Question: Why most of alternative alleles are the alleles with major frequency?
0
gravatar for star
3.0 years ago by
star60
Netherlands
star60 wrote:

I find set of SNPs that in 4 different population have same minor allele frequency and also same alleles. but I find that most of my alternative alleles are the alleles with major frequency! how can I genetically explain it ?

 

ADD COMMENTlink modified 3.0 years ago by Adrian Pelin2.2k • written 3.0 years ago by star60
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gravatar for Adrian Pelin
3.0 years ago by
Adrian Pelin2.2k
Canada
Adrian Pelin2.2k wrote:

Well... if it's something you expect to be heterozygous, 50/50, than major and minor make no difference, in one population you can see it as 45/55 and in another 51/49, so major and minor change places but that has no biological impact. Need more info on what it is you are actually doing, is this for human genome?

ADD COMMENTlink written 3.0 years ago by Adrian Pelin2.2k

Yes, it is for human genome. I find alternative allele for my data according to reference allele and I expect most of  alternative alleles be minor allele but they are major allele?

ADD REPLYlink written 3.0 years ago by star60

In human genomes you would just be looking at heterozygous or homozygous SNPs, not major/minor. If you alternate allele is 0.9-1.0 in frequency, I would call this as a homozygous SNP. If it is 0.35-0.65, I would call it a heterozygous SNP.

This is assuming each of your datasets represents one individuals sequencing, rather then populations as you previously mentioned.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Adrian Pelin2.2k
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