Date   
A new Hartley member

Jared Smith
 

I'd like to welcome Michael Hartley to the group. He has kit #617805
and has recently done the Y67 DNA test. He likely shows as a match to
some of you (he is GD=7 to me at Y67). I've added him to the STR and
GDs spreadsheets - http://dna.smithplanet.com/str

I also added another Hartley from their surname project - there are
now 5 Hartleys and Sanchez (who is a Hartley) in addition to Joel.
These are all very good candidates for additional testing on the
Hartley branch of Z17911.

Michael's most distant known ancestor originates in England around
1660, then came to Pennsylvania in a Quaker emigration. Having such an
old ancestor defined for our tree is very helpful. Hopefully we can
establish Michael's location on our tree.

Welcome aboard Michael!

Jared

Re: YFull tree updates

Jared Smith
 

As a quick follow-up, Merrick's BAM file was analyzed by FTDNA and
they've confirmed that Merrick is positive for Y29969, so this
confirms my suspicion that it is equivalent to BY11573. This also
means that Goff has this SNP because he's on the downstream branch at
BY11565 with Merrick.

Jared

On Sun, Feb 12, 2017 at 9:01 PM, Jared Smith <jared@...> wrote:
Joel noted on the R-L513 list that YFull has updated their tree based
on Bennett's results - https://www.yfull.com/tree/R-S5668/

R-Z16351 is our branch (what I call Z16357). They have Joel alone at
the base of this branch because there's not yet other results to
differentiate him.

They now have Thomas and Bennett on the Y29969 branch. I had
identified this SNP as being distinctive to Thomas and Bennett at
http://dna.smithplanet.com/snp

They don't show BY11573 for them (like I, FTDNA, and Big Tree do),
probably because it was a questionable read for both - and they don't
have Merrick's results or SNP Pack results to add validity to it.
Merrick had no or poor test coverage for Y29969, so for now we should
consider Y29969 and BY11573 to be phylogenetically equivalent. I'll
update my tree to reflect this.

They also updated the Time to Most Recent Common Ancestor (TMRCA)
estimates - moving Z16351/Z16357 (Hartley) a bit older to 1550 ybp and
Y29969 (Thomas and Bennett) to 1200 ybp.

Jared

My Big-Y results

Jared Smith
 

My Big-Y results (kit #307773) are in. I am firmly (still) at
R-Z17911. I had hoped that I would share some private/novel SNPs with
Hartley, or maybe a few with Bennett or Thomas, but it appears that my
branch split near the same time as the Harley and BY11573 (and
downstream) branches. I do have quite a few of my own private/novel
SNPs for this new potential Smith branch below Z17911, but there are
no new branches (yet) from my test results.

I'm just off on a road trip, but will try to find some time to analyze
things more fully.

Jared

Re: My Big-Y results

Joel Hartley
 

Hi Jared,

So I suspect on your Z16357 SNP Tree, you will be branching off on a pink box parallel to me under Z17911.

Joel

On 2/16/2017 10:27 AM, Jared Smith wrote:
My Big-Y results (kit #307773) are in. I am firmly (still) at
R-Z17911. I had hoped that I would share some private/novel SNPs with
Hartley, or maybe a few with Bennett or Thomas, but it appears that my
branch split near the same time as the Harley and BY11573 (and
downstream) branches. I do have quite a few of my own private/novel
SNPs for this new potential Smith branch below Z17911, but there are
no new branches (yet) from my test results.

I'm just off on a road trip, but will try to find some time to analyze
things more fully.

Jared

Re: My Big-Y results

Joel Hartley
 

Jared,

You are my top BigY match now:



Joel

On 2/16/2017 10:27 AM, Jared Smith wrote:
My Big-Y results (kit #307773) are in. I am firmly (still) at
R-Z17911. I had hoped that I would share some private/novel SNPs with
Hartley, or maybe a few with Bennett or Thomas, but it appears that my
branch split near the same time as the Harley and BY11573 (and
downstream) branches. I do have quite a few of my own private/novel
SNPs for this new potential Smith branch below Z17911, but there are
no new branches (yet) from my test results.

I'm just off on a road trip, but will try to find some time to analyze
things more fully.

Jared




Re: My Big-Y results

Jared Smith
 

Yes, I now form a new theoretical branch from Z17911 (well, theoretical until I can get a closer cousin to test). My branch will be a sibling to your Hartley branch, which is a sibling to the BY11573 branch with Thomas, Bennett, Merrick, and Goff. As soon as I can update it, I'll add my pink box to the SNP tree.

Of note is that your Hartley theoretical branch is depicted with A11130, but that just represents one of the dozen or so private SNPs that have been identified for you. My box will also fill with a dozen or so of similar (but not yet named) SNPs.

Joel, you are also my top match, followed by Bennett, then Thomas, as you'd expect considering these results.

I'm a bit disappointed that no new branches were formed with my results, but this paves the road for others to follow. Now to redouble my research efforts to find a distant Smith cousin!

Jared


On Thu, Feb 16, 2017 at 12:34 PM, Joel Hartley <joel@...> wrote:
Jared,

You are my top BigY match now:



Joel

On 2/16/2017 10:27 AM, Jared Smith wrote:
My Big-Y results (kit #307773) are in. I am firmly (still) at
R-Z17911. I had hoped that I would share some private/novel SNPs with
Hartley, or maybe a few with Bennett or Thomas, but it appears that my
branch split near the same time as the Harley and BY11573 (and
downstream) branches. I do have quite a few of my own private/novel
SNPs for this new potential Smith branch below Z17911, but there are
no new branches (yet) from my test results.

I'm just off on a road trip, but will try to find some time to analyze
things more fully.

Jared





Re: My Big-Y results

Joel Hartley
 

Hi Jared,

It seems like with the people that we had, all the branching that was going to happen already happened. The good news is that Michael Hartley has expressed interest in the Big Y. This could produce some extra resolution between your branch of YDNA and mine.

I think that the reason I have some named SNPs is that I believe my Hartley administrator, William Hartley, probably went in and named some of my SNPs after I took the Big Y test.

Sorry for your disappointment. As you know, this BigY is a long term thing. It's good to be a pioneer, but being way out in front of the pack can be lonely!

Joel

On 2/17/2017 1:03 AM, Jared Smith wrote:
Yes, I now form a new theoretical branch from Z17911 (well, theoretical until I can get a closer cousin to test). My branch will be a sibling to your Hartley branch, which is a sibling to the BY11573 branch with Thomas, Bennett, Merrick, and Goff. As soon as I can update it, I'll add my pink box to the SNP tree.

Of note is that your Hartley theoretical branch is depicted with A11130, but that just represents one of the dozen or so private SNPs that have been identified for you. My box will also fill with a dozen or so of similar (but not yet named) SNPs.

Joel, you are also my top match, followed by Bennett, then Thomas, as you'd expect considering these results.

I'm a bit disappointed that no new branches were formed with my results, but this paves the road for others to follow. Now to redouble my research efforts to find a distant Smith cousin!

Jared


On Thu, Feb 16, 2017 at 12:34 PM, Joel Hartley <joel@...> wrote:
Jared,

You are my top BigY match now:



Joel

On 2/16/2017 10:27 AM, Jared Smith wrote:
My Big-Y results (kit #307773) are in. I am firmly (still) at
R-Z17911. I had hoped that I would share some private/novel SNPs with
Hartley, or maybe a few with Bennett or Thomas, but it appears that my
branch split near the same time as the Harley and BY11573 (and
downstream) branches. I do have quite a few of my own private/novel
SNPs for this new potential Smith branch below Z17911, but there are
no new branches (yet) from my test results.

I'm just off on a road trip, but will try to find some time to analyze
things more fully.

Jared






a Smith lineage

Charles Thomas
 

Hi Jared,

It's of no consequence to my Y-DNA lineage or to your research, but in another line I'm supposedy a descendant of Nicholas Smith d.1719 Surry County, VA, and wife Elizabeth Flood. His Y-lineage seems to be I-M223-group 1 (#134470) at the Smith Project, but R-M269-group 32 is another possibility.

Best,

Charles 

Re: a Smith lineage

Jared Smith
 

Charles -

That is interesting. It does appear that your (supposed) ancestor is
probably I-M223. Sylvia and Lenita (our Z16357 people) and I are in
the Smith R-M269-16 group. Many or most of the other Smiths in that
group are also Z16357 people.

I have some exciting news coming soon regarding our tree!

Jared

On Fri, Feb 17, 2017 at 9:53 PM, Charles Thomas <charles_002@...> wrote:
Hi Jared,

It's of no consequence to my Y-DNA lineage or to your research, but in
another line I'm supposedy a descendant of Nicholas Smith d.1719 Surry
County, VA, and wife Elizabeth Flood. His Y-lineage seems to be I-M223-group
1 (#134470) at the Smith Project, but R-M269-group 32 is another
possibility.

Best,

Charles

Re: a Smith lineage

Joel Hartley
 

Jared,

You have piqued my interest concerning your exciting news.

Joel

On 2/18/2017 12:16 AM, Jared Smith wrote:
Charles -

That is interesting. It does appear that your (supposed) ancestor is
probably I-M223. Sylvia and Lenita (our Z16357 people) and I are in
the Smith R-M269-16 group. Many or most of the other Smiths in that
group are also Z16357 people.

I have some exciting news coming soon regarding our tree!

Jared


On Fri, Feb 17, 2017 at 9:53 PM, Charles Thomas <charles_002@...> wrote:
Hi Jared,

It's of no consequence to my Y-DNA lineage or to your research, but in
another line I'm supposedy a descendant of Nicholas Smith d.1719 Surry
County, VA, and wife Elizabeth Flood. His Y-lineage seems to be I-M223-group
1 (#134470) at the Smith Project, but R-M269-group 32 is another
possibility.

Best,

Charles

Phillips Big-Y - new Bennett/Phillips branch

Jared Smith
 

The Big-Y results for Brent Phillips are in. He is confirmed R-Y29969
with Bennett and Thomas. This is phylogenetically equivalent to
BY11573. You'll notice FTDNA has changed the terminal SNP for Bennett
and Thomas to Y29969 - it's a more reliable SNP to check.

Beyond this, there's also a new tentative Bennett/Phillips branch.
They both share the following markers (and perhaps some others that
are yet to be discovered):
7488239-G-A
22486193-A-T
25311291-T-C

These are in rather poor read areas for the Y-DNA test, but I believe
at least the first one should hold up under further analysis to create
this new branch.

I had thought that Bennett and Phillips would share more good SNPs
(i.e., they had a more recent common ancestor), but this proves that
their lines split after Y29969. But both of them have around 10 good
unique SNPs that would provide distinct Bennett and Phillips branches
with additional cousin testers.

Another good discover with the Phillips and my Smith Big-Y is
validation of 5 or 6 other SNP markers that those of us on the Z17911
block share. This means that Z17911 is a bigger/longer block than we
had previously thought, thus moving our more recent ancestor in that
block closer to modern day.

My own VERY rough estimate based on what we know now is that our most
recent Z17911 lived probably around 1200 years ago, with the
Bennett/Phillips/Thomas/Merrick/Goff Y29969/BY11573 ancestor living
around 800 years ago.

Brent's results add some very useful information to our project!

Jared

Re: Phillips Big-Y - new Bennett/Phillips branch

Jared Smith
 

I forgot to mention that I've updated the charts at
http://dna.smithplanet.com/snp to reflect these changes, in case you
prefer a visual view of what's happening.

Jared

On Sat, Feb 18, 2017 at 12:45 PM, Jared Smith <jared@...> wrote:
The Big-Y results for Brent Phillips are in. He is confirmed R-Y29969
with Bennett and Thomas. This is phylogenetically equivalent to
BY11573. You'll notice FTDNA has changed the terminal SNP for Bennett
and Thomas to Y29969 - it's a more reliable SNP to check.

Beyond this, there's also a new tentative Bennett/Phillips branch.
They both share the following markers (and perhaps some others that
are yet to be discovered):
7488239-G-A
22486193-A-T
25311291-T-C

These are in rather poor read areas for the Y-DNA test, but I believe
at least the first one should hold up under further analysis to create
this new branch.

I had thought that Bennett and Phillips would share more good SNPs
(i.e., they had a more recent common ancestor), but this proves that
their lines split after Y29969. But both of them have around 10 good
unique SNPs that would provide distinct Bennett and Phillips branches
with additional cousin testers.

Another good discover with the Phillips and my Smith Big-Y is
validation of 5 or 6 other SNP markers that those of us on the Z17911
block share. This means that Z17911 is a bigger/longer block than we
had previously thought, thus moving our more recent ancestor in that
block closer to modern day.

My own VERY rough estimate based on what we know now is that our most
recent Z17911 lived probably around 1200 years ago, with the
Bennett/Phillips/Thomas/Merrick/Goff Y29969/BY11573 ancestor living
around 800 years ago.

Brent's results add some very useful information to our project!

Jared

Re: Phillips Big-Y - new Bennett/Phillips branch

Charles Thomas
 

Thanks for the update. I checked and yes FTDNA does indeed show me as R-Y29969 now with BY11573 shown in light brown meaning presumed positive beside Y29969 on the tree. I also noticed that Rodney Martin is shown as BY11573 on my match list.

Thanks also to Joel a week or so ago for the heads-up on the YFull tree update.

Charles  




From: Z16357@groups.io <Z16357@groups.io> on behalf of Jared Smith <jared@...>
Sent: Saturday, February 18, 2017 1:45 PM
To: Z16357@groups.io
Subject: [Z16357] Phillips Big-Y - new Bennett/Phillips branch
 
The Big-Y results for Brent Phillips are in. He is confirmed R-Y29969
with Bennett and Thomas. This is phylogenetically equivalent to
BY11573. You'll notice FTDNA has changed the terminal SNP for Bennett
and Thomas to Y29969 - it's a more reliable SNP to check.

Beyond this, there's also a new tentative Bennett/Phillips branch.
They both share the following markers (and perhaps some others that
are yet to be discovered):
7488239-G-A
22486193-A-T
25311291-T-C

These are in rather poor read areas for the Y-DNA test, but I believe
at least the first one should hold up under further analysis to create
this new branch.

I had thought that Bennett and Phillips would share more good SNPs
(i.e., they had a more recent common ancestor), but this proves that
their lines split after Y29969. But both of them have around 10 good
unique SNPs that would provide distinct Bennett and Phillips branches
with additional cousin testers.

Another good discover with the Phillips and my Smith Big-Y is
validation of 5 or 6 other SNP markers that those of us on the Z17911
block share. This means that Z17911 is a bigger/longer block than we
had previously thought, thus moving our more recent ancestor in that
block closer to modern day.

My own VERY rough estimate based on what we know now is that our most
recent Z17911 lived probably around 1200 years ago, with the
Bennett/Phillips/Thomas/Merrick/Goff Y29969/BY11573 ancestor living
around 800 years ago.

Brent's results add some very useful information to our project!

Jared



Re: Phillips Big-Y - new Bennett/Phillips branch

Joel Hartley
 

Thanks Jared,

I was wondering what happened to that test. Also I'm wondering why I can't see Phillips on my match list? Hopefully, it should show up soon.

Joel

On 2/18/2017 2:45 PM, Jared Smith wrote:
The Big-Y results for Brent Phillips are in. He is confirmed R-Y29969
with Bennett and Thomas. This is phylogenetically equivalent to
BY11573. You'll notice FTDNA has changed the terminal SNP for Bennett
and Thomas to Y29969 - it's a more reliable SNP to check.

Beyond this, there's also a new tentative Bennett/Phillips branch.
They both share the following markers (and perhaps some others that
are yet to be discovered):
7488239-G-A
22486193-A-T
25311291-T-C

These are in rather poor read areas for the Y-DNA test, but I believe
at least the first one should hold up under further analysis to create
this new branch.

I had thought that Bennett and Phillips would share more good SNPs
(i.e., they had a more recent common ancestor), but this proves that
their lines split after Y29969. But both of them have around 10 good
unique SNPs that would provide distinct Bennett and Phillips branches
with additional cousin testers.

Another good discover with the Phillips and my Smith Big-Y is
validation of 5 or 6 other SNP markers that those of us on the Z17911
block share. This means that Z17911 is a bigger/longer block than we
had previously thought, thus moving our more recent ancestor in that
block closer to modern day.

My own VERY rough estimate based on what we know now is that our most
recent Z17911 lived probably around 1200 years ago, with the
Bennett/Phillips/Thomas/Merrick/Goff Y29969/BY11573 ancestor living
around 800 years ago.

Brent's results add some very useful information to our project!

Jared

Re: Phillips Big-Y - new Bennett/Phillips branch

Jared Smith
 

Charles -

Oh, that must be Chuck Martin's SNP pack results. I don't see those
results at all yet, but that would put him at the same place on the
tree as you. We don't know if he's on the same branch as Bennett and
Phillips because none of those SNPs are yet in the SNP pack - heck, we
just discovered them a few hours ago. :-)

Chuck, if this is all correct, that confirms your placement on the
tree as Y29969/BY11573 (with BY11573 being the SNP you've actually
tested positive for).

Joel, I don't see Brent Phillips in my Big-Y matches list either. It
seems they're still processing this batch of results.

Two new family lines positioned on our tree in one day! Excellent!

Jared

On Sat, Feb 18, 2017 at 2:23 PM, Joel Hartley <joel@...> wrote:
Thanks Jared,

I was wondering what happened to that test. Also I'm wondering why I can't
see Phillips on my match list? Hopefully, it should show up soon.

Joel


On 2/18/2017 2:45 PM, Jared Smith wrote:

The Big-Y results for Brent Phillips are in. He is confirmed R-Y29969
with Bennett and Thomas. This is phylogenetically equivalent to
BY11573. You'll notice FTDNA has changed the terminal SNP for Bennett
and Thomas to Y29969 - it's a more reliable SNP to check.

Beyond this, there's also a new tentative Bennett/Phillips branch.
They both share the following markers (and perhaps some others that
are yet to be discovered):
7488239-G-A
22486193-A-T
25311291-T-C

These are in rather poor read areas for the Y-DNA test, but I believe
at least the first one should hold up under further analysis to create
this new branch.

I had thought that Bennett and Phillips would share more good SNPs
(i.e., they had a more recent common ancestor), but this proves that
their lines split after Y29969. But both of them have around 10 good
unique SNPs that would provide distinct Bennett and Phillips branches
with additional cousin testers.

Another good discover with the Phillips and my Smith Big-Y is
validation of 5 or 6 other SNP markers that those of us on the Z17911
block share. This means that Z17911 is a bigger/longer block than we
had previously thought, thus moving our more recent ancestor in that
block closer to modern day.

My own VERY rough estimate based on what we know now is that our most
recent Z17911 lived probably around 1200 years ago, with the
Bennett/Phillips/Thomas/Merrick/Goff Y29969/BY11573 ancestor living
around 800 years ago.

Brent's results add some very useful information to our project!

Jared




New variants spreadsheet

Jared Smith
 

I have uploaded a new spreadsheet to
http://dna.smithplanet.com/media/Z16357-Variants.xlsx

This likely has limited utility for anyone other than me, but I
thought I'd share it. This file is used for analyzing Y-DNA mutation
variants (SNPs, insertions/deletions, etc.) that us Z16357 people
have. It's a very large spreadsheet with complex calculations - minor
changes like sorting can take a long time to calculate.

The Variants tab includes all 68,355 unique variants that we have.
These were collected from Big-Y VCF files.

You can use the Lookup tab to query specific DNA position numbers to
see the values each of us have at that position.

The Shared Variants tab shows all known variants ***AT OR BELOW
Z16357*** that at least 2 of us have. This allows easy analysis of the
consistency of SNPs and determination of their position on our
branches. A "+" indicates a positive test for that variant. A "***"
indicates the variant was identified, but the test quality is
questionable. A blank box indicates EITHER a negative result OR no
test coverage (be careful - you can't assume too much from a blank box
without analyzing the BED file for read coverage).

The Unique Variants tab lists most of the variants that are unique to
only one of us. I'd be happy to add any new ones from YFull, if any of
you who have tested there would like to e-mail them to me. Note that
some Insertions/Deletions (these are kinda like hiccups in your DNA)
show "Count" as 0 because Big Tree calculates the position info for
INDELs a bit differently than the VCF file. These are retained for
reference.

The primary function of this spreadsheet is to easily add VCF data to
Variants for new Big-Y testers, then immediately determine which
existing SNPs from our branch they have, and which Unique Variants are
then no longer unique and need to be moved to Shared Variants.

Jared

Re: New variants spreadsheet

Joel Hartley
 

Thanks, Jared,

That should be a great resource. I'll send some of my SNPs your way once I sort them out. YFull has them as:

Best Quality (5)
Acceptable (6)
Ambiguous (20)

I'm guessing you just want the 1st 2 categories?

Joel

On 2/20/2017 6:44 PM, Jared Smith wrote:
I have uploaded a new spreadsheet to
http://dna.smithplanet.com/media/Z16357-Variants.xlsx

This likely has limited utility for anyone other than me, but I
thought I'd share it. This file is used for analyzing Y-DNA mutation
variants (SNPs, insertions/deletions, etc.) that us Z16357 people
have. It's a very large spreadsheet with complex calculations - minor
changes like sorting can take a long time to calculate.

The Variants tab includes all 68,355 unique variants that we have.
These were collected from Big-Y VCF files.

You can use the Lookup tab to query specific DNA position numbers to
see the values each of us have at that position.

The Shared Variants tab shows all known variants ***AT OR BELOW
Z16357*** that at least 2 of us have. This allows easy analysis of the
consistency of SNPs and determination of their position on our
branches. A "+" indicates a positive test for that variant. A "***"
indicates the variant was identified, but the test quality is
questionable. A blank box indicates EITHER a negative result OR no
test coverage (be careful - you can't assume too much from a blank box
without analyzing the BED file for read coverage).

The Unique Variants tab lists most of the variants that are unique to
only one of us. I'd be happy to add any new ones from YFull, if any of
you who have tested there would like to e-mail them to me. Note that
some Insertions/Deletions (these are kinda like hiccups in your DNA)
show "Count" as 0 because Big Tree calculates the position info for
INDELs a bit differently than the VCF file. These are retained for
reference.

The primary function of this spreadsheet is to easily add VCF data to
Variants for new Big-Y testers, then immediately determine which
existing SNPs from our branch they have, and which Unique Variants are
then no longer unique and need to be moved to Shared Variants.

Jared

Re: New variants spreadsheet

Joel Hartley
 

Addendum, there are actually more categories:



I assume that ambiguous is better than Low quality. Perhaps you do want the Ambiguous ones.

Joel

On 2/20/2017 6:44 PM, Jared Smith wrote:
I have uploaded a new spreadsheet to
http://dna.smithplanet.com/media/Z16357-Variants.xlsx

This likely has limited utility for anyone other than me, but I
thought I'd share it. This file is used for analyzing Y-DNA mutation
variants (SNPs, insertions/deletions, etc.) that us Z16357 people
have. It's a very large spreadsheet with complex calculations - minor
changes like sorting can take a long time to calculate.

The Variants tab includes all 68,355 unique variants that we have.
These were collected from Big-Y VCF files.

You can use the Lookup tab to query specific DNA position numbers to
see the values each of us have at that position.

The Shared Variants tab shows all known variants ***AT OR BELOW
Z16357*** that at least 2 of us have. This allows easy analysis of the
consistency of SNPs and determination of their position on our
branches. A "+" indicates a positive test for that variant. A "***"
indicates the variant was identified, but the test quality is
questionable. A blank box indicates EITHER a negative result OR no
test coverage (be careful - you can't assume too much from a blank box
without analyzing the BED file for read coverage).

The Unique Variants tab lists most of the variants that are unique to
only one of us. I'd be happy to add any new ones from YFull, if any of
you who have tested there would like to e-mail them to me. Note that
some Insertions/Deletions (these are kinda like hiccups in your DNA)
show "Count" as 0 because Big Tree calculates the position info for
INDELs a bit differently than the VCF file. These are retained for
reference.

The primary function of this spreadsheet is to easily add VCF data to
Variants for new Big-Y testers, then immediately determine which
existing SNPs from our branch they have, and which Unique Variants are
then no longer unique and need to be moved to Shared Variants.

Jared




Re: New variants spreadsheet

Jared Smith
 

Please send all of them (with an indication of or grouping by YFull's
quality level). I'm curious how their quality levels align with those
from the other sources I used - Mike W.'s analysis, Alex's Big-Y
analysis, and my own.

I don't really include much grading information in the spreadsheet,
beyond FTDNA's read data (PASS or REJECTED, though they have an
extremely high threshold for "PASS"), and the indication of the Region
and STR data (anything in these columns will suggest lower quality).

I didn't think it necessary to create a complex quality analysis
metric in the spreadsheet seeing as this is what Mike, Alex, and YFull
do best, and I can always reference their work in instances where
things are questionable.

Jared

On Mon, Feb 20, 2017 at 4:56 PM, Joel Hartley <joel@...> wrote:
Thanks, Jared,

That should be a great resource. I'll send some of my SNPs your way once I
sort them out. YFull has them as:

Best Quality (5)
Acceptable (6)
Ambiguous (20)

I'm guessing you just want the 1st 2 categories?

Joel



On 2/20/2017 6:44 PM, Jared Smith wrote:

I have uploaded a new spreadsheet to
http://dna.smithplanet.com/media/Z16357-Variants.xlsx

This likely has limited utility for anyone other than me, but I
thought I'd share it. This file is used for analyzing Y-DNA mutation
variants (SNPs, insertions/deletions, etc.) that us Z16357 people
have. It's a very large spreadsheet with complex calculations - minor
changes like sorting can take a long time to calculate.

The Variants tab includes all 68,355 unique variants that we have.
These were collected from Big-Y VCF files.

You can use the Lookup tab to query specific DNA position numbers to
see the values each of us have at that position.

The Shared Variants tab shows all known variants ***AT OR BELOW
Z16357*** that at least 2 of us have. This allows easy analysis of the
consistency of SNPs and determination of their position on our
branches. A "+" indicates a positive test for that variant. A "***"
indicates the variant was identified, but the test quality is
questionable. A blank box indicates EITHER a negative result OR no
test coverage (be careful - you can't assume too much from a blank box
without analyzing the BED file for read coverage).

The Unique Variants tab lists most of the variants that are unique to
only one of us. I'd be happy to add any new ones from YFull, if any of
you who have tested there would like to e-mail them to me. Note that
some Insertions/Deletions (these are kinda like hiccups in your DNA)
show "Count" as 0 because Big Tree calculates the position info for
INDELs a bit differently than the VCF file. These are retained for
reference.

The primary function of this spreadsheet is to easily add VCF data to
Variants for new Big-Y testers, then immediately determine which
existing SNPs from our branch they have, and which Unique Variants are
then no longer unique and need to be moved to Shared Variants.

Jared




New Thomas/Martin branch

Jared Smith
 

The S5668 SNP pack results are in for Chuck Martin and they confirm a
new Thomas/Martin branch of the tree.

First, I had indicated Chuck's kit # previously as 161394. That was
incorrect. His actual kit # is 495859.

One of Thomas' (previously) unique SNPs is FGC33966. FTDNA included
this SNP in the S5668 SNP Pack. Chuck Martin is positive for FGC33966
(and also BY11573), thus verifying this new branch!

I've updated my charts at http://dna.smithplanet.com/snp to reflect
the new branching (you may need to hit Refresh). You'll notice that we
currently don't have anyone left right at S59969/BY11573 - they've all
moved to downstream blocks in just the last few weeks due to new test
results.

This places the common Thomas/Martin ancestor at probably 500-700
years ago. It's likely that Thomas and Martin also share some of
Thomas' other 'unique' SNPs - such as FGC33968 and FGC33967 - see
http://www.ytree.net/SNPinfoForPerson.php?personID=413 Each new SNP
match would move your common ancestor 100+ years closer to present
day. But you are GD=6 at Y67, so this does suggest that your common
ancestor is still probably at least a few hundred years back, and that
we got lucky and hit gold with your FGC33966 SNP match.

In other news, I see that FTDNA has updated their tree with some of
our recent changes (I'll request that FGC33966 be added). If I'm
reading it correctly, the new terminal SNP for Bennett and Phillips (I
currently have as ??? on my charts) is labelled BY15420. They also
list BY15419 upstream of this and BY11565, but I'm not sure what this
SNP is. I'll try to figure it out.

Discovering new branches is what this project is about, and new ones
always make my day!

Thanks,

Jared

PS - Chuck, I don't see you in the Martin project. Maybe try
re-joining - or maybe something odd is happening there.