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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 charts can be displayed for 1000 Genomes allele frequencies. If a pie chart is shown on the view for the 1000 Genomes Project, 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 populations are grouped by project when possible (e.g. 1000 Genomes, HapMap and ESP for human, Mouse Genomes Project for Mouse).

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

Allele frequencies and counts: In this separate example, the alleles found in the Utah Residents (CEPH) with Northern and Western European ancestry (CEU) HapMap population are C (a frequency of 0.492, or 49.2% of all alleles) and G (0.508 or 50.8%). 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 58(C) + 60(G), which adds up to 118 alleles. Therefore, the C allele has a frequency of 58/118, or 0.492.

Genotypes frequencies and counts: Genotypes detected in this population are C|C (a frequency of 0.220 or 22%), C|G (0.542 or 54.2%) and G|G (0.237 or 23.7%). Allele count represents the number of each type of allele found in the population studied. In the example above, out of 59 individuals (118 alleles), the allele C was found 58 times and allele G was detected 60 times.