To cover a scenario where the mutation-frequencies are distributed according to a natural existing population, we used resequencing data from 120 individuals from the African YRI population and 119 individuals from the Central European CEU population. In this example, we test for overrepresentation of rare exonic variants in the YRI population compared to the CEU population in each Encode region. Such an overrepresentation is expected since the YRI population generally shows higher diversity than the CEU population [39], and hence more rare variants are expected. Exonic variants are grouped for each ENCODE region, to mimic a disease-resequencing study like the ones reported in human resequencing studies [5],[7],[16]; as a result, 5 groups of 2–72 polymorphic variants are obtained (see Table 2).
