Exon 4 of CD58. (a) RefSeq genes from the human genome are plotted at the top with arrows indicating their orientation and exons; the transcript analyzed is in red. The gray square denotes regions without any repeat content. The compared exon/intron pair is shown highlighted in green/dark blue, respectively. Each line represents a mapped read: top macaque, and bottom human WGS reads. Each base pair in the alignment has a color indicating low quality (black), gap (white), high-quality identity (gray), and high-quality substitution (purple if it is intronic, red if it is nonsynonymous, yellow if it is synonymous). In this example there are no stop codons. (b) Zoom of the region showing an excess of nonsynonymous differences (in red). The exonic rate of differences per nucleotide is fivefold increased relative to its adjacent introns (0.20 = exonic rate, versus 0.04 in the introns).