Fig. 4

Complexity of infection analysis by site based on the optimized GATK4 pipeline with ploidy of 6 and 2 versus GATK3. This analysis included SNPs with minor allele frequencies > 1% and missingness rates < 10% on the core region of chromosome 13 from public Illumina reads of field isolate samples (n = 6626). Ploidy 6 and ploidy 2 refer to the optimized GATK4 pipeline ran at hexaploid and diploid modes that were compared to GATK3 (publically available callset from MalariaGEN Pf6). Ploidy 6 showed significant increase in polyclonal sample detection compared to ploidy 2 and GATK3 after pairwise statistical analysis between pipelines (P < 0.05, Wilcoxon test). DRC: Democratic Republic of Congo. COI: complexity of infection