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Minor allele frequency differences between populations in 1000 Genomes

I downloaded frequencies of about 10K SNPs from 1000 Genomes. I computed the average frequency for each population ( I believe the standard reported frequency refers to the minor allele). In general, Europeans had the highest frequencies, around 40% but all the other populations had lower frequencies. Can someone explain what this phenomenon is due to? I know that the original population is CEU, so the MAF is defined in reference to Europeans, but I don't see why this would lead it to be systematically higher. I suppose a few SNPs that are European-specific will be absent among other populations but there are not enough to explain this big discrepancy. Here are the frequencies for some populations:

CEU: 0.472 CHB: 0.331 FIN: 0.402 MXL: 0.369 YRI: 0.326

snp genome
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written by pifferdavide pifferdavide

How did you select your 10k SNPs. Are they Europe specific I am confused when you say the original populations is CEU but Europeans have higher frequencies while others have lower

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written by Santosh Anand Santosh Anand

I just randomly selected SNPs using SNPSNAP. They were not European specific. I assumed that the first population sequenced by 1000 Genomes was CEU and that there might be a bias towards European SNPs but I am not sure, just my conjecture.

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written by pifferdavide pifferdavide

Please use ADD COMMENT for comments to keep the post organized.

I assumed that the first population sequenced by 1000 Genomes was CEU

That's not true. Although the sequencing was done in different phases, there was no preferential sequencing for a particular population in any phase. You can get all the information here

http://www.internationalgenome.org/about http://www.bioinf.jku.at/research/sharingShortIBD/hapFabia1000Genomes_html/node34.html

That said, I wii check again if selection of SNPs from snpsnap is bringing some bias

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written by Santosh Anand Santosh Anand

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