ParsEval Summary

Started:                06 Mar 2015, 03:25PM
Reference annotations:  OGS
Prediction annotations: NCBI
Executing command:      bin/parseval --datashare=data/share/ --outformat=html --outfile=pe.temp --overwrite --refrlabel=OGS --predlabel=NCBI data/gff3/amel-ogs-g716.gff3 data/gff3/amel-ncbi-g716.gff3 

Sequences compared

Click on a sequence ID below to see comparison results for individual loci.

Sequence Refr genes Pred genes Loci
Group7.161088

Gene loci [?]If a gene annotation overlaps with another gene annotation, those annotations are associated with the same gene locus. See this page for a formal definition of a locus annotation.

shared7
unique to reference1
unique to prediction0
Total8

Reference annotations

genes10
average per locus1.250
transcripts10
average per locus1.250
average per gene1.000

Prediction annotations

genes8
average per locus1.000
transcripts10
average per locus1.250
average per gene1.250

Comparisons

Total comparisons8
(+) perfect matches [?]Prediction transcripts (exons, coding sequences, and UTRs) line up perfectly with reference transcripts.0 (0.0%)
(+) perfect matches with mislabeled UTRs [?]5'/3' orientation of UTRs is reversed between reference and prediction, but a perfect match in all other aspects.0 (0.0%)
(+) CDS structure matches [?]Not a perfect match, but prediction coding sequence(s) line up perfectly with reference coding sequence(s).4 (50.0%)
average length8691.00 bp
average # refr exons5.75
average # pred exons6.00
average refr CDS length455.25 aa
average pred CDS length455.25 aa
(+) exon structure matches [?]Not a perfect match or CDS match, but prediction exon structure is identical to reference exon structure.0 (0.0%)
(+) UTR structure matches [?]Not a perfect match, CDS match, or exon structure match, but prediction UTRs line up perfectly with reference UTRs.0 (0.0%)
(+) non-matches [?]Differences in CDS, exon, and UTR structure.4 (50.0%)
average length13661.75 bp
average # refr exons6.50
average # pred exons6.25
average refr CDS length398.25 aa
average pred CDS length391.50 aa

CDS structure comparison

reference CDS segments49
match prediction44 (89.8%)
don't match prediction5 (10.2%)
prediction CDS segments48
match prediction44 (91.7%)
don't match prediction4 (8.3%)
Sensitivity0.898
Specificity0.917
F1 score0.907
Annotation edit distance0.093

Exon structure comparison

reference exons49
match prediction33 (67.3%)
don't match prediction16 (32.7%)
prediction exons49
match prediction33 (67.3%)
don't match prediction16 (32.7%)
Sensitivity0.673
Specificity0.673
F1 score0.673
Annotation edit distance0.327

UTR structure comparison

reference UTR segments10
match prediction0 (0.0%)
don't match prediction10 (100.0%)
prediction UTR segments16
match prediction0 (0.0%)
don't match prediction16 (100.0%)
Sensitivity0.000
Specificity0.000
F1 score--
Annotation edit distance1.000

Nucleotide-level comparison

 CDSUTRsOverall
matching coefficient0.9950.9640.802
correlation coefficient0.9780.430--
sensitivity0.9760.371--
specificity0.9840.540--
F1 score0.9800.440--
annotation edit distance0.0200.544--