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[Preprint]. 2023 Feb 14:rs.3.rs-2561857. [Version 1] doi: 10.21203/rs.3.rs-2561857/v1

Figure 4. Complexity of infection analysis by site based on the optimized GATK4 pipeline with ploidy of 6 and 2 versus GATK3.

Figure 4

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 = 6,626). 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.