Fig. 2
In silico analysis demonstrates that MAD4HatTeR’s microhaplotypes capture high genetic diversity within African samples. We reconstructed alleles (microhaplotypes) from publicly available WGS data to estimate genetic diversity. For SpotMalaria, SNP barcodes are used instead of microhaplotypes based on intended design and current usage. We note that additional information may be present within the amplified targets if microhaplotype sequences are accurately identifiable with appropriate bioinformatic processing. As such, alternate results for microhaplotypes reconstructed for the targets that contain the SNPs in SpotMalaria are shown in Supplementary Fig. 2. A. Diversity module pool D1 includes more highly heterozygous targets than other published highly multiplexed panels. Only targets for diversity in each panel are included and heterozygosity is calculated for samples across Africa. B. We performed principal coordinate analysis on alleles on global, African or Mozambican data. The percentage of variance explained by each principal component is indicated in parentheses.
