Gene Stats Detail


Summary

  count total len % cov % gc min len max len median len mean len
Contig 210 41700345 99.82 48.70 927 1198896 116463.50 198573.07
Gene 15869 30859581 69.99 50.08 93 22934 1635.00 1944.65
Exon 62476 44266080 64.75 50.48 2 22934 414.00 708.53
Coding 20553 28605528 51.28 51.59 93 22842 1173.00 1391.79
Intergenic 13462 12536683 30.01 45.49 1 50904 594.00 931.26
5' UTR 13135 7542965 8.67 48.52 1 7625 302.00 574.26
3' UTR 13670 8117587 9.35 46.30 1 8585 319.00 593.82

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 20553 predictions to 10149 reference models.

  cov sn sp TP TN FP FN unknown
nucleotide 0.5918 0.9907 0.9906 26059375 1551990 248497 244603 19382640
splices 0.4794 0.9216 0.9223 55251 - 4655 4701 65046
exons 0.5195 0.8187 0.8229 26709 - 24 45 30017