FIG. 3.

(A–C). Allele-specific alignments. Allele-specific read alignments showing the mean coverage for Drosophila melanogaster reads (red) and D. simulans reads (blue) per exon in (A) Ugt-35b, (B) Hexo1, (C) Iris. Custom wiggle tracks for reads separated by allele assignment were visualized using the UCSC Genome Browser (Kent et al. 2002). Wiggle tracks for publication including overlays and gene models (Flybase 5.26 annotations) were created using R (R Development Core Team 2011). Gene models are from the FlyBase Protein-Coding Genes track (R5.12). The genome version is D. melanogaster April 2006 BDGP R5/dm3 assembly.