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Archiver > GENEALOGY-DNA > 2010-11 > 1289201894


From: Dienekes Pontikos <>
Subject: Re: [DNA] Autosomal alleles reported as A/B
Date: Mon, 8 Nov 2010 09:38:14 +0200
References: <SNT139-w43E9EDC67FC2B5C0688456C84F0@phx.gbl>
In-Reply-To: <SNT139-w43E9EDC67FC2B5C0688456C84F0@phx.gbl>


A/B is Illumina's strand-independent coding. It's explained quite well here

http://www.illumina.com/documents/products/technotes/technote_topbot.pdf

To answer Doug's question, the data can be found here:

http://www.ncbi.nlm.nih.gov/geo/

under:

GSE22494

I've already used it here:

http://dienekes.blogspot.com/2010/11/multidimensional-scaling-and-admixture.html
http://dienekes.blogspot.com/2010/11/admixture-in-siberia-greenland-and.html

On Mon, Nov 8, 2010 at 3:36 AM, argiedude <> wrote:
>
> http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM558710
>
> The study by Rasmussen (2010) that covered the sequencing of the ancient Eskimo dna included some freely available supplementary genotype data on some 200 Siberians and North American Indians. In the link above is a randomly selected sample, and you can see that the alleles, in the column "value", are reported as AA, AB, BB. There's no clarification, for each SNP, of what A and B refer to (A, C, G, T). Neither in these samples or in the full multi-GB download of all the data. I've dealt with a previous dataset like this, that reported the alleles as A or B, but it clarified for each SNP the values of the alleles, such as A/G, C/T, pr other, followed by the chain of A's and B's.
>
> Sincerely,
> argiedude
>
>
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--
Dienekes' Anthropology Blog: http://dienekes.blogspot.com


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