Topics

Z17911 BigY

Joel Hartley
 

Does anyone know why I have a 0 SNP difference to Thomas and Bennett and a 2 SNP difference to Merrick on the Big Y?

Jared Smith
 

There are really four levels of reporting for each SNP: positive,
negative, maybe, and no coverage.

The 'maybe' results (this is my terminology, not FTDNA's) are markers
where you show the SNP in your raw results, but it was in a
questionable read area of the test. This means you probably have the
SNP, but FTDNA takes a very conservative approach and does not report
these. If additional people on your branch get 'maybe' results for
that same SNP, the more likely it is a valid SNP for that haplogroup.
A positive test for that SNP verifies it as a good one and (usually)
establishes it on the tree.

No coverage means the test didn't read in this area, so you can't
really know from that test alone. If you do, however, test positive
for a downstream SNP, then you'll know you also have all upstream
SNPs, even if your test results show 'maybe' or no coverage results
for them.

My tree and FTDNA's tree has Merrick two branches downstream (BY11573
and a terminal SNP of BY11565), from you and I who are at Z17911. So
this is the 2 SNP differences.

But Thomas and Bennett also have BY11573, so this means they should
show a 1 SNP difference to you, right? The answer would be yes, except
that Merrick, Thomas, and Bennett all were 'maybe' results for
BY11573, so FTDNA doesn't count these. You'll see that Thomas and
Bennett still show terminal SNP at FTDNA of Z17911, not BY11573.

So why does Merrick get credit for BY11573 when his 'maybe' result is
the same as Thomas and Bennett? Because we know BY11573 is a valid SNP
because of Goff's positive result for it. This established its
definitive location on the tree. While Thomas and Bennett don't get
credit for it because of their 'maybe' results (they show 0 SNP
differences to you), Merrick does because his terminal SNP is
downstream from it. He can't NOT have it, even though his results were
'maybe'.

This highlights how valuable Goff's SNP pack results were to our part
of the tree. They really verified two more haplogroups - BY11573 (the
first positive result after three 'maybe' results) and BY11565 (the
second positive result with Merrick).

Hopefully that helps.

Jared

On Thu, Feb 2, 2017 at 7:16 AM, Joel Hartley <joel@...> wrote:
Does anyone know why I have a 0 SNP difference to Thomas and Bennett and a 2
SNP difference to Merrick on the Big Y?

Jared Smith
 

To add a some additional thoughts on this...

- You can see the four SNP test result states in Alex's mutations
matrix at the Big Tree.

- How do we know Thomas and Bennett are BY11573 if their results are
'maybe'? Because it would be incredibly unlikely that it's mere chance
that they both show this particular mutation at this exact location
that also aligns with a proven SNP. FTDNA, however, is super
conservative about making such assumptions.

- While FTDNA does not report 'maybe' results for Big-Y, it does for
SNP Packs. It shows these with an asterisk and describes them as "no
calls". My SNP results show BY4028*, for example. Even though this SNP
was a 'maybe' test result, because my terminal SNP is downstream from
it, I know I have it.

- FTDNA uses some unknown formula or method to sometimes define 'solo'
terminal SNPs - when only one person has tested positive for it. For
example, Pillsbury shows terminal SNP of BY13850 even though he's the
only one to have ever tested positive for it. Hays (N28178) similarly
is alone with BY13845. On the other hand, Joel Hartley shows terminal
SNP of Z17911, even though he alone has the A11130 SNP. I'm not sure
how they determine which solo SNPs are worthy of 'terminal' status. I
generally use FTDNA's determination in marking the haplogroups of my
tree - http://dna.smithplanet.com/media/Z16357-SNP-Tree.pdf - as
verified or theoretical.

- Remember the term "terminal SNP" is a misnomer - it really means
"temporary terminal SNP" - it's the last one we can reasonably
verify... for now.

Jared

On Thu, Feb 2, 2017 at 7:25 PM, Jared Smith <jared@...> wrote:
There are really four levels of reporting for each SNP: positive,
negative, maybe, and no coverage.

The 'maybe' results (this is my terminology, not FTDNA's) are markers
where you show the SNP in your raw results, but it was in a
questionable read area of the test. This means you probably have the
SNP, but FTDNA takes a very conservative approach and does not report
these. If additional people on your branch get 'maybe' results for
that same SNP, the more likely it is a valid SNP for that haplogroup.
A positive test for that SNP verifies it as a good one and (usually)
establishes it on the tree.

No coverage means the test didn't read in this area, so you can't
really know from that test alone. If you do, however, test positive
for a downstream SNP, then you'll know you also have all upstream
SNPs, even if your test results show 'maybe' or no coverage results
for them.

My tree and FTDNA's tree has Merrick two branches downstream (BY11573
and a terminal SNP of BY11565), from you and I who are at Z17911. So
this is the 2 SNP differences.

But Thomas and Bennett also have BY11573, so this means they should
show a 1 SNP difference to you, right? The answer would be yes, except
that Merrick, Thomas, and Bennett all were 'maybe' results for
BY11573, so FTDNA doesn't count these. You'll see that Thomas and
Bennett still show terminal SNP at FTDNA of Z17911, not BY11573.

So why does Merrick get credit for BY11573 when his 'maybe' result is
the same as Thomas and Bennett? Because we know BY11573 is a valid SNP
because of Goff's positive result for it. This established its
definitive location on the tree. While Thomas and Bennett don't get
credit for it because of their 'maybe' results (they show 0 SNP
differences to you), Merrick does because his terminal SNP is
downstream from it. He can't NOT have it, even though his results were
'maybe'.

This highlights how valuable Goff's SNP pack results were to our part
of the tree. They really verified two more haplogroups - BY11573 (the
first positive result after three 'maybe' results) and BY11565 (the
second positive result with Merrick).

Hopefully that helps.

Jared


On Thu, Feb 2, 2017 at 7:16 AM, Joel Hartley <joel@...> wrote:
Does anyone know why I have a 0 SNP difference to Thomas and Bennett and a 2
SNP difference to Merrick on the Big Y?

Joel Hartley
 

Here are the two SNPs that the Big Y shows as being different between me and Merrick:

CTS3563 CTS11841

According to the Big Tree website:

CTS3563 is 15022900-G-A

That shows up as a unique mutation for Merrick. So I wouldn't think that if Merrick has this as a unique mutation that that would count as a one SNP difference. I don't know much about CTS11841. Apparently I have that one and Merrick doesn't. I have also read that it is unreliable, so I'm not sure why this would be listed as a difference between me and anyone.

Joel


Jared Smith
 

Then scratch what I posted before - though this is the logic used for
positioning on the tree. I recall now that I had written earlier about
these 2 SNPs.

These are both known SNPs, but for totally different haplogroups. They
are in poor coverage regions on your tests, so I think they are either
misreads or they are private SNPs that just happen to coincide with
the other known SNPs. It seems FTDNA has identified them as
differences for you because they were in some database somewhere at
the time the results were processed.

CTS3563 is an SNP for the E haplogroup (search for CTS3563 at
http://isogg.org/tree/ISOGG_HapgrpE.html). Alex has it highlighted
pink on Merrick's results which means it's on the edge of a coverage
region.

CTS11841 is very similar. This is C>T at position 23311208. This is an
I haplogroup SNP in the ISOGG list. This is one that you have that
Merrick doesn't. This mutation isn't listed by Alex for you, probably
because it is on the very edge of a coverage region - so probably a
misread for you.

CTS11841 should also show as a difference between you and Bennett
(he's negative for it). But it is a 'maybe' for some of the others on
our branch (Thomas, one of the Hays men, etc.). This reinforces that
it's in a poor read area. I suspect that FTDNA dropped this one from
consideration between the time your results were processed and
Bennett's were, so that's why it's not showing for you two... or
something.

This is what differentiates Alex's analysis from FTDNA's tools - Alex
takes the time to analyze these things to weed out such anomalies and
questionable reads, and he look for possibilities (especially between
multiple men) that don't fit within FTDNA's automated processes. Rumor
has it some new SNP tools will be coming to FTDNA soon - their current
tools seem to be rather lacking.

Jared

On Fri, Feb 3, 2017 at 4:46 AM, Joel Hartley <joel@...> wrote:
Here are the two SNPs that the Big Y shows as being different between me and
Merrick:

CTS3563 CTS11841

According to the Big Tree website:

CTS3563 is 15022900-G-A

That shows up as a unique mutation for Merrick. So I wouldn't think that if
Merrick has this as a unique mutation that that would count as a one SNP
difference. I don't know much about CTS11841. Apparently I have that one and
Merrick doesn't. I have also read that it is unreliable, so I'm not sure why
this would be listed as a difference between me and anyone.

Joel


Joel Hartley
 

Thanks Jared,

I guess that the FTDNA algorithms work most of the time - not so well in this case. It seems like they should have some exceptions for SNPs that are in other Haplogroups.

Joel

-----Original Message-----
From: Z16357@groups.io [mailto:Z16357@groups.io] On Behalf Of Jared Smith
Sent: Friday, February 3, 2017 10:19 AM
To: Z16357@groups.io
Subject: Re: [Z16357] Z17911 BigY

Then scratch what I posted before - though this is the logic used for positioning on the tree. I recall now that I had written earlier about these 2 SNPs.

These are both known SNPs, but for totally different haplogroups. They are in poor coverage regions on your tests, so I think they are either misreads or they are private SNPs that just happen to coincide with the other known SNPs. It seems FTDNA has identified them as differences for you because they were in some database somewhere at the time the results were processed.

CTS3563 is an SNP for the E haplogroup (search for CTS3563 at http://isogg.org/tree/ISOGG_HapgrpE.html). Alex has it highlighted pink on Merrick's results which means it's on the edge of a coverage region.

CTS11841 is very similar. This is C>T at position 23311208. This is an I haplogroup SNP in the ISOGG list. This is one that you have that Merrick doesn't. This mutation isn't listed by Alex for you, probably because it is on the very edge of a coverage region - so probably a misread for you.

CTS11841 should also show as a difference between you and Bennett (he's negative for it). But it is a 'maybe' for some of the others on our branch (Thomas, one of the Hays men, etc.). This reinforces that it's in a poor read area. I suspect that FTDNA dropped this one from consideration between the time your results were processed and Bennett's were, so that's why it's not showing for you two... or something.

This is what differentiates Alex's analysis from FTDNA's tools - Alex takes the time to analyze these things to weed out such anomalies and questionable reads, and he look for possibilities (especially between multiple men) that don't fit within FTDNA's automated processes. Rumor has it some new SNP tools will be coming to FTDNA soon - their current tools seem to be rather lacking.

Jared


On Fri, Feb 3, 2017 at 4:46 AM, Joel Hartley <joel@...> wrote:
Here are the two SNPs that the Big Y shows as being different between
me and
Merrick:

CTS3563 CTS11841

According to the Big Tree website:

CTS3563 is 15022900-G-A

That shows up as a unique mutation for Merrick. So I wouldn't think
that if Merrick has this as a unique mutation that that would count as
a one SNP difference. I don't know much about CTS11841. Apparently I
have that one and Merrick doesn't. I have also read that it is
unreliable, so I'm not sure why this would be listed as a difference between me and anyone.

Joel