Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population

Table 3 Concordant SNP calls made from the HiSeq, Ion Proton, and Omni 2.5-8 SNP array data

Samples	Total calls	Omni 2.5	HiSeq	Proton	All concordant	HO concordant	HP concordant	OP concordant	Proton support
01	17031	16902	16782	15678	15549	16733	15576	15571	0.929
02	17168	17007	16872	14033	13879	16820	13896	13907	0.825
03	17156	17009	16860	15025	14855	16806	14889	14898	0.884
04	16964	16847	16712	15668	15552	16663	15580	15572	0.933
05	17029	16930	16782	16326	16208	16732	16238	16247	0.969
06	17151	17033	16873	15863	15723	16832	15744	15765	0.934
07	17193	17058	16918	16060	15905	16862	15939	15947	0.943
08	17223	17099	16939	16095	15935	16892	15965	15988	0.943
09	17282	17173	17017	16220	16084	16965	16114	16133	0.948
10	17030	16922	16800	16180	16067	16747	16098	16094	0.959
11	17086	16944	16802	14332	14182	16768	14199	14207	0.846
12	17234	17100	16938	16163	15996	16889	16028	16046	0.947
Average	17129	17002	16858	15637	15495	16809	15522	15531	0.922
%CV	0.56	0.54	0.49	4.7	4.8	0.49	4.8	4.8	4.7

HO concordant, HiSeq 2500 and Omni 2.5-8 chip SNP calls were concordant but not the Ion Proton calls. HP concordant, HiSeq 2500 and Ion Proton SNP calls were concordant but not the Omni 2.5-8 chip calls. OP concordant, Omni 2.5-8 chip and Ion Proton SNP calls were concordant but not the HiSeq 2500 calls. Calculation of proton support = All concordant/HO concordant.

ISSN: 1471-2164