Gene Stats Detail


Summary

  count total len % cov % gc min len max len median len mean len
Contig 87 11135996 94.91 43.79 1093 2268246 4213.00 127999.95
Gene 4878 10053146 76.27 44.15 102 16518 1785.00 2060.92
Exon 10266 9637355 72.73 44.39 3 14133 464.00 938.76
Coding 4878 6846852 58.35 45.50 102 14907 1146.00 1403.62
Intergenic 3152 2784560 23.73 42.33 1 229431 288.00 883.43
5' UTR 3594 980462 8.08 41.14 1 5517 172.50 272.81
3' UTR 3569 1810041 14.31 41.49 5 6155 274.00 507.16

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 4878 predictions to 4883 reference models.

  cov sn sp TP TN FP FN unknown
nucleotide 0.9500 0.9962 0.9995 9154304 356160 4913 35208 502561
splices 0.5770 0.9789 0.9422 11161 - 685 241 8686
exons 0.8010 0.8883 0.9053 7444 - 6 21 2043