Gene Stats Detail


Summary

  count total len % cov % gc min len max len median len mean len
Contig 1362 59936783 97.68 48.40 706 439130 20208.00 44006.45
Gene 20925 39334632 59.51 49.77 93 22869 1593.00 1879.79
Exon 81093 55425136 54.57 50.19 1 16038 407.00 683.48
Coding 27347 35760474 42.79 51.35 93 22596 1101.00 1307.66
Intergenic 18179 24842342 40.49 46.27 1 178157 672.00 1366.54
5' UTR 17948 8786825 7.60 48.05 1 7731 280.00 489.57
3' UTR 18087 10877837 9.58 46.98 1 9564 335.00 601.42

Specificity/Sensitivity Analysis

close

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 27347 predictions to 13524 reference models.

  cov sn sp TP TN FP FN unknown
nucleotide 0.5789 0.9897 0.9879 31956045 1917936 389987 332231 25162215
splices 0.4609 0.8928 0.9232 69001 - 5743 8281 87442
exons 0.5262 0.7843 0.8108 34594 - 34 75 38425