Figure 1 summarizes the results of a standard logistic regression analysis, where SNPs are grouped by MAF. For each collection of SNPs, we found the Genomic Control λ (in black) and the percentage of SNPs with p < 5 × 10−8 (in gray). Results from the soft call analysis are shown in solid lines, while those from the hard call analysis are shown in dashed lines. In Figure 1a, we see that λ ≈ 1 among the 139,732 SNPs measured on both chips, and the percentage of highly significant SNPs is close to 0 across all MAFs; the error measures in this setting are virtually identical whether we use hard call or soft call imputation. Thus, when we consider only the SNPs measured on both chips, we have no evidence from these two measures that the distribution of the test statistics deviates from the null.
