Extended Data Fig. 2. Evidence for association with HbS in three regions of the Pf genome using directly-typed HbS genotypes.

Points show evidence for association with HbS (log₁₀ Bayes Factor for test in N = 4,071 samples, y axis) based on direct typing of HbS for variants in the Pfsa1, Pfsa2 and Pfsa3 regions of the Pf genome (panels). Variants which alter protein coding sequence are denoted by plusses, while other variants are denoted by circles. Results are computed by logistic regression including an indicator of country as a covariate and assuming an additive model of association; missing and mixed Pf genotype calls were excluded. A corresponding plot using imputed HbS genotypes can be found in Fig. 1. The variant with the strongest association in each region is annotated and the panels show regions of length 50kb centred at this variant. Below, regional genes are annotated, with gene symbols given where the gene has an ascribed name in the PlasmoDB annotation (after removing 'PF3D7_' from the name where relevant); the three genes containing the most-associated variants are shown in red.