Supplementary Figure 5: Genetic structure of individual infections.

Each of the 148 samples from western Thailand (WTH), western Cambodia (WKH) and Papua Indonesia (PID) is displayed. The box on the left displays a histogram of nonreference allele frequency (NRAF) across all heterozygous SNPs. The horizontal axis is NRAF on a scale of 0 to 1. The vertical axis is the number of SNPs on a scale of 0 to 500. The box on the right displays heterozygosity in 20-kb bins across the genome. The horizontal axis represents genomic position, with vertical lines separating the 14 chromosomes. The vertical axis shows the proportion of heterozygous SNPs in a given bin on a scale of 0 to 0.03. The legend for each sample gives its geographical origin, average read depth, F_WS, RoH and the inferred number of dominant clones. The line above each of these plots is colored according to the classification in Figure 3a (right). The inferred number of dominant clones is based on these criteria: one dominant clone, F_WS ≥ 0.99; two dominant clones, F_WS < 0.99 and NRAF histogram is bimodal and symmetric; three or more dominant clones, F_WS < 0.99 and NRAF histogram is not bimodal and symmetric. RoH is the proportion of the genome occupied by runs of homozygosity, defined here as the proportion of 100-kb bins for which mean heterozygosity < 0.005. Samples are ordered by RoH. In samples with two dominant clones, the clones are classified as either unrelated (if RoH < 0.1) or related (if RoH > 0.1).