Comprehensive comparison of three commercial human whole-exome capture platforms

Table 3 Concordance of genotypes and SNPs

	Concordance with 1 M bead genotyping data							Concordance with WGSS data
Replicate^a	All genotypes	SNPs in 1 M chip	SNPs in exome capture	Homs in 1 M chip	Homs in exome capture	Hets in 1 M chip	Hets in exome capture	All genotypes	SNPs in WGSS	SNPs in exome capture	Homs in WGSS	Homs in exome capture	Hets in WGSS	Hets in exome capture
NA-r1	99.846	99.641	99.826	99.649	99.987	99.633	99.687	99.999	99.216	98.636	99.951	99.868	98.683	97.750
NA-r2	99.854	99.670	99.835	99.708	99.975	99.637	99.714	99.999	99.264	98.616	99.943	99.850	98.768	97.724
NS-r1	99.854	99.679	99.819	99.682	99.951	99.676	99.707	99.998	99.211	98.396	99.974	99.747	98.657	97.426
NS-r2	99.849	99.660	99.841	99.684	99.987	99.640	99.716	99.999	99.197	98.706	99.979	99.752	98.629	97.949
AS-r1	99.816	99.526	99.823	99.571	99.948	99.486	99.712	99.998	98.783	98.021	99.917	99.824	97.945	96.703
AS-r2	99.815	99.514	99.805	99.556	99.880	99.477	99.738	99.998	98.762	97.972	99.927	99.771	97.893	96.645

For each replicate, the 30-fold data set used for Table 2 analyses was also used for the analyses. ^aAS, Agilent solution; NA, NimbleGen array; NS, NimbleGen solution; r1 and r2 are two replicate experiments for each platform. Hets, heterozygotes; Homs, homozygotes.

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