Figure 3.

Chromosome 2 is a supernumerary chromosome. (A) Read depths at SNPs in unique regions across the whole nuclear genome (black) or on chr02 only (blue). Chr02 median depth (170) is roughly double the whole-genome median depth (88), indicating chr02 may have double the copy number of the rest of the genome. (B) Proportion of reads with minor allele for all SNPs in unique regions across the genome (black) or on chr02 only (blue). 0.5 (1:1 ratio) indicates two copies; a mixture of 0.25 (1:3 ratio) and 0.5 indicates four copies.