Pf1: Catalogue of Genetic Variation in P. falciparum v1.0

Description This record describes version 1.0 of the P. falciparum Community Project: 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 227 parasite samples collected at six different locations in Africa, Asia and Oceania, we identified more than 86,000 exonic single nucleotide polymorphisms (SNPs). This download includes data on these SNPs and their allele frequencies. These data are described in detail in Manske, Miotto et al, Nature (2012), PMID 22722859. http://www.ncbi.nlm.nih.gov/pubmed/22722859. These data were also used for the analysis published in Miotto et al, Nature Genetics (2013), PMID 23624527. http://www.ncbi.nlm.nih.gov/pubmed/23624527 These data are made available open access. If you use these data, please cite:Manske M., Miotto O. et al. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature. 2012 July 19; 487: 375-379. PMID 22722859 Files in the record: snp_complete_pgv.csv.zip: The complete catalogue of SNPs, including coordinates, alleles, allele frequencies for all populations and references to genes. snp_alleles_pgv.csv.zip: Set of alleles for all the SNPs in the catalog, including references to genes. snp_maf_pgv.csv.zip: Set of minor allele frequencies by population for all the SNPs in the catalogue, including references to genes. snp_daf_pgv.csv.zip: Set of derived allele frequencies by population for all the SNPs in the catalogue, including references to genes. snp_nraf_pgv.csv.zip: Set of non-reference allele frequencies by population for all the SNPs in the catalogue, including references to genes.