Re: New Hartley/Smith SNP block?

Jared Smith
 

I searched Michael's novel variants at yBrowse.org and see that
William Hartley submitted at least one of them for naming.
14806931-C-G is named A15733 - so I propose that this be the
designator for Michael's novel branch.

If you've not used yBrowse before, it's a bit clunky, but very
powerful. To search for an SNP name at the position above, you'd
search for "ChrY:14806931..14806931". After the results load, there is
an SNP area of the page. Click on the SNP name (if present) to get the
details (such as who submitted it).

You need to make sure that the mutation is correct. For example,
Michael also has 14403766-C-A. Searching this position shows SNP
ZS1551 here, but it is C-G, not C-A.

You can also search an SNP name to find its position.

Another of Michael's novel variants was already named some time ago
-19110373-C-T is Y30173. So this one aligns with an SNP in another
haplogroup.

I don't see any other "good" SNPs of his that have been named. William
submits the variants to YSEQ.net for analysis and naming. I suspect
that William probably submitted the others of Michael's variants to
YSEQ, but I think they only submit ones to ISOGG for naming that can
be adequately tested with their current test panels. William's
subscribed here, so can probably provide better insight into this
process.

The SNP prefix indicates who submitted it for naming. A=YSEQ.net,
BY=FTDNA (Big-Y), FGC=Full Genomes Corp., and Y=Y Full. The full list
is at https://isogg.org/tree/

So A15733 is our current best SNP for Michael's branch.

Jared

On Mon, Apr 24, 2017 at 7:30 AM, Joel Hartley <joel@...> wrote:
Hi Jared,

What is the process for giving Michael Hartley a provisional identifying
named SNP (or SNPs) of his own? Are we waiting for the best SNP before we
name one? Also who does the naming? I think that when I did my BigY, William
Hartley, the administer of the Hartley YDNA Project went in and named a
bunch of my SNPs. I'm not sure why this didn't happen for Michael.

Joel


On 3/25/2017 11:13 AM, Jared Smith wrote:

It's official - my terminal SNP is now A11138! FTDNA did a BAM analysis to
verify this and has added this SNP to the tree. I've updated my charts at
http://dna.smithplanet.com/snp I also added a bit more aging info.

Because we now know that A11138 is above the A11132 block and not below it
as a novel variant with Joel, this does decrease the number of novel
variants Joel has, effectively moving the shared Hartley ancestor date for
Joel and Michael back a bit (at least according to the math of my
calculations).

This also places the Hartley/Smith ancestor just below Z17911 somewhere
around 800 years ago (give or take a century or so).

It is quite incredible that just a few months ago we had no branches below
Z17911, and now we have 7 downstream branches with 13 known shared SNPs!

Jared


On Fri, Mar 24, 2017 at 12:24 PM, Joel Hartley <joel@...> wrote:

Hi Jared,

I'm never sure when this YFull analysis is finalized or not. At any rate,
on my list of SNPs, A11138 is the first one that is not listed as private.
So I assume that means I share it with you. If we hadn't done the YFull
analysis, I'm not sure if anyone would've picked up on this branching SNP.

Also it appears that the Z16357 SNP Tree needs to be modified again. It
looks like everyone has left Z17911 behind and that it is now a "ghost
town".

Joel


On 3/21/2017 8:03 AM, Jared Smith wrote:

No, I don't show A11138 as being a matching SNP with you. That's what is
particularly confusing to me.

But I clearly show positive for A11138 in my SNP list in my "Hg and SNPs"
list. A11138 is the very first one on my list.

I'm pretty sure the light green + indicates that there was only one read
at that location, so it is only suspected positive.

Jared


On Tue, Mar 21, 2017 at 5:44 AM, Joel Hartley <joel@...> wrote:

Hi Jared,

This is all very interesting. I wonder if my YFull has not been updated
yet. Do you show me as an A11138 match under the SNP Matches Tab?



I see A11138 under my Hg and SNPs but not at the SNP Matches.



Do you know what the light green + means compared to the dark green +?

Joel


On 3/20/2017 10:12 PM, Jared Smith wrote:

First, I see that FTDNA has pushed the updates to the tree for the
Hartley branch. Joel and Michael, your terminal SNP is now recorded as
A11132.

I just got my YFull results processed and they show me as positive for
A11138 (19477032-A-T). This is an SNP that Joel has, but that Michael
did not test positive for. However, it is right on the edge of a read
area for Michael, so it's quite possible that he also has A11138.

On the other hand, it's right in the middle of a read area for me, so
I would have thought I was negative because FTDNA didn't report it,
but it seems YFull's BAM analysis shows me as positive for it with a 5
star rating.

If this holds up, then this will make a small A11138 Hartley/Smith SNP
block just below Z17911 and above the Hartley A11132 block. This also
means that Michael has to be positive for this SNP (he can't be
downstream of this block and not have this SNP), which will increase
your shared SNPs by one and decrease Joel's novel variants by one -
effectively moving your shared ancestor closer to present day than
previously estimated by maybe 50-100 years.

I'm going to run all this past Mike W. He can request that FTDNA to a
BAM analysis on this region to see if I and Michael are both A11138.

Jared




Join Z16357@groups.io to automatically receive all group messages.