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Vcf file (bgzip compression) containing variants from patient sample 1, 2 and 3, which were sequenced with the Nanopore adaptive sampling mode selecting for reads aligning to the P. falciparum 3D7 reference genome. Variants were called using Clair3, and combined with GATK. No variant filtration was applied.

Supplementary Figures 1-2 and Supplementary Tables 1-6 and 8-10

Supplementary Figures 1-3 and Supplementary Tables 1-9.

Total sequencing depth and depth of the resistance allele for drug-resistance associated markers in P. falciparum (1) in patient 1, 2 and 3. The higher multiplicity of infection (MOI) of patient 1 and 3 explains the presence of both resistant and non-resistant alleles at some loci. For 38 of the resistance associated markers, a PCR fragment was Sanger sequenced to assess whether the SNP was called correctly with Nanopore sequencing. (1) WHO. 2020. Report on antimalarial drug efficacy, resistance and response: 10 years of surveillance (2010-2019). WHO, Geneva.

Total sequencing depth and depth of the resistance allele for drug-resistance associated markers in P. falciparum (1) in patient 1, 2 and 3. The higher multiplicity of infection (MOI) of patient 1 and 3 explains the presence of both resistant and non-resistant alleles at some loci. For 38 of the resistance associated markers, a PCR fragment was Sanger sequenced to assess whether the SNP was called correctly with Nanopore sequencing. (1) WHO. 2020. Report on antimalarial drug efficacy, resistance and response: 10 years of surveillance (2010-2019). WHO, Geneva.

Vcf file (bgzip compression) containing variants from patient sample 1, 2 and 3, which were sequenced with the Nanopore adaptive sampling mode selecting for reads aligning to the P. falciparum 3D7 reference genome. Variants were called using Clair3, and combined with GATK. No variant filtration was applied.

Supplementary Figures 1-3 and Supplementary Tables 1-9.

Supplementary Figures 1-3 and Supplementary Tables 1-9.