[ensembl-dev] allele and population_genotype

Will McLaren wm2 at ebi.ac.uk
Thu Jun 2 18:22:55 BST 2011

Hi Sung,

The tables show similar, but not the same information.

population_genotype gives the frequency (and count) of observed
genotypes (e.g. A|G) in a population; allele gives the frequency of
alleles (e.g. A)

Here's an example. Suppose we are looking at a SNP with alleles A and
G, in a population with 10 members. The members have the following


So we have 3 A|A, 5 A|G and 2 G|G. The frequency of A|A is therefore 3
/ 10 = 0.3, similarly A|G is 0.5 and G|G is 0.2. These are the values
that would be stored in the population_genotype table.

To get allele frequencies we count the individual alleles that make up
the genotypes. So for A we have 6 (3 x A|A) + 5 (5 x A|G), from a
total of 20, so the allele frequency is 11 / 20 = 0.55. Similarly for
G we have 5 (5 x A|G) + 4 (2 x G|G), frequency = 9 / 20 = 0.45. Of
course you can also subtract one frequency from 1 to get the other for
biallelic SNPs!

Hope this helps

Will McLaren
Ensembl Variation

(sorry forgot to copy in dev first time!)

On 2 June 2011 18:03, Sung Gong <sung at bio.cc> wrote:
> Hi,
> I am wondering the difference between the two table; allele and
> population_genotype in the Ensembl variation database.
> Both the tables have 'count' and 'frequency' information along with
> the allele type.
> Do they reflect the same information, but in different level?
> Cheers,
> Sung
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