Variation in nucleotide diversity over the core genome. Nucleotide diversity is shown for each cross in 500-bp half-overlapping windows across the core genome (which excludes hypervariable regions containing var, rif, or stevor genes) using SNPs combined from both variant calling methods and passing all quality filters. The peak of nucleotide diversity on Chromosome 10 is expanded to show four distinct peaks due to genes encoding merozoite surface antigens MSP3, MSP6, DBLMSP, and DBLMSP2. All labeled loci (with the exception of AMA1) are sites of complex variation where assembly of sequence reads is required to determine the nonreference alleles.
