Gene Stats Detail


Summary

  count total len % cov % gc min len max len median len mean len
Contig 433 36223641 99.39 48.33 558 473223 44810.00 83657.37
Gene 13321 21076905 57.54 50.44 90 34078 1355.00 1582.23
Exon 37516 19051094 51.98 51.16 1 29066 284.00 507.81
Coding 13322 17842161 48.95 51.57 90 33594 1101.00 1339.30
Intergenic 13091 15474252 42.46 45.43 1 74674 773.00 1182.05
5' UTR 2446 392993 1.08 46.67 1 4754 111.00 160.67
3' UTR 3084 815940 2.21 44.38 1 3601 190.00 264.57

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 13322 predictions to 7147 reference models.

  cov sn sp TP TN FP FN unknown
nucleotide 0.6227 0.9818 0.9969 12125767 738330 37453 225093 7952815
splices 0.3386 0.8921 0.8495 21582 - 3823 2609 49627
exons 0.4801 0.8216 0.7975 14363 - 50 204 19506