Figure 3

Imperfect mappability causes inaccurate measures of relative allelic abundance. For unbiased differentiating sites (i.e., those with fewer neighboring differentiating sites than the number of mismatches allowed) with either perfect (white) or imperfect (grey) mappability, the distribution of relative allelic abundance (measured as the proportion of mapped reads assigned to the reference allele) is shown for the 36-base (A-D) and 50-base (E-H) reads simulated from the two D. melanogaster genotypes as well as for the 36-base reads simulated from D. melanogaster and D. simulans (I-L) aligned to a single genome, allowing one (A, E, I), two (B, F, J), or three (C, G, K) mismatches. The distribution of relative allelic abundance for unbiased differentiating sites with perfect (white) and imperfect (grey) mappability is also shown for all three simulated datasets after aligning reads to both the reference and alternative genomes, allowing no mismatches (D, H, L).