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Fig. 3 | Malaria Journal

Fig. 3

From: An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis

Fig. 3

Local population structure in sub-Saharan Africa. t-distributed stochastic neighbour embedding (tSNE) was computed from the variance-standardized genetic relationship matrix generated using A SNPs and indels combined, B indels only and C SNPs only. Variant data (from chromosome 1) were pruned for linkage disequilibrium and only samples with less than 20% missing genotypes (n = 3008) were kept. DRC: Democratic Republic of Congo

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Malaria Journal

ISSN: 1475-2875

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