Need assistance: Haplogroup, Gedmatch

Question

1) I received by Big Y results from FTDNA just the other day. My confirmed haplogroup moved from R-M269 to R-CTS13034. I can't find any info on this new haplogroup. Can one help?

2) Also, I downloaded my raw results and have tried four times uploading to Gedmatch, but I keep getting error messages. Why would this be? The messages are not always the same, but they indicate a line number and state that I have to have 4 - 5 columns (of something).

Thanks for your help with these two questions!

Edited: typo

Comments

Googled that R-CTS13034 AND there's a website and how helpful it wail be is ... unknown.  FamilyTreeDNA - McShane, McShain and there's also FamilyTreeDNA - American Indian DNA Project

I have my doubts bout the utility for you of these pages 

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Befuddled, as usual when it comes to charts like these. Thanks for trying, Susan!

I googled R-CTS13034 and got nothing!

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My results a few years ago were R-M269 also, but I am not up to speed on the newer designation R-CTS13034.

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Hi Pip,

For your 2nd question - are you trying to upload Y-DNA or autosomal DNA (auDNA/atDNA) test results to GEDmatch? GEDmatch only accepts auDNA/atDNA test data. So from FTDNA to GEDmatch, you could download/upload Family Finder test results, if you've also purchased that test from them.

My understanding is that you can upload Y-DNA test results to mitoYDNA.org.

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CTS has been in haplogroups for a while

mutations within the larger haplogroup

as the testing becomes more refined, better subgroups are being created, particularly in reference to geographics

An example of some older CTS groupings

https://en.wikipedia.org/wiki/Haplogroup_R_(Y-DNA)

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PIP !  PIP !!

You're a mutant human ! 

I knew all along you weren't normal 

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CTS is an abbreviation for Chris Tyler-Smith of The Wellcome Trust Sanger Institute.  He has identified thousands of Y SNPs.

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@Rick: Ah, that's why! I never knew and kept trying to upload. Duh!

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@Eddie: You're just now finding out how mutant I am? C'mon, Eddie! I though you were sharper than that! 

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@Peter: Thanks, Peter! I'll check it out.

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You should know my DNA

I am E-M215 E-V68

I am Watusi

The archaeologists find E-M215 in the Pharaohs' mummies

I AM ROYAL EGYPTIAN  

Kneel before me. I am your god  (stole that from Stargate SG1 LOL)

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posted this back in the dinosaur days

https://www.wikitree.com/g2g/486811/now-anyhow

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That post was from well before I joined. Good thing you posted it again!

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rb1 anychance? their was some new sub groups discovered recently

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That will b th new branch,  try googling the long version of it

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Hi Pip,

this is in regards to the mitoydna.org site. I've tried to access it and it looks as if there may be an error because the site wont pull up. I also have problems trying to pull up the sister site for the mtdna site. Do you or does anyone have the correct link for either site? It would be greatly appreciated!

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Hello Connie,

You must be registered at mitoYDNA.org to view anything there (like GEDmatch).  Here is a video which shows how to register https://www.youtube.com/watch?v=I0WWnDdWKKw

mitoYDNA is free (like WikiTree).

Pip’s mtDNA is viewable at mitoYDNA.  Unfortunately he did not correctly upload his Y-DNA.  

At https://www.wikitree.com/wiki/Roberts-7085 you can view my Y-DNA (and mtDNA) at mitoYDNA.  

Here is a video of some of mitoYDNA’s features https://www.youtube.com/watch?v=gufZ8hJPM7s

Sincerely, Peter

mitoYDNA, team member

WikiTree DNA Project, co-leader

Answer 1

I did a search, too, and I did find something. If you got the snp right, that is, it seems rather shy of any terminal snp you might have. The same snp occurs in the Big Y haplogroup of one Patrick McShea in the McShane, McShain DNA project, terminal snp R-BY595.. I'd say it looks like you must be somewhere in the R1b L21 Atlantic Celtic haplogroup (Celtic British rather than English, Anglo-Saxon) if so. I used the snp Tracker tool with his terminal snp, and it came up L21. http://scaledinnovation.com/gg/snpTracker.html

Comments

 Well PIP, according to the wikipedia article on Celts --  Celtic refers to a family of languages and, more generally, means "of the Celts" or "in the style of the Celts". ... The four are Irish Gaelic, Scottish Gaelic, Welsh, and Breton; plus two recent revivals, Cornish (one of the Brittonic languages) and Manx (one of the Goidelic languages). Continental Celts are the Celtic-speaking people of mainland Europe and Insular Celts are the Celtic-speaking peoples of the British and Irish islands and their descendants. The Celts of Brittany derive their language from migrating insular Celts, mainly from Wales and Cornwall, and so are grouped accordingly.  The Celtic League and the International Celtic Congress bring together Ireland, Wales,Scotland, the Isle of Man, the French Brittany and Conualles – nations united by languages with a Celtic origin, and that have become the most known and recognized heirs of the culture. 

Answer 2

Hello Pip,

Your Big Y-700 test is a Y chromosome test.  GEDmatch is only for autosomal DNA and X chromosomes.

Your Y-STRs should be uploaded to mitoYDNA.org.  You can choose to upload your Y-STR Results from your regular Y-DNA test (up to 111 markers) or from your Big Y Test (over 700 markers).  It is the .csv file at the bottom right of the results page.  Instructions are at https://www.wikitree.com/wiki/Space:Instructions_to_Upload_Family_Tree_DNA_Y-DNA_Test_Information_to_mitoYDNA.org and also at mitoYDNA.org.

Enter R-CTS13034 as your Y haplogroup at mitoYDNA and then clicking on your haplogroup will automatically link to it’s age, hierarchy, and ancient migration shown at SNP Tracker.

Be sure to enter your mitoyDNA ID under your Y-DNA info at https://www.wikitree.com/wiki/Special:DNATests . Doing so will automatically associate your Y-DNA information with your direct paternal line in WikiTree.

Comments

Got it! Thanks, Peter.

Answer 3

Pip   ---   You want to look at the many branches you passed through as you went from R-M269 to R-CTS13034.  At M269 you were one of 65,500 who tested positive for this SNP at FTDNA.  At CTS13034 you are one of 3.  Coming down the haplotree from M269, the 1st major split is U106 or P312; you are P312; one of 39,300.  The next split is L21, DF27 or U152; you are U152; one of 6,000.  Then you branch to Z36 which makes you one of 670.  I don't look much at U152, but look at this then R-Z36.  You can see this progression on FTDNA's Public Y-DNA Haplotree.

Comments

Now I get it! Much appreciated, Fred.

Answer 4

Hi Pip,

Just sending this along as an FYI. I administrate my brother's FTDNA along with mine. His haplogroup, too, was R-M269. I paid for his Y700 and his confirmed DNA haplogroup now is R-BY62081. There are no others in this group (yet). I told him he was in a class all his own (which would not surprise you if you met him). I'm still trying to understand fully what his confirmed group means; hence, study genetic genealogy!

Comments

Yup, mine appears (at this time) to be pretty unique!

Answer 5

I think FTDNA might have chosen a wrong SNP amongst the 33 equivalent SNPs to name your haplogroup with. ISOGG's Ybrowse does know CTS13034 but finds it not qualified and not belonging to any particular haplogroup and Yfull has it 3 times in haplogroup O. Sometimes the same mutation will appear independently in different haplogroups and is normally not used for the naming of nodes. And after FTDNA has done the manual examinations of yours and the 2 other CTS13034 SNPs you might end with another name of your haplogroup.

As Fred pointed out your haplogroup is a subhaplogroup of R-Z36. You can read about it at Eupedia - go to the Italo-Celtic branch.

Comments

Ole, what does “not qualified” mean?

So, if more people test, this haplogroup might change to another place in the SNP tree?

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Hi, Ole. Actually, if looked you at the Ybrowse full data set to find CTS13034 as not qualified, you'll see that single reference is only to the original 2011 naming of the SNP by Chris Tyler-Smith, using data extracted from the 1,000 Genomes Project. In fact, most (I can't say all, but I believe it may be) of CTF's naming designations from that 2011 1,000 Genomes extraction are flagged as "not qualified."

He submitted a significant number of variants to dbSNP for naming as a result of that 2011 effort (thousands of them) and, since these were the result of looking at an anonymous compilation and not of verification by separate test results, they are flagged as "not qualified"...as in, not verified via direct, multiple sequencing runs. But that doesn't mean the SNP isn't really a SNP. That's why you'll see no YCC haplogroup for these 1,000 Genomes extractions....at least, not the vast majority of them (there are over 11,000).

In that same Ybrowse dataset, there are 28 other references to CTS13034, and on all of those the YCC haplogroup designation reads "R-BY32412>R-CTS13034," or CTS13034 as a child of BY32412. The oldest of those was reported in 2016, and the newest this year.

I looked at Yfull, and I see what you mean about them, for some reason, displaying three SNPs (though grayed-out) that are definitely in the "O" haplogroup. There is zero association anywhere else of CTS13034 or BY32412 to haplogroup "O." But I'll freely admit that some of the time I can't figure out what Vadim Urasin and company are doing at Yfull.

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Pip; I didn't know what "not qualified" exactly meant here, but I think Edison has given us a thorough explanation.

No, not another place, but a more exact place on the tree. For now, you have a branch with no side branches for 33 SNPs, the SNPs you share with the two others in haplogroup CTS13034. If a new tester only shares 15 of them a new branch will be formed, and the branches will be renamed according to which SNPs are shared. And if another test that shares some of your private variants, a new branch will also be formed. You can actively test a distant cousin on your male line to find your own Sheppard haplogroup :-)

Edison; thank you, that explains. Where do you find the 28 other references to CTS13034?

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Evening, Ole. Thomas Krahn (of YSEQ and, prior to that, who FTDNA had moved to Houston to help design, build, and operationalize its Gene by Gene testing laboratory), does a great job--as an unpaid volunteer, I might add--of keeping YBrowse as up-to-date as possible. As a courtesy to the genetic genealogy community, he also makes available the source data files he uses in YBrowse's instance of GBrowse: ybrowse.org/gbrowse2/gff/. The most recent main upload of Y-SNPs was 28 May. Just FYI, the .CSV file contains--let me look--1,177,810 rows counting the header, so you'd want to open it in a database tool rather than Excel, which can only load 1,048,576 rows.

And, unfortunately, dbSNP doesn't offer compiled release data by chromosome, so the files there, even the VCFs, can get truly massive. But you can always get to the latest data at ftp.ncbi.nih.gov/snp/latest_release/.

And since I don't think Pip will ever again ask me about yDNA  please tell him that I agree with your assessment of the associated SNPs he sees with his CTS13034. With so many SNPs that have, as yet, not been determined to define a new haplotree branch or node, that location is ripe to see new branching sometime soon.

I know it's an odd way to put it, but this truly is the golden age of yDNA testing for genealogy. The FTDNA haplotree contains over 170,000 SNPs; the YBrowse primary dataset consists of 1,177,809 SNPs; the BigY-700 full-sequence test targets about 23.6 million base pairs. New SNPs will continue to be named, and they along with SNPs already in the catalog will drive the Y-haplotree deeper and deeper...and closer to the current generation in all clades. My own "terminal" SNP is R-BY35083, with which only BY35082 is shown as associated, and I have one private variant. Pip has much more room for refinement very soon.

And BTW, I paid Yfull for an analysis last year, and they show me as BY19276, on a completely different sub-branch of BY3332 than does FTDNA. Many of the detailed, Big Y results I've seen are in disagreement between FTDNA and Yfull. Since I'm R-P312, I've also made my BAM available to Alex Williamson's Big Tree: www.ytree.net/DisplayTree.php?blockID=1058, which agrees with FTDNA that BY19276 is not on my branch.

Answer 6

Hi Pip, just wanted to encourage you to join the Ftdna projects. It may help you on your search and will also help others as the more kits they can compare the more complete the picture becomes. Also, Your DNAportal.com is a good site I did notice FTDNA now has a similar ethnicity estimate.

Comments

Hi, Sherry! I’m in on a few projects on FTDNA. Need to join one more for some matches I have there.

Answer 7

The current terminal SNP you've been assigned is too new to have much info out there floating around about it. That Terminal will likely change at some point.

While waiting for more matches and info you'll have to use the upstream SNPs to find information;

R-P312 > ZZ11 > U152 > Z36 > BY1328 > BY2151 > A7992 > FGC59783 > FGC71023 > BY32412 > CTS13034

Comments

Hi CR!  Just got notified yesterday that I have new subclade under CTS13034: BY108000. 

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Cool! :) Looks like it's downstream one step (for now) from CTS13034.  So, that Z36 Eupedia link is likely the best place to start for now...and search each step down in order...BY1328 info would be the next to look for...;) I try to pay close attention to the regions they mention in the literature... Sometimes you can get a feel for a migratory route and match that up with some archeology and or linguistics and such...;) Likely over the next several years as more kits come in the picture will become much more clearer and begin to match up with known history. Gonna be an exciting time...;)

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The CTS13034 fit my paper trail and oral history, according to the geography of that subclade, Scotland of course. I’ve got a lot of work to do!