FIGURE 3.

Genomic distribution of heterozygous positions in Saccharomyces cerevisiae genomes. Each genome was divided into 40 kbp windows, the number of variants was counted within each window, and this count was divided by the window size. While most windows had a typical number of heterozygous positions (2–8 per kbp) there were a substantial number of windows that contained very few heterozygous positions. Note that these are raw variants from the VCF file produced by the variant caller (in our case, GATK HaplotypeCaller). Because most variant callers take an aggressive perspective on variant calling, the values presented are likely an over-estimate of heterozygosity.