A and B hg. SNPs

From 1000 Genomes & Other Full Y Sequence Data

Moderators: Rootsy, GregRM

User avatar
Posts: 102
Joined: Thu Mar 15, 2012 4:26 pm
Location: USA
YDNA:
J2a1i (father)
MtDNA:
I1a1b
PostPosted: Wed May 29, 2013 6:58 pm
I've been working on the vcf file kindly provided by Greg which includes haplogroups A, B, C, and unknown others.

I just thought folks might be interested to know the kinds of number of SNPs I'm seeing for the very early clades.

There are only two A0 samples, but at least they belong to quite distant clades, A0a1 and A0b. I've found, so far, 1543 SNPs that separate them from all other samples! Some of these must be derived in A0, while others are no doubt actually derived in all other downstream branches of the tree. We'll have to compare these SNPs with the data from the Neanderthal, Chimp, etc., to find out which are really derived in A0 and which are derived in everyone else.

There are also, so far, 1517 SNPs derived only in the three A1a samples.

If we had a full Y sequence for an A00 sample, we would know right away which SNPs are actually downstream, because they'd be shown as derived in both A00 and A0. In other words, those would be A1-T SNPs.

Imagine how interesting it would be to be able to compare the numbers of SNPs in A00 in comparison to A0, A1a, and all the other haplogroups!

In order for this to happen, we need to receive donations to fund a full Y sequence for A00. Either that, or perhaps we can convince Full Genomes to donate a test for the sake of science. What do you all think?

Bonnie
User avatar
Posts: 102
Joined: Thu Mar 15, 2012 4:26 pm
Location: USA
YDNA:
J2a1i (father)
MtDNA:
I1a1b
PostPosted: Thu May 30, 2013 1:44 pm
Don't all reply at once, now! ;)

Guess I'll need to post in some of the more active forums if I hope to get a conversation going. This sure isn't like the old DNA-forums. :|

I know, I need to introduce our new research project, the subtle approach isn't the best way to generate excitement!

Posts: 623
Joined: Wed Mar 14, 2012 2:16 pm
PostPosted: Thu May 30, 2013 2:31 pm
Here is perhaps the difficulty: Full Y sequencing is so new that everyone is still saving up for their own test (or that of someone in their own haplogroup). "Charity begins at home." :)

Full Y sequencing of an A00 individual would indeed be an important milestone.
User avatar
Posts: 150
Joined: Fri Mar 30, 2012 4:31 am

YDNA:
G P303+
MtDNA:
C4a1
PostPosted: Thu May 30, 2013 7:39 pm
Hi Bonnie,
This is exciting!
Crowd sourcing is the way to go. Once you have a project page and paypal link, I will chip in .

Return to Y-SNP Data Mining

Who is online

Users browsing this forum: No registered users and 1 guest