The HapMap Project identified a set of approximately four million common SNPs, and genotyped these SNPs in four populations. The intent is that this data can be used as a reference for future studies of human disease. This track displays the genotype counts and allele frequencies of those SNPs. The data displayed are from release 22 (HapMap Phase II), based on dbSNP build 126. This track also provides orthologous alleles from chimp and macaque.
The HapMap data are from these four human populations:
The CEU and YRI data are comprised of 90 individuals in parent-child trios. The UCSC display removes the data for the children, leaving 60 individuals in each population. The CHB and JPT data are comprised of 45 individuals.
The HapMap assays provide biallelic results. Over 99.9% of HapMap SNPs are included in dbSNP build126 as biallelic; approximately 3,000 are more complex. Two-thirds of the HapMap SNPs are transitions: one-third are A/G, one-third are C/T.
The orthologous alleles in chimp (panTro2) and macaque (rheMac2) were derived using liftOver.
No two HapMap SNPs occupy the same position. Aside from seven SNPs from the pseudoautosomal region of chrX, no rsIds are included more than once. No HapMap SNPs occur on chrM or on "random" chromosomes.
Note: calculation of heterozygosity has changed since this version of the track. In this track, expected heterozygosity is calculated as follows: the allele counts from all populations are summed (not normalized for population size) and used to determine overall major and minor allele frequencies. Assuming Hardy-Weinberg equilibrium, overall expected heterozygosity is calculated as two times the product of major and minor allele frequencies (see Modern Genetic Analysis, section 17-2). [In the updated HapMap SNPs track, observed heterozygosity is calculated as follows: each population's heterozygosity is computed as the proportion of heterozygous individuals in the population. The population heterozygosities are averaged to determine the overall observed heterozygosity.]
The human SNPs are displayed in gray using a color gradient based on minor allele frequency. The higher the minor allele frequency, the darker the display. By definition, the maximum minor allele frequency is 50%. When zoomed to base level, the major allele is displayed for each population.
Reversing the base position track will cause the HapMap display to reverse as well. This is the recommended configuration for SNPs on the negative strand.
The orthologous alleles from chimp and macaque are displayed in brown using a color gradient based on quality score. Quality scores range from 0 to 100 representing low to high quality. For orthologous alleles, the higher the quality, the darker the display. Quality scores are not available for chimp chromosomes chr21 and chrY; these were set to 98, consistent with the panTro2 browser quality track.
Filters are provided for the data attributes described above. Additionally, a filter is provided for heterozgosity over all populations. The measure of heterozygosity used is 2pq (from Hardy-Weinberg equilibrium). Filters are applied to all six subtracks. This is true, even if a subtrack is not displayed.
Notes on orthologous allele filters:
This track is based on International HapMap Project release 22 data, provided by the HapMap Data Coordination Center.
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The source for this track are the genotypes_chr*_*_r22_nr.b36.txt.gz files from
http://www.hapmap.org/genotypes/2007-03/rs_strand/non-redundant.