Table 5

Genotype correlations with the genome-wide SNP genotyping chip for lower sequencing coverages

Sequencing depth 1× to 5×

Sequencing depth 6× to 10×

Sequencing depth 11× to 15×




Exome capture method

Number of concordant SNPs

Number of discordant SNPs

Genotype correlation

Number of concordant SNPs

Number of discordant SNPs

Genotype correlation

Number of concordant SNPs

Number of discordant SNPs

Genotype correlation


Agilent SureSelect

779

258

75.12%

802

46

94.58%

647

17

97.44%

Agilent SureSelect 50 Mb

846

243

77.69%

1,127

37

96.82%

1,109

14

98.75%

NimbleGen SeqCap

206

60

77.44%

361

19

95.00%

459

13

97.25%

NimbleGen SeqCap v2.0

110

39

73.83%

338

9

97.41%

486

3

99.39%


Sulonen et al. Genome Biology 2011 12:R94   doi:10.1186/gb-2011-12-9-r94

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