Gene Stats Detail


Summary

  count total len % cov % gc min len max len median len mean len
Contig 3 12571820 100.00 36.06 2452883 5579133 4539804.00 4190606.67
Gene 5144 11164990 81.29 37.14 99 15182 1911.00 2170.49
Exon 10497 10760848 77.78 37.47 3 14362 509.00 1025.14
Coding 5163 7213050 57.20 39.63 75 14775 1137.00 1397.07
Intergenic 3513 2352742 18.71 31.37 1 78172 357.00 669.72
5' UTR 4576 1400961 10.78 33.36 2 4397 187.00 306.15
3' UTR 4619 2146837 15.93 32.64 3 5911 289.00 464.78

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 5163 predictions to 4176 reference models.

  cov sn sp TP TN FP FN unknown
nucleotide 0.6981 0.9972 0.9993 7401469 394751 4816 20606 3382406
splices 0.6333 0.9899 0.9776 12998 - 298 132 7698
exons 0.7800 0.9438 0.9587 7850 - 3 2 2309