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

BMC Genomics

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

	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)

^aThe numbers of parentheses refer to known or unknown variant loci in dbSNP databases

ISSN: 1471-2164

	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)