Figure 4

Insertions and deletions (indels) cause biased allele-specific assignment when reads are aligned to a single reference genome. For differentiating sites with perfect mappability and fewer neighboring differentiating sites than the number of mismatches allowed, the distributions of relative allelic abundance are shown for differentiating sites with (grey) and without (white) one or more nearby indel(s) after aligning the 36-base reads simulated from D. melanogaster and D. simulans to either the D. melanogaster genome with one (A), two (B), or three (C) mismatches allowed or to both the D. melanogaster and D. simulans genomes with no mismatches allowed (D).