Hi,

I was wondering how databases as 1000genomes and ESP6500 deal with allele frequencies for positions on the X chromosome. Do they only take females to calculate the number of alleles & allele frequencies or do they take into account that a male only has one X?
They just count how many of each allele exist overall.

Let's say we have a variant on X and a group of two men, two women. Their genotypes are A, G, AG and GG - that's six alleles, two A and four G. We would call A as the minor allele with a frequency of 0.33.

[Here][1] is an example. Look at the top line of the table, ie ALL. There are 384 C alleles and 1275 T alleles in the total population, so the MAF is 0.231 (384/1659 = 0.231). The genotypes are 129 C men, 396 T men, 37 CC women, 181 CT women and 349 TT women. C frequency = 129 (C men) + 2 x 37 (CC women) + 181 (CT women) = 384. T frequency = 396 (T men) + 181 (CT women) + 2 x 349 (TT women) = 1275.

 [1]: http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=X:84436603-85257871;v=rs509717;vdb=variation;vf=364091