Question: Mafs Do Not Match Allele En Population Diversity
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gravatar for Martijn
4.7 years ago by
Martijn0
Martijn0 wrote:

Dear,

I was looking on dbSNP.

When I looked at the Minor Allele Frequences of some SNPs and I compared them to the Population Diversity Overview below, I noticed that some MAF were not correct.

Here an example of SNP rs2760320

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=2760320

The MAF of this SNP is: C=0.045/98

But when we look at its population diversity, you can see that C is totally not the minor allele, but G. According that population diversity, C has an allele frequency of 0.9.

What is the reason of this?

maf frequency allele • 1.4k views
ADD COMMENTlink modified 4.7 years ago by Emily_Ensembl15k • written 4.7 years ago by Martijn0
0
gravatar for Emily_Ensembl
4.7 years ago by
Emily_Ensembl15k
EMBL-EBI
Emily_Ensembl15k wrote:

The confusion here is because dbSNP are displaying the reverse stranded alleles (see table of genomic positions on their page), whereas 1000 genomes have reported the MAF for the forward strand allele. Here's the same variant in Ensembl, where all variant alleles are reported as the forward strand. As you can see, the alleles are listed as G/C with the MAF reported as C 0.04. If you click on population genetics, you'll see the frequency of the two alleles across the populations reflects this MAF.

Both Ensembl and 1000 genomes only report alleles on the forward strand, as this makes everything more consistent and clear. Unfortunately, dbSNP have many old records in their database which are reported on the reverse strand, which can be very confusing. When these are imported into Ensembl and 1000 genomes, they are moved onto the forward strand.

ADD COMMENTlink written 4.7 years ago by Emily_Ensembl15k
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