log{P(Yi=1)1−P(Yi=1)}=β0+β1Ai where β1 is the effect of SNP i and β0 is an intercept term. We stored the p-value and the χ2 test statistic for the Wald test of β1. For the soft call genotypes, where Ai is the expected number of rare alleles given the observed data (0 ≤ Ai ≤ 2), the software mach2dat was used (http://www.sph.umich.edu/csg/yli/mach/index.html) (Li et al. 2009, 2010). For the hard call genotypes, where Ai ∈ {0, 1, 2}, we used the software PLINK version 1.07 (http://pngu.mgh.harvard.edu/purcell/plink) (Purcell et al. 2007). Figures were generated in the statistical software R version 2.9.0 (R Development Core Team 2009).
