Gene Stats Detail


Summary

  count total len % cov % gc min len max len median len mean len
Contig 18 11262981 96.81 37.55 1353 2566365 17994.50 625721.17
Gene 4986 10116365 80.86 38.45 99 14922 1763.00 2028.95
Exon 10519 9702676 77.31 38.74 3 14361 450.00 922.40
Coding 4986 6922074 59.49 40.65 69 14721 1131.00 1388.30
Intergenic 3396 2226816 19.14 32.98 1 174833 297.00 655.72
5' UTR 3937 1247118 10.26 34.05 2 5187 201.00 316.77
3' UTR 3937 1533484 12.32 33.34 2 4602 239.00 389.51

Specificity/Sensitivity Analysis

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Terminology is from Burset M and Guigo R, "Evaluation of gene structure prediction programs." Genomics, 1996 Jun 15;34(3):353-67.
TP (true positives): nucleotides predicted as exonic in predictions and EST evidence; splice junctions with exact agreement, in position and type (donor:donor, acceptor:acceptor), between predictions and EST evidence; exons with both splice sites in exact agreement with EST evidence.
TN (true negatives): nucleotides predicted as intronic in predictions and EST evidence; not defined for splice sites or exons.
FP (false positives/overpredictions): nucleotides predicted as exonic where EST evidence indicates an intron; predicted splice junctions where the EST alignments do not have a splice*; predicted exons which fall entirely within an intron supported by EST evidence ("wrong" in Guigo's terminology).
FN (false negatives/underpredictions): nucleotides predicted as intronic where EST evidence indicates an exon; EST alignment splice junctions where the predictions do not have a splice*; EST-based exons that fall entirely within a predicted intron ("miss" in Guigo's terminology).
unknown (cannot be scored): nucleotides that do not touch an EST alignment; splices that do not touch an EST alignment, and initial/terminal splices that fall within an initial/terminal exon of a partial EST alignment; exons that either do not touch an EST alignment or fully encapsulate a single-exon partial EST alignment.
sn (sensitivity): TP/(TP+FN)
sp (specificity): TP/(TP+FP)
cov (coverage): percentage of predicted elements that are not "unknown"

In the very rare cases where the query predicts a donor site exactly where EST evidence indicates an acceptor (or vice versa), we count it as both FP and FN. Certain classes of incorrect exon predictions are not labeled TP, FP nor FN.

Compared 4986 predictions to 3000 reference models.

  cov sn sp TP TN FP FN unknown
nucleotide 0.6733 0.9980 0.9997 6583771 212326 1781 13377 3305110
splices 0.4009 0.9906 0.9660 8148 - 287 77 12603
exons 0.5155 0.9390 0.9432 5115 - 1 4 5096