Correlation of sequenced genotypes to the SNP chip genotypes. SAMtools' pileup genotype calls recalled with quality ratios in the VCP were compared with the Illumina Human660W-Quad v1 SNP chip genotypes. (a) The correlations for Agilent SureSelect- and NimbleGen SeqCap-captured sequenced genotypes. (b) The correlations for SureSelect 50 Mb- and SeqCap v2.0-captured sequenced genotypes. Correlations for heterozygous, reference homozygous and variant homozygous SNPs (according to the chip genotype call) are presented on separate lines, though the lines for homozygous variants, laying near 100% correlation, cannot be visualized. The x-axis represents the accumulative minimum coverage of the sequenced SNPs.