swapping of internal and external controls. We note that in each of the four studies considered the vast majority of SNPs ranked in the top 1% by the test with PC adjustment were ranked within the top 5% by the test without PC adjustment (Figures 6A, 7A, S5A, and S6A). Figures 5 and S3 show that both ranks of the most discordant SNPs are close to the threshold.
