A common practice in GWAS is to plot the observed –log10 p-value versus that expected under the null, where the latter are derived assuming uniformity of the p-value. Due to the discreteness of the test statistic p-values derived from an exact test are not uniform under the null, however. The correct MAF-specific distribution can be derived by enumerating all counts under the null for that MAF in the sample. In this context it is also difficult to use the q-value methodology (Storey, 2003) due to the nonuniformity of the null distribution.
