QQ-plots for quantitative phenotypes in the presence 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, and Wright’s F
was assumed to be 0.01. (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.