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

From: 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

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
  1. 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.