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+)
|field||example||SQL type ||description |
|bin ||590||smallint(6) ||Indexing field to speed chromosome range queries.|
|chrom ||chr1||varchar(255) ||Reference sequence chromosome or scaffold|
|chromStart ||752565||int(10) unsigned ||Start position in chromosome|
|chromEnd ||752566||int(10) unsigned ||End position in chromosome|
|name ||rs3094315||varchar(255) ||SNP ID (dbSNP reference SNP rsNNNNN ID)|
|ancestralAllele ||G||char(1) ||Ancestral allele on forward strand of reference genome assembly|
|derivedAllele ||A||char(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.|
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
HGDP Allele Freq (hgdpGeo) Track Description
This track shows the 657,000 SNPs genotyped in 53 populations worldwide by the
Genome Diversity Project in collaboration with the
du Polymorphisme Humain (HGDP-CEPH).
This track and several others are available from the
HGDP Selection Browser.
Samples collected by the HGDP-CEPH from 1,043 individuals from around the
world were genotyped for 657,000 SNPs at
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.
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.
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.
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.