ParsEval Summary

Started:                28 Aug 2014, 11:26PM
Reference annotations:  OGS
Prediction annotations: NCBI
Executing command:      bin/parseval --datashare=data/share/ --outformat=html --png --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
Group7.16	10	8	8

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.

shared	7
unique to reference	1
unique to prediction	0
Total	8

Reference annotations

genes	10
average per locus	1.250
transcripts	10
average per locus	1.250
average per gene	1.000

Prediction annotations

genes	8
average per locus	1.000
transcripts	10
average per locus	1.250
average per gene	1.250

Comparisons

Total comparisons	8
perfect matches [?]Prediction transcripts (exons, coding sequences, andUTRs) 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 length	8691.00 bp
average # refr exons	5.75
average # pred exons	6.00
average refr CDS length	455.25 aa
average pred CDS length	455.25 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 length	13661.75 bp
average # refr exons	6.50
average # pred exons	6.25
average refr CDS length	398.25 aa
average pred CDS length	391.50 aa

CDS structure comparison

reference CDS segments	49
match prediction	44 (89.8%)
don't match prediction	5 (10.2%)
prediction CDS segments	48
match prediction	44 (91.7%)
don't match prediction	4 (8.3%)
Sensitivity	0.898
Specificity	0.917
F1 score	0.907
Annotation edit distance	0.093

Exon structure comparison

reference exons	49
match prediction	33 (67.3%)
don't match prediction	16 (32.7%)
prediction exons	49
match prediction	33 (67.3%)
don't match prediction	16 (32.7%)
Sensitivity	0.673
Specificity	0.673
F1 score	0.673
Annotation edit distance	0.327

UTR structure comparison

reference UTR segments	10
match prediction	0 (0.0%)
don't match prediction	10 (100.0%)
prediction UTR segments	16
match prediction	0 (0.0%)
don't match prediction	16 (100.0%)
Sensitivity	0.000
Specificity	0.000
F1 score	nan
Annotation edit distance	1.000

Nucleotide-level comparison

	CDS	UTRs	Overall
matching coefficient	0.995	0.964	0.802
correlation coefficient	0.978	0.430	--
sensitivity	0.976	0.371	--
specificity	0.984	0.540	--
F1 score	0.980	0.440	--
annotation edit distance	0.020	0.544	--