Pooling reads across heterozygous and homozygous regions clearly identified SNPs. (A) For each homozygous strain independently, the number of positions with max-to-sum ratio <0.7 were considered ‘putative SNPs’; the total number of putative SNPs on each chromosome was called SNPs
, and this number was divided by the corresponding value for wild type; to avoid confusion, the plotted number is the minimum of this quotient and 100%. (B) Putative SNP locations were identified in the wild-type strain, and the corresponding positions in homozygous strains were investigated for SNP status: if a putative SNP position from wild type was not a SNP in the indicated strain, it was shaded green (or pink, depending on the allele), whereas if both were SNPs, the latter was shaded white. (C) Scatterplot of max-to-sum ratios in heterozygous and homozygous regions for every position in the genome. Histograms at top and right show the distribution of data on each perpendicular axis as indicated, with bars in linear space and lines in log space. (D) The number of unphased SNPs in non-overlapping 50 kb windows tiled across the genome, with telomere and centromere locations as indicated.