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Archiver > GENEALOGY-DNA > 2011-02 > 1296890679


From: Vince Tilroe <>
Subject: Re: [DNA] Approx. hg: R-L21: L459
Date: Sat, 05 Feb 2011 00:24:39 -0700
References: <825DC33309DE4B0FB61E09005FB5C8AD@YOURC7CB43EF61> <AANLkTimDy1bT_GQtdLapwCHPY=5NyVJ7ZGACjPHKQHJM@mail.gmail.com> <4D4CCAD7.5050802@gmail.com><AANLkTim0z8k414g4bWJdwRjV0G-byFqX3n=Eyrs+OgP_@mail.gmail.com>
In-Reply-To: <AANLkTim0z8k414g4bWJdwRjV0G-byFqX3n=Eyrs+OgP_@mail.gmail.com>


True, but if say you widen the scope to the region between
ChrY:5334701..5335371 (671 basepairs), which is more in line with the
segment lengths we're using, the hit on the X produces a 665/671 match
between the Ref. X and the Ref. Y sequences, which is enough to filter
out recent X-Y transpositions if the primers are designed to consider
those differences.

The WTY trace which had the L459+ mutation was very unambiguous on both
forward and reverse segments, the reverse less so than the forward by a
small degree, but not enough to warrent concern. If any of the primers
bonded to both X and Y chromosomes, we should have expected an ambiguous
heterozygous call at that position in either direction. There was none.

On 2011-02-04 11:54 PM, Stephen Forrest wrote:
> Using FTDNA's chromosome browser I expanded the region surrounding the L459
> SNP to 71 bp (ChrY:5335001..5335071), downloaded this 71-bp sequence and ran
> a blast query on it against human sequences.
>
> It had four good matches (three at 100%, one at 98%), and from the
> alignments it appears that all four hits have the ancestral C.value. Most
> importantly however, two of the hits were against the X chromosome.
>

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