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Archiver > GENEALOGY-DNA > 2006-07 > 1152517379


From: "John McEwan" <>
Subject: RE: [DNA] How many SNPs on the Y chromosome?
Date: Mon, 10 Jul 2006 19:42:59 +1200
In-Reply-To: <E1FziIz-000H9h-2e@mk-webmail-2.b2b.uk.tiscali.com>


Dear Gareth

This is how I do it. Go to golden path
http://genome.ucsc.edu/cgi-bin/hgGateway

select the region of interest on chromosome Y say chrY:20000000-30000000
for hg17 and submit then click the tables menu at the top and this takes
you to a menu page where you select the variations and repeats group and
then track as SNPs. The position field should already be be filled as
chrY:20000000-30000000 and click the get output and hey presto: you have
11,244 SNPs from dbsnp125 build in a table format from that region of
the genome that you can load into excel.

At about that point you mutter expletives about the lack of a conversion
table between all "known" M, P and S SNPs we talk about on the list and
the rs number dbSNP uses and wonder why.....

Cheers

John

......
Gareth said

Ken & List

further research suggests that the "SNPs" in the X-transposed region are

just differences detected (by computer!) between parallel sequences on
the X
and Y chromosome reference sequences, rather than differences between 2
actual human samples at the same location on the same chromosome.
A paper published at the time the Y reference sequence was "completed"
(Skaletsky et al 2003) estimated that this region was copied from the X
to
the Y chromosome about 3 to 4 million years ago. Most of the variation
detected would therefore be much older than Y chromosome "Adam". The
higher
density of reported SNPs in this region reflects this timescale plus the

fact that the SNP detecters had two complete sequences to compare.
So we can discount most of the 36,259 as not relevant to even the
"deepest"
investigations into the paternal ancestry of modern humans. I wonder if
there is a way of extracting the number of "real" SNPs in the database?

Gareth




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