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Human Genome Diversity Project Smoothed Expected Heterozygosity on 7 Continents   (All Variation and Repeats tracks)

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 Hetzgty Africa  Human Genome Diversity Proj Smoothd Expec Heterozygosity (Africa)   Schema 
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 Hetzgty Bantu  Human Genome Diversity Proj Smoothd Expec Heterozygosity (Bantu pops. in Africa)   Schema 
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 Hetzgty Mideast  Human Genome Diversity Proj Smoothd Expec Heterozygosity (Mideast)   Schema 
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 Hetzgty Europe  Human Genome Diversity Proj Smoothd Expec Heterozygosity (Europe)   Schema 
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 Hetzgty S. Asia  Human Genome Diversity Proj Smoothd Expec Heterozygosity (S. Asia)   Schema 
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 Hetzgty E. Asia  Human Genome Diversity Proj Smoothd Expec Heterozygosity (E. Asia)   Schema 
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 Hetzgty Oceania  Human Genome Diversity Proj Smoothd Expec Heterozygosity (Oceania)   Schema 
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 Hetzgty Americas  Human Genome Diversity Proj Smoothd Expec Heterozygosity (Americas)   Schema 
    

Description

This track shows a 3-SNP moving average of p(1-p) where p is the major allele frequency (i.e. half of the expected heterozygosity) on seven continents, from 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. The 53 populations were divided into seven continental groups: Africa, Middle East, Europe, South Asia, East Asia, Oceania and the Americas. Allele frequencies were used to calculate p(1-p) for each SNP, and then a 3-SNP average was computed for each SNP and its two neighboring SNPs.

The associated analysis tracks HGDP FST, HGP iHS, and HGDP XP-EHH (Pickrell et al.) did not make use of all African populations, but instead used only the Bantu populations because a more closely related group was desired for comparison with other continental groups. For this track, separate subtracks show the expected heterozygosity of all African populations and of only Bantu populations.

Credits

Thanks to the HGDP-CEPH and Joe Pickrell in the Pritchard lab at the University of Chicago for providing these data.

References

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.

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.

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.