large degree of dissimilarity, which is not surprising given the small sample sizes here. The discreteness of the p-values from the exact test is apparent also, and the distribution away from zero (which corresponds principally to null SNPs) is far from uniform. To reinforce this point we plot the histogram of exact p-values in panel (b), the most probable configuration of genotypes has probability 1 and for these data more than a third (consisting of 37,253 SNPs) have a p-value of 1. This plot shows a great similarity to Figure 2 of Rohlfs and Weir (2008) (except that we have truncated the vertical axis so that more detail in the bulk of the distribution can be revealed). In panel (c), we plot the observed –log10 p-values versus those expected under a uniform null. A plot containing this information is almost universally presented in GWAS, but it is not strictly valid because it assumes uniformity under the null. The Bonferroni threshold is indicated on this plot and leads to HWE being rejected for 191 SNPs.
