Date   
Re: Mike Hartley BigY

Jared Smith
 

I did some additional analysis of Michael's results from his raw data.
There's not too much more to add, but I did find a couple other
variants that Joel and Michael share:
22425308 G A
25297201 T A
26310965 T C

As a brief explanation of this, 22425308 (for example) is the position
on the Y chromosome. The ancestral value (meaning the one that pretty
much everyone else has) for this position is G, but both of them have
an A here.

However, all three of these are in rather questionable areas on the
chromosome where poor reads can occur, so it's possible (though not
very likely) that these are both mis-reads that just happen to be the
same, or that some other relative could also have this variant, but
the test might not catch it due to its location.

I also found one solid INDEL that they both share:
18721623 A AA

Think of an INDEL (short for Insertion/Deletion) as a 'hiccup' on the
DNA - where the transfer of DNA from father to son results in one or
more extra segments of the DNA getting injected, or where a segment of
the DNA disappears. In this case, the ancestral marker is A, but you
two both have an extra A (thus AA) here.

We don't typically count INDELs as "SNPs", but this is certainly a
high quality mutation that you almost certainly got from a common
ancestor, so it can be used for comparing future matches.

I'm sure Mike W. and Alex will likely find some additional novel
variants for Michael when they do their analysis, but I think this is
probably everything that they share that is worth tracking.

I'll send the data to Michael Sager soon and ask him to update the
FTDNA tree and update your terminal SNPs to A11132.

Jared


On Fri, Mar 17, 2017 at 10:57 AM, Michael W. Hartley
<@MWH> wrote:
I finally found this place. My raw data is on it's way to Jared and Mike
Walsh. Let me know what else you need.

Re: Mike Hartley BigY

Joel Hartley
 

I see that Mike Hartley's results are at the Big Tree site awaiting analysis with several others in the lower right in pink:



Joel

On 3/17/2017 10:40 PM, Jared Smith wrote:
I did some additional analysis of Michael's results from his raw data.
There's not too much more to add, but I did find a couple other
variants that Joel and Michael share:
22425308 G A
25297201 T A
26310965 T C

As a brief explanation of this, 22425308 (for example) is the position
on the Y chromosome. The ancestral value (meaning the one that pretty
much everyone else has) for this position is G, but both of them have
an A here.

However, all three of these are in rather questionable areas on the
chromosome where poor reads can occur, so it's possible (though not
very likely) that these are both mis-reads that just happen to be the
same, or that some other relative could also have this variant, but
the test might not catch it due to its location.

I also found one solid INDEL that they both share:
18721623 A AA

Think of an INDEL (short for Insertion/Deletion) as a 'hiccup' on the
DNA - where the transfer of DNA from father to son results in one or
more extra segments of the DNA getting injected, or where a segment of
the DNA disappears. In this case, the ancestral marker is A, but you
two both have an extra A (thus AA) here.

We don't typically count INDELs as "SNPs", but this is certainly a
high quality mutation that you almost certainly got from a common
ancestor, so it can be used for comparing future matches.

I'm sure Mike W. and Alex will likely find some additional novel
variants for Michael when they do their analysis, but I think this is
probably everything that they share that is worth tracking.

I'll send the data to Michael Sager soon and ask him to update the
FTDNA tree and update your terminal SNPs to A11132.

Jared


On Fri, Mar 17, 2017 at 10:57 AM, Michael W. Hartley
<mwhlaw1@...> wrote:
I finally found this place.  My raw data is on it's way to Jared and Mike
Walsh.  Let me know what else you need.




Z16357 In-depth Age Analysis

Jared Smith
 

Aging our ancestors using Y-DNA data is far from an exact science. I'd
be happy to have you poke holes in any of this.

An analysis of the 11 Z16357 people who have taken Big-Y results in
the following number of 'good', unique/novel variants/mutations:

C. Hays 4
R. Hays 3
Pillsbury 5
Merrick 11
Thomas 6
Phillips 7
Bennett 9
M. Hartley 5
J. Hartley 5
J. Smith 12
Smith 27

These are variants that each person has that are not shared with
anyone else who has tested. The higher the number of novel variants,
the further back one would expect to be related to someone else
listed. I use the same metric for a 'good' variant as Alex does on his
Big Tree. This is a bit more aggressive than what YFull uses.

There are, however, some inconsistencies with this. Merrick, for
example, has nearly twice as many novel variants as Thomas, even
though Merrick connects lower/later on the tree than Thomas - one
would thus expect Merrick to have fewer novel variants. This is
primarily a factor of test coverage, but this is all we have to work
with, so we partially account for this variability by averaging. This
is why each new Big-Y test gives us increased accuracy.

When I add the novel variants above to the number of 'good' SNPs in
each block or haplogroup of our tree and average the results, I end up
with the following average number of variants downstream from each
listed SNP block:

ZS349 - 3.5
Z16854 - 9.3
BY15420 - 8.0
BY15419 - 9.7
Y29969 - 9.5
A11132 - 5
Z17911 - 10.9
Z16343 - 13
Z16357 - 36.1

This means, for example, that there's an average of 3.5 variants that
were formed after the most recent ZS349 ancestor that the two Hays men
share. For Z17911, we average 10.9 variants downstream (more recent
than) our most recent common Z17911 ancestor. Altogether, we average
36.1 SNPs downstream of Z16357.

To use these variant numbers to help us in aging, we need to calculate
a "years per SNP" value. YFull has our last Z16357 ancestor at around
3300 years ago (though they've acknowledged this is probably too
high). Other recent estimates put it as young as 2300 years ago. Until
someone digs up some Z16357 remains or we get enough DNA testers to
give us better data, we have to use our best informed estimate. I'll
assume our most recent Z16357 ancestor lived a minimum of 2500 and
maximum of 3000 years ago.

If we divide these age estimates by 36.1 SNPs (on average), this is a
minimum of 69.3 years per SNP and a maximum of 83.1 years per SNP. We
can then use these values to assign age estimates to notable
branchings as follows:

ZS349 - 327-376 years before present
Z16854 - 732-861
BY15420 - 639-750
BY15419 - 755-889
Y29969 - 743-875
A11132 - 431-501
Z17911 - 837-987
Z16343 - 986-1166
Z16357 - 2585-3085

The values are years before present, and include an additional 35
years (one generation?) to account for the age of the last ancestor
that had this SNP - and also adds 50 years as a guessed average of how
old the 11 Z16357 people are.

So this estimates that the common ZS349 ancestor for Hays was born
347-376 years ago. We know this ancestor was George Hays who was born
in 1655 - 362 years ago, so these numbers align perfectly!

This places our Z17911 ancestor being born between 837 and 987 years
ago. It places the Hartley common ancestor between 431 and 501 years
ago, the Bennett/Phillips ancestor 639-750 years ago, etc.

Do keep in mind that accuracy is more variable near the end of the
branches (closer to present day), especially with data from only 2 or
3 people. And SNPs are not always formed at a consistent rate. So this
all a bit rough, but should give us fairly reasonable estimations.

Jared

Re: Z16357 In-depth Age Analysis

Joel Hartley
 

This sounds reasonable to me. I'd like to hear what folks at the L513 Yahoo Forum would have to say about it.

Joel

On 3/20/2017 10:52 AM, Jared Smith wrote:
Aging our ancestors using Y-DNA data is far from an exact science. I'd
be happy to have you poke holes in any of this.

An analysis of the 11 Z16357 people who have taken Big-Y results in
the following number of 'good', unique/novel variants/mutations:

C. Hays 4
R. Hays 3
Pillsbury 5
Merrick 11
Thomas 6
Phillips 7
Bennett 9
M. Hartley 5
J. Hartley 5
J. Smith 12
Smith 27

These are variants that each person has that are not shared with
anyone else who has tested. The higher the number of novel variants,
the further back one would expect to be related to someone else
listed. I use the same metric for a 'good' variant as Alex does on his
Big Tree. This is a bit more aggressive than what YFull uses.

There are, however, some inconsistencies with this. Merrick, for
example, has nearly twice as many novel variants as Thomas, even
though Merrick connects lower/later on the tree than Thomas - one
would thus expect Merrick to have fewer novel variants. This is
primarily a factor of test coverage, but this is all we have to work
with, so we partially account for this variability by averaging. This
is why each new Big-Y test gives us increased accuracy.

When I add the novel variants above to the number of 'good' SNPs in
each block or haplogroup of our tree and average the results, I end up
with the following average number of variants downstream from each
listed SNP block:

ZS349 - 3.5
Z16854 - 9.3
BY15420 - 8.0
BY15419 - 9.7
Y29969 - 9.5
A11132 - 5
Z17911 - 10.9
Z16343 - 13
Z16357 - 36.1

This means, for example, that there's an average of 3.5 variants that
were formed after the most recent ZS349 ancestor that the two Hays men
share. For Z17911, we average 10.9 variants downstream (more recent
than) our most recent common Z17911 ancestor. Altogether, we average
36.1 SNPs downstream of Z16357.

To use these variant numbers to help us in aging, we need to calculate
a "years per SNP" value. YFull has our last Z16357 ancestor at around
3300 years ago (though they've acknowledged this is probably too
high). Other recent estimates put it as young as 2300 years ago. Until
someone digs up some Z16357 remains or we get enough DNA testers to
give us better data, we have to use our best informed estimate. I'll
assume our most recent Z16357 ancestor lived a minimum of 2500 and
maximum of 3000 years ago.

If we divide these age estimates by 36.1 SNPs (on average), this is a
minimum of 69.3 years per SNP and a maximum of 83.1 years per SNP. We
can then use these values to assign age estimates to notable
branchings as follows:

ZS349 - 327-376 years before present
Z16854 - 732-861
BY15420 - 639-750
BY15419 - 755-889
Y29969 - 743-875
A11132 - 431-501
Z17911 - 837-987
Z16343 - 986-1166
Z16357 - 2585-3085

The values are years before present, and include an additional 35
years (one generation?) to account for the age of the last ancestor
that had this SNP - and also adds 50 years as a guessed average of how
old the 11 Z16357 people are.

So this estimates that the common ZS349 ancestor for Hays was born
347-376 years ago. We know this ancestor was George Hays who was born
in 1655 - 362 years ago, so these numbers align perfectly!

This places our Z17911 ancestor being born between 837 and 987 years
ago. It places the Hartley common ancestor between 431 and 501 years
ago, the Bennett/Phillips ancestor 639-750 years ago, etc.

Do keep in mind that accuracy is more variable near the end of the
branches (closer to present day), especially with data from only 2 or
3 people. And SNPs are not always formed at a consistent rate. So this
all a bit rough, but should give us fairly reasonable estimations.

Jared

Re: Z16357 In-depth Age Analysis

Charles Thomas
 

Great analysis, Jared, but I think the SNP names are confusing me. Did you include an equivalent to FGC33966 for Martin and me?

Charles


From: Z16357@groups.io <Z16357@groups.io> on behalf of Jared Smith <jared@...>
Sent: Monday, March 20, 2017 9:52 AM
To: Z16357@groups.io
Subject: [Z16357] Z16357 In-depth Age Analysis
 
Aging our ancestors using Y-DNA data is far from an exact science. I'd
be happy to have you poke holes in any of this.

An analysis of the 11 Z16357 people who have taken Big-Y results in
the following number of 'good', unique/novel variants/mutations:

C. Hays 4
R. Hays 3
Pillsbury 5
Merrick 11
Thomas 6
Phillips 7
Bennett 9
M. Hartley 5
J. Hartley 5
J. Smith 12
Smith 27

These are variants that each person has that are not shared with
anyone else who has tested. The higher the number of novel variants,
the further back one would expect to be related to someone else
listed. I use the same metric for a 'good' variant as Alex does on his
Big Tree. This is a bit more aggressive than what YFull uses.

There are, however, some inconsistencies with this. Merrick, for
example, has nearly twice as many novel variants as Thomas, even
though Merrick connects lower/later on the tree than Thomas - one
would thus expect Merrick to have fewer novel variants. This is
primarily a factor of test coverage, but this is all we have to work
with, so we partially account for this variability by averaging. This
is why each new Big-Y test gives us increased accuracy.

When I add the novel variants above to the number of 'good' SNPs in
each block or haplogroup of our tree and average the results, I end up
with the following average number of variants downstream from each
listed SNP block:

ZS349 - 3.5
Z16854 - 9.3
BY15420 - 8.0
BY15419 - 9.7
Y29969 - 9.5
A11132 - 5
Z17911 - 10.9
Z16343 - 13
Z16357 - 36.1

This means, for example, that there's an average of 3.5 variants that
were formed after the most recent ZS349 ancestor that the two Hays men
share. For Z17911, we average 10.9 variants downstream (more recent
than) our most recent common Z17911 ancestor. Altogether, we average
36.1 SNPs downstream of Z16357.

To use these variant numbers to help us in aging, we need to calculate
a "years per SNP" value. YFull has our last Z16357 ancestor at around
3300 years ago (though they've acknowledged this is probably too
high). Other recent estimates put it as young as 2300 years ago. Until
someone digs up some Z16357 remains or we get enough DNA testers to
give us better data, we have to use our best informed estimate. I'll
assume our most recent Z16357 ancestor lived a minimum of 2500 and
maximum of 3000 years ago.

If we divide these age estimates by 36.1 SNPs (on average), this is a
minimum of 69.3 years per SNP and a maximum of 83.1 years per SNP. We
can then use these values to assign age estimates to notable
branchings as follows:

ZS349 - 327-376 years before present
Z16854 - 732-861
BY15420 - 639-750
BY15419 - 755-889
Y29969 - 743-875
A11132 - 431-501
Z17911 - 837-987
Z16343 - 986-1166
Z16357 - 2585-3085

The values are years before present, and include an additional 35
years (one generation?) to account for the age of the last ancestor
that had this SNP - and also adds 50 years as a guessed average of how
old the 11 Z16357 people are.

So this estimates that the common ZS349 ancestor for Hays was born
347-376 years ago. We know this ancestor was George Hays who was born
in 1655 - 362 years ago, so these numbers align perfectly!

This places our Z17911 ancestor being born between 837 and 987 years
ago. It places the Hartley common ancestor between 431 and 501 years
ago, the Bennett/Phillips ancestor 639-750 years ago, etc.

Do keep in mind that accuracy is more variable near the end of the
branches (closer to present day), especially with data from only 2 or
3 people. And SNPs are not always formed at a consistent rate. So this
all a bit rough, but should give us fairly reasonable estimations.

Jared



Re: Z16357 In-depth Age Analysis

Jared Smith
 

Charles -

FGC33966 is your terminal SNP shared with Martin, but I only analyzed
Big-Y testers so I could include the novel variants. So FGC33966 is
counted as one of your 6 novel variants.

This methodology is a fairly standard way of doing age estimates, but
I don't think it had been done to this level for our tree before.

Jared

On Mon, Mar 20, 2017 at 3:05 PM, Charles Thomas <charles_002@...> wrote:
Great analysis, Jared, but I think the SNP names are confusing me. Did you
include an equivalent to FGC33966 for Martin and me?

Charles

________________________________
From: Z16357@groups.io <Z16357@groups.io> on behalf of Jared Smith
<jared@...>
Sent: Monday, March 20, 2017 9:52 AM
To: Z16357@groups.io
Subject: [Z16357] Z16357 In-depth Age Analysis

Aging our ancestors using Y-DNA data is far from an exact science. I'd
be happy to have you poke holes in any of this.

An analysis of the 11 Z16357 people who have taken Big-Y results in
the following number of 'good', unique/novel variants/mutations:

C. Hays 4
R. Hays 3
Pillsbury 5
Merrick 11
Thomas 6
Phillips 7
Bennett 9
M. Hartley 5
J. Hartley 5
J. Smith 12
Smith 27

These are variants that each person has that are not shared with
anyone else who has tested. The higher the number of novel variants,
the further back one would expect to be related to someone else
listed. I use the same metric for a 'good' variant as Alex does on his
Big Tree. This is a bit more aggressive than what YFull uses.

There are, however, some inconsistencies with this. Merrick, for
example, has nearly twice as many novel variants as Thomas, even
though Merrick connects lower/later on the tree than Thomas - one
would thus expect Merrick to have fewer novel variants. This is
primarily a factor of test coverage, but this is all we have to work
with, so we partially account for this variability by averaging. This
is why each new Big-Y test gives us increased accuracy.

When I add the novel variants above to the number of 'good' SNPs in
each block or haplogroup of our tree and average the results, I end up
with the following average number of variants downstream from each
listed SNP block:

ZS349 - 3.5
Z16854 - 9.3
BY15420 - 8.0
BY15419 - 9.7
Y29969 - 9.5
A11132 - 5
Z17911 - 10.9
Z16343 - 13
Z16357 - 36.1

This means, for example, that there's an average of 3.5 variants that
were formed after the most recent ZS349 ancestor that the two Hays men
share. For Z17911, we average 10.9 variants downstream (more recent
than) our most recent common Z17911 ancestor. Altogether, we average
36.1 SNPs downstream of Z16357.

To use these variant numbers to help us in aging, we need to calculate
a "years per SNP" value. YFull has our last Z16357 ancestor at around
3300 years ago (though they've acknowledged this is probably too
high). Other recent estimates put it as young as 2300 years ago. Until
someone digs up some Z16357 remains or we get enough DNA testers to
give us better data, we have to use our best informed estimate. I'll
assume our most recent Z16357 ancestor lived a minimum of 2500 and
maximum of 3000 years ago.

If we divide these age estimates by 36.1 SNPs (on average), this is a
minimum of 69.3 years per SNP and a maximum of 83.1 years per SNP. We
can then use these values to assign age estimates to notable
branchings as follows:

ZS349 - 327-376 years before present
Z16854 - 732-861
BY15420 - 639-750
BY15419 - 755-889
Y29969 - 743-875
A11132 - 431-501
Z17911 - 837-987
Z16343 - 986-1166
Z16357 - 2585-3085

The values are years before present, and include an additional 35
years (one generation?) to account for the age of the last ancestor
that had this SNP - and also adds 50 years as a guessed average of how
old the 11 Z16357 people are.

So this estimates that the common ZS349 ancestor for Hays was born
347-376 years ago. We know this ancestor was George Hays who was born
in 1655 - 362 years ago, so these numbers align perfectly!

This places our Z17911 ancestor being born between 837 and 987 years
ago. It places the Hartley common ancestor between 431 and 501 years
ago, the Bennett/Phillips ancestor 639-750 years ago, etc.

Do keep in mind that accuracy is more variable near the end of the
branches (closer to present day), especially with data from only 2 or
3 people. And SNPs are not always formed at a consistent rate. So this
all a bit rough, but should give us fairly reasonable estimations.

Jared



New Hartley/Smith SNP block?

Jared Smith
 

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

Re: Z16357 In-depth Age Analysis

Charles Thomas
 

Thanks, Jared. The new age estimates are very helpful. One more question if I may:

the L513 Descendant Tree Chart has Bennett and I at BY11382. Is that an equivalent for

a SNP included on your Z16357 SNP tree?

Charles




From: Z16357@groups.io <Z16357@groups.io> on behalf of Jared Smith <jared@...>
Sent: Monday, March 20, 2017 8:53 PM
To: Z16357@groups.io
Subject: Re: [Z16357] Z16357 In-depth Age Analysis
 
Charles -

FGC33966 is your terminal SNP shared with Martin, but I only analyzed
Big-Y testers so I could include the novel variants. So FGC33966 is
counted as one of your 6 novel variants.

This methodology is a fairly standard way of doing age estimates, but
I don't think it had been done to this level for our tree before.

Jared



On Mon, Mar 20, 2017 at 3:05 PM, Charles Thomas <charles_002@...> wrote:
> Great analysis, Jared, but I think the SNP names are confusing me. Did you
> include an equivalent to FGC33966 for Martin and me?
>
> Charles
>
> ________________________________
> From: Z16357@groups.io <Z16357@groups.io> on behalf of Jared Smith
> <jared@...>
> Sent: Monday, March 20, 2017 9:52 AM
> To: Z16357@groups.io
> Subject: [Z16357] Z16357 In-depth Age Analysis
>
> Aging our ancestors using Y-DNA data is far from an exact science. I'd
> be happy to have you poke holes in any of this.
>
> An analysis of the 11 Z16357 people who have taken Big-Y results in
> the following number of 'good', unique/novel variants/mutations:
>
> C. Hays 4
> R. Hays 3
> Pillsbury 5
> Merrick 11
> Thomas 6
> Phillips 7
> Bennett 9
> M. Hartley 5
> J. Hartley 5
> J. Smith 12
> Smith 27
>
> These are variants that each person has that are not shared with
> anyone else who has tested. The higher the number of novel variants,
> the further back one would expect to be related to someone else
> listed. I use the same metric for a 'good' variant as Alex does on his
> Big Tree. This is a bit more aggressive than what YFull uses.
>
> There are, however, some inconsistencies with this. Merrick, for
> example, has nearly twice as many novel variants as Thomas, even
> though Merrick connects lower/later on the tree than Thomas - one
> would thus expect Merrick to have fewer novel variants. This is
> primarily a factor of test coverage, but this is all we have to work
> with, so we partially account for this variability by averaging. This
> is why each new Big-Y test gives us increased accuracy.
>
> When I add the novel variants above to the number of 'good' SNPs in
> each block or haplogroup of our tree and average the results, I end up
> with the following average number of variants downstream from each
> listed SNP block:
>
> ZS349 - 3.5
> Z16854 - 9.3
> BY15420 - 8.0
> BY15419 - 9.7
> Y29969 - 9.5
> A11132 - 5
> Z17911 - 10.9
> Z16343 - 13
> Z16357 - 36.1
>
> This means, for example, that there's an average of 3.5 variants that
> were formed after the most recent ZS349 ancestor that the two Hays men
> share. For Z17911, we average 10.9 variants downstream (more recent
> than) our most recent common Z17911 ancestor. Altogether, we average
> 36.1 SNPs downstream of Z16357.
>
> To use these variant numbers to help us in aging, we need to calculate
> a "years per SNP" value. YFull has our last Z16357 ancestor at around
> 3300 years ago (though they've acknowledged this is probably too
> high). Other recent estimates put it as young as 2300 years ago. Until
> someone digs up some Z16357 remains or we get enough DNA testers to
> give us better data, we have to use our best informed estimate. I'll
> assume our most recent Z16357 ancestor lived a minimum of 2500 and
> maximum of 3000 years ago.
>
> If we divide these age estimates by 36.1 SNPs (on average), this is a
> minimum of 69.3 years per SNP and a maximum of 83.1 years per SNP. We
> can then use these values to assign age estimates to notable
> branchings as follows:
>
> ZS349 - 327-376 years before present
> Z16854 - 732-861
> BY15420 - 639-750
> BY15419 - 755-889
> Y29969 - 743-875
> A11132 - 431-501
> Z17911 - 837-987
> Z16343 - 986-1166
> Z16357 - 2585-3085
>
> The values are years before present, and include an additional 35
> years (one generation?) to account for the age of the last ancestor
> that had this SNP - and also adds 50 years as a guessed average of how
> old the 11 Z16357 people are.
>
> So this estimates that the common ZS349 ancestor for Hays was born
> 347-376 years ago. We know this ancestor was George Hays who was born
> in 1655 - 362 years ago, so these numbers align perfectly!
>
> This places our Z17911 ancestor being born between 837 and 987 years
> ago. It places the Hartley common ancestor between 431 and 501 years
> ago, the Bennett/Phillips ancestor 639-750 years ago, etc.
>
> Do keep in mind that accuracy is more variable near the end of the
> branches (closer to present day), especially with data from only 2 or
> 3 people. And SNPs are not always formed at a consistent rate. So this
> all a bit rough, but should give us fairly reasonable estimations.
>
> Jared
>
>
>
>



Re: New Hartley/Smith SNP block?

Joel Hartley
 

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




Re: Z16357 In-depth Age Analysis

Jared Smith
 

Charles -

It appears Mike made a mistake when he updated the chart. This should
be FGC33966. None of us have BY11382. I'll let him know.

Thanks,

Jared

On Mon, Mar 20, 2017 at 11:40 PM, Charles Thomas
<charles_002@...> wrote:
Thanks, Jared. The new age estimates are very helpful. One more question if
I may:

the L513 Descendant Tree Chart has Bennett and I at BY11382. Is that an
equivalent for

a SNP included on your Z16357 SNP tree?

Charles



________________________________
From: Z16357@groups.io <Z16357@groups.io> on behalf of Jared Smith
<jared@...>
Sent: Monday, March 20, 2017 8:53 PM
To: Z16357@groups.io
Subject: Re: [Z16357] Z16357 In-depth Age Analysis

Charles -

FGC33966 is your terminal SNP shared with Martin, but I only analyzed
Big-Y testers so I could include the novel variants. So FGC33966 is
counted as one of your 6 novel variants.

This methodology is a fairly standard way of doing age estimates, but
I don't think it had been done to this level for our tree before.

Jared



On Mon, Mar 20, 2017 at 3:05 PM, Charles Thomas <charles_002@...>
wrote:
Great analysis, Jared, but I think the SNP names are confusing me. Did you
include an equivalent to FGC33966 for Martin and me?

Charles

________________________________
From: Z16357@groups.io <Z16357@groups.io> on behalf of Jared Smith
<jared@...>
Sent: Monday, March 20, 2017 9:52 AM
To: Z16357@groups.io
Subject: [Z16357] Z16357 In-depth Age Analysis

Aging our ancestors using Y-DNA data is far from an exact science. I'd
be happy to have you poke holes in any of this.

An analysis of the 11 Z16357 people who have taken Big-Y results in
the following number of 'good', unique/novel variants/mutations:

C. Hays 4
R. Hays 3
Pillsbury 5
Merrick 11
Thomas 6
Phillips 7
Bennett 9
M. Hartley 5
J. Hartley 5
J. Smith 12
Smith 27

These are variants that each person has that are not shared with
anyone else who has tested. The higher the number of novel variants,
the further back one would expect to be related to someone else
listed. I use the same metric for a 'good' variant as Alex does on his
Big Tree. This is a bit more aggressive than what YFull uses.

There are, however, some inconsistencies with this. Merrick, for
example, has nearly twice as many novel variants as Thomas, even
though Merrick connects lower/later on the tree than Thomas - one
would thus expect Merrick to have fewer novel variants. This is
primarily a factor of test coverage, but this is all we have to work
with, so we partially account for this variability by averaging. This
is why each new Big-Y test gives us increased accuracy.

When I add the novel variants above to the number of 'good' SNPs in
each block or haplogroup of our tree and average the results, I end up
with the following average number of variants downstream from each
listed SNP block:

ZS349 - 3.5
Z16854 - 9.3
BY15420 - 8.0
BY15419 - 9.7
Y29969 - 9.5
A11132 - 5
Z17911 - 10.9
Z16343 - 13
Z16357 - 36.1

This means, for example, that there's an average of 3.5 variants that
were formed after the most recent ZS349 ancestor that the two Hays men
share. For Z17911, we average 10.9 variants downstream (more recent
than) our most recent common Z17911 ancestor. Altogether, we average
36.1 SNPs downstream of Z16357.

To use these variant numbers to help us in aging, we need to calculate
a "years per SNP" value. YFull has our last Z16357 ancestor at around
3300 years ago (though they've acknowledged this is probably too
high). Other recent estimates put it as young as 2300 years ago. Until
someone digs up some Z16357 remains or we get enough DNA testers to
give us better data, we have to use our best informed estimate. I'll
assume our most recent Z16357 ancestor lived a minimum of 2500 and
maximum of 3000 years ago.

If we divide these age estimates by 36.1 SNPs (on average), this is a
minimum of 69.3 years per SNP and a maximum of 83.1 years per SNP. We
can then use these values to assign age estimates to notable
branchings as follows:

ZS349 - 327-376 years before present
Z16854 - 732-861
BY15420 - 639-750
BY15419 - 755-889
Y29969 - 743-875
A11132 - 431-501
Z17911 - 837-987
Z16343 - 986-1166
Z16357 - 2585-3085

The values are years before present, and include an additional 35
years (one generation?) to account for the age of the last ancestor
that had this SNP - and also adds 50 years as a guessed average of how
old the 11 Z16357 people are.

So this estimates that the common ZS349 ancestor for Hays was born
347-376 years ago. We know this ancestor was George Hays who was born
in 1655 - 362 years ago, so these numbers align perfectly!

This places our Z17911 ancestor being born between 837 and 987 years
ago. It places the Hartley common ancestor between 431 and 501 years
ago, the Bennett/Phillips ancestor 639-750 years ago, etc.

Do keep in mind that accuracy is more variable near the end of the
branches (closer to present day), especially with data from only 2 or
3 people. And SNPs are not always formed at a consistent rate. So this
all a bit rough, but should give us fairly reasonable estimations.

Jared





Re: New Hartley/Smith SNP block?

Jared Smith
 

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





Re: New Hartley/Smith SNP block?

Joel Hartley
 

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






Re: New Hartley/Smith SNP block?

Jared Smith
 

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







Re: New Hartley/Smith SNP block?

Charles Thomas
 

Congrats on the new discovery, Jared! With your extensive knowledge and help I hope there are many more discoveries for each of us in the group.

Charles Thomas


From: Z16357@groups.io <Z16357@groups.io> on behalf of Jared Smith <jared@...>
Sent: Saturday, March 25, 2017 10:13 AM
To: Z16357@groups.io
Subject: Re: [Z16357] New Hartley/Smith SNP block?
 
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.

dna.smithplanet.com
SNP Overview. By analyzing certain SNP mutations that developed in men long ago and were then passed to their descendants today, we can begin to build a family tree ...



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







Autosomal DNA

Charles Thomas
 

Hey Jared,

I was looking for something online in addtion to dna-explained.com to send to an autosomal DNA match of mine for explanation of the possibilities of the match and I found the following nice page of yours:

http://smithplanet.com/stuff/gedmatch.htm

I recommend it to others here looking to understand autosomal matches.

Thanks,

Charles Thomas

DNA Day Sale - Big-Y $150 off

Jared Smith
 

I hope everyone is doing well. We haven't had any new tests on our
branch of the tree lately, but now is the optimal time for us to
recruit new Big-Y testers. Big-Y is on sale for only $450 through
Thursday of this week.

If everyone on this list would send just a couple e-mails to some of
their close Y-DNA matches, we likely could recruit several new
testers.

Someone asked for some positive messaging to help recruit Big-Y
testers, so I wrote the following, in case you'd like to use or modify
it:

*****
Big-Y testing maps the genetic tree of humanity. We're slowly mapping
every Y-DNA mutation to particular ancestors - some known by name and
some too ancient to be known. Even for very old common ancestors,
these markers provide a unique identifier for them - a way to identify
family tree connections that could not possibly be made using
genealogical records.

Traditional genealogy works from modern day and builds the tree
backward from us to our ancestors. Y-DNA genealogy works in reverse -
we've identified mutations in our ancient ancestors and are
identifying new cousin relationships, new branches, and more defined
family timelines with each new Big-Y test. For many family lines,
we're still very much in the early days of this research, but each new
test provides better clarity.

On our own Z16357 part of the Y-DNA tree
(http://dna.smithplanet.com/), we are getting much better defined
branches. We're getting closer to knowing geographies of some of our
ancestors - where and when they lived in the British Isles in the last
few thousand years. As we define and verify the individual mutations
that form new branches on our tree, we are paving the path for others
to eventually take very inexpensive DNA tests to see how their direct
male line connects with the rest of humanity. This future is only
possible if we pave the way by investing in Big-Y!
*****

Thanks,

Jared Smith

Re: New Hartley/Smith SNP block?

Joel Hartley
 

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








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




Re: New Hartley/Smith SNP block?

Joel Hartley
 

Thanks, Jared for the fast response! Also thanks for roaming around YBrowse to find Michael Hartley's named SNP.

It looks like for now, Michael's A15733 could be called the Quaker Hartley Line SNP.

I know that Michael Walsh had mentioned that it would be good if the Hartleys could continue on with the 'A' named SNPs, so I'm happy that Michael got a SNP starting with 'A'.

Joel

On 4/24/2017 10:28 AM, Jared Smith wrote:
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



Re: DNA Day Sale - Big-Y $150 off

Fran Pillsbury
 

Happy to report that Kit 601582, my new project member, ordered Big-Y last Thursday. So there will soon be a Pillsbury SNP below the Hays-Pillsbury node on the R1b-L513 Tree.!

He is currently a member of R1b (Y-111 ), but not L21 or L513. His MDKA is  the same as  mine: Wm. Pilsbury, b. 1605 -- not yet updated on his account.

Cheers,

Fran Pillsbury

At 06:23 PM 4/22/2017 -0600, you wrote:

I hope everyone is doing well. We haven't had any new tests on our