Supplementary data for published paper

Haplotype homozygosity and derived alleles in the human genome

Andrew Fry, Clare Trafford, Martin Kimber, Man-Suen Chan, Kirk Rockett and Dominic Kwiatkowski

Am. J. Hum. Genet., 78, 2006

Using simulations and empirical data from the International HapMap Project, this paper reports that a simple pairwise metric of haplotype homozygosity gives significantly higher mean values for human SNP alleles that appear to be derived than for those that appear to be ancestral.

The MARKER application calculates this haplotype homozygosity metric individually for all markers in a dataset, each time using a 25kb region either side of the target SNP. Separate values are calculated for the major allele (HH1C) and the minor allele (HH2C), and the results are plotted to the left of the MARKER maps.

Please note that HHxC values are currently available for HapMap and Perlegen MARKER datasets only.

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MARKER lets you query and view HapMap data in various ways but doesn't display the primary data, in accordance with the terms and conditions of the International HapMap Project Public Access Licence.]