Pf3: Catalogue of Genetic Variation in P. falciparum v3.1

Description This record describes version 3.1 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 3,251 parasite samples collected at 40 different locations in Africa, Asia, America and Oceania, we identified more than 600,000 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 (ftp://ftp.sanger.ac.uk/pub/pathogens/Plasmodium/falciparum/3D7/3D7.latest_version/version3). 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.Description 本记录介绍了恶性疟原虫社区项目（P. falciparum Community Project）的3.1版本：恶性疟原虫遗传变异目录，其收录内容如下： 1. 通过深度测序鉴定得到的单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）； 2. 不同地理种群的等位基因频率； 3. 基因组可及性评估指标——包括GC含量、比对质量及覆盖度——用于可视化展示单核苷酸多态性鉴定与样本精准基因分型过程中可能存在的技术难点。 研究团队对采集自非洲、亚洲、美洲及大洋洲40个不同采样点的3251份疟原虫样本开展分析，共鉴定出超过60万个外显子区域单核苷酸多态性。本次发布的数据包含上述单核苷酸多态性及其等位基因频率的相关信息。生成该数据集的实验方法已详细发表于Manske、Miotto等于2012年发表于《自然》（Nature）的研究论文，PubMed编号（PMID）为22722859，访问链接：http://www.ncbi.nlm.nih.gov/pubmed/22722859。 本研究将短读长DNA序列数据比对至参考基因组3D7 v3版本（ftp://ftp.sanger.ac.uk/pub/pathogens/Plasmodium/falciparum/3D7/3D7.latest_version/version3），基因注释及外显子边界信息采用PlasmoDB GFF v9版本（http://plasmodb.org/common/downloads/release-9.0/Pfalciparum3D7/gff/data/）。本数据集已开放获取，若您使用本数据，请引用如下文献： Manske M., Miotto O. 等. 通过深度测序分析自然感染中的恶性疟原虫多样性. 自然. 2012年7月19日; 487: 375-379. PMID 22722859 本记录包含的文件： snp_alleles_pgv.tab.zip：完整的单核苷酸多态性目录，包含位点坐标、等位基因及基因关联注释信息。 snp_maf_pgv.tab.zip：目录中所有单核苷酸多态性的种群次要等位基因频率数据集。 snp_daf_pgv.tab.zip：目录中所有单核苷酸多态性的种群衍生等位基因频率数据集。 snp_nraf_pgv.tab.zip：目录中所有单核苷酸多态性的种群非参考等位基因频率数据集。 snp_fst_pgv.tab.zip：目录中所有单核苷酸多态性的种群分化统计量（FST）数据集。