We then removed monomorphic SNPs or those with a genotyping completion rate <95%. After this step, 991 221 SNPs were retained. We note that using a genotyping completion rate of 95% or more allows some SNPs of poor genotyping quality to enter the analysis; the alternative is to use a more stringent completion rate, such as 99%, which has the advantage of removing low-quality SNPs at the cost of removing some high-quality SNPs. Recognizing the tradeoff, we chose to use the less stringent criterion for association analysis, and follow up SNPs with small P-values, by manual inspection of genotype clusters. However, for the figures in the manuscript, we use the more stringent criterion for genotyping completion rate, which more accurately reflects the final results after manual inspection of genotype clusters.
