Fig. 5

Variance of allele balance calculated for downsampled S. cerevisiae isolates exhibiting ploidy variation. Whole-genome sequencing datasets of isolates were downsampled to 10×, 20×, 30×, 40×, and 50×. a Variance of allele balance was calculated from downsampled variant calls. Observations calculated from the same isolate are joined by a line. The contours provided as a guide were calculated using B. lactucae data (Fig. 3). Histograms of allele balance were investigated for the two labelled isolates. b Isolate YJM954 had bimodal distribution of allele balance frequencies inconsistent with diploidy. c Isolate YJM676 had a Gaussian distribution consistent with diploidy. d The percentage of high-quality SNPs called as heterozygous could differentiate haploid isolates from polyploidy isolates. At all coverages the percentage of SNPs passing the allele balance filter never exceeded 55% for haploid isolates and was never less than 55% for diploid or polyploid isolates. The closest points were 53.1% for haploid isolate CBS1227 calculated from 135 polymorphisms at 10× and 57.1% for diploid isolate CBS2910 calculated from 2377 SNPs at 50×. See Additional file 2: Fig S5 for more details