Figure 4

Box plots showing coverage analysis of P. falciparum chromosome 11. (i) P. falciparum 3D7; mapped reads normalized to 21× genome coverage (1 normalized depth represents 21×). (ii) Clinical isolate PK0076; mapped reads normalized to 11× genome coverage (1 normalized depth represents 11×). Subplots B, C and D in both i & ii show coverage of sub-regions of the P. falciparum 3D7 chromosome 11. A) Coverage depth variability plotted for each library on the entire chromosome. B) Distribution of base coverage depth for each library over gene Pf11_0074 and its neighboring introns. C) Distribution of base coverage depth at positions 259985-260864 (extreme AT-region). D) Distribution of base coverage depth at positions 29092-30361 (VAR gene and introns). Top and bottom sides of a box plot represent 75^th and 25^th percentile of base coverage-depth distribution respectively. The middle line represents 50^th percentile. A narrow box indicates less variation in coverage depth across that locus and vice versa. Kapa HiFi, Kapa2G and Platinum pfx enzymes were used in the presence of TMAC. All P. falciparum 3D7and most clinical isolate libraries were prepared in duplicate and each replicate data plotted independently as shown.