Gene Stats Detail


Summary

  count total len % cov % gc min len max len median len mean len
Contig 3578 28324259 92.40 50.14 493 165902 2194.00 7916.23
Gene 9075 17209324 55.09 52.73 151 15194 1639.00 1896.34
Exon 24973 16055151 50.77 53.19 3 13345 381.00 642.90
Coding 9153 12269413 39.66 54.68 150 14889 1062.00 1340.48
Intergenic 9760 13767387 44.91 46.32 1 33099 546.00 1410.59
5' UTR 6214 1732845 5.53 49.63 1 3740 188.00 278.86
3' UTR 6282 2052893 6.30 46.96 1 4281 240.00 326.79

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 9153 predictions to 0 reference models.

  cov sn sp TP TN FP FN unknown
nucleotide - - - 0 0 0 0 17399231
splices - - - 0 - 0 0 49946
exons - - - 0 - 0 0 24973