Fig. 3

Molecular karyotyping of Bge3 cell line with read depth coverage and single-nucleotide variant allele frequency. Short paired-end Illumina reads from Bge3 and B. glabrata were mapped to version 1 of the strain BB02 reference genome. a Total normalized coverage for Bge3 and B. glabrata reads were similar (left), while coverage distributions for 7 of the 18 largest linkage groups (LGs) were significantly different (right, P < 0.05, highlighted in red). The Kolmogorov-Smirnov test was used to test the null hypothesis that the two LG RDC samples are drawn from the same distribution. b SNVs were filtered for quality and biallelism and grouped by LG. Reads supporting the alternative allele for each SNV were counted and plotted as a frequency to total reads at that site. Given a population with stable chromosome copy number (CCN), alternative allele frequency from independently inherited LGs should correlate to CCN. Allele frequencies greater than 0.875 and less than 0.125 were trimmed to theoretically accommodate octosomies. Frequencies in our data do not coalesce around predictable ratios, suggesting that CCN as measured by allele frequency is masked by a mixed aneuploid population