Schema for HGDP Allele Freq - Human Genome Diversity Project SNP Population Allele Frequencies
  Database: hg19    Primary Table: hgdpGeo    Row Count: 667,349
Format description: Human Genome Diversity Project population allele frequencies (bed 4+)
fieldexampleSQL type description
bin 590smallint(6) Indexing field to speed chromosome range queries.
chrom chr1varchar(255) Reference sequence chromosome or scaffold
chromStart 752565int(10) unsigned Start position in chromosome
chromEnd 752566int(10) unsigned End position in chromosome
name rs3094315varchar(255) SNP ID (dbSNP reference SNP rsNNNNN ID)
ancestralAllele Gchar(1) Ancestral allele on forward strand of reference genome assembly
derivedAllele Achar(1) Derived allele on forward strand of reference genome assembly
popFreqs 0.0882,0.1667,0.6818,0.25,0...longblob For each population in alphabetical order, the proportion of the population carrying the ancestral allele.

Sample Rows
 
binchromchromStartchromEndnameancestralAllelederivedAllelepopFreqs
590chr1752565752566rs3094315GA0.0882,0.1667,0.6818,0.25,0.2292,0.2778,0.5909,0.26,0.18,0.0,0.0,0.0,0.1111,0.2143,0.1786,0.0455,0.1,0.1818,0.2222,0.125,0.125,0 ...
590chr1768447768448rs12562034GA0.8824,0.75,0.9091,0.9375,0.8958,0.7444,0.9773,0.76,0.8,0.75,1.0,0.9,0.7222,0.8214,0.8929,0.5,0.5,0.7955,0.5556,0.9583,0.5179,0. ...
592chr110058051005806rs3934834CT0.7941,0.7917,0.6818,0.6875,0.7917,0.7222,0.4773,0.86,0.88,0.95,1.0,0.9,1.0,0.8214,0.8214,0.8382,0.85,0.7955,0.9444,0.6667,0.892 ...
592chr110187031018704rs9442372GA0.5588,0.5625,0.5,0.625,0.5417,0.4444,0.5682,0.7,0.48,0.95,0.7143,0.8,0.7778,0.5238,0.5893,0.8235,0.85,0.6818,0.6667,0.4167,0.82 ...
592chr110214141021415rs3737728GA0.7647,0.8125,0.6364,0.875,0.7917,0.7667,0.7727,0.78,0.66,1.0,0.7143,0.9,0.7778,0.7024,0.7679,0.9853,1.0,0.8864,0.7222,0.75,0.92 ...
592chr110216571021658rs11260588GA1.0,0.9792,0.7727,0.75,1.0,0.9889,0.8864,0.92,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.75,1.0,0.769 ...
592chr110216941021695rs9442398GA0.7353,0.7083,0.4545,0.6875,0.8125,0.7222,0.5682,0.78,0.6,1.0,0.7143,0.9,0.7778,0.6786,0.7679,0.9559,1.0,0.8864,0.7222,0.75,0.87 ...
592chr110305641030565rs6687776CT0.8824,0.7083,0.4545,0.375,0.8125,0.7667,0.5682,0.78,0.82,0.9,0.7143,0.8,0.6667,0.7143,0.875,0.8235,0.95,0.7727,0.8333,0.8333,0. ...
592chr110315391031540rs9651273GA0.8235,0.7917,0.9545,1.0,0.6667,0.6444,0.9773,0.76,0.94,1.0,1.0,1.0,1.0,0.631,0.7321,1.0,0.95,0.8636,0.9444,0.6667,0.9464,0.7174 ...
593chr110489541048955rs4970405AG0.9118,0.8125,1.0,1.0,0.8542,0.8333,1.0,0.94,0.9,1.0,0.7143,0.8,0.7222,0.8452,0.8929,0.8676,0.9,0.8409,0.7778,0.8333,0.8571,0.91 ...

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

HGDP Allele Freq (hgdpGeo) Track Description
 

Description

This track shows the 657,000 SNPs genotyped in 53 populations worldwide by the Human Genome Diversity Project in collaboration with the Centre d'Etude du Polymorphisme Humain (HGDP-CEPH). This track and several others are available from the HGDP Selection Browser.

Methods

Samples collected by the HGDP-CEPH from 1,043 individuals from around the world were genotyped for 657,000 SNPs at Stanford. Ancestral states for all SNPs were estimated using whole genome human-chimpanzee alignments from the UCSC database. For each SNP in the human genome (NCBI Build 35, UCSC database hg17), the allele at the corresponding position in the chimp genome (Build 2 version 1, UCSC database pantro2) was used as ancestral.

Allele frequencies were plotted on a world map using programs included in the Generic Mapping Tools.

Credits

Thanks to the HGDP-CEPH, the Pritchard lab at the University of Chicago, Joe Pickrell and John Novembre for sharing the data and plotting scripts for this track.

References

Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A et al. A human genome diversity cell line panel. Science. 2002 Apr 12;296(5566):261-2.

Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, Myers RM. Worldwide human relationships inferred from genome-wide patterns of variation. Science. 2008 Feb 22;319(5866):1100-4.

Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li J, Absher D, Srinivasan BS, Barsh GS, Myers RM, Feldman MW, Pritchard JK. Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 2009 May;19(5):826-37.

Wessel P, Smith WHF. New, improved version of Generic Mapping Tools released. EOS, Trans. Amer. Geophys. U. 1998;79(47):579.