with internal and external controls (results shown in Figures S3, S4, S5). Comparing Figure 5A with 5B shows the high correlation of the two sets of ranks in the original study with internal controls and the lower correlation in the reconstructed studies using external controls. Figures 6 and 7 show the histogram of ranks according to the test without PC adjustment for SNPs ranked within a given range by the test with PC adjustment. Again, the discordance between two ranks in the analyses with external controls is more prominent than in the original study.
