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Table 2 Comparison of software performance in intra-individual InDel detection

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

Softwarea True InDels (%) Size-correct InDels with wrong bases (%) Missed InDels (%) False positive InDels (%)
DiSNPindel 43(53.1 %) 20 (24.7 %) 18 (22.2 %) 0 (0.0 %)
novoSNP 6 (7.4 %) 7 (8.6 %) 68 (84.0 %) 34 (72.3 %)
Mutation surveyor 7 (8.6 %) 7 (8.6 %) 67 (82.8 %) 26 (65.0 %)
PrimeIndel 15 (18.5 %) 10 (12.3 %) 56 (69.1 %) 0 (0.0 %)
  1. The numbers of true, size-correct but base-wrong, missed and false positive InDels were detected with 77 single traces containing SSR-associated InDels [23]. More data were given in Additional file 3: Table S3
  2. aPolyPhred did not detect any InDels and was thus excluded from the comparison