SNPs with multiple nucleotides
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Entering edit mode
2.4 years ago
Sebastian ▴ 10

Hello people,

I just have a dataset of imputed data and i see for the first time of my life some "SNP" that contain multiple nucleotides in a single allele.

ex :

pos: 4:90048466

A0/A1: A:AAAAACAAACAAAC

Do you know where I can read and fully understand what this is and where it is from?


extra question:

Do you know a r package where I can find the locus ( and not the position) for the SNP ?

For snp rs114073636 we have the position 1:62066340 and the locus 1p31.3

I have lots of SNPs where i would like to have their locus.

Thanks a lot!

SNP multiple locus nucleotide GWAS • 719 views
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Entering edit mode
2.4 years ago
Jautis ▴ 570

Those are the ways insertion/deletions are represented. In this case, it's a "AAAACAAACAAAC" insertion following the "A" position.

(I would ask about rsid/position/locus in a separate question)

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Thanks for replying.

But how is that possible ? An SNP is not supposed to be a just Sincle Nucleotide? Do you know where i can read more about that? thanks.

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Imputation (and VCF files) include common genetic variation, not just common SNPs.

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