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JimT
04-04-2014, 06:32 PM
My FullGenomes haplogroupCompare report shows 53 new high-reliablity SNPs under DF27. 68 of the 69 other DF27+ men in the report share none of the new SNPs with me. One of the DF27+ men, HG00107 from the 1000 Genomes Project, shares 36 of the new SNPs. I've uploaded an excerpt from the report with the 53 new SNPs to:
https://drive.google.com/file/d/0BxkbmZJ7aYSYeWNUUlROTkEwV2c/edit?usp=sharing

I belong to the Rox2 subclade of DF27+, and HG00107 apparently does too, based on his STRs. Rox2 has gone from DF27* to having 36 new SNPs under DF27+. It will be interesting to see how many are synonymous and how many define new branches.

In addition to the 36 Rox2 SNPs, the spreadsheet contains my 13 private SNPs (highlighted in blue) and 4 that may or may not be private (highlighted in yellow).

Jim Turner

Webb
04-04-2014, 07:10 PM
Jim, that is sweet.

razyn
06-04-2014, 07:36 PM
I created a Rox2 group in the R1b-DF27 haplogroup project today. It's currently Group N, and a horrible dark olive color -- both may be changed, but I'm still busy with music stuff and had to get off the computer. I also moved JimT into that project, so he could be in it -- I think he's on the road or something. (The GAP tools won't let me remove him from a haplogroup project, but I can join him to one -- so I did.)

corner
06-04-2014, 09:34 PM
I created a Rox2 group in the R1b-DF27 haplogroup project today.
Good news, thanks. The recently identified subclade under DF27 that FGC11395 'Rox2' is positive for (and DF84 too) is Z2571, by the way, not DF2571.

razyn
06-04-2014, 09:52 PM
Oopsie. Guess I'll fix that stuff. But I copied that from Bob Dickinson's email to the DF27 Yahoo group, today...

OK, some corrections made, look at it again. Now it's pale yellow, not olive. And I must away.

corner
06-04-2014, 10:38 PM
OK, some corrections made, look at it again. Now it's pale yellow, not olive. And I must away.
Just one thing.. regarding Group N, Rox2 is negative for DF84, I could have phrased it better. DF84 is parallel with Rox2, both are under Z2571. Cheers.

razyn
06-05-2014, 08:29 AM
If you want to phrase it better, phrase it. I would care more if there actually were a DF84+ person in the project. It seems to me the only guys we have who currently want Z2571 explored are Rox2 guys (apparently quite a few of those), and I put that first so some of them might see it. Maybe a new subgroup Na, for DF84+ under the Z2571 group? And that Na also means N/A, vis a vis "Rox2" -- which AFAIK is not a SNP, per se.

I could also phrase that "tests available" part better, for group Uf -- but we have certain rules that prohibit (or at least inhibit) making actual sense, about that. The testing that is breaking down this phylogeny is for the most part from FGC -- I've just set up a place to look at the similar results because Bob requested one yesterday. We currently have a lot of balls in the air, as you know. And FTDNA is dancing on a tightrope with NatGeo. And I am too old to want to join the circus.

corner
06-05-2014, 10:45 AM
If you want to phrase it better, phrase it. I would care more if there actually were a DF84+ person in the project. It seems to me the only guys we have who currently want Z2571 explored are Rox2 guys (apparently quite a few of those), and I put that first so some of them might see it. Maybe a new subgroup Na, for DF84+ under the Z2571 group? And that Na also means N/A, vis a vis "Rox2" -- which AFAIK is not a SNP, per se.

I could also phrase that "tests available" part better, for group Uf -- but we have certain rules that prohibit (or at least inhibit) making actual sense, about that. The testing that is breaking down this phylogeny is for the most part from FGC -- I've just set up a place to look at the similar results because Bob requested one yesterday. We currently have a lot of balls in the air, as you know. And FTDNA is dancing on a tightrope with NatGeo. And I am too old to want to join the circus.
I meant I could have phrased my post #4, above, better. I understand the difficulties, thanks for tackling it.

Group N. at the DF27 Project has, 'N. Rox2 (R1b-P312>DF27>Z2571>FGC11395, FGC11397 or DF84) ' at the moment. It just needs 'or DF84' removing as Rox2 are DF84-.

DF84 and FGC11395 (aka 'Rox2') are parallel and both downstream of Z2571. Z2571 is downstream of DF27.

1934

The DF27>Z2571>DF84 results are from the 1000 Genomes Project, I've yet to see anyone mention a DF84+ result elsewhere. It is available at FTDNA and is on the Chromo2 chip. Luckily there was a Rox2 cluster match in 1000 Genomes from Orkney who matched Jim and Bob's many new FGC SNP results. Nothing had turned up in previous testing (other than DF27 itself). Regarding Z2571 being 'explored', we already know it's the SNP above FGC11395 and DF84. DF27** (those who remain DF27+ and negative for all currently known SNPs downstream) might be interested in Z2571 and any newly identified subclades below DF27. Another similar early DF27 subclade looks to be Z2552.

Anyway, hope the music went well yesterday :drum:

razyn
06-06-2014, 02:44 PM
@ Chris, be sure to tell me when you get your YSEQ results. I haven't yet moved you into the Rox2 group (because nominally it isn't supposed to be based on the members' STR off-modals -- whatever we may personally believe about that).

Also I've asked Mike to add "Rox2" to the title of this thread.

Also, it hasn't been obvious to me until today that your subtle "Rox2" tag (at the bottom of posts here by corner) is a link to your site: https://sites.google.com/site/rox2cluster/home

I trust you'll shortly be moved to update the News there with a link to your new group N, which (unless you reset the default display of 500 kits) is on the second page in this project: https://www.familytreedna.com/public/R1b-DF27/default.aspx?vgroup=R1b-DF27&section=ycolorized

[[[Mikewww: "so let it be written, so let it be done." ]]]

corner
06-06-2014, 06:29 PM
Will do. It seems right that those with FGC11395 or FGC11397 confirmed positive results are in Group N. and the rest of us remain in Group Uf. until we get either of those SNP results.

As well as the 8 kits already in the 'Uf. Unable to confirm DF27 but matches Rox2 Cluster' section at the FTDNA DF27 Project, there are 10 more Rox2 kits with 67 or 111 markers in other parts of the DF27 Project:

91628
228365
187534
U2408
60417
146399
302792
E14895
244412
440

Hope I haven't missed anyone. Most, if not all, of the 18 kits that match the Rox2 key off-modal markers in the DF27 Project at present (that haven't tested the new SNPs yet) are likely to be FGC11395+. There might be less confidence with only 67 markers but most should be FGC11395+. There is little doubt of a match with 111 markers.

FGC11397 is the branch below the founder, FGC11395. I am not aware of any certain way of predicting which FGC SNP a match might be positive for just yet. FGC11397+ Bob Dickinson and Jim Turner are two of my closer matches at 111 markers. I look to be on the same branch as Bob on a phylogenetic tree made using 111 marker matches, so I ordered FGC11397. If negative for FGC11397, then FGC11395 would be the one to go for. If in doubt, or in a rush, a match might just order both at the same time (only available at YSEQ at the moment).

Lots more Rox2 STR matches, tested to at least 67 markers and above, are to be found in other FTDNA projects and on YSearch (YSearch ID: 3QNM8). Hopefully they might join the DF27 Project. I will look at the FTDNA R1b-P312 Project as there are probably a few there who have yet to join the DF27 Project.

corner
06-08-2014, 05:32 PM
be sure to tell me when you get your YSEQ results.
Just got my FGC11397+ so I (N3461) am in the same Rox2 subclade (DF27>Z2571>FGC11395>FGC11397) as Jim Turner, Bob Dickinson and an anonymous 1000 Genomes Project man with origins in Orkney.

razyn
06-08-2014, 07:22 PM
Well that was quick. And [ping] you are moved.

razyn
10-15-2014, 01:24 AM
Contra what I said in post #7 on this thread, FGC11395 can be tested, sort of, at FTDNA -- because it is a position that shows up in Big Y tests, as "novel variants," if one has that mutation. (And btw there are a bunch of others.)

On the basis of novel variant evidence I have just added 66501 and 330933 to Rox2, group N. Both had Big Y results that match 92933 Wilson, and each other, on a string of variants that they share with nobody else with Big Y results to date. One of these variants is the correct mutation at position 14861066, defining FGC11395+.

None of these three displays a call the position 7332619, so I see no proof that any one of them is FGC11397+. Of course, this evidence is just from the selected and displayed novel variants -- not from their .bed files or BAM files.

corner
10-15-2014, 11:50 AM
Contra what I said in post #7 on this thread, FGC11395 can be tested, sort of, at FTDNA -- because it is a position that shows up in Big Y tests, as "novel variants," if one has that mutation. (And btw there are a bunch of others.)

On the basis of novel variant evidence I have just added 66501 and 330933 to Rox2, group N. Both had Big Y results that match 92933 Wilson, and each other, on a string of variants that they share with nobody else with Big Y results to date. One of these variants is the correct mutation at position 14861066, defining FGC11395+.

None of these three displays a call the position 7332619, so I see no proof that any one of them is FGC11397+. Of course, this evidence is just from the selected and displayed novel variants -- not from their .bed files or BAM files.

FGC11397 (position 7332619 G>A) is one of the 45-ish SNPs shared below Z2571 by two Rox2 matches who took FGC tests but is not covered by BigY. FGC11395 is in BigY. There look to be 17 Rox2 SNPs present in BigY out of the 45 in FGC tests, although four positive BigY SNPs, shared in the FGC tests, are marked as 'rejected' in BigY.

Both FGC11395 and FGC11397 are now thought to be equivalent at the moment. Those two were chosen by Jim Turner and Thomas Krahn as useful SNPs to help define the cluster. Either might be ordered by Rox2 STR matches as relatively inexpensive 'one-offs' to confirm what the clear off-modal STR patterns suggest.

Key Rox2 off-modal STR markers over 67 markers: DYS391=10 (P312 modal=11), DYS389ii=30 (29), DYS449=30 (29), DYS607=14 (15), DYS534=14 (15)

The 68-111 marker section in the FTDNA STR test contains the following key off-modal STRs for Rox2, including: 540=13 (12), 717=20 (19), 589=11 (12), 636=11 (12), 532=14 (13), 504=16 (17)

Z2571, FGC11395 and FGC11397 are available to order as 'one-offs' from YSEQ.net. Z2571 is also available at FTDNA. FGC11397 has recently been made available at FTDNA, both are found at 'Advanced Orders'.

The following kits in other parts of the DF27 project will also probably have the Rox2 SNPs:

A. DF27+ (R1b-DF27)

228365
187534 (111 markers)
U2408
146399 (111 markers)

Uf. Unable to confirm DF27 but matches Rox2 Cluster (Should test Z2571 and below)

202611
241356
115452
N18197
86047
122148 (111 markers)
300626 (111 markers)

Ul1. Unable to confirm DF27 (Consider Big Y or Geno 2 or DF27)

440

Ungrouped

328073