QQ-plots for dichotomous phenotypes in the absence of population substructure. QQ-plots were generated from results of 10,000 replicates for quantitative phenotypes. We assumed that the number of markers was 2, and that their minor allele frequencies were generated as U(0.1, 0.5). ρ was assumed to be 0.2. (a)
Q=2 and D'=0, (b)
Q=2 and D'=0.5, (c)
Q=5 and D'=0, and (d)
Q=5 and D'=0.5 were assumed respectively.