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Table 1 Comparison of software performance in intra-individual SNP detection

From: DiSNPindel: improved intra-individual SNP and InDel detection in direct amplicon sequencing of a diploid

Softwarea Grade or score thresholdb Found SNPs (%) Missed SNPs (%)
DiSNPindel 1 60 (90.9 %) 6 (9.1 %)
  2 61 (92.4 %) 5 (7.6 %)
  3 61 (92.4 %) 5 (7.6 %)
  4 63 (95.4 %) 3 (4.6 %)
  5 63 (95.4 %) 3 (4.6 %)
  6 63 (95.4 %) 3 (4.6 %)
novoSNP 18 0 (0.0 %) 66 (100.0 %)
  13 11 (16.7 %) 55 (83.3 %)
  9 16 (24.4 %) 50 (75.6 %)
  6 19 (28.8 %) 47 (71.2 %)
  3 25 (37.9 %) 41 (62.1 %)
  1 25 (37.9 %) 41 (62.1 %)
Mutation surveyor Medium sensitivity 20 (30.3 %) 46 (69.7 %)
  High sensitivity 20 (30.3 %) 46 (69.7 %)
  1. The numbers of found and missed SNPs were experimentally verified with 66 CAPS-associated intra-individual SNPs originating from 62 single traces [22]
  2. aPolyPhred did not detect any SNPs at ranks 1–6 and was thus excluded from the comparison
  3. bGrade 2, score 13 and medium sensitivity could be a high threshold for reliable SNP detection in DiSNPindel, novoSNP and Mutation Surveyor, respectively, where Grade 4, score 6 and high sensitivity could be a low threshold