Fig. 1

The five isolates representing each of the lineages were assessed for ploidy and aneuploidy (largest five supercontigs presented). A Non-overlapping 10 kb windows of the normalized depth of coverage (normalized by total sequencing depth across percentiles of GC content, and excluding ambiguous sites) shows evidence for aneuploidies (supercontig 2, 3 and 5) among each of the Bd isolates apart from BdCH ACON. B Allele frequencies (percent of reads agreeing with the reference base) are shown from 25% agree to 75% disagree, with red-dotted lines indicating greatest support for bi-allelic/diploidy between 47 and 53% and greatest support for tri-allelic/triploidy between 30–36% and 63–69%