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Problems with raw data download

Problems with raw data download

Posted: 22 Mar 2013 2:38AM GMT
Classification: Query
I rec'd the following results from 23andme (build 37)
# rsid chromosome position genotype
rs4477212 1 82154 AA

and the following from Ancestry.com (also build 37)
rsid chromosome position allele1 allele2
rs4477212 1 82154 T T

Can you explain why there would be a difference if the build is the same and the snp is the same? Should both be reporting the same allele values?

Re: Problems with raw data download

Posted: 22 Mar 2013 3:22AM GMT
Classification: Query
Checked on the http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs4477212 site and the snp should have values of A or G. Looks like the TT reported by Ancestry shouldn't be possible. Am I reading this wrong?

Re: Problems with raw data download

Posted: 22 Mar 2013 7:17PM GMT
Classification: Query
It looks like AncestryDNA reported the reverse (minus) strand of the double helix for that particular SNP. The complementary bases on the double helix are A<->T and C<->G, so your alleles would be AA.

A few other SNPs with different strand orientations have been reported. Some of those could actually be because 23andMe or FTDNA reported the minus strand. Maybe at some point we'll get a consolidated list of those SNPs, but in the meantime, most 3rd party utilities allow a little bit of wiggle room for non-matching SNPs.

Re: Problems with raw data download

Posted: 22 Mar 2013 7:29PM GMT
Classification: Query
Thanks for the info.

According to Ancestry's data they are supposed to be reporting the forward strand for all of the data. It says that right in the downloaded data. 23nMe reports using the forward strand for that same SNP. Something isn't adding up here...

Re: Problems with raw data download

Posted: 22 Apr 2015 7:18AM GMT
Classification: Query
So what ever became of this? I have seen this exact issue as well. Would love to know what is going on.

Re: Problems with raw data download

Posted: 22 Apr 2015 10:11PM GMT
Classification: Query
I haven't pursued it any further, got busy with other things. If you find out I would love to know. Hopefully I'll have more time to devote to all of this in the future.
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