PfCP: MalariaGEN P. falciparum Community Project (January 2016 Release)

This record provides data files for the paper ‘Genomic epidemiology of artemisinin resistant malaria’ by the MalariaGEN P. falciparum Community Project, and provides links to data resources and citation information.

Data Resources

This record contains the following data associated with the Community Project January 2016 release:

• Supplementary data file: For each P. falciparum gene, this table lists: the systematic ID, position and description of the gene; the ortholog gene in P. chabaudi; the conservation score; the count of all (N)on-synonymous and (S)ynonymous mutation in Africa (AFR) and Southeast Asia (SEA); the count of the rare (i.e. present in only 1 or 2 samples) mutations; the N/S log fold-change in SEA vs AFR; the Fisher’s test p-value of N/S in AFR vs SEA.
• Sample metadata file: contains sample information, accession numbers and genotype calls for 3,411 samples from 23 countries.
• Catalogue of genetic variations (SNPs) and allele frequencies (v4.0): a catalogue with more than 900,000 SNPs and allele frequency data based on an analysis of 3,488 samples from 43 locations in 23 countries. Contains the following zip files:
  • snp_alleles_pgv.tab.zip: The complete catalogue of SNPs, including coordinates, alleles and references to genes.
  • snp_maf_pgv.tab.zip: Set of minor allele frequencies by population for all the SNPs in the catalogue.
  • snp_daf_pgv.tab.zip: Set of derived allele frequencies by population for all the SNPs in the catalogue.
  • snp_nraf_pgv.tab.zip: Set of non-reference allele frequencies by population for all the SNPs in the catalogue.
  • snp_fst_pgv.tab.zip: Population differentiation statistic (FST) for all the SNPs in the catalogue.
  • README file containing further information for the catalogue

About the collaboration

The sequence data used in this analysis were generated by the Wellcome Trust Sanger Institute and contributed to the MalariaGEN P. falciparum Community Project by several independent research groups. These data form part of ongoing projects that are investigating a number of scientific questions that go beyond the scope of this particular publication. Some of the intended scientific analyses will be published through the MalariaGEN P. falciparum Community Project which includes all of the samples and data listed here, and other intended analyses will be published through the Pf3k Project which includes a large subset of the samples and data.

These data are made available open access. If you use these data, please cite:

MalariaGEN Plasmodium falciparum Community Project, Genomic epidemiology of artemisinin resistant malaria. eLife, 2016 (DOI: 10.7554/eLife.08714).