See here and here and here That last one concerns Brent Pedersen's and colleagues' Indexcov, see here. There is also an article The Genome Sequence of the Jean-Talon Strain, an Archeological Beer Yeast from Québec, Reveals Traces of Adaptation to Specific Brewing Conditions by Fijarczyk et al that goes into determining ploidy per chromosome in Figure 1 and has the accompanying code for making the figures here, in particular there is R code for plotting coverage across the genome that produces a plot reminiscent of my script plot_expression_across_chromosomes.py discussed below.

I tried to make a tool that would do this for ngs data. See here. It should work with humans if you have a genome annotation file.

Even though my script was developed with RNA-Seq data, if you can point plot_expression_across_chromosomes.py at the components of a baseline vs. coverage for your other genomes as columns in a spreadsheet, it should work with DNA coverage data, I think. Actually, you may need to use coverage among different chromosomes as the columns, i.e., baseline vs. experimental, depending on how you have your data.

People looking into this might be interested in this discussion and related pre-print.