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Table 3 Concordance of genotypes and SNPs

From: Comprehensive comparison of three commercial human whole-exome capture platforms

  Concordance with 1 M bead genotyping data Concordance with WGSS data
Replicatea 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
  1. 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.