Archiver > GENEALOGY-DNA > 2010-02 > 1265440658

From: Thomas Krahn <>
Subject: Re: [DNA] 23andMe mtDNA results, two different SNPs at same position
Date: Sat, 06 Feb 2010 01:17:38 -0600
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In-Reply-To: <>


The position myDNA:16129 can in deed have 3 different alleles (G, A or
in rare cases C) in different persons.
16129C can be found in haplogroup U2e I believe (don't pin me down on
the exact haplogroup name. It may be outdated; mtDNA haplogroups are
still a foreign language for me which I'll never learn. Other persons at
FTDNA are taking care of this).

The intention of the designer of the i3001605 probe was apparently to
pick up the rare C variant. This can of course only work if there is no
A allele at this position because the Illumina bead chip can only detect
2 different bases. Therefore a second probe location was necessary.

So in order to interpret these two markers the analyst must consider the
quality scores of the base calls. If they are not available it is at
least necessary to consider the haplogroup context. Only if the other
alleles are already pointing to haplogroup U2 the probe i3001605 should
be taken into consideration. In all other cases this probe should be
simply ignored because it may show a weak false positive signal.

I hope this helps,


> Can someone explain the following 23andMe results:
> 16129 rs5005270 G (tests for A and G)
> 16129 i3001605 C (tests for C and G)
> As expected, some people will have a G at both.
> However, lots of people have both a G and a C at the same 16129
> position as in the example above.
> At FTDNA the same people will only have a G and no C, with no
> heteroplasmy listed.
> Does this mean there is an insertion that is normally ignored between
> 16129 and 16130 at FTDNA?
> Note that I translated the 16130 into 16129 CRS position from the raw
> data at 23andMe in order to compare with the standard.
> Kathy J.
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