Figure 2.

Distribution of mutations along chromosomes. (A) SNV density is plotted across chromosomes I and X for the aggregate variants for mutant strains (Mu) and the wild isolates (WI). The SNV density is essentially uniform along the length of both the autosome and X chromosome in the mutant strains. In contrast, for the wild isolates SNV density on chromosome I is much higher on the arms, where recombination is high and gene density is in general lower than in the centers, where recombination is low and gene density is higher. SNV density along the wild isolates' X chromosome is more uniform. (B) Similar density plots for all short indels and (C) only those outside of homopolymer runs. There is enrichment for short indels on the autosomal arms of both the WI and mutant strains, although this is much more pronounced for the WI. However, the distribution in the mutant strains is much more uniform when only considering the small indel events that do not involve homopolymer runs. The bias toward higher density on the autosomal arms remains for the WI.