Fig. 5: Analysis of length polymorphism and nucleotide identity of msp2-derived reads.

a Read length distributions of msp2 alleles across 24 mock samples. Each dot represents the length of a single read that was trimmed to the extent of msp2 coding-sequence (CDS) after mapping. Individual reads are coloured by the laboratory strain to which they have the highest identity alignment. Multi-modal distributions are indicative of mixed infections. b Hierarchically clustered heatmaps of msp2-derived reads showing pairwise alignment scores. Each cell is coloured by the global pairwise alignment score between two msp2-derived reads, which have been hierarchically clustered along both rows and columns. Colours of rows and columns indicate the laboratory strain to which each read has the highest identity alignment, as in (a). Heatmaps are shown for two different mock samples: clonal 3D7 (top); mixture of 3D7 and Dd2 (middle); and mixture of 3D7, Dd2 and GB4 (bottom). Note how reads cluster based on allele type. GB4 reads are under-represented in the bottom heatmap, likely due to lower DNA quality. c, d are the same as (a, b), but for 28 field samples from Zambia. In (c), read lengths distributions suggest the presence of both clonal and mixed infections. In (d), examples of likely clonal infection (top); two-strain infection (middle); and three-strain infection (bottom).