Pf4: Catalogue of Genetic Variation in P. falciparum v4.0

Description

This record describes version 4.0 of the P. falciparum Community Project is the Catalogue of Genetic Variation in P. falciparum, which includes:

• Single nucleotide polymorphisms (SNPs) identified via deep sequencing
• Allele frequencies in different geographical populations
• Measures of genome accessibility – such as %GC, mapping quality and coverage – to visualise potential difficulties in identifying SNPs and accurately genotyping samples

Through an analysis of 3,488 parasite samples collected at 43 different locations in Africa, Asia, America and Oceania, we identified more than 930,000 exonic single nucleotide polymorphisms (SNPs). This download includes data on these SNPs and their allele frequencies.

The methods used to generate the data are described in detail in MalariaGEN Plasmodium falciparum Community Project, eLife (2016), DOI: 10.7554/eLife.08714.

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).

Files in the record:

• 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.