# ParsEval Summary

    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
--- | --- | --- | ---
Group7.16 | 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, 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 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 | --
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 | --