Extended Data Fig. 6: Pfsa3+ genotypes are correlated with PF3D7_1127000 transcript levels in trophozoite-stage infections.

Plot shows the ratio of RNA-seq reads carrying the non-reference allele at the chr11:1,057,437 T > C mutation (x axis) against the estimated transcript abundance of PF3D7_1127000 (log2 TPM, y axis), for 32 children from Mali ascertained with HbAA or HbAS genotype (colours, as detailed in the legend). Underlying data is as published by Saelens et al¹⁶ and is further detailed in Supplementary Table 6. The plot is separated by parasite stage (panel labels) as previously inferred¹⁶. Among trophozoite-stage infections, we noted one infection of an HbAS individual (AS08) that has low expression of PF3D7_1127000 (TPM = 28.3); this sample appears to have Pfsa3- genotype although we caution that only two reads with reasonable mapping quality were observed. Conversely, one ring-stage infection of an HbAA genotype individual (AA01) has relatively high expression (TPM = 253.2) of PF3D7_1127000; this sample is likely mixed as it appears to express gene copies with both Pfsa3- and Pfsa3+ genotypes, with Pfsa3+ predominant.