Schematic diagram of scaffolds analysed in M and S relative to the An. gambiae PEST reference. Horizontal rectangle (labeled at left) represents genomic sequence from the PEST reference genome, with green shaded sections indicating flanking sequence at the telomeric and centromeric ends, red sections indicating repetitive sequence at both breakpoints, and the blue section indicating the 2R+barrangement. Horizontal arrows indicate the relative position (not to scale) and orientation of assembly or manual scaffolds used in the analysis. The scaffold number (if applicable), approximate length, and source (An. gambiae M or S genome sequence) is indicated at left. Vertical gray rectangles highlight the ~10 kb breakpoint regions whose sequence was compared between the PEST, M and S genomes.