Quality of the Illumina data was assessed using PLINK (http://pngu.mgh.harvard.edu/purcell/plink/) (Purcell et al., 2007). SNPs (n=315 980) were submitted for quality checks. Call rates exceeded 98% for all 452 individuals, one individual was excluded because of a sex discrepancy, and two individuals were excluded because of per-family Mendelian errors in excess of 1%. Out of the 315 980 SNPs submitted, 6109 SNPs were excluded because of a minor allele frequency (MAF) less than 0.05, 13 SNPs were excluded because of Mendelian errors in more than 4 families, and 629 SNPs were excluded because of deviations from Hardy–Weinberg equilibrium (HWE) (P<0.000001). In total, three individuals and 6751 SNPs did not pass our quality control checks.
