert(out, DeepEquals, []interface{}{".", "."}) - - in = []interface{}{"1", "2"} - out, err = splitGT(in, 2) - c.Assert(err, IsNil) - c.Assert(out, DeepEquals, []interface{}{".", "1"}) - -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/sv_test.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/sv_test.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/sv_test.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/sv_test.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,116 +0,0 @@ -package vcfgo_test - -import ( - "io" - "strings" - - "github.com/brentp/vcfgo" - - . "gopkg.in/check.v1" -) - -var cnvStr = `##fileformat=VCFv4.1 -##fileDate=20100501 -##reference=1000GenomesPilot-NCBI36 -##assembly=ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/sv/breakpoint_assemblies.fasta -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##ALT= -##ALT= -##ALT= -##ALT= -##ALT= -##ALT= -##ALT= -##ALT= -##ALT= -##ALT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 -2 321682 . T 6 PASS SVTYPE=DEL;END=321887;SVLEN=-205;CIPOS=-56,20;CIEND=-10,62 GT:GQ 0/1:12 -2 14477084 . C 12 PASS SVTYPE=DEL;END=14477381;CIPOS=-22,18;CIEND=-12,32 GT:GQ 0/1:12 -3 9425916 . C 23 PASS SVTYPE=INS;SVLEN=6027;CIPOS=-16,22 GT:GQ 1/1:15 -3 12665100 . A 14 PASS SVTYPE=DUP;END=12686200;SVLEN=21100;CIPOS=-500,500;CIEND=-500,500 GT:GQ:CN:CNQ ./.:0:3:16.2 -4 18665128 . T 11 PASS SVTYPE=DUP;END=18665204;SVLEN=76;CIPOS=-10,10;CIEND=-10,10 GT:GQ:CN:CNQ ./.:0:5:8.3 -4 18665128 . T 11 PASS SVTYPE=INS;END=18665204;SVLEN=76;CIPOS=-10,10;CIEND=-10,10 GT:GQ:CN:CNQ ./.:0:5:8.3 -4 18665128 . T 11 PASS SVTYPE=DUP;END=18665204;SVLEN=76;CIPOS=-10,10;CIEND=-10,10 GT:GQ:CN:CNQ ./.:0:5:8.3 -4 43266825 rs369548269 T . . ON=0;OLD_MULTIALLELIC=4:43266825:T/TAC/ GT 0/1 -5 755892 175981_1 N ]1:759001]N 112.69 PASS AC=4;AF=0.01361;ALG=PROD;AN=294;CIEND=-10,29;CIEND95=0,34;CIPOS=-30,29;CIPOS95=28,32;EVENT=175981;EXVAR=0.00508;HW=0.00;HetPct=2.7;HomRefPct=97.3;HomVarPct=0.0;IMPRECISE;MATEID=1 GT 0/1` - -//1 2827694 rs2376870 CGTGGATGCGGGGAC C . PASS SVTYPE=DEL;END=2827762;HOMLEN=1;HOMSEQ=G;SVLEN=-68 GT:GQ 1/1:13.9 - -type CNVSuite struct { - reader io.Reader - vcfStr string -} - -var _ = Suite(&CNVSuite{vcfStr: cnvStr}) - -func (s *CNVSuite) SetUpTest(c *C) { - s.reader = strings.NewReader(s.vcfStr) -} - -func (s *CNVSuite) TestDupIns(c *C) { - r, err := vcfgo.NewReader(s.reader, false) - c.Assert(err, IsNil) - var v *vcfgo.Variant - - v = r.Read() //.(*vcfgo.Variant) - c.Assert(int(v.End()), Equals, 321887) - - left, right, ok := v.CIPos() - c.Assert(ok, Equals, true) - c.Assert(int(left), Equals, 321682-56-1) - c.Assert(int(right), Equals, 321682+20) - - eleft, eright, ok := v.CIEnd() - c.Assert(ok, Equals, true) - c.Assert(int(eleft), Equals, 321887-10-1) - c.Assert(int(eright), Equals, 321887+62) - - v = r.Read() //.(*vcfgo.Variant) - c.Assert(int(v.End()), Equals, 14477381) - - v = r.Read() //.(*vcfgo.Variant) - c.Assert(int(v.Start()), Equals, 9425915) - c.Assert(int(v.End()), Equals, 9431943) - - v = r.Read() //.(*vcfgo.Variant) - c.Assert(int(v.End()), Equals, 12686200) - - v = r.Read() //.(*vcfgo.Variant) - c.Assert(int(v.End()), Equals, 18665204) - - v = r.Read() //.(*vcfgo.Variant) // INS - c.Assert(int(v.End()), Equals, 18665204) - - v = r.Read() //.(*vcfgo.Variant) // CNV - c.Assert(int(v.End()), Equals, 18665204) - - v = r.Read() //.(*vcfgo.Variant) // CNV - c.Assert(int(v.End()), Equals, 43266825) - - left, right, ok = v.CIPos() - c.Assert(left, Equals, v.Start()) - c.Assert(right, Equals, v.Start()+uint32(1)) - c.Assert(ok, Equals, false) - - eleft, eright, ok = v.CIEnd() - c.Assert(eleft, Equals, v.End()-1) - c.Assert(right, Equals, v.End()) - c.Assert(ok, Equals, false) - - v = r.Read() //.(*vcfgo.Variant) // BND - c.Assert(int(v.Start()), Equals, 755891) - c.Assert(int(v.End()), Equals, 755891+1) - -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/test-dp.vcf golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/test-dp.vcf --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/test-dp.vcf 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/test-dp.vcf 1970-01-01 00:00:00.000000000 +0000 @@ -1,63 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##fileDate=20190823 -##reference=GRCh38_full_analysis_set_plus_decoy_hla.fa -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##ALT= -##ALT= -##ALT= -##ALT= -##ALT= -##ALT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##smoove_count_stats=16239X1:12295708,26753588,800025,6216842 -##bcftools_viewVersion=1.9+htslib-1.9 -##smoove_version=0.2.4 -##contig= -##bcftools_annotateVersion=1.9+htslib-1.9 -##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Oz -o 16239X1-smoove.genotyped.vcf.gz; Date=Fri Aug 23 18:11:55 2019 -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tumor -chr1 180214710 1836 N 1711.24 . SVTYPE=DEL;SVLEN=-242;END=180214952;STRANDS=+-:16;IMPRECISE;CIPOS=-30,184;CIEND=-241,29;CIPOS95=-12,26;CIEND95=-23,14;SU=16;PE=16;SR=0;SNAME=tow19_tumor:605;ALG=PROD;GCF=0.563786;AN=2;AC=2 GT:GQ:SQ:GL:DP ./.:.:.:.:0 diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/test-h.vcf golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/test-h.vcf --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/test-h.vcf 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/test-h.vcf 1970-01-01 00:00:00.000000000 +0000 @@ -1,277 +0,0 @@ -##fileformat=VCFv4.2 -##FILTER= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##SAMPLE= -##PEDIGREE= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER==14)"> -##FILTER= -##FILTER= -##FILTER= 0.05, thus not somatic"> -##FILTER= -##FILTER== 4.25, thus likely false positive"> -##FILTER= 0.01/5**vd2"> -##FILTER= 0.9"> -##FILTER= -##FILTER= -##FILTER= -##FILTER= 0.35) and low p-value for somatic (SPV < 0.05)"> -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= 1 indicates MSI"> -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##GATKCommandLine= -##Mutect Version=2.1-beta -##SnpEffCmd="SnpEff -cancer -i vcf -o vcf -csvStats /data/projects/punim0010/projects/Grimmond_Patients/brigibFFPE/work/vardict/batch1-effects-stats.csv -s /data/projects/punim0010/projects/Grimmond_Patients/brigibFFPE/work/vardict/batch1-effects-stats.html GRCh37.75 /data/projects/punim0010/projects/Grimmond_Patients/brigibFFPE/work/vardict/batch1.vcf.gz " -##SnpEffVersion="4.3i (build 2016-12-15 22:33), by Pablo Cingolani" -##bcftools_annotateCommand=annotate --set-id +%INFO/rs_ids -o /data/projects/punim0010/projects/Grimmond_Patients/brigibFFPE/work/bcbiotx/tmpgXBf2A/batch1-1_0_16151943.vcf.gz -O z; Date=Sun Sep 17 09:57:35 2017 -##bcftools_annotateVersion=1.5+htslib-1.5 -##bcftools_filterCommand=filter -i 'QUAL >= 0'; Date=Sun Sep 17 09:57:28 2017 -##bcftools_filterVersion=1.5+htslib-1.5 -##bcftools_viewCommand=view -f PASS,. -O z -o /data/projects/punim0010/projects/Grimmond_Patients/brigibFFPE/work/bcbiotx/tmpjSPYhS/batch1-ensemble-work/txtmp6440159648747552230/vardict-batch1-effects-annotated-damage-ann-nofilter.vcf.gz /data/projects/punim0010/projects/Grimmond_Patients/brigibFFPE/work/vardict/batch1-effects-annotated-damage-ann.vcf.gz; Date=Tue Sep 19 18:31:21 2017 -##bcftools_viewVersion=1.5+htslib-1.5 -##filtering_status=These calls have been filtered by FilterMutectCalls to label false positives with a list of failed filters and true positives with PASS. -##normal_sample=BriGibBld -##reference=file:///data/projects/punim0010/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -##source=VarScan2 -##tumor_sample=BriGibFFPE -##bcftools_viewCommand=view -r 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y batch1-ensemble-annotated.vcf.gz; Date=Wed Sep 20 16:30:20 2017 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BriGibFFPE BriGibBld -1 16234 . T C 210 PASS ACGTNacgtnMINUS=0,12,0,40,0,0,15,0,8,0;ACGTNacgtnPLUS=0,7,0,36,0,0,13,0,4,0;ANN=C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328|processed_transcript||n.*1825T>C|||||1825|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene||n.*1822T>C|||||1822|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene||n.*1825T>C|||||1825|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene||n.*2564T>C|||||2564|,C|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene|8/11|n.1098-287A>G||||||,C|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene|7/8|n.880+620A>G||||||,C|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene|7/9|n.982-287A>G||||||,C|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene|8/10|n.1068-287A>G||||||,C|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene|9/12|n.1303-287A>G||||||;CALLERS=vardict,varscan,mutect2;LSEQ=CCATGCTCTGACAGTCTCAG;MSI=2;MSILEN=1;RSEQ=TGCACACACGAGCCAGCAGA;SAMPLE=BriGibFFPE;SHIFT3=0;SOMATIC;SOR=inf;SSF=0;STATUS=StrongSomatic;TYPE=SNV;fitcons=0.2558;encode_consensus_gm12878=T;encode_consensus_h1hesc=CTCF;encode_consensus_helas3=T;encode_consensus_hepg2=T;encode_consensus_huvec=CTCF;encode_consensus_k562=CTCF;dgv=CopyNumber;tfbs=CTCF;hapmap1=2.9818;hapmap2=0;stam_mean=18.7689;stam_names=CD34,CMK,Fibrobl,HFF,SK_N_MC 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NA21098 NA21099 NA21100 NA21101 NA21102 NA21103 NA21104 NA21105 NA21106 NA21107 NA21108 NA21109 NA21110 NA21111 NA21112 NA21113 NA21114 NA21115 NA21116 NA21117 NA21118 NA21119 NA21120 NA21122 NA21123 NA21124 NA21125 NA21126 NA21127 NA21128 NA21129 NA21130 NA21133 NA21135 NA21137 NA21141 NA21142 NA21143 NA21144 -22 16061250 rs60160543 T A,C 100 PASS AC=8,5000;AF=0.00159744,0.998403;AN=5008;NS=2504;DP=22899;EAS_AF=0.005,0.995;AMR_AF=0,1;AFR_AF=0.0008,0.9992;EUR_AF=0,1;SAS_AF=0.002,0.998;AA=.|||;VT=SNP;MULTI_ALLELIC GT 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 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2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 2|2 diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/test-weird-header.vcf golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/test-weird-header.vcf --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/test-weird-header.vcf 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/test-weird-header.vcf 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-##contig= -##contig= -##contig= -##contig= -##contig= -##contig= -##filtering_status=These calls have been filtered by FilterMutectCalls to label false positives with a list of failed filters and true positives with PASS. -##source=FilterMutectCalls -##source=Mutect2 -##tumor_sample=UKB_1098724_0230794985 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT UKB_1098724_0230794985 diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/.travis.yml golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/.travis.yml --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/.travis.yml 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/.travis.yml 1970-01-01 00:00:00.000000000 +0000 @@ -1,17 +0,0 @@ -language: go - -go: - - 1.3 - - 1.4.2 - - 1.5 - - 1.6 - - 1.7 - - tip - -before_install: - - go get github.com/axw/gocov/gocov - - go get github.com/mattn/goveralls - - if ! go get code.google.com/p/go.tools/cmd/cover; then go get golang.org/x/tools/cmd/cover; fi -script: - - $HOME/gopath/bin/goveralls -service=travis-ci - diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/variant.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/variant.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/variant.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/variant.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,420 +0,0 @@ -package vcfgo - -import ( - "errors" - "fmt" - "log" - "strconv" - "strings" - - "github.com/brentp/irelate/interfaces" -) - -// Variant holds the information about a single site. It is analagous to a row in a VCF file. -type Variant struct { - Chromosome string - Pos uint64 - Id_ string - Reference string - Alternate []string - Quality float32 - Filter string - Info_ interfaces.Info - Format []string - Samples []*SampleGenotype - // if lazy parsing, then just save the sample strings here. - sampleString string - Header *Header - LineNumber int64 -} - -func (v *Variant) Info() interfaces.Info { - return v.Info_ -} - -func (v *Variant) Id() string { - return v.Id_ -} - -func (v *Variant) Ref() string { - return v.Reference -} - -func (v *Variant) Alt() []string { - return v.Alternate -} - -// Chrom returns the chromosome name. -func (v *Variant) Chrom() string { - return v.Chromosome -} - -// Start returns the 0-based start -func (v *Variant) Start() uint32 { - return uint32(v.Pos - 1) -} - -// CIPos reports the Left and Right end of an SV using the CIPOS tag. It is in -// bed format so the end is +1'ed. E.g. If there is not CIPOS, the return value -// is v.Start(), v.Start() + 1 -func (v *Variant) CIPos() (uint32, uint32, bool) { - if v.Header == nil { - v.Header = NewHeader() - } - s := v.Start() - v.Header.RLock() - if _, ok := v.Header.Infos["CIPOS"]; !ok { - v.Header.RUnlock() - v.Header.Lock() - v.Header.Infos["CIPOS"] = &Info{Id: "CIPOS", Number: "2", Description: "CIPOS", Type: "Integer"} - v.Header.Unlock() - } else { - v.Header.RUnlock() - } - - ipair, err := v.Info().Get("CIPOS") - if ipair == nil && err != nil { - return s, s + 1, false - } - pair, ok := ipair.([]int) - if !ok { - return s, s + 1, false - } - left := pair[0] - right := pair[1] - return uint32(int(s) + left), uint32(int(s) + right + 1), true -} - -// CIEnd reports the Left and Right end of an SV using the CIEND tag. It is in -// bed format so the end is +1'ed. E.g. If there is no CIEND, the return value -// is v.End() - 1, v.End() -func (v *Variant) CIEnd() (uint32, uint32, bool) { - if v.Header == nil { - v.Header = NewHeader() - } - e := v.End() - v.Header.RLock() - if _, ok := v.Header.Infos["CIEND"]; !ok { - v.Header.RUnlock() - v.Header.Lock() - v.Header.Infos["CIEND"] = &Info{Id: "CIEND", Number: "2", Description: "CIEND", Type: "Integer"} - v.Header.Unlock() - } else { - v.Header.RUnlock() - } - ipair, err := v.Info().Get("CIEND") - if ipair == nil && err != nil { - return e - 1, e, false - } - pair, ok := ipair.([]int) - if !ok { - return e - 1, e, false - } - left := pair[0] - right := pair[1] - return uint32(int(e)+left) - 1, uint32(int(e) + right), true -} - -// End returns the 0-based start + the length of the reference allele. -func (v *Variant) End() uint32 { - /* - if len(v.Alt()[0]) == 0 { - log.Println(v.Chrom(), v.Start()+1, v.Ref(), v.Alt()) - }*/ - a := v.Alt()[0] - if len(a) == 0 || a[0] != '<' { - return uint32(v.Pos-1) + uint32(len(v.Ref())) - } - if strings.HasPrefix(v.Alt()[0], " 0.02 || v < -0.02 { - val = fmt.Sprintf("%.4f", v) - } else { - val = fmt.Sprintf("%.5g", v) - } - val = strings.TrimRight(strings.TrimRight(val, "0"), ".") - if val == "" || val == "-" { - val = "0" - } - return val -} - -func fmtFloat64(v float64) string { - var val string - if v > 0.02 || v < -0.02 { - val = fmt.Sprintf("%.4f", v) - } else { - val = fmt.Sprintf("%.5g", v) - } - val = strings.TrimRight(strings.TrimRight(val, "0"), ".") - if val == "" || val == "-" { - val = "0" - } - return val -} - -// SampleGenotype holds the information about a sample. Several fields are pre-parsed, but -// all fields are kept in Fields as well. -type SampleGenotype struct { - Phased bool - GT []int - DP int - GL []float64 - GQ int - MQ int - Fields map[string]string -} - -// RefDepth returns the depths of the alternates for this sample -func (s *SampleGenotype) RefDepth() (int, error) { - if ad, ok := s.Fields["AD"]; ok { - idx := strings.Index(ad, ",") - return strconv.Atoi(ad[:idx]) - } - if ro, ok := s.Fields["RO"]; ok { - return strconv.Atoi(ro) - } - return 0, errors.New("only freebayes and gatk depths supported at this time") -} - -// AltDepths returns the depths of the alternates for this sample -func (s *SampleGenotype) AltDepths() ([]int, error) { - var svals []string - if ad, ok := s.Fields["AD"]; ok { - idx := strings.Index(ad, ",") - svals = strings.Split(ad[idx+1:], ",") - } else if ro, ok := s.Fields["AO"]; ok { - svals = strings.Split(ro, ",") - } else { - return []int{}, errors.New("only freebayes and GATK supported for ref/alt depths") - } - vals := make([]int, len(svals)) - for i := range svals { - v, err := strconv.Atoi(svals[i]) - if err != nil { - return []int{}, err - } - vals[i] = v - } - return vals, nil -} - -// String returns the string representation of the sample field. -func (sg *SampleGenotype) String(fields []string) string { - if len(fields) == 0 { - return "." - } - - s := make([]string, len(fields)) - for i, f := range fields { - s[i] = sg.Fields[f] - } - return strings.Join(s, ":") -} - -// NewSampleGenotype allocates the internals and returns a *SampleGenotype -func NewSampleGenotype() *SampleGenotype { - s := &SampleGenotype{} - s.GT = make([]int, 0, 2) - s.GL = make([]float64, 0, 3) - s.Fields = make(map[string]string) - return s -} - -// String gives a string representation of a variant -func (v *Variant) String() string { - var qual string - if v.Quality == MISSING_VAL { - qual = "." - } else { - qual = fmt.Sprintf("%.1f", v.Quality) - } - s := fmt.Sprintf("%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s", v.Chromosome, v.Pos, v.Id_, v.Ref(), strings.Join(v.Alt(), ","), qual, v.Filter, v.Info()) - if len(v.Samples) > 0 { - samps := make([]string, len(v.Samples)) - for i, s := range v.Samples { - samps[i] = s.String(v.Format) - } - s += fmt.Sprintf("\t%s\t%s", strings.Join(v.Format, ":"), strings.Join(samps, "\t")) - } else if v.sampleString != "" { - s += fmt.Sprintf("\t%s\t%s", strings.Join(v.Format, ":"), v.sampleString) - } - return s -} - -// GetGenotypeField uses the information from the header to parse the correct time from a genotype field. -// It returns an interface that can be asserted to the expected type. -func (v *Variant) GetGenotypeField(g *SampleGenotype, field string, missing interface{}) (interface{}, error) { - if g == nil { - return missing, fmt.Errorf("GetGenotypeField: empty genotype when requesting %s", field) - } - h := v.Header - format, ok := h.SampleFormats[field] - if !ok { - return nil, fmt.Errorf("GetGenotypeField: field not found in formats: %s", field) - } - value, ok := g.Fields[field] - if !ok { - return nil, fmt.Errorf("GetGenotypeField: field not found in genotypes: %s", field) - } - switch format.Type { - case "Integer": - var mv int - var ok bool - if mv, ok = missing.(int); !ok { - return nil, fmt.Errorf("GetGenotypeField: bad non-int missing value: %v", missing) - } - return handleNumberType(format.Number, value, len(v.Alt()), len(g.GT), true, mv) - - case "Float": - var mv float32 - var ok bool - if mv, ok = missing.(float32); !ok { - return nil, fmt.Errorf("GetGenotypeField: bad non-float missing value: %v", missing) - } - return handleNumberType(format.Number, value, len(v.Alt()), len(g.GT), false, mv) - - case "String", "Character", "Unknown": - return value, nil - - case "Flag": - return field, nil - - } - - return nil, fmt.Errorf("unknown format: %s", format.Type) -} - -func handleNumberType(number string, value string, nAlts int, nGTs int, isInt bool, mv interface{}) (interface{}, error) { - if number == "1" || !strings.Contains(value, ",") || number == "." || number == "" { - if isInt { - if value == "" || value == "." { - return (mv).(int), nil - } - return strconv.Atoi(value) - } - if value == "" || value == "." { - return (mv).(float32), nil - } - return strconv.ParseFloat(value, 32) - } - if count, err := strconv.Atoi(number); err == nil || number == "G" || number == "A" || number == "R" { - if err != nil { - switch number { - case "G": - count = nGTs * (nGTs + 1) / 2 - case "A": - count = nAlts - case "R": - count = nAlts + 1 - } - err = nil - } - var ret interface{} - split := strings.Split(value, ",") - if isInt { - ret = make([]int, len(split), len(split)) - } else { - ret = make([]float32, len(split), len(split)) - } - - var countErr error - - // caller can ignore error if they want, we still fill what we can. - if len(split) != count { - countErr = fmt.Errorf("number of fields (%d) does not match expected (%d) in '%s'", len(split), count, value) - } - for i, s := range split { - if isInt { - ri, err := strconv.Atoi(s) //, 10, 32) - if err != nil { - // if it's an error, we allow empty - if s == "" || s == "." { - ret.([]int)[i] = mv.(int) - err = nil - } else { - return nil, fmt.Errorf("non integer type: %s", s) - } - } else { - ret.([]int)[i] = int(ri) - } - } else { - rf, err := strconv.ParseFloat(s, 32) - if err != nil { - // if it's an error, we allow empty - if s == "" || s == "." { - ret.([]float32)[i] = mv.(float32) - err = nil - } else { - return nil, fmt.Errorf("non float type: %s", s) - } - } else { - ret.([]float32)[i] = float32(rf) - } - } - } - return ret, countErr - } else if number == "." || number == "" { - return value, nil - } else { - return nil, fmt.Errorf("unknown number field: %s", number) - } -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/variant_test.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/variant_test.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/variant_test.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/variant_test.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,91 +0,0 @@ -package vcfgo_test - -import ( - "fmt" - "io" - "strings" - - "github.com/brentp/vcfgo" - - . "gopkg.in/check.v1" -) - -type VariantSuite struct { - reader io.Reader -} - -var _ = Suite(&VariantSuite{}) - -func (s *VariantSuite) SetUpTest(c *C) { - s.reader = strings.NewReader(vcfStr) -} - -func (s *VariantSuite) TestVariantGetInt(c *C) { - rdr, err := vcfgo.NewReader(s.reader, true) - c.Assert(err, IsNil) - v := rdr.Read() //.(*vcfgo.Variant) - v.Info() - - ns, err := v.Info_.Get("NS") - c.Assert(err, IsNil) - c.Assert(ns, Equals, 3) - - dp, err := v.Info_.Get("DP") - c.Assert(dp, Equals, 14) - c.Assert(err, IsNil) - - nsf, err := v.Info_.Get("NS") - c.Assert(err, IsNil) - c.Assert(nsf, Equals, int(3)) - - dpf, err := v.Info_.Get("DP") - c.Assert(err, IsNil) - c.Assert(dpf, Equals, int(14)) - - hqs, err := v.Info_.Get("AF") - c.Assert(hqs, DeepEquals, []float32{0.5}) - c.Assert(err, IsNil) - - dpfs, err := v.Info_.Get("DP") - c.Assert(err, IsNil) - c.Assert(dpfs, DeepEquals, 14) - -} - -func (s *VariantSuite) TestInfoField(c *C) { - rdr, err := vcfgo.NewReader(s.reader, false) - c.Assert(err, IsNil) - v := rdr.Read() //.(*vcfgo.Variant) - vstr := fmt.Sprintf("%s", v.Info()) - c.Assert(vstr, Equals, "NS=3;DP=14;AF=0.5;DB;H2") -} - -func (s *VariantSuite) TestInfoMap(c *C) { - rdr, err := vcfgo.NewReader(s.reader, false) - c.Assert(err, IsNil) - v := rdr.Read() //.(*vcfgo.Variant) - - vstr := fmt.Sprintf("%s", v) - c.Assert(vstr, Equals, "20\t14370\trs6054257\tG\tA\t29.0\tPASS\tNS=3;DP=14;AF=0.5;DB;H2\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t1|0:48:8:51,51\t1/1:43:5:.,.") - - v.Info_.Set("asdf", 123) - v.Info_.Set("float", 123.2001) - has, err := v.Info_.Get("asdf") - c.Assert(has, Equals, "123") - _, err = v.Info_.Get("float") - c.Assert(err, ErrorMatches, ".*float not found in header.*") - - c.Assert(fmt.Sprintf("%s", v.Info_), Equals, "NS=3;DP=14;AF=0.5;DB;H2;asdf=123;float=123.2001") - - rdr.Clear() - -} - -func (s *VariantSuite) TestStartEnd(c *C) { - rdr, err := vcfgo.NewReader(s.reader, false) - c.Assert(err, IsNil) - v := rdr.Read() - - c.Assert(int(v.Start()), Equals, 14369) - c.Assert(int(v.End()), Equals, 14370) -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/vcf.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/vcf.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/vcf.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/vcf.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,65 +0,0 @@ -package vcfgo - -import ( - "fmt" - "strings" -) - -// VCFError satisfies the error interface and allows multiple errors. -// This is useful because, for example, on a single line, every sample may have -// a field that doesn't match the description in the header. We want to keep parsing -// but also let the caller know about the error. -type VCFError struct { - Msgs []string - Lines []int64 -} - -// Error returns a string with all errors delimited by newlines. -func (e *VCFError) Error() string { - var msgs []string - seen := make(map[string]struct{}) - for i, m := range e.Msgs { - // remove duplicates - if _, ok := seen[m]; !ok { - seen[m] = struct{}{} - msgs = append(msgs, fmt.Sprintf("%s. [line: %d]", m, e.Lines[i])) - } - } - return strings.Join(msgs, "\n") -} - -// NewVCFError allocates the needed ingredients. -func NewVCFError() *VCFError { - e := VCFError{Msgs: make([]string, 0), Lines: make([]int64, 0)} - return &e -} - -// Add adds an error and the line number within the vcf where the error took place. -func (e *VCFError) Add(err error, line int64) { - if err != nil { - if ierr := err.Error(); ierr != "" { - if len(e.Msgs) == 5000 { - // only keep at most 5K errors. - m := make([]string, 0, 5000) - l := make([]int64, 0, 5000) - m = append(m, e.Msgs[3000:]...) - l = append(l, e.Lines[3000:]...) - e.Msgs = m - e.Lines = l - } - e.Msgs = append(e.Msgs, ierr) - e.Lines = append(e.Lines, line) - } - } -} - -// IsEmpty returns true if there no errors stored. -func (e *VCFError) IsEmpty() bool { - return len(e.Msgs) == 0 -} - -// Clear empties the Messages -func (e *VCFError) Clear() { - e.Msgs = e.Msgs[:0] - e.Lines = e.Lines[:0] -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/vcf_test.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/vcf_test.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/vcf_test.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/vcf_test.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,140 +0,0 @@ -package vcfgo - -import ( - "os" - "testing" - - . "gopkg.in/check.v1" -) - -func Test(t *testing.T) { TestingT(t) } - -type VCFSuite struct{} - -var _ = Suite(&VCFSuite{}) - -var infotests = []struct { - input string - exp *Info -}{ - {`##INFO=`, - &Info{Id: "NS", Number: "1", Type: "Integer", Description: "Number of Samples With Data"}}, - {`##INFO=`, - &Info{Id: "DP", Number: "1", Type: "Integer", Description: "Total Depth"}}, - {`##INFO=`, - &Info{Id: "AF", Number: "A", Type: "Float", Description: "Allele Frequency"}}, - {`##INFO=`, - &Info{Id: "AA", Number: "1", Type: "String", Description: "Ancestral Allele"}}, - {`##INFO=`, - &Info{Id: "DB", Number: "0", Type: "Flag", Description: "dbSNP membership, build 129"}}, - {`##INFO=`, - &Info{Id: "H2", Number: "0", Type: "Flag", Description: "HapMap2 membership"}}, -} - -var formattests = []struct { - input string - exp *SampleFormat -}{ - {`##FORMAT=`, - &SampleFormat{Id: "GT", Number: "1", Type: "String", Description: "Genotype"}}, - {`##FORMAT=`, - &SampleFormat{Id: "GQ", Number: "1", Type: "Integer", Description: "Genotype Quality"}}, - {`##FORMAT=`, - &SampleFormat{Id: "HQ", Number: "2", Type: "Integer", Description: "Haplotype Quality"}}, - {`##FORMAT=`, - &SampleFormat{Id: "DP", Number: "1", Type: "Integer", Description: "Read Depth"}}, -} - -var filtertests = []struct { - filter string - exp []string -}{ - {`##FILTER=`, - []string{"q10", "Quality below 10"}}, - {`##FILTER=`, - []string{"s50", "Less than 50% of samples have data"}}, -} - -var samplelinetests = []struct { - line string - exp []string -}{ - {`#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003`, []string{"NA00001", "NA00002", "NA00003"}}, - {`#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT`, []string{}}, -} - -func (s *VCFSuite) TestHeaderInfoParse(c *C) { - for _, v := range infotests { - obs, err := parseHeaderInfo(v.input) - c.Assert(err, IsNil) - c.Assert(obs, DeepEquals, v.exp) - c.Assert(obs.String(), Equals, v.input) - } -} - -func (s *VCFSuite) TestHeaderFormatParse(c *C) { - for _, v := range formattests { - obs, err := parseHeaderFormat(v.input) - c.Assert(err, IsNil) - c.Assert(obs, DeepEquals, v.exp) - c.Assert(obs.String(), Equals, v.input) - - } -} - -func (s *VCFSuite) TestHeaderFilterParse(c *C) { - - for _, v := range filtertests { - obs, err := parseHeaderFilter(v.filter) - c.Assert(err, IsNil) - c.Assert(obs, DeepEquals, v.exp) - } -} - -func (s *VCFSuite) TestHeaderVersionParse(c *C) { - obs, err := parseHeaderFileVersion(`##fileformat=VCFv4.2`) - c.Assert(err, IsNil) - c.Assert(obs, Equals, "4.2") -} - -func (s *VCFSuite) TestHeaderBadVersionParse(c *C) { - _, err := parseHeaderFileVersion(`##fileformat=VFv4.2`) - c.Assert(err, ErrorMatches, "file format error.*") -} - -func (s *VCFSuite) TestHeaderContigParse(c *C) { - m, err := parseHeaderContig(`##contig=`) - c.Assert(err, IsNil) - c.Assert(m, DeepEquals, map[string]string{"assembly": "B36", "md5": "f126cdf8a6e0c7f379d618ff66beb2da", "species": "\"Homo sapiens\"", "taxonomy": "x", "ID": "20", "length": "62435964"}) -} - -func (s *VCFSuite) TestHeaderExtra(c *C) { - obs, err := parseHeaderExtraKV("##key=value") - c.Assert(err, IsNil) - c.Assert(obs[0], Equals, "key") - c.Assert(obs[1], Equals, "value") -} - -func (s *VCFSuite) TestHeaderSampleLine(c *C) { - - for _, v := range samplelinetests { - r, err := parseSampleLine(v.line) - c.Assert(err, IsNil) - c.Assert(r, DeepEquals, v.exp) - } -} - -func (s *VCFSuite) TestIssue5(c *C) { - rdr, err := os.Open("test-multi-allelic.vcf") - c.Assert(err, IsNil) - vcf, err := NewReader(rdr, false) - c.Assert(err, IsNil) - - variant := vcf.Read() - samples := variant.Samples - - c.Assert(samples[0].GT, DeepEquals, []int{2, 2}) - c.Assert(samples[1].GT, DeepEquals, []int{2, 2}) - c.Assert(samples[2].GT, DeepEquals, []int{2, 2}) - -} diff -Nru golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/writer.go golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/writer.go --- golang-github-brentp-irelate-0.0~git20180801.1bf7c8f+ds/vendor/github.com/brentp/vcfgo/writer.go 2020-07-04 18:01:59.000000000 +0000 +++ golang-github-brentp-irelate-0.0.1+ds/vendor/github.com/brentp/vcfgo/writer.go 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -package vcfgo - -import ( - "fmt" - "io" - "sort" - "strings" -) - -// Writer allows writing VCF files. -type Writer struct { - io.Writer - Header *Header -} - -// NewWriter returns a writer after writing the header. -func NewWriter(w io.Writer, h *Header) (*Writer, error) { - fmt.Fprintf(w, "##fileformat=VCFv%s\n", h.FileFormat) - - for _, imap := range h.Contigs { - fmt.Fprintf(w, "##contig=") - } - - // Samples - keys := make([]string, 0, len(h.Samples)) - for sampleId := range h.Samples { - keys = append(keys, sampleId) - } - sort.Strings(keys) - for _, sampleId := range keys { - fmt.Fprintln(w, h.Samples[sampleId]) - } - - for i := range h.Pedigrees { - fmt.Fprintln(w, h.Pedigrees[i]) - } - - // Filters - keys = keys[:0] - for k := range h.Filters { - keys = append(keys, k) - } - sort.Strings(keys) - for _, k := range keys { - fmt.Fprintf(w, "##FILTER=\n", k, h.Filters[k]) - } - - // Infos - keys = keys[:0] - for k := range h.Infos { - keys = append(keys, k) - } - sort.Strings(keys) - for _, k := range keys { - fmt.Fprintf(w, "%s\n", h.Infos[k]) - } - - // SampleFormats - keys = keys[:0] - for k := range h.SampleFormats { - keys = append(keys, k) - } - sort.Strings(keys) - for _, k := range keys { - fmt.Fprintf(w, "%s\n", h.SampleFormats[k]) - } - for _, line := range h.Extras { - fmt.Fprintf(w, "%s\n", line) - } - - fmt.Fprint(w, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT") - var s string - if len(h.SampleNames) > 0 { - s = "\t" + strings.Join(h.SampleNames, "\t") - } - - fmt.Fprint(w, s+"\n") - return &Writer{w, h}, nil -} - -// WriteVariant writes a single variant -func (w *Writer) WriteVariant(v *Variant) { - fmt.Fprintln(w, v) -}