Figure 6

Relative allelic abundance can be estimated for most exons after excluding sites problematic sites. The proportion of differentiating sites (blue) and exons with at least one differentiating site (red) suitable for quantifying ASE after excluding sites with an excess of neighboring differentiating sites, imperfect mappability (black) and an indel(s) nearby (grey) are shown for the 36-base reads simulated from the two D. melanogaster genotypes (left) and from the D. melanogaster and D. simulans exomes (right). Each pair of bars results from aligning reads to either a single reference genome (Ref) or both the maternal and paternal genomes (M + P) with zero (0), one (1), two (2), or three (3) mismatches allowed. The two D. melanogaster genotypes compared did not include any indels, as described in the main text.