DOI: 10.5281/zenodo.18744958
title: Pf6: An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples

description: This record provides information about the Pf6 dataset which contains genome variation data on 7,000 worldwide samples of Plasmodium falciparum. The key publication is MalariaGEN et al, Wellcome Open Research 2021642 DOI: 10.12688/wellcomeopenres.16168.1. 

Content of the data release

This release contains details on contributing partner studies, sample metadata and key sample attributes inferred from genomic data, and genomic data including raw sequence reads. Further details and analytical results can be found in the accompanying data release paper.

These data are available open access. Publications using these data should acknowledge and cite the source of the data using the following format: "This publication uses data from the MalariaGEN Plasmodium falciparum Community Project as described in ‘An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. MalariaGEN et al, Wellcome Open Research 2021642 DOI: 10.12688/wellcomeopenres.16168.1.'".



Study information: Details of the 49 contributing partner studies, including description, contact information and key people.

Sample provenance and sequencing metadata: sample information including partner study information, location and year of collection, ENA accession numbers, and QC information for 7,113 samples from 28 countries.

Measure of complexity of infections: characterisation of within-host diversity (FWS) for 5,970 QC pass samples.

Drug resistance marker genotypes: genotypes at known markers of drug resistance for 7,113 samples, containing amino acid and copy number genotypes at six loci: crt, dhfr, dhps, mdr1, kelch13, plasmepsin 2-3.

Inferred resistance status classification: classification of 5,970 QC pass samples into different types of resistance to 10 drugs or combinations of drugs and to RDT detection: chloroquine, pyrimethamine, sulfadoxine, mefloquine, artemisinin, piperaquine, sulfadoxine- pyrimethamine for treatment of uncomplicated malaria, sulfadoxine- pyrimethamine for intermittent preventive treatment in pregnancy, artesunate-mefloquine, dihydroartemisinin-piperaquine, hrp2 and hrp3 genes deletions.

Drug resistance markers to inferred resistance status: details of the heuristics utilised to map genetic markers to resistance status classification.

Gene differentiation: estimates of global and local differentiation for 5,561 genes.

Extended methods: detailed bioinformatic methods for Pf6.


A README file describes in fine detail all the files included in the release, the format and interpretation of each column, and contains some tips and tricks for accessing genotype data in VCF and zarr files.

Supplementary data

The following supplementary data is available as a single document download: Supplementary data



Supplementary Note



Analysis of local differentiation score

The classic 76T chloroquine resistance mutation in crt is found on multiple haplotypes

Suplhadoxine-pyrimethamine resistance is widespread and associated with many haplotypes

mdr1 duplications have many different breakpoints

Artemisinin, piperaquine, and mefloquine resistance

No evidence of resistance to less commonly used antimalarials



Supplementary Table 1. Breakdown of analysis set samples by geography

Supplementary Table 2. Studies contributing samples

Supplementary Table 3. Summary of discovered variant positions

Supplementary Table 4. Breakpoints of duplications of gch1

Supplementary Table 5. Breakpoints of duplications of mdr1

Supplementary Table 6. Breakpoints of duplications of plasmepsin 2-3

Supplementary Table 7. Genes ranked by global differentiation score

Supplementary Table 8. Genes ranked by local differentiation score

Supplementary Table 9. Number of samples used to determine proportions in Table 2

Supplementary Table 10. Frequencies of mutations associated with mono- and multi-drug resistance pre- and post-2011

Supplementary Table 11. Frequency of crt amino acid 72-76 haplotypes

Supplementary Table 12. Frequencies of dhfr (51, 59, 108, 164) and dhps (437, 540, 581, 613) multi-locus haplotypes

Supplementary Table 13. Frequency of HRP2 and HRP3 deletions by country

Supplementary Table 14. Alleles at six mitochondrial positions used for the species identification

Supplementary Figure 1. Histogram of local differentiation score for all genes