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TigerMW
04-15-2016, 03:41 PM
I was told today that FTDNA would start releasing the first of several SNP Packs for U152.

It is a very important period once we see what the packs are and they are posted in the Advanced Tests menu (select SNP Pack and click on the name of the pack for SNP details). The reason there is some urgency now is that FTDNA has been able to do last minute adds of SNPs in the past. Once they submit the first run of orders to their lab for processing, the late adds are closed off and we are left waiting until a V2/update (months from now).

Please keep an eye on the Advanced Tests. I think this will be a series of packs and it will be obvious what's coming in the future as there will be holes or lack of coverage of some big branches in the first pack(s) of the series. They do intend to have full coverage of U152.

I've not watched the haplotree for U152 lately, but I've heard on other forums of people getting haplogroup labels. That was probably an indicator that the packs were getting ready to be released. Getting FTDNA to update their haplotree has been a two steps forward, one back, two forward, one back kind of thing. This takes time.

razyn
04-15-2016, 03:49 PM
Are they doing any sort of reality check about ZZ11? It's not on the DF27 pack. Seems to me that would be a fairly straightforward way of moving toward a broader acceptance (or finding contrary evidence, if any) of Alex's suggestion that U152 and DF27 are brother clades.

TigerMW
04-15-2016, 04:27 PM
Are they doing any sort of reality check about ZZ11? It's not on the DF27 pack. Seems to me that would be a fairly straightforward way of moving toward a broader acceptance (or finding contrary evidence, if any) of Alex's suggestion that U152 and DF27 are brother clades.
Z11 is really almost a R1b-P312 Pack kind of thing. It should be there, right?

lgmayka
04-15-2016, 05:18 PM
The reason there is some urgency now is that FTDNA has been able to do last minute adds of SNPs in the past. Once they submit the first run of orders to their lab for processing, the late adds are closed off and we are left waiting until a V2/update (months from now).
I see absolutely no coverage of the FGC11577 clade (https://yfull.com/tree/R-FGC11577/) in the R-L2 SNP Pack.

lgmayka
04-15-2016, 05:22 PM
The reason there is some urgency now is that FTDNA has been able to do last minute adds of SNPs in the past. Once they submit the first run of orders to their lab for processing, the late adds are closed off and we are left waiting until a V2/update (months from now).
I see no coverage of the Y18894 clade (https://yfull.com/tree/R-Y18894/) in the R-L2 SNP Pack.

Is it possible that the designer of the R-L2 SNP Pack never checked YFull's haplotree?

Kwheaton
04-15-2016, 06:02 PM
Can someone post a list of what is included? I am not seeing a list.

TigerMW
04-15-2016, 06:10 PM
Can someone post a list of what is included? I am not seeing a list.
Here it is. You have to go to your myFTDNA account, click on the blue "Upgrade" at the top and then click on the blue "Buy Now" in the "Advanced Tests" box. On the "Select a Product" screen, select "SNP Pack" and then a list will pop up. Click on any pack to see what's in it.

Here is what it has:
SNP Pack R1b-L2 SNP Pack
Includes the following SNPs on the haplotree:
U152, L2, Z49, Z367, L196, PF7610, CTS10009, CTS3080, CTS5689, A6454, BY2823, DF110, FGC10516, FGC22501, FGC5301, FGC5344, L408, PF6658, S1567, DF103, FGC14641, L199, FGC22538, FGC22516, FGC22528, FGC22533, FGC22500, FGC22503, FGC22512, FGC22513, A1704, A1706, A1717, A1722, A6455, BY1020, BY1145, BY2381, BY2825, BY2826, BY3477, BY3478, BY3479, BY3480, BY3481, BY3482, BY3483, BY3484, BY3485, BY3486, BY3490, BY3491, BY3492, BY3493, BY3496, BY3497, BY3501, BY3503, BY3504, BY3505, BY3506, BY3507, BY3508, BY3509, BY3510, BY3512, BY3513, BY3514, BY771, BY806, BY831, FGC13617, FGC32882, FGC36273, FGC4166, FGC4177, FGC4183, FGC4193, FGC4213, FGC5303, FGC5306, FGC5308, FGC8154, FGC8158, FGC8178, L409, PF7609, PH3790, PR5365, S1555, S1561, S1566, S1569, S1570, S1573, S18462, Y11667, Y11931, Y11932, Y11933, Y3960, Y3961, Y3964, Y6763, Z7054

Includes the following SNPs that are NOT on the haplotree:
BY2895, FGC13620, FGC5338, FGC5345, FGC5356, BY2824, BY3487, BY3489, BY3498, BY3499, BY3500, BY3502, BY3511, FGC10525, FGC10536, FGC10543, FGC13619, FGC13621, FGC13623, FGC29428, FGC29470, FGC4220, PF7599, PF7603, PF7604, PF7605, Y11232

This is not an all encompassing L2 Pack. It is more of a L2 top and misc branches pack. I'll have to pull out my notes and go the U152 tree.

MitchellSince1893
04-15-2016, 08:56 PM
Here it is. You have to go to your myFTDNA account, click on the blue "Upgrade" at the top and then click on the blue "Buy Now" in the "Advanced Tests" box. On the "Select a Product" screen, select "SNP Pack" and then a list will pop up. Click on any pack to see what's in it.

Here is what it has:
SNP Pack R1b-L2 SNP Pack
Includes the following SNPs on the haplotree:
U152, L2, Z49, Z367, L196, PF7610, CTS10009, CTS3080, CTS5689, A6454, BY2823, DF110, FGC10516, FGC22501, FGC5301, FGC5344, L408, PF6658, S1567, DF103, FGC14641, L199, FGC22538, FGC22516, FGC22528, FGC22533, FGC22500, FGC22503, FGC22512, FGC22513, A1704, A1706, A1717, A1722, A6455, BY1020, BY1145, BY2381, BY2825, BY2826, BY3477, BY3478, BY3479, BY3480, BY3481, BY3482, BY3483, BY3484, BY3485, BY3486, BY3490, BY3491, BY3492, BY3493, BY3496, BY3497, BY3501, BY3503, BY3504, BY3505, BY3506, BY3507, BY3508, BY3509, BY3510, BY3512, BY3513, BY3514, BY771, BY806, BY831, FGC13617, FGC32882, FGC36273, FGC4166, FGC4177, FGC4183, FGC4193, FGC4213, FGC5303, FGC5306, FGC5308, FGC8154, FGC8158, FGC8178, L409, PF7609, PH3790, PR5365, S1555, S1561, S1566, S1569, S1570, S1573, S18462, Y11667, Y11931, Y11932, Y11933, Y3960, Y3961, Y3964, Y6763, Z7054

Includes the following SNPs that are NOT on the haplotree:
BY2895, FGC13620, FGC5338, FGC5345, FGC5356, BY2824, BY3487, BY3489, BY3498, BY3499, BY3500, BY3502, BY3511, FGC10525, FGC10536, FGC10543, FGC13619, FGC13621, FGC13623, FGC29428, FGC29470, FGC4220, PF7599, PF7603, PF7604, PF7605, Y11232

This is not an all encompassing L2 Pack. It is more of a L2 top and misc branches pack. I'll have to pull out my notes and go the U152 tree.

This will be really disapointing if there is no Z49 SNP pack to follow.

As it is there is not one SNP test for any of the subclades of Z49, the largest branch of L2.

No Z142. S8183, F2083 or their subclades.
Without a separate Z49 SNP pack that's a big oversight/makes no sense. Over 130 SNPs selected, yet they don't test any, 1 level down from the largest L2 branch?

Thus I gotta hope/believe there is a separate Z49 SNP pack right behind this one. If so, then I retract my criticism. Otherwise I have to question the choice of SNPs.

Osiris
04-15-2016, 09:07 PM
My little subgroup BY3493 is there so yay for me. One of the many little groups hanging off of L2. Since I know of no male cousin lines between 300 years ago and 5000 years ago hopefully this shakes some out for me. Of course the only way to test the 30 or so SNPs that cropped up in those hundreds of generations is to do a Big Y or Y Elite. We'll see if this helps drive people to those solutions.

TigerMW
04-15-2016, 09:48 PM
My little subgroup BY3493 is there so yay for me. One of the many little groups hanging off of L2. Since I know of no male cousin lines between 300 years ago and 5000 years ago hopefully this shakes some out for me. Of course the only way to test the 30 or so SNPs that cropped up in those hundreds of generations is to do a Big Y or Y Elite. We'll see if this helps drive people to those solutions.
I still haven't had a chance to pull this up, but this makes sense. I think this is the L2 "top-layer" and "misc subclades" SNP Pack. As we will see, it is very important that the M343 Backbone Pack has pointer SNPs into the pack series so people don't have to go through three steps... just two, the Backbone and then one of the U152 series. Hopefully, this was planned out and executed correctly. I need to check what's in the M343 Backbone pack.

TigerMW
04-15-2016, 09:52 PM
...
Without a separate Z49 SNP pack that's a big oversight/makes no sense. Over 130 SNPs selected, yet they don't test any, 1 level down from the largest L2 branch?

Because they want to be able to jump directly to a Z49 pack from the M343 Backbone Pack. The customer won't have to order three packs, just the Backbone and then the specialized one for Z49.

MitchellSince1893
04-15-2016, 10:00 PM
Because they want to be able to jump directly to a Z49 pack from the M343 Backbone Pack. The customer won't have to order three packs, just the Backbone and then the specialized one for Z49.

That was what I surmised/hoped.

So you are confirming there is indeed a Z49 SNP pack?

lgmayka
04-15-2016, 11:18 PM
The customer won't have to order three packs, just the Backbone and then the specialized one for Z49.
Of course, the many people who ordered the Deep Clade-R back in 2009 and got a result of L2+ L20- may end up ordering two more SNP packs (first L2, then possibly Z49).

A.Morup
04-16-2016, 05:45 AM
Being Z367 (from the R343 backbone pack), is this new pack meaningful for me, or should I start saving up for a Big Y in the name of science?
And will a Big Y also give me at least the same STR's as Y111 (I'm at Y37 now)?

Thanks

emmental
04-16-2016, 01:03 PM
Are there any plans for a Z36 pack?

If so, would they consider adding SNPs not yet found through Big Y. I have done FGC Elite 1.0 and share 26 SNPs with a 1KG person. Another surname matches at least 6 of the 26 (FGC6420, 6421, 6423, 6424, 6430, 6434); and a third surname matches at least 3 of the 26 (FGC6421, 6423,6424). Both of these men confirmed this through YSEQ.

I still have not been able to break down the group of 26 SNPs with a mix of positive and negative results.

Kwheaton
04-16-2016, 06:46 PM
For anyone interested The L2 SNP pack has some interesting but rather random subclades of FGC22501
Includes FGC22501
FGC22538, FGC22516, FGC22528, FGC22533, FGC22500, Broad based group which is shared by about 15 surnames and many countries of origin.
FGC22503, FGC22512, FGC22513 WHEATON MALLENBY

They did not include the SNPS shared with WHIFFING (England), LAGERBERG (Sweden from Germany long ago) and 6Driff22 (Roman Age York)which I really think these would make a lot of sense. Since they are found in one ancient and two modern samples.
7866684 (A/G), 14287006 (C/A), 133294319 (C/T)

emmental
04-17-2016, 01:07 AM
Are there any plans for a Z36 pack?

If so, would they consider adding SNPs not yet found through Big Y. I have done FGC Elite 1.0 and share 26 SNPs with a 1KG person. Another surname matches at least 6 of the 26 (FGC6420, 6421, 6423, 6424, 6430, 6434); and a third surname matches at least 3 of the 26 (FGC6421, 6423,6424). Both of these men confirmed this through YSEQ.

I still have not been able to break down the group of 26 SNPs with a mix of positive and negative results.


I guess not.

razyn
04-17-2016, 10:06 PM
Z11 [i.e. ZZ11] is really almost a R1b-P312 Pack kind of thing. It should be there, right?
It should IMO be in the U152 and the DF27 Packs, to create a stronger body of evidence less expensively than with BigY tests. I have yet to see any result hit the DF27 project from a P312 Pack; so I question either its popularity or its usefulness (whichever is causing the complete dearth of reported DF27 results), for addressing the ZZ11 question I raised in my original comment here.

And to get ZZ11 into the U152 Pack, I gather you have a window closing Wednesday.

The U152 project at FTDNA has 1655 members and the DF27 project has 1467, as of today. One of the several ways in which they are looking more like brothers now than formerly -- in part because U152 had been discovered about seven years earlier.

TigerMW
04-18-2016, 01:05 AM
It should IMO be in the U152 and the DF27 Packs, to create a stronger body of evidence less expensively than with BigY tests. I have yet to see any result hit the DF27 project from a P312 Pack; so I question either its popularity or its usefulness (whichever is causing the complete dearth of reported DF27 results), for addressing the ZZ11 question I raised in my original comment here.

And to get ZZ11 into the U152 Pack, I gather you have a window closing Wednesday.

The U152 project at FTDNA has 1655 members and the DF27 project has 1467, as of today. One of the several ways in which they are looking more like brothers now than formerly -- in part because U152 had been discovered about seven years earlier.

We have had DF27+ people come from the M343 Pack as you know. I think the P312 pack is almost more of a P312*, DF19, DF99, L238 pack. The top layer of the other branches are just there for those old R-P312 testers who haven't moved forward yet. It doesn't look like there are many of those around who want to advance.

Do you question that Z11 is ancestral to both U152 and DF27? What are we trying to prove to who? If I was writing an academic paper I would understand the importance but to U152 people interested in genetic genealogy it may not be that valuable.
However, we are jumping the gun a bit anyway. The U152 top-layer pack has not been released.

TigerMW
04-18-2016, 04:21 PM
Are there any plans for a Z36 pack? Yes.


If so, would they consider adding SNPs not yet found through Big Y. I have done FGC Elite 1.0 and share 26 SNPs with a 1KG person. Another surname matches at least 6 of the 26 (FGC6420, 6421, 6423, 6424, 6430, 6434); and a third surname matches at least 3 of the 26 (FGC6421, 6423,6424). Both of these men confirmed this through YSEQ. They can add them. I don't know what's in a future Z36 pack. I can ask but I don't see FGC6420 on a draft tree. What is the branch it hangs under?

TigerMW
04-18-2016, 04:44 PM
The BY named SNPs above BY3000 may not be in YBrowse. I asked for the details on the newer SNPs last week. Here is what I have for details on the BY SNPs in the R1b-L2 SNP top-layer and misc. subclades Pack.

BY1020 13803706-A-T
BY1145 15078369-A-G
BY2381 25729973-T-
BY2823 07664023-C-T
BY2824 14144251-C-G
BY2825 14311608-G-A
BY2826 21916166-A-G
BY2895 06182427-C-G
BY3477 08316544-T-C
BY3478 08389832-C-T
BY3479 08427596-A-G
BY3480 08447979-A-G
BY3481 08512043-A-G
BY3482 08515713-G-A
BY3483 08536951-G-A
BY3484 08557048-G-A
BY3485 08600829-A-G
BY3486 08878221-C-G
BY3487 14287006-C-A
BY3489 15393864-C-G
BY3490 15929351-T-C
BY3491 18759999-A-G
BY3492 19215602-A-T
BY3493 21391079-C-T
BY3496 02783738-A-C
BY3497 02889012-G-C
BY3498 03134021-A-C
BY3499 03780174-T-A
BY3500 04829349-C-T
BY3501 06643898-A-G
BY3502 06711888-G-A
BY3503 06810920-C-T
BY3504 06812286-A-G
BY3505 07147847-A-G
BY3506 07283648-T-C
BY3507 07411270-T-C
BY3508 07426675-A-C
BY3509 07543417-A-T
BY3510 07553614-T-C
BY3511 07722917-CTA-CA
BY3512 07902196-T-A
BY3513 08093829-A-G
BY3514 08117769-G-C
BY771 08203243-C-G
BY806 08440744-G-A
BY831 08639381-C-T

razyn
04-18-2016, 04:52 PM
Do you question that Z11 is ancestral to both U152 and DF27? What are we trying to prove to who?
No, I'm among the few, the proud, the people who think Alex is right. And YFull, ISOGG, that part of the haplotree at FTDNA, all the academic papers yet in print, Eupedia maps, etc. (whoever fails so far to mention ZZ11, or otherwise to note that DF27 and U152 share an ancestor) are a little remiss. Maybe if some routine test results started showing it, ZZ11 would be more generally noticed.

TigerMW
04-18-2016, 05:07 PM
Here is a summary of what I think the U152 SNP pack series will be - seven packs providing complete coverage. They have been in the works since late last year.

U152 top layer and misc subclades

. L2 top layer and L2 misc subclades

. . Z367 subclade and downstream only

. . Z49 subclade and downstream only

. Z36 and downstream only

. Z43(~Z56) subclade and downstream only

. Z192(~PF6658,Z193) and downstream only

You want to test for the SNP Pack that is most specialized for your subclade, if you know what it is. If you don't know what you are other than U152+, then the R1b-U152 SNP Pack is the right one to start with. It's not out yet, but it must be coming soon. If your terminal haplogroup (public, documented, most youthful) turns out to be one of the misc. subclades of U152 then you are done after taking the SNP packs as you have reached your terminal haplogroup.

We can look at the tree information from the R1b U152 project results page.
https://www.familytreedna.com/groups/r-1b-u152/about/results

A274, A275 and Z5805 are examples of SNPs that should be in the future R1b-U152 SNP Pack. If you have one of those and take the U152 pack you will be done as you've reached your terminal haplogroup.

The larger subclades that are named by a "lead with" SNP (i.e. Z367, Z49, etc.) should have those "lead with" SNPs in the R1b-U152 SNP Pack as well as the R1b-M343 Backbone Pack. Having these SNPs included in the U152 pack is like saying it has pointers or bridges to the more specialized packs. The same would be true for the R1b-L2 SNP Pack just released. It has the bridge SNPs Z49 and Z367.

This brand new R1b-L2 SNP Pack is a little bit like the U152 pack in that the L2 pack also has a top layer with bridge SNPs. Z367 and Z49, since they are downstream of L2 but have their own specialized packs, are included as bridge SNPs in the L2 pack. That way if you know you are L2+ but are not sure where you fit in L2 you can safely take the R1b-L2 SNP Pack test.

Here are examples of people who should NOT consider the R1b-L2 SNP Pack:

1. Already tested L2-

2. Already tested Z36+, Z43+, Z56+, Z192+, PF6658+ (since the tree shows they must be L2-)

3. Already tested Z367+ or anything downstream, like L20+ (since a more specialized pack is expected, the R1b-Z367 SNP Pack)

4. Already tested Z49+ or anything downstream, like Z142+ (since a more specialized pack is expected - the R1b-Z49 SNP Pack)

5. Already tested Big Y unless you have a specific reason that are you comfortable with.

If the situations one through five don't apply to you and you are L2+ or match an L2+ person closely you should consider the R1b-L2 SNP Pack. This could include people who are L2+ and lightly tested downstream. For instance, if you think you are A6454+ but don't know much beyond that you will see there are eight (8) SNPs downstream of the A6454 subclade in the R1b-L2 SNP Pack. The introductory price is $99 so this a good time to blast through those SNPs.

TigerMW
04-18-2016, 05:12 PM
No, I'm among the few, the proud, the people who think Alex is right. And YFull, ISOGG, that part of the haplotree at FTDNA, all the academic papers yet in print, Eupedia maps, etc. (whoever fails so far to mention ZZ11, or otherwise to note that DF27 and U152 share an ancestor) are a little remiss. Maybe if some routine test results started showing it, ZZ11 would be more generally noticed.
I agree but the trade-off is from a U152 genetic genealogy advocate's point of view. The U152 pack will be bursting with misc. subclades and could have other pursuits like near private SNPs and busting a block or two of phylogenetic equivalents inside of the U152 subclade. They all know they are ZZ11+ anyway.

razyn
04-18-2016, 05:56 PM
I agree but the trade-off is from a U152 genetic genealogy advocate's point of view. The U152 pack will be bursting with misc. subclades and could have other pursuits like near private SNPs and busting a block or two of phylogenetic equivalents inside of the U152 subclade.
Then I hope you can pick the couple dozen most important, NextGen-tested U152 families (to stay under the 160 SNP limit), by Wednesday. Personally, I think getting the phylogeny right (and published) is more worthwhile.


They all know they are ZZ11+ anyway.
I seriously doubt that.

TigerMW
04-18-2016, 07:03 PM
For anyone interested The L2 SNP pack has some interesting but rather random subclades of FGC22501
Includes FGC22501
FGC22538, FGC22516, FGC22528, FGC22533, FGC22500, Broad based group which is shared by about 15 surnames and many countries of origin.
FGC22503, FGC22512, FGC22513 WHEATON MALLENBY

They did not include the SNPS shared with WHIFFING (England), LAGERBERG (Sweden from Germany long ago) and 6Driff22 (Roman Age York)which I really think these would make a lot of sense. Since they are found in one ancient and two modern samples.
7866684 (A/G), 14287006 (C/A), 133294319 (C/T)
This branch is covered by second of those three SNPs:
BY3487 14287006-C-A
It is reportedly part of a Big Y "gold" region as well as a CombBed region. This may have been why it was selected.

Are there any branches of FGC2250 not covered by any SNPs?

A.Morup
04-18-2016, 08:30 PM
Thanks Mikewww for a great write up on the various potential future SNP packs - hope you are right!

emmental
04-18-2016, 08:44 PM
Yes.

They can add them. I don't know what's in a future Z36 pack. I can ask but I don't see FGC6420 on a draft tree. What is the branch it hangs under?

On "The Big Tree" it is listed as the FGC6424 branch (Mosimann and NA12144) under Z36. On the YFull tree it is listed as the Y3577(FGC6418) branch under Z36.

TigerMW
04-18-2016, 08:54 PM
Then I hope you can pick the couple dozen most important, NextGen-tested U152 families (to stay under the 160 SNP limit), by Wednesday. Personally, I think getting the phylogeny right (and published) is more worthwhile.
I agree, but it might be that genetic genealogists within U152 are more interested in the phylogeny below U152 than above it.


They all know they are ZZ11+ anyway.

I seriously doubt that.
I misstated that. We (not they) know they are ZZ11+ and they could know if they wanted too. They may not care.

There are many, many SNPs in the M269 phylogenetic block that could use better documentation. Not all trees are consistent in how they treat them. Where do upstream research SNP additions end? and who pays?

TigerMW
04-18-2016, 08:59 PM
Thanks Mikewww for a great write up on the various potential future SNP packs - hope you are right!Thank you.

I don't want to make commitments for other people, i.e. FTDNA, but it is important for testers to know what is and isn't, at least generally. The knowledge that there is a series of packs is important. I do not want to see a high probability Z49+ person take the R1b-L2 SNP Pack test when the R1b-Z49 SNP Pack is just around the corner (same for Z367).

I don't think I'm wrong on what packs. I know what they are working on anyway. When is another question but they are behind already so it should be soon.

TigerMW
04-18-2016, 09:55 PM
.....
Here are examples of people who should NOT consider the R1b-L2 SNP Pack:

1. Already tested L2-
2. Already tested Z36+, Z43+, Z56+, Z192+, PF6658+ (since the tree shows they must be L2-)
3. Already tested Z367+ or anything downstream, like L20+ (since a more specialized pack is expected, the R1b-Z367 SNP Pack)
4. Already tested Z49+ or anything downstream, like Z142+ (since a more specialized pack is expected - the R1b-Z49 SNP Pack)
5. Already tested Big Y unless you have a specific reason that are you comfortable with.

If the situations one through five don't apply to you and you are L2+ or match an L2+ person closely you should consider the R1b-L2 SNP Pack. This could include people who are L2+ and lightly tested downstream. For instance, if you think you are A6454+ but don't know much beyond that you will see there are eight (8) SNPs downstream of the A6454 subclade in the R1b-L2 SNP Pack. The introductory price is $99 so this a good time to blast through those SNPs.

The R1b-L2 SNP Pack covers the "top-layer" of L2 branching plus the "misc. subclades". However, the "misc." list appears long and well covered. The only two branches not covered by downstream SNPs are Z367 and Z49. There is a reason for this. Both of these SNPs are included in the L2 pack as bridge pointers to specialized packs for Z367 and Z49. You could call this the R1b-L2 (xZ367 xZ49) Pack.

In alphabetical orders here are SNPs that mark each of the nineteen (19) branches of L2, at least according to what FTDNA has.

A6454
BY1145
BY2823
BY2895
CTS5689
DF103
DF110
FGC10543
FGC13620
FGC14641
FGC22501
FGC5301
FGC5338
L199
PF7609
S1555
Y11667
Z367
Z49

Seventeen (17) of these nineteen branches have downstream branching covered in the L2 pack. This how the pack gets to over the 120-125 odd SNPs in the pack, by covering the downstream branching.

As mentioned, Z367 and Z49 are stubs in the L2 pack as there will be specific packs for each of these two, with lots of SNPs in them.

Here https://dl.dropboxusercontent.com/u/17907527/R1b-L2-Pack.pdf is an .PDF outline tree of what's in the R1b-L2 SNP Pack with position number detail. As you can see, selected SNPs from phylogenetic equivalent blocks are included. In other haplogroups of R1b, we've found that phylogenetic equivalent blocks are busted from time to time to discover more layering in the branch. Testing multiple SNPs in a block also is a form of validation (cross-checking).

This is critical. If you see a key branch or SNP missing, please reply back ASAP. FTDNA has accepted late adds to the intoductory versions of a pack but we may have only a 24-36 hour window to submit late-adds. What's missing? I don't know if it is problematic but it looks like S18827 might mark a branch?

lgmayka
04-18-2016, 10:34 PM
This is critical. If you see a key branch or SNP missing, please reply back ASAP. FTDNA has accepted late adds to the intoductory versions of a pack but we may have only a 24-36 hour window to submit late-adds. What's missing? I don't know if it is problematic but it looks like S18827 might mark a branch?
I'll ask once again: Have you included the FGC11577 clade (https://yfull.com/tree/R-FGC11577/) which is directly under L2? It is on the official U152 tree. The two examples, Ukrainian and British, diverged 3000 years ago.

TigerMW
04-19-2016, 02:33 AM
I'll ask once again: Have you included the FGC11577 clade (https://yfull.com/tree/R-FGC11577/) which is directly under L2? It is on the official U152 tree. The two examples, Ukrainian and British, diverged 3000 years ago.
Good eyes, Lawrence. Thank you. I don't see it on the current list but need to doublecheck the use of BY SNPs. In any case, I'll request it.

TigerMW
04-19-2016, 02:36 AM
On "The Big Tree" it is listed as the FGC6424 branch (Mosimann and NA12144) under Z36. On the YFull tree it is listed as the Y3577(FGC6418) branch under Z36.
I haven't seen any final details on a Z36 SNP Pack, but yes, this branch (including both of these two SNPs) have been submitted (months ago.)

MitchellSince1893
04-19-2016, 03:38 AM
Here is a summary of what I think the U152 SNP pack series will be...

. . Z49 subclade and downstream only


Do you know when the Z49 SNP pack will be available for review?

TigerMW
04-19-2016, 02:45 PM
Do you know when the Z49 SNP pack will be available for review?
No, it's not at all under my control. As I mentioned before, only Lawrence was able to get me to predict a time-line (for DF27), which turned out to be credible. I just know they are working on it. I'll see if I can find anything else. What are critical SNPs that you want to make sure are included?

MitchellSince1893
04-19-2016, 03:42 PM
...What are critical SNPs that you want to make sure are included?
At least one of the following from this terminal branch:
-FGC12401/Y10984 (FGC12401 is FTDNA name for this terminal branch)
-FGC12402/Y10985
-FGC12403/Y9080 (Y9080 is Yfull's name for this terminal branch)
-FGC12404/Y10986
-FGC12405/Y4272

As FTDNA currently only shows FGC12401, FGC12402, and FGC12404, it's probably best to limit to these.

If limited to one then make it FGC12401.

jbarry6899
04-19-2016, 06:06 PM
What are critical SNPs that you want to make sure are included?

Probably goes without saying, but S8183 and Y4354, Y4355 and Y4356. If there is room, there are some downstream SNPs that currently are private or geographically restricted, but would be useful to explore: Y11179, Y13610, Y13860, Y17276, Y16875 and Y14088.

lgmayka
04-19-2016, 06:54 PM
What are critical SNPs that you want to make sure are included?
Please be sure that the R1b-Z49 SNP Pack includes the exotic Polish Y18894 clade (https://yfull.com/tree/R-Y18894/).

MitchellSince1893
04-19-2016, 07:26 PM
Richard Rocca hasn't posted much recently...maybe he's a CPA (tax season in the US)

But Mikwww says he's been involved.

I want to thank him for what he's doing behind the scenes...if he's involved then I have no worries the U152 SNP packs will be done right.

Kwheaton
04-19-2016, 08:32 PM
Mike,
I highly recommend adding at least one of the three SNPS that was identified in the 6DRif22 sample. We have a WHIFFING from the UK and Lagerberg From Sweden (origins from Germany) that match this York Roman age skeleton. I would expect this will be a major subdivision under FGC22501. I think its inclusion might build some interest in the test.

7866684 (A/G)
14287006 (C/A)
133294319(C/T)

Regards
Kelly

TigerMW
04-19-2016, 08:44 PM
Good eyes, Lawrence. Thank you. I don't see it on the current list but need to doublecheck the use of BY SNPs. In any case, I'll request it.
Okay, I went ahead and submitted over a dozen additional SNPs based on feedback and re-reviews of YFull, etc. I hope most of them get in. A few I'd already submitted so they may be problematic.

Kelly, see reply #26 below. I think 14287006 (C/A) is already covered.

I think the L2 top-layer and misc subclades (xZ367 xZ49) pack will be a pretty good pack.

I'll see what info we have for Z49 and Z367.

razyn
04-19-2016, 09:05 PM
It should IMO be in the U152 and the DF27 Packs, to create a stronger body of evidence less expensively than with BigY tests. I have yet to see any result hit the DF27 project from a P312 Pack; so I question either its popularity or its usefulness (whichever is causing the complete dearth of reported DF27 results), for addressing the ZZ11 question I raised in my original comment here.
I ran a filtered report of completed results, and find that I misspoke, here. The first part in boldface (above) is flat wrong; there are 14 guys with P312 pack results, although none got a DF27 from it (most got ZZ12_1+, a few some specific SNP below DF27 such as Z209) and one was in fact a U152 guy who joined us in error. The other boldface part is wrong too, but not in the sense I intended. They got some result with a recommendation for another test (DF27 SNP pack, or a specific SNP below ZZ12 that they ordered and then joined the DF27 project after its result came in). So, what I saw (or at least noticed) may have been the subsequent (DF27 SNP Pack, or whatever) result coming in.

Anyway, I'll yield the point that it's an issue that could, and really should, be dealt with at the P312 pack level. Or higher. However, it isn't being so dealt with; and ZZ11 needs to be tested somewhere, if the haplotree is ever supposed to reflect phylogenetic reality as we understand it.

In that regard, I notice that at present there are ten SNPs shown at the same level, immediately below P312: L21; L194 (a subclade of DF27 and probably ZZ12, see kit N2642); U152 (should be a level lower, under unrecognized ZZ11); DF19; L238; and DF99 (probably on the right level, but they shouldn't come between brothers U152 and DF27); DF27 (also should be under unrecognized ZZ11); Z29645 and Z30600 (both subclades of unrecognized ZZ37/ZZ38); and A9063, that appears actually to belong on that level.

That much room for improvement is evident without looking at FGC or YFull, and they're always turning up stuff, too.

TigerMW
04-19-2016, 09:56 PM
Probably goes without saying, but S8183 and Y4354, Y4355 and Y4356. If there is room, there are some downstream SNPs that currently are private or geographically restricted, but would be useful to explore: Y11179, Y13610, Y13860, Y17276, Y16875 and Y14088.
I can't find Y13860 in Z49. Do you have a link to a tree that shows this? It looks like it might be recurrent. I found the others.

TigerMW
04-19-2016, 09:58 PM
Please be sure that the R1b-Z49 SNP Pack includes the exotic Polish Y18894 clade (https://yfull.com/tree/R-Y18894/).
As far as the Z49 tree, I see this and will track it.

jbarry6899
04-19-2016, 10:00 PM
I can't find Y13860 in Z49. .

Sorry, typo! It's Y16860, right below S8183 in the YFull tree.

TigerMW
04-19-2016, 10:00 PM
At least one of the following from this terminal branch:
-FGC12401/Y10984 (FGC12401 is FTDNA name for this terminal branch)
-FGC12402/Y10985
-FGC12403/Y9080 (Y9080 is Yfull's name for this terminal branch)
-FGC12404/Y10986
-FGC12405/Y4272

As FTDNA currently only shows FGC12401, FGC12402, and FGC12404, it's probably best to limit to these.

If limited to one then make it FGC12401.
As far as Z49, yes, this FGC12401 branch should be included.

TigerMW
04-19-2016, 10:14 PM
Sorry, typo! It's Y16860, right below S8183 in the YFull tree.
Thanks. Rocca doesn't seem to track this one even though he has some that YFull thinks are equivalents, like Y16862. I do see it in the YFull tree for Z49. Y16860 doesn't look like a particularly good region but I'm not an expert on that stuff.

Kwheaton
04-19-2016, 10:50 PM
This branch is covered by second of those three SNPs:
BY3487 14287006-C-A
It is reportedly part of a Big Y "gold" region as well as a CombBed region. This may have been why it was selected.

Are there any branches of FGC2250 not covered by any SNPs?

Thanks Mike...I did not know it had been named! :) Yay!

Kelso
04-20-2016, 05:00 AM
. Z192(~PF6658,Z193) and downstream only

You want to test for the SNP Pack that is most specialized for your subclade, if you know what it is.

Mike,

Thanks for the hard work on keeping track of these new SNP packs.

You may not have looked at the "Z192(~PF6658,Z193) and downstream only" pack yet but if possible we would like a number of the SNPs under FGC5033 and then the next layer down a group under FGC5029. Not sure how many of these groups can be added but for us more the merrier.

Rich has a newer SNP 7717741(T/C) listed above FGC5033. Not sure if this one will work but it probably should be added. Thanks, Tim

edit: These SNPs are under PF6658+>Z193+>Z192- on Rich's U152 excel chart

TigerMW
04-20-2016, 01:43 PM
The best thing you can do to make sure your SNPs are known for packs (and I think panels too) is get on Alex Williamson's Big Tree. It's free, it's visual and it is easy to copy from. It's a real descendants tree type format rather than the crazy outline format where you have to try to look at the indentations.

The easy way to get on the tree is to download your Big Y raw results VCF zipped folder. Don't unzip it, just rename the file and upload it to the files section of the U152 yahoo group. It has free storage. The VCF zipped folder is small, unlike the BAM file, but it has a tremendous amount of relevant information (much that FTDNA filters out on your Y SNP page). You don't have to participate in the yahoo group to join. You can turn it on "no email/web viewing only" and forget about it. You can use a nickname and fake birthdate in the profile so you can be anonymous.
https://groups.yahoo.com/neo/groups/R1b-U152-Project/info
https://groups.yahoo.com/neo/groups/R1b-U152-Project/files

However, please rename the zipped VCF folder so we can list the kit# and MDKA surname (mark as unknown if need to). Here is the format that is consistent with the rest of P312.
L513_N54638_Walsh_BigY_RawData_20140616
This the major haplogroup (i.e. could be L2, Z192, Z56, etc.), kit #, MDKA surname and ending with the yyyymmdd date of the file.

I go back and forth looking at YFull, FGC, ISOGG and the U152 project trees, but the Big Tree is the easiest to read once you get used to it.
http://ytree.net/DisplayTree.php?blockID=28

If you can drill down on the branch boxes for details and look at subsets (subclades) of the bigger tree, i.e. Z49
http://ytree.net/DisplayTree.php?blockID=420&star=false

He already has 190 NGS results on the Big Tree, including the 1K Genomes public study results. He will take your BAM file links too and uses that for in-depth analysis and tie-breaking. However, don't underestimate the VCF zipped folders. They are an easy, quick start. Alex is an FGC elite tester so he can handle those results too, although I'm not familiar with how he receives those files.

What the heck! It's a second opinion and it's free.

This does not mean you shouldn't send your BAM files elsewhere. That's fine. I'm on the Big Tree and have both FGC and YFull interpretations. I do have to get my compatriot to do YFull so my youthful SNPs actually show up. Richard Rocca is a citizen-scientist so he's the main man in U152 land and you want to get him your data for sure. I think he uses CSV file some and takes BAM files but I'm not sure how he processes things. I nearly killed myself getting my line down to about 300-400 year-old SNP on to ISOGG and was able to get my 600-800 year-old SNPs into Geno 2 Next Gen.

I want people to know about my Y SNPs and folks out there to stumble upon them. It's hard telling what we will find out.


Mike,

Thanks for the hard work on keeping track of these new SNP packs.

You may not have looked at the "Z192(~PF6658,Z193) and downstream only" pack yet but if possible we would like a number of the SNPs under FGC5033 and then the next layer down a group under FGC5029. Not sure how many of these groups can be added but for us more the merrier.

Rich has a newer SNP 7717741(T/C) listed above FGC5033. Not sure if this one will work but it probably should be added. Thanks, Tim

edit: These SNPs are under PF6658+>Z193+>Z192- on Rich's U152 excel chart
Keslo, I tried to get both Z193 and PF6658 in the R1b-M343 Backbone SNP Pack. Z193 was rejected outright and PF6658 was tried in the pack but apparently was problematic. I think FTDNA is still trying on PF6658 but I'm not hopeful.

The net is that Z193+ Z192- subclades will not likely be in a Z192 SNP Pack. SNPs from this branching will have to be in the U152 top-layer and misc. subclades SNP pack.

P.S. I may be going over the top here but I'm proud of P312, very proud. I have multiple paternal lineages in my family (duh) and most of them appear to be P312. I want it to be the best documented, most studied, best understood haplogroup. In P312-land, Alex's Big Tree is like a national treasure.

TigerMW
04-20-2016, 02:15 PM
This branch is covered by second of those three SNPs:
BY3487 14287006-C-A .....

Thanks Mike...I did not know it had been named! :) Yay!

Since I'm on roll on this, let me extoll more virtues of the Big Tree. Here is the U152 section. You can click any box and drill down, but that's not what I want to you look at.
http://ytree.net/DisplayTree.php?blockID=28&star=false

Please note that there are the synonym names for the SNPs, not just one brand of name. Alex downloads YBrowse to pull in all of the synonyms he can. BY SNPs are problematic because FTDNA is slow at getting them to TK, or something. However, I ask FTDNA for the latest BY SNP position detail every few weeks and send them to Alex so he grafts them into the Big Tree too. He and I use (actually I copied him) the positionnum-anc-der format for unnamed SNPs but if you click an any branch box you can get all of the details anyway plus an assessment of the regions, i.e. palindromes, centromeres, etc.

TigerMW
04-20-2016, 04:19 PM
Are they doing any sort of reality check about ZZ11? It's not on the DF27 pack. Seems to me that would be a fairly straightforward way of moving toward a broader acceptance (or finding contrary evidence, if any) of Alex's suggestion that U152 and DF27 are brother clades.

Razyn and Gotten, I've created a new thread for this. I'll move these ZZ11 related posts over to this new thread tomorrow.
http://www.anthrogenica.com/showthread.php?6965-What-is-ZZ11-and-what-do-we-do-with-it

It is relevant to U152 but also to DF27 and maybe should be in the M343 Backbone. Anyway, I'm not proficient on these ZZ Y chromosome locations so let's talk about it over on the new thread.

razyn
04-20-2016, 04:31 PM
OK by me. I just posted about it on the R1b-YDNA Yahoo group, your current thread -- have a look. I'm going to root through the P312 SNP pack results of the guys in the DF27 project who had it, to see if that ZZ11 is actually showing up but just being ignored in the haplotree. (I can't look at the U152 guys.) If the test is just missing the SNP, that might be tweakable.

Armenis
04-22-2016, 10:22 AM
The BY named SNPs above BY3000 may not be in YBrowse. I asked for the details on the newer SNPs last week. Here is what I have for details on the BY SNPs in the R1b-L2 SNP top-layer and misc. subclades Pack.

BY1020 13803706-A-T
BY1145 15078369-A-G
BY2381 25729973-T-
BY2823 07664023-C-T
BY2824 14144251-C-G
BY2825 14311608-G-A
BY2826 21916166-A-G
BY2895 06182427-C-G
BY3477 08316544-T-C
BY3478 08389832-C-T
BY3479 08427596-A-G
BY3480 08447979-A-G
BY3481 08512043-A-G
BY3482 08515713-G-A
BY3483 08536951-G-A
BY3484 08557048-G-A
BY3485 08600829-A-G
BY3486 08878221-C-G
BY3487 14287006-C-A
BY3489 15393864-C-G
BY3490 15929351-T-C
BY3491 18759999-A-G
BY3492 19215602-A-T
BY3493 21391079-C-T
BY3496 02783738-A-C
BY3497 02889012-G-C
BY3498 03134021-A-C
BY3499 03780174-T-A
BY3500 04829349-C-T
BY3501 06643898-A-G
BY3502 06711888-G-A
BY3503 06810920-C-T
BY3504 06812286-A-G
BY3505 07147847-A-G
BY3506 07283648-T-C
BY3507 07411270-T-C
BY3508 07426675-A-C
BY3509 07543417-A-T
BY3510 07553614-T-C
BY3511 07722917-CTA-CA
BY3512 07902196-T-A
BY3513 08093829-A-G
BY3514 08117769-G-C
BY771 08203243-C-G
BY806 08440744-G-A
BY831 08639381-C-T

Any info or knowledge regarding BY4246+

I have seen this SNP in an individual who is L2>FGC13620+ (BY3485)

lamahorse
04-24-2016, 10:29 PM
We're down as U152 > Y17059 on ytree.net now. :)

R.Rocca
06-25-2016, 10:48 PM
Posted yesterday by Mikewww...


FTDNA put out some additional SNP packs for R1b-U152 subclades. The line-up now looks like:

R1b-U152 top-layer and misc subclades (bridges to the below)
R1b-Z43 (~Z56)

R1b-L2 (xZ367 xZ49) top-layer and misc subclades
R1b-Z367
R1b-Z49

I have not looked at these closely yet but I think this means there are two more packs come and then U152 will have coverage of all major branches.

TigerMW
06-27-2016, 09:03 PM
Any info or knowledge regarding BY4246+

I have seen this SNP in an individual who is L2>FGC13620+ (BY3485)

I submit a request to FTDNA (anyway can through the FTDNA web "contact" page) and get a list of the position details. They sent me this:

BY4246 23073902-A-T

emmental
08-30-2016, 05:11 PM
Any recent news of a Z36 SNP pack?

TigerMW
09-08-2016, 01:02 PM
The details from the FTDNA Orders/Advanced Tests/SNP Pack (select a product) web page shows the SNP list as posted in the Z36 news thread.

Here is my attempt to put that SNP list into an outline tree format with position numbers, synonyms, etc.
https://dl.dropboxusercontent.com/u/17907527/R1b-Z36-Pack.pdf

This is an urgent question - Is any branch missing?

I've got a request for Y19751 to be added, which is a subclade of Y16884. Anything else? We probably get one chance in the next 24-48 hours to add last minute SNPs.

I don't think Y16884 is actually in the pack, but I see t equivalent A8031 is

Please download this PDF file if you want it as I'll delete it in a week or two.

TigerMW
09-08-2016, 01:17 PM
Here is the current Pack coverage for R1b-U152 Subclades.

R1b-U152 top-layer and misc subclades (bridges to all the below)
R1b-Z36
R1b-Z43 (~Z56)
R1b-L2 (xZ367 xZ49) top-layer and misc subclades (bridges to the below)
R1b-Z367
R1b-Z49

I still see one gap. Z92 itself is in the U152 top-layer pack, but there is no coverage for Z92 subclades. If you know you are Z92, wait for that pack.