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Population genetics

Example page

For the top panel describing variation details such as source and class, see this help page.

Populations: Who was studied?  Populations are described by three-letter codes such as CEU (Utah residents).  1000 genomes data is separated into five super-populations: AFR, AMR, ASN, EUR, and SAN.  See this FAQ for a description of what they mean.  ALL stands for all 1000 Genomes data, not separated by population.  Most of these data are imported through dbSNP.

Pie charts

Pie graphs are available for 1000 genomes allele frequencies. If a pie graph is shown on the view, it represents the distribution of the alleles in a 1000 genomes super population for a specific variation. In the example above, 50% of the alleles found in Utah residents studied (CEU) are T (frequency of 0.5), and 50% are G. In the CHB (Beijing) and JPT (Japan) populations, there is only one allele found (T), so the percentage of this allele is 100%. The third graph shows that 61% of alleles found in the Yoruba (YRI) population are T, and 39% are G.

Frequency tables

The first table shown is for 1000 Genomes populations, if known.  The second table shown will be for HapMap populations.  A third, other data table is displayed

The populations studied and data sources (submitters) are shown in the first three columns. Allele and genotype frequencies are displayed in the next columns, followed by allele and genotype counts.

Allele frequencies: In this separate example, the alleles found in the Yoruba (YRI) HapMap population are C (a frequency of 0.175, or 17.5% of all alleles) and G (0.825 or 82.5%). The allele frequency is calculated by dividing one allele's count (C) by the number of alleles detected. In this case, the total allele count is 21(C) + 99(G), which adds up to 120 alleles. Therefore, the C allele has a frequency of 21/120, or 0.175.

Genotypes and counts: Genotypes detected in this population are C|C (a frequency of 0.017 or 1.7%), C|G (0.317 or 31.7%) and G|G (0.667 or 66.7%). Allele count represents the number of each type of allele found in the population studied. In the example above, out of 60 individuals (120 alleles), the allele C was found 21 times and allele G was detected 99 times.

In this example, the genotype count adds up to 60 individuals, and shows only one individual with the C|C genotype.