SNPs with multiple nucleotides

Question

[Sebastian]

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?

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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!

Answer 1

[Jautis]

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)

[Sebastian]

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.

[Jautis]

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