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Table 1 Comparison of the efficiency of VarDetect, PolyPhred, Genalys, novoSNP and Mutation Surveyor.

From: VarDetect: a nucleotide sequence variation exploratory tool

Gene (contigs) Verified SNPs VarDetect PolyPhred Genalys novoSNP Mut. Surveyor
   TP FP FN TP FP FN TP FP FN TP FP FN TP FP FN
ACOX2 (5) 10 10 28 0 3 1 7 6 277 4 9 352 1 6 40 4
ADM (2) 2 1 4 1 0 0 2 1 260 1 2 220 0 1 11 1
ARRB1 (6) 16 15 7 1 9 1 7 16 30 0 15 58 1 13 13 3
CACNA1D (11) 26 23 9 3 12 4 14 20 363 6 26 361 0 22 60 4
CACNB3 (3) 6 5 4 1 4 1 2 5 191 1 5 308 1 3 51 3
CCL2 (2) 3 3 10 0 1 0 2 3 196 0 3 130 0 2 34 1
CCL3 (2) 12 11 4 1 4 0 8 9 171 3 12 123 0 9 31 3
CCL4 (2) 10 8 11 2 6 3 4 8 136 2 8 96 2 7 20 3
CCL5 (2) 3 3 2 0 3 1 0 3 28 0 3 21 0 2 3 1
CCR7 (2) 2 2 3 0 1 0 1 2 75 0 2 129 0 1 3 1
ITGAM (13) 27 19 20 8 17 7 10 19 552 8 23 618 4 22 63 5
ITGAX (15) 25 24 28 1 13 4 12 22 704 3 24 1166 1 19 131 6
ITGB7 (9) 16 15 13 1 11 1 5 15 435 1 16 521 0 11 32 5
LIPG (1) 4 2 2 2 1 2 3 3 82 1 3 102 1 3 2 1
NPY (2) 9 7 4 2 5 0 4 8 228 1 9 334 0 7 11 2
Total 15 genes 171 148 149 23 90 25 81 140 3728 31 160 4539 11 128 505 43
77 contigs                 
Precision (%)   49.83 78.26 3.62 3.40 20.22
Recall (%)   86.55 52.63 81.87 93.57 74.85
F-score (%)   63.25 62.94 6.93 6.56 31.84
  1. Our testing set comprises 77 exonic contigs from 15 human genes. Of these 77 contigs, there are 171 SNPs experimentally validated by the experts [14]. novoSNP has lowest false negative result while generates heighest false positive result (4539). The number of detected SNPs and the false positive result identified by VarDetect are better than Genalys, novoSNP and Mutation Surveyor. Although VarDetect has worse performance on false positive, its SNP identification coverage (148 out of 171) is much higher than that of PolyPhred (90 out of 171) resulting in higher false positive and lower false negative result than PolyPhred' s. From these experiments, VarDetect had the best F-score (63.25%) that slightly greater than PolyPhred (62.94%). Mutation Surveyor, Genalys and novoSNP had low F-score that had 31.84%, 6.93% and 6.56%, respectively.