Copy number/segmentation analyses showing amplified and highly variable or deleted regions on 14 chromosomes. Amplified/deleted regions were displayed as a signal heat map (red, amplified; blue, deleted or highly polymorphic) from each parasite. The 14 chromosome diagrams showed amplified (red, > 1.5) or deleted/highly variable regions (blue, < 0.67) after filtering for regions 0.3 kb or larger. The dashed lines separate the four parasites in each chromosome in the order of 7G8, Dd2, FCR3, and HB3. The arrow indicates the chromosome 5 regions amplified in Dd2 and FCR3.