Within the Mfangano isolates there were 4 genes of interest identified with SNPs that had significant iHS values ((− log10[1–2|ΦiHS–0.5|]) > 4.0), including: P. falciparum apical membrane protein 1 (Pfama1), one of the leading malaria vaccine candidates, merozoite surface protein 3 (Pfmsp3), associated with erythrocyte invasion and host immunity, and the Peptidase family C50 which are associated with the pathogenicity of P. falciparum through parasite immune evasion or invasion of host cells (Supplementary Fig. S3, Supplementary Table S5). Here, LAP3 is linked to malaria.