Ploidy number definition

For the calculation of chromosome copy number, we followed the methodology of Zhang et al. [48]. Prior to that, we used the bamCoverage tool from the deepTools package (https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html), to estimate sequencing depth from each chromosome, and normalized using the RPKM method. The median depth of each chromosome (d_chr) was then determined followed by calculation of the total median depth for all chromosomes (d_T = median[d_chr1…d_chr35]). These values were then divided by two in order to represent the median depth for a haploid allele of a chromosome. The chromosome copy number was given by S_chr = d_chr/(d_T/2). These steps were implemented in a R script to perform the analysis automatically. We assumed that in general all chromosomes were diploid.