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Table 3 Pairwise comparison of variants called for four samples by TargetSeq-Proton and SureSelect-HiSeq

From: Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling

  TargetSeq-Proton-specific(dbSNP|novel)a Concordant(dbSNP|novel) SureSelect-HiSeq-specific(dbSNP|novel)
  Total SNPs InDels Total SNPs InDels Total SNPs InDels
S1 1470 (1021|449) 1274 (998|276) 196 (23|173) 17202 (16288|914) 16833 (15943|890) 369 (345|24) 6682 (6348|334) 5851 (5606|245) 831 (742|89)
S2 1432 (1018|414) 1229 (996|233) 203 (22|181) 19039 (18038|1001) 18655 (17683|972) 384 (355|29) 4833 (4533|300) 4044 (3839|205) 789 (694|95)
S3 1518 (1073|445) 1305 (1046|259) 213 (27|186) 18087 (17149|938) 17720 (16810|910) 367 (339|28) 5689 (5390|299) 4897 (4671|226) 792 (719|73)
S4 1462 (1069|393) 1326 (1051|275) 136 (18|118) 17808 (16891|917) 17409 (16521|888) 399 (370|29) 5681 (5353|328) 4922 (4674|248) 759 (679|80)
  1. aThe numbers of parentheses refer to known or unknown variant loci in dbSNP databases