We first made a series of simulations in the absence of population structure. (Some additional details are in the Methods section.) Our first set of runs had 100 individuals and 5,000 unlinked SNPs, and the second 200 individuals and 50,000 unlinked SNPs. In each case we ran 1,000 simulations and show in Figure 2A and 2B probability–probability (P–P) plots of the empirical and TW tail areas. The results seem entirely satisfactory, especially for low p-values in the top right of Figures 2A and 2B. For assessment of statistical significance, it is the low p-value range that is relevant. The simulations show more generally that the TW theory is relevant in a genetic context, that the normalizations of Equations 5–7 are appropriate, and that the calculation of the effective marker size has not seriously distorted the TW statistic.
