Figure 5.

Estimated mapping accuracy for 100 000 real 36-bp reads from D. melanogaster, mapped to the D. simulans genome. Circles indicate a score cutoff of 150. The dotted line shows the mapping accuracy when we model the sequencer errors but not the real differences. The solid line shows the accuracy when we model both. The dashed red line shows the accuracy when we model both but forbid insertions and deletions. Correctness was estimated by mapping the reads to the D. melanogaster genome (modeling sequencer errors only), and using the UCSC D. melanogaster / D. simulans pairwise genome alignment to cross-reference the mappings.