Pf2: Catalogue of Genetic Variation in P. falciparum v2.2

Description

This record describes version 2.2 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 2,155 parasite samples collected at 35 different locations in Africa, Asia, America and Oceania, we identified more than 500,000 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 Manske, Miotto et al, Nature (2012), PMID 22722859. http://www.ncbi.nlm.nih.gov/pubmed/22722859. Short-read DNA sequence data were mapped against the reference genome 3D7 v3. PlasmoDB GFF v9 was used for gene annotations and exon boundaries (http://plasmodb.org/common/downloads/release-9.0/Pfalciparum3D7/gff/data/). 

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_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.