allele frequencies interpretation
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9 weeks ago

Hi everyone, I have downloaded some pieces of information about different markers from the UCSC table browser. And this is the output I got:

enter image description here

As you can see, for some markers, the reference is different from the alleles, and I do not know how to consider the locus, is it biallelic or triallelic? The output gives only two frequencies whose sum result in 1, so this make me to think it is biallelic. So which alleles should I consider?

I hope to have been clear! Thank you in advance for your help and opinion, Giulia

locus bedfile alleles frequencies • 272 views
Entering edit mode

(Disclaimer: I have no expertise in interpreting genetic variants, but the issue aroused my scientific curiosity)

According to dbSNP, it is either G or A in basically any population for study. So, I guess it is an odd technical artefact from sequencing the wrong strand or a bioinformatic mistake assuming strand-specificity where there was none?

The only biological explanation I can think of is an inversion - which I would however rather expect to see in a patient sample and not in some reference dataset in the UCSC Genome Browser.


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