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mafe
11-10-2013, 10:06 AM
25000 known SNPs
10 million base-pair coverage
$495 (sale ends December 1st 2013)


Is there a reasonable chance they will find new "U152" SNPs not tested by Geno 2.0?

Kwheaton
11-10-2013, 03:51 PM
Mafe,

I am taking a wait and see attitude after seeing some posts and private communications elsewhere. Especially given Thomas Krahn's concerns and he developed the product! I have noted comments by others and heard directly that less expensive products will be offered by Full Genomes so I am keeping my FTDNA wallet in my back pocket and let somebody else be the guinea pig. I was not impressed with the GENO 2.0 roll out and would just as soon avoid that fiasco. [For those that don't remember one of my Group participants got someone else's results and many of the first batch of SNPs turned out be unreliable due to probe problems].

It's tempting but My wait and see attitude has proved prudent with Chromo 2 and Geno 2.0. And after waiting for the first batches of Full Genomes to return I am going to go for the whole thing and probably save money in the long run. Also I can say their customer support is excellent so far.

mafe
11-10-2013, 05:10 PM
Seeing these concerns, I think I'll adopt the wait and see attitude. If BIG Y is like WTY there is no guarantee they will find new SNPs...and $495 is alot of money for nothing. Testing the full shebang with Full Genomes seems to be the only guarantee to find new SNPs at the moment, but unfortunately their current price is too hefty for my wallet.

Solothurn
11-11-2013, 10:07 AM
I have heard Geno 3.0 will appear sooner than first thought.

Q. So what is the answer for * paying $$$ to search for new SNPs?

A. I have heard on the mailing lists that FTDNA are going to produce a new Y backbone test to search for new SNPs. As $39 each time could work out expensive, especially with new chips revealing new SNPs :)

"FTDNA announced at their conference that they will be bringing back a redesigned backbone test. No exact date was given, but I expect that it will be by mid-year."



Seeing these concerns, I think I'll adopt the wait and see attitude. If BIG Y is like WTY there is no guarantee they will find new SNPs...and $495 is alot of money for nothing. Testing the full shebang with Full Genomes seems to be the only guarantee to find new SNPs at the moment, but unfortunately their current price is too hefty for my wallet.

Alessio B. Bedini
11-11-2013, 10:35 AM
Considering that we will have soon the results of FGS, I'll wait for the new SNPs discovered with FGS and I'll test those.

If the test on the new SNPs will not give results then BIG-Y will seem like a good option since I've tested 111mrk and I don't care full-mtDNA-seq

mafe
11-11-2013, 12:45 PM
I have heard Geno 3.0 will appear sooner than first thought.

Q. So what is the answer for * paying $$$ to search for new SNPs?

A. I have heard on the mailing lists that FTDNA are going to produce a new Y backbone test to search for new SNPs. As $39 each time could work out expensive, especially with new chips revealing new SNPs :)

"FTDNA announced at their conference that they will be bringing back a redesigned backbone test. No exact date was given, but I expect that it will be by mid-year."

I guess it all depends on how the U152* group will break up. If U152* breaks up in a few bigger subclades you might be able to find SNPs through Chip-based testing like Geno/Chromo. If it breaks up in alot of smaller subclades or private SNPs the current chip-based products will be pretty useless for people who are already well tested (Geno/WTY).

I think sequencing might be the only way forward for U152*, the big question is; which company does the best sequence for the best price? FTDNA BIG Y claims to sequence 10 millions base-pairs, but we haven't seen results yet and I don't know if they also provide raw data. Full Genomes is developing entry-level products, hopefully quality sequencing for a reasonable price with raw data!

Individual SNP testing might be useful for people who belong to an obvious cluster and want to test SNPs found in a sequence belonging to that cluster.

Solothurn
11-11-2013, 01:10 PM
Thanks mafe

I read Thomas Krahn posted this at Full Genomes on Facebook:

"Since I have designed this "Big Y" test by myself I can confirm that the
enrichment assay is designed to cover about 18 Mb and I took special care
for tweaking it so that the final coverage is in fact around 10MB. This was
confirmed by a couple of test runs that have been done at Illumina. No such
testing has been done in the FTDNA lab yet. However FTDNA is planning on
doing 15000 of those tests on the HiSeq machines which means that they'll
combine quite a lot of samples on a single run with "DNA barcoding". I am
very worried that this will bring up a lot of crosstalk which will lead to
confusing results across the combined samples. David Mittelmann didn't even
get the numbers right for the WTY so I doubt that he'll be able to do the
correct math for the Next Gen sequencing. In either case customers will be
excited about the price and will not care about quality."

R.Rocca
11-11-2013, 01:59 PM
Just one thing to keep in mind...a very important amount of SNPs that are found using full Y-sequencing (Full Genomes or Big-Y) will never be available for single order. This happens because primers are sometimes impossible to create for some of these SNPs.

Kwheaton
11-11-2013, 02:46 PM
Just one thing to keep in mind...a very important amount of SNPs that are found using full Y-sequencing (Full Genomes or Big-Y) will never be available for single order. This happens because primers are sometimes impossible to create for some of these SNPs.

Rich,
That is very interesting. So that will mean the necessity of a test that can cover the area in question. thinking out loud here: So if we discover say 3 new L2 downstream public SNPs and 5 private ones in a sample and primers are only possible for 4 of them then the only way to get at the remaining 4 is to sequence those areas where they occur. That seems like something that FG would be looking at.

I am on the ISOGG list and Thomas Krahn's concerns about the barcoding have been addressed by Elliot there as well. It also appears that the Big Y is having a very successful rollout in part due to the price point and great marketing. To be fair Thomas pointed out that each test may pick up SNPs not picked up in the other thus there may be a false assumption if a SNP is found one place and not another. It may turn out that the Big Y is excellent and a good investment for some but not so much for others. If money is an issue and you have a little patience I suspect that the new GENO product and the new backbone products due within the next year will catch many of the newly discovered SNPs with a certain amount of time lag. and they will most certainly have a lower price point. Individual SNP testing at a $39 price point is cost prohibitive. Better to buy a panel nut patience is needed.

I have a 91 year old participant in my group who is also one of my most generous supporters and so I feel a certain time pressure to get as much as I can although I expect he may make it to 100 at the rate he is going. :-)

In the long wrong competition is good and will spur better product development and downward pressure on pricing. My concern is that it not be at the cost of accuracy. I think we will have some better answers in 6 months, just like we did with GENO 2.0. If your particular sub clade is already well tested the only realistic hope is that the FG or BigY will provide new SNPs. You pay your money and take your chances. Our WTY and GENO 2 testers came up with 1 private SNP and empty thus my reluctance to encourage anyone jumping on the bandwagon too soon. But perhaps one can overthink it all. My gut simply suggests proceed with caution on the new Big Y. I have been cautious with the FG as well.....waiting to see that people were happy with the results.

And if some of you are thinking about the cost going up that us a marketing ploy that they all use. the cost may temporarily go up but it will almost invariably go down again. Either through sale or permanent lowering of cost.

haleaton
11-11-2013, 05:27 PM
Just one thing to keep in mind...a very important amount of SNPs that are found using full Y-sequencing (Full Genomes or Big-Y) will never be available for single order. This happens because primers are sometimes impossible to create for some of these SNPs.

Would't "impossible" imply that traditional Sanger Y sequencing cannot fully measure the readable sequences that current NGS can? Typically primers for one SNP yield a range of base pairs of various lengths and I thought could be make to overlap with multiple primers and enough time and money. Unless you are talking about long indels or something?

Though I would agree that many of the non-Private SNPs may never be available as individual orders.

R.Rocca
11-11-2013, 06:14 PM
Would't "impossible" imply that traditional Sanger Y sequencing cannot fully measure the readable sequences that current NGS can? Typically primers for one SNP yield a range of base pairs of various lengths and I thought could be make to overlap with multiple primers and enough time and money. Unless you are talking about long indels or something?

Though I would agree that many of the non-Private SNPs may never be available as individual orders.

Typically, the issue is when a sequence is almost identical on the X chromosome.

Kwheaton
11-12-2013, 02:58 AM
Full Genomics Corp Greg Magoon posted this elsewhere on FACEBOOK for those who may not have seen it

Greg Magoon on our work: vs FTDNA


Quote
Regarding the breadth of coverage on chrY: The mapped coverage of the FGC raw data is about 23 million base pairs (mbp). We have estimated the region of reliable mappings in the FGC raw data (corresponding to the high-reliability novel variants) to be 12-16 mbp, but haven't gotten around to precisely quantifying this (not to mention the fact that the concept of 'reliable' is fluid.) Plus, many of the variants classified with lower reliability will likely turn out to be genuine, but further study is needed in those cases. As far as I can tell, the region of chrY that is covered by this test is the same as would be obtained through whole genome sequencing, and since FTDNA basically seems to be targeting a smaller subset of chrY, while using similar next-gen sequencing technology (2x100 bp read length Illumina sequencing), their coverage will almost certainly be lower than the FGC test (it will not be higher). If I make some educated guesses about the approach they are using, am expecting that the larger region covered by the FGC option will give roughly 20-60% more reliable SNPs than the FTDNA option. So, bottom line is that it is difficult to make a head-to-head comparison until FTDNA releases some additional details including example data (I understand that one FGC customer with results has ordered the FTDNA test, which will provide an informative comparison). But it seems clear that there will be significant regions that are not covered by the new FTDNA offering that are available through the FGC results.

Also, in terms of results analysis and interpretation, my sense is that FTDNA will not be offering much here, and may encounter some challenges. The issue of false positives in NGS results is a non-trivial problem, and I wouldn't be surprised if their analysis has problems in this regard. In any case, we have put a lot of resources into making this aspect of FGC;s analysis as solid as possible. We also have worked hard to develop a large database of sequence results (from 1000 Genome Project, Personal Genome Project, and elsewhere) to aid in interpreting the results and help place the new variants on the Y-tree.

Finally, my understanding from some posts on various forums is that FTDNA is not planning on making the raw read and alignment data available, whereas FGC provides this as an option.

And regarding two specific questions I asked him
QUESTION 1) for a surname project like mine will there be less expensive ways around this issue (primers unable to be developed as Rich mentioned)? Or will multiple Full sequences be necessary for each participant IF critical SNPs are unable to have primers developed or that the SNPS are private and there is no cost benefit for any company to develop them?


Answer this is an open question from my perspective...it is not yet clear how the pricing of the various options and technical capabilities will evolve in the future. Often if a SNP is particularly important (e.g. DF27) there are ways to work around the issues (Thomas Krahn developed a nested primer approach for this case)...there is a cost-benefit tradeoff. Usually, in cases where there is suspicion about a variant from NGS, there is a desire to confirm a SNP by developing primers and doing Sanger sequencing, so that is another factor to consider. But if it is a reliable variant, then additional testing of paternal relatives through NGS should provide the desired information (though at higher cost, as you mention).

QUESTION 2 Part of the reason to go ahead with the FG is that no one else can do it for us as the closest GD is something like -23 at 67 markers. But then I read this comment from Thomas Krahn and wondered if someone could explain this.

"Thomas Krahn on FACEBOOK: Bonnie Sure it would be perfect to run a sample with both methods. Cost will be the limiting factor. Another thought is that both companies use different enrichment assays, therefore the covered regions will only partially overlap. If you want more coverage this would be a way. However this also means that not all data can be crosschecked.

Can someone explain the bolded portion? Does this mean that depending on the enrichment technology some areas will be more available for detecting SNPs than others? And can you guesstimate how much might not overlap? And does this mean that in order to get full benefit one must test in different methodologies? Or is it more a matter of unstable areas of the Y that are unlikely to give reliable results.


ANSWER: Regarding your question 2, my experience is that the enrichment used for the BGI sequencing considers chrY regions that are essentially equivalent to what you would get with whole-genome sequencing (i.e. there are no obvious gaps due to targeting). So, although I respect Thomas' expertise, I'm having a hard time seeing how the FTDNA "Big Y" option will cover regions that aren't covered by the FGC/BGI approach. (As my past messages alluded to, I expect the converse will be true, where Big Y will miss regions covered in FGC results so far.) Of course, I could be proven wrong, but we'll have to wait to see some example data before doing a comparison.


Refreshing to have such candid commentary and answers to specific questions. Bravo!

Bolgeris
11-14-2013, 09:30 PM
Now I ordered the Big Y test..
i hope also.. others L20+ will order .. to compare.
Ciao

Rathna
11-15-2013, 06:04 AM
Now I ordered the Big Y test..
i hope also.. others L20+ will order .. to compare.
Ciao

I don't understand this order: if you did Geno 2.0 and are waiting for Chromo2 (like me), probably this Big Y shouldn't add any more. Probably you should have ordered the Full Y which would have been definitive.
Anyway these results of yours will be able to verify my hypothesis, i.e. that Big Y is the same of Geno 2.0 plus Chromo2.

Bolgeris
11-15-2013, 06:27 AM
We will see..
what happened?!

TigerMW
11-15-2013, 02:22 PM
... Anyway these results of yours will be able to verify my hypothesis, i.e. that Big Y is the same of Geno 2.0 plus Chromo2.
No, Big Y is more like a super Walk the Y test that also includes SNPs that are in Geno 2 and Chromo 2. We don't have the Chromo 2 SNP address locations so there may be SNPs they have that no one else has. There are a number articles on Big Y like this one. http://cruwys.blogspot.co.uk/2013/11/the-new-big-y-test-from-family-tree-dna.html

From what I've read, Big Y is covering over 10 M base pairs reliably but possibly another 6-8 M. This is would be in comparison to something like 420,000 for WTY so odds of discovery are much, much better. They claim the testing method is more accurate, but I think that you have recognize this is a highly technical field and technical comparisons, well, they can be hard to understand. In the end, its the results that count.

Is anyone keeping track of U152 Big Y orders? I need to start doing that for DF27. I've been monitoring L21 and I can now count 113 Big Y orders for them.

R.Rocca
11-15-2013, 03:04 PM
No, Big Y is more like a super Walk the Y test that also includes SNPs that are in Geno 2 and Chromo 2. We don't have the Chromo 2 SNP address locations so there may be SNPs they have that no one else has. There are a number articles on Big Y like this one. http://cruwys.blogspot.co.uk/2013/11/the-new-big-y-test-from-family-tree-dna.html

From what I've read, Big Y is covering over 10 M base pairs reliably but possibly another 6-8 M. This is would be in comparison to something like 420,000 for WTY so odds of discovery are much, much better. They claim the testing method is more accurate, but I think that you have recognize this is a highly technical field and technical comparisons, well, they can be hard to understand. In the end, its the results that count.


Correct Mike, Geno 2.0 and Chromo 2 have no potential to find SNPs in your specific sample whereas Big-Y is more like a WTY on steroids.



Is anyone keeping track of U152 Big Y orders? I need to start doing that for DF27. I've been monitoring L21 and I can now count 113 Big Y orders for them.

I am keeping track of all U152 orders for both Full Genomes and Big-Y (too much work to have them in two separate places). I am also going to add all of the discovered SNPs along with those of other U152 genomes (1KG, PGP, etc.)

https://docs.google.com/spreadsheet/ccc?key=0AgHBsIq9ZUahdFJ4MUdicTVKUmJvSmFsVTFOa2RPX 3c&usp=drive_web#gid=0

mafe
11-15-2013, 04:01 PM
From yourgeneticgenealogist.com:

Throughout the genetic genealogy community for the last couple of days, there has been speculation that Family Tree DNA's Big Y product will not include raw data downloads. I found this very difficult to believe with FTDNA's track record of transparency, so I asked Gene by Gene's new Chief Scientific Officer Dr. David Mittelman for clarification on this matter. He confirmed that, while the Big Y results will consist of SNP calls, the raw data will be available for those who want it - just as it is for the company's exome and whole genome products. He added, "We will want to set up some infrastructure to support downloading these big raw files and we will need to clarify for customers that our CSRs are obviously not able to offer advice or support on how to use them."


So is BIG Y a definitive test for the base-pairs covered? Like the FG test?

Rathna
11-15-2013, 04:01 PM
Correct Mike, Geno 2.0 and Chromo 2 have no potential to find SNPs in your specific sample whereas Big-Y is more like a WTY on steroids.


Yes, but we do know the SNPs which are important for us, those tested by Geno 2.0 and Chromo2. The others are probably so rare that are linked to a family line, which probably won't say anything for our researches. Better the Full Y then.
Anyway also about this we will bring it to account at the end.

R.Rocca
11-15-2013, 04:24 PM
Yes, but we do know the SNPs which are important for us, those tested by Geno 2.0 and Chromo2. The others are probably so rare that are linked to a family line, which probably won't say anything for our researches. Better the Full Y then.
Anyway also about this we will bring it to account at the end.

I don't think anyone can speak to which SNPs are available on Chromo 2, and I'd imagine that for folks in the North Sea and the British Isles a lot will be revealed, but for many continentals, there may be nothing new. We know that Geno 2.0 missed many important SNPs as well.

Either way, there is no doubt that the Full Genomes test is the ultimate product, but Big-Y is definitely going to show a lot of new/important SNPs.

mafe
11-16-2013, 12:52 PM
I took the plunge and ordered BIG Y, as an outlier in the U152* group I have doubts I will share many SNPs with others but I hope for the best.

Solothurn
11-16-2013, 01:42 PM
Very best of luck with this mafe :)

If I had the funds I would certainly join you.

I wish I could find a way to word a plea to members of my U152 A:a:a:a group to pool resources. There are 11 of us so would only be only roughly $45 each.

Any suggestions on how to put this to them would be very appreciated :)





I took the plunge and ordered BIG Y, as an outlier in the U152* group I have doubts I will share many SNPs with others but I hope for the best.

mafe
11-16-2013, 02:04 PM
Thanks Solothurn, maybe you can use the $50 coupon of the WTY participant in your cluster?


Very best of luck with this mafe :)

If I had the funds I would certainly join you.

I wish I could find a way to word a plea to members of my U152 A:a:a:a group to pool resources. There are 11 of us so would only be only roughly $45 each.

Any suggestions on how to put this to them would be very appreciated :)

Solothurn
11-16-2013, 02:29 PM
Nice one mafe :)

I had forgotten about that!

I will email him and ask :)


Thanks Solothurn, maybe you can use the $50 coupon of the WTY participant in your cluster?

Solothurn
11-16-2013, 06:17 PM
I have emailed all in my U152 group to chip in. With the WTY $50 off, If all 11 agree it would only be $41 EACH :party:

Fingers crossed :)

MitchellSince1893
11-17-2013, 12:59 AM
Ah screw it...it's only money...took the plunge on the Big Y.

As I told my wife this hobby is still cheaper than my old one...Ford Mustangs.

Plus it's for Science! :)

Best I can tell from Richard Rocca's spreadsheet, no other J1: U152> L2> Z49> Z142 (L562- L594-) types have ordered the Big Y or the FG.

Solothurn
11-17-2013, 10:47 AM
I sent the emails from my hotmail, but suspect all or most got trashed as I selected 'read receipt'.

I have resent it again today using a non hotmail account, so hopefully hear back today.

* Had one reply from Australia (as ahead of me in time) they have said they are interested at $41 :)

Also had another reply asking what will it show and how would they benefit. I answered as best as I could.

I am not anticipating much interest or rather $$ >:(






I have emailed all in my U152 group to chip in. With the WTY $50 off, If all 11 agree it would only be $41 EACH :party:

Fingers crossed :)

Solothurn
11-17-2013, 04:14 PM
I asked Steve about how to go about ordering it from different sources, i.e. pooling resources from a subgroup!

He has been told it is not yet possible to order the BigY through the project funds!

Not good IMHO >:(


Thanks Solothurn, maybe you can use the $50 coupon of the WTY participant in your cluster?

lgmayka
11-17-2013, 09:09 PM
He has been told it is not yet possible to order the BigY through the project funds!
It can't be done on the web site. The administrator has to contact FTDNA for that.

Solothurn
11-18-2013, 09:48 AM
Thanks lgmayka

Only had two replies from ten, so It looks like the BIG Y may not be an option this time around for our cluster :(

I did hear SNPs are produced around every 100 years or so. I have since heard every two generations!
This would be a major breakthrough for us all and for admin calculations farther back, re brick walls etc.
Potentially c3,500 years since our U152 marker is 112 more SNPs. I don't know if this will ever become reality though :unsure:





It can't be done on the web site. The administrator has to contact FTDNA for that.

Kwheaton
11-18-2013, 02:20 PM
Solothurn,

Do not lose heart. I have done this several times. First for a WTY and second for a Full Y. I don't know if it would help but you could link to this lesson in my beginner's guide. It includes Links to Debbie Kennett and Roberta Estes Blog Posts and I have given an example of how refining SNPs can be relevant in a genealogical time frame. Lesson 15 the Future of Y testing Is Here (https://sites.google.com/site/wheatonsurname/beginners-guide-to-genetic-genealogy/lesson-15-the-future-y-is-here)
Kelly

Solothurn
11-18-2013, 02:37 PM
Thanks Kelly :)




Solothurn,

Do not lose heart. I have done this several times. First for a WTY and second for a Full Y. I don't know if it would help but you could link to this lesson in my beginner's guide. It includes Links to Debbie Kennett and Roberta Estes Blog Posts and I have given an example of how refining SNPs can be relevant in a genealogical time frame. Lesson 15 the Future of Y testing Is Here (https://sites.google.com/site/wheatonsurname/beginners-guide-to-genetic-genealogy/lesson-15-the-future-y-is-here)
Kelly

Kwheaton
11-18-2013, 02:49 PM
Your welcome. And I probably should have added it took a couple of weeks and some coaxing. Then I got one big donation and the rest fell into place. It's really helpful if you can lay out possible historical scenarios. Many folks like the one in my example had tested these individual SNPs but really had no clue what it means. Only DNA geeks care about Z5050 but if it defines a particular group of Roman Soldiers or Vikings or descendants of the Earl of Nottingham....well that's another thing altogether.

Solothurn
11-21-2013, 12:06 PM
Now FOUR U152** (L2- Z36- Z56- Z192-) samples awaiting BigY or FGS results - yDNA Sequencing

Duncan, Fulfisk, Engelen and now Wear from my cluster :)

Hope this is the end of the U152*

mafe
11-21-2013, 05:11 PM
Great news Solothurn! :beerchug:

Solothurn
11-21-2013, 06:19 PM
Thanks mafe

I hope Colangelo can order the BigY! It should determine his L159.2 once and for all :)


Great news Solothurn! :beerchug:

MitchellSince1893
11-22-2013, 01:14 AM
There's now two of us Z142+ L562- types doing the Big Y.

1370 John Graves, b.c. 1665, England/Virginia and myself.

Solothurn
11-22-2013, 11:13 AM
Andereggen and Zafonte are also in 'the mix' now :)

Full genome results are coming in now so Duncan's results will be in soon :beerchug:


Great news Solothurn! :beerchug:

mafe
11-22-2013, 03:02 PM
Andereggen and Zafonte are also in 'the mix' now :)

Full genome results are coming in now so Duncan's results will be in soon :beerchug:

It's looking good...and still a week to go before the sale ends, hopefully some more people will order, the more the merrier.

MitchellSince1893
11-29-2013, 10:56 PM
There's now 3 of us Z142+ L562- types doing the Big Y.

Kit 1620 is now the 3rd.

Not much time left before the sale ends.

Solothurn
11-30-2013, 12:13 PM
Many have taken the plunge, including 10 U152*.
Hope there is some 'positive' progress!

*Sale ends 1st December :)

haleaton
12-04-2013, 02:20 AM
As expected recent update from FTDNA. Glad they put "BETA" in there.



PENDING TESTS






Tests
Lab Procedure
Batch
Expected
Notes


Big Y
HiYNGS
543
2/28/2014
We will release results from the BIG Y Pre-Sale with the BETA myFTDNA results pages in mid February 2014.

MitchellSince1893
12-04-2013, 05:32 AM
:pout: Darn. It used to say 6 Jan...

Kwheaton
12-06-2013, 05:31 AM
New information now says Feb 28. And I predicted somewhere I would not be the least bit surprised if this date gets pushed forward a couple of times landing in March or April. Even though that may be disappointing I would rather see that they do due diligence and get it right rather than rolling out before things are fully vetted.

TigerMW
12-06-2013, 08:43 PM
New information now says Feb 28. And I predicted somewhere I would not be the least bit surprised if this date gets pushed forward a couple of times landing in March or April. Even though that may be disappointing I would rather see that they do due diligence and get it right rather than rolling out before things are fully vetted.

I agree 100%. We all want as much accuracy as possible.

It is my understanding there was no "slip" in the schedule and this has always been part of the planned "public" release of Big Y results.

"We plan to release the first set of BIG Y results in February 2014."
http://www.familytreedna.com/faq/answers.aspx?id=27

Roberta Estes of DNAeXplain was at the FTDNA conference and wrote this on November 13th, "For the answers to many of these questions, we will have to wait until the first Big Y results start to be returned in approximately 10-12 weeks."
http://www.yourgeneticgenealogist.com/2013/11/news-from-family-tree-dna-big-y.html

The problem is that their system has been errantly reporting the December date for the batch results. I can't find it now, but somewhere I read that is because Big Y is a new product and FTDNA wants to go through extra quality control steps. In other words, they will have tests done earlier but they won't release them until February as a precautionary review process step, but I'm kind of with you - they need to get it right, not early.

MitchellSince1893
12-09-2013, 06:10 AM
Now up to 4 U152>L2>Z49>Z142* (L562- Z150 not tested) signed up for BigY results:

1370 John Graves, b.c. 1665, England/Virginia R1b1a2a1a1b3c
1620 R1b1a2a1a1b3c
249822 Edward Leopold Mitchell (NPE) 1893-1969 London UK R1b1a2a1a1b3c
7181 Thomas Davenport - 1615-1685 of Dorchester, MA R1b1a2a1a1b3c

I'm glad to see the addition of Davenport as he has a closer GD to me.

R.Rocca
12-09-2013, 03:10 PM
Now up to 4 U152>L2>Z49>Z142* (L562- Z150 not tested) signed up for BigY results:

1370 John Graves, b.c. 1665, England/Virginia R1b1a2a1a1b3c
1620 R1b1a2a1a1b3c
249822 Edward Leopold Mitchell (NPE) 1893-1969 London UK R1b1a2a1a1b3c
7181 Thomas Davenport - 1615-1685 of Dorchester, MA R1b1a2a1a1b3c

I'm glad to see the addition of Davenport as he has a closer GD to me.

On a Z49+Z412+ related note, Beaugrand's Chromo 2 results have him as S7402/Z12222+ which is approximately at the same level as Z150.

Solothurn
12-10-2013, 02:34 PM
AND Aulicino is in too. I am 51/67 with him.

And he is also the less common DYS458=16 :)

On 12 markers I am 6/12 and one would say we are too distant, however on looking at myself with Wear I am 9/12 and still 60/67 :music:




Andereggen and Zafonte are also in 'the mix' now :)

Full genome results are coming in now so Duncan's results will be in soon :beerchug:

MitchellSince1893
12-14-2013, 07:26 PM
Was trying to find a more general big y thread but this will do. Just read on https://www.facebook.com/groups/isogg/ that Thomas Krahn said

Good news for Big Y! I was at FTDNA yesterday and Max has told me that they have the first successful runs in house completed. He didn't say on which machine they were running (MiSeq or HiSeq) and he didn't comment on possible barcoding problems, but this gives us hope that some customers may not need to wait until next year to see their results.

Pigmon
12-23-2013, 04:10 PM
Now up to 4 U152>L2>Z49>Z142* (L562- Z150 not tested) signed up for BigY results:

1370 John Graves, b.c. 1665, England/Virginia R1b1a2a1a1b3c
1620 R1b1a2a1a1b3c
249822 Edward Leopold Mitchell (NPE) 1893-1969 London UK R1b1a2a1a1b3c
7181 Thomas Davenport - 1615-1685 of Dorchester, MA R1b1a2a1a1b3c

I'm glad to see the addition of Davenport as he has a closer GD to me.

Mitchell,

Steve Gilbert told me some time ago that although my matches are not close to anyone, Davenport is my closest match!

I think I am in this bucket with you, Graves, and Davenport.

Other matches on FTDNA matches at a genetic distance of 3 are surnames Fortenberry, VanValkenburg, and Faulkenberry which, if I am not mistaken, are in the same family.

Cheers,
Curtis

Biloo
01-02-2014, 11:32 PM
There is an update in my awaiting tests table :

Batch 542
Lab Procedure : gDNAQC
Expected 12/31/2013

mafe
01-03-2014, 12:18 PM
Same here!, I guess gDNAQC stands for Quality Control!!! :beerchug:

AWAITING TESTS
Tests Lab Procedure: Big Y gDNAQC
Batch: 543
Expected: 6-1-2014

MitchellSince1893
01-03-2014, 01:42 PM
Ditto for me.




AWAITING TESTS
Tests Lab Procedure: Big Y gDNAQC
Batch: 543
Expected: 6-1-2014

haleaton
01-03-2014, 06:56 PM
AWAITING TESTS


Tests
Lab Procedure
Batch
Expected
Notes


Big Y
gDNAQC
543
1/6/2014

GailT
01-03-2014, 07:29 PM
I'm curious to see if they will also report high confidence and low confidence SNPs for Big Y. It will be interesting to see how well the results match up with the Full Y. I suppose if you get hits on a low confidence SNP on both tests, it might be more reliable.

haleaton
01-04-2014, 03:38 AM
I'm curious to see if they will also report high confidence and low confidence SNPs for Big Y. It will be interesting to see how well the results match up with the Full Y. I suppose if you get hits on a low confidence SNP on both tests, it might be more reliable.

Yes, I was interested if heterozygosity was a function of the test/sample or if it was unique to the individual--carrying multiple types of Y-DNA. Also if you get two 50x tests will that be equivalent to a 100x test?

GailT
01-05-2014, 08:38 PM
Sounds like we will not see BigY results at FTDNA until sometime in March. At the FTDNA discussion forum, Rebecca said "the very, very, very end of February".

Based on past experience with other tests, and given that this is a new technology and new analysis method for FTDNA, I would not be surprised if this gets extended into May or June.

Stellaritic
01-06-2014, 04:20 PM
Sounds like we will not see BigY results at FTDNA until sometime in March. At the FTDNA discussion forum, Rebecca said "the very, very, very end of February".

Based on past experience with other tests, and given that this is a new technology and new analysis method for FTDNA, I would not be surprised if this gets extended into May or June.

I noticed that the huge "the big Y is here "icon appeared shortly after people started receiving the "gDNAQC" notifications which in my opinion could mean that ftDNA are somewhat satisfied with the raw data results to the point where they feel now more confident to market their product,but don't want to release results until the IT team will come up with some kind of SNP matching new feature or something of the sort.

MitchellSince1893
01-06-2014, 05:53 PM
Sounds like we will not see BigY results at FTDNA until sometime in March. At the FTDNA discussion forum, Rebecca said "the very, very, very end of February".

Based on past experience with other tests, and given that this is a new technology and new analysis method for FTDNA, I would not be surprised if this gets extended into May or June.
Based on previous comments from FTDNA, it might be that the IT side of displaying the results is the reason...jmo.

mafe
01-09-2014, 05:44 PM
Thomas Krahn on the gDNAQC notification (L21 yahoo group):

"Well, this likely points to the fact that FTDNA has some real trouble with the BigY at the moment if they need to use an explicit genomic DNA quality control. Likely they had several runs failing already so that they had to establish a quality control system to prevent critical samples from being included in the expensive BigY pipeline. My guess is that the barcoded mass production on the HiSeq didn't work out and they'll be forced to go back to the MiSeq."

MitchellSince1893
01-10-2014, 03:15 AM
My gDNAQC notification is now gone. I now only have this message



Big Y HiYNGS 543 2/28/2014 We will release results from the BIG Y Pre-Sale with the BETA myFTDNA results pages in mid February 2014.

Maybe that means I cleared QC?

haleaton
01-10-2014, 06:05 AM
My gDNAQC notification is now gone. I now only have this message

Maybe that means I cleared QC?

Same here. It will be interesting do see just how they roll the whole thing--which tree they will use and how they might provide new SNP definitions to the public. How the raw data will be provided. And who do go to for individual Sanger SNP tests. SNP Tsunami or SNPnado?

These are the good times.

MitchellSince1893
01-29-2014, 10:19 PM
This must be the part of the "SNP tsunami" where the water gets sucked way out into the bay before the big one hits.

Anybody heard anything recently...good, bad, or otherwise, on how the Big Y is going?

MitchellSince1893
02-03-2014, 03:26 AM
Big Y update from FTDNA Web Presence and Customer Engagement rep Rebeckah Canada on 2nd February 2014, 03:19 PM

Update

--------------------------------------------------------------------------------

So far, so good. :-) Results should still be out at the end of the month.
http://forums.familytreedna.com/showthread.php?t=33717&page=5

26 days left...but who's counting ;)

MitchellSince1893
02-09-2014, 02:43 AM
Today, according to Rebekah Canada, Web Presence and Customer Engagement at Family Tree DNA


If it is going to be pushed back, I will let you guys know right away. So far... all is looking good.


http://forums.familytreedna.com/showpost.php?p=377425&postcount=27

Fingers crossed that it doesn't slip.

Kwheaton
02-28-2014, 08:42 PM
Anyone get results yet?

haleaton
02-28-2014, 08:51 PM
No, but my status changed in last few hours to:

Big Y HiYNGS 543 3/28/2014

"We expect that all samples ordered during the initial sale (last November & December) will be delivered by March 28th. We are processing samples in first come first serve order. If a sample doesn't pass quality control, we will place it in the next set of results to be processed as long as we have enough DNA sample. If we require an additional sample, we will send a new test kit and place the new sample in the first set to be processed when it is returned."

tbartold
02-28-2014, 09:01 PM
I have results!

However, I was surprised with the number of undefined results.
36,566 tested.
613 Yes
25,046 No
10,907 Undefined.

Unfortunately, Z367, Z49, and Z35 all came in as undefined. But I think I'm still L2* anyway, since Z34, Z142 and Z258 all came up No.

It says I have to wait a few days (March 3) before I can download the raw results, but once I do, is anyone keen on collecting/seeing them?

One more interesting number, is that it says that only 91 of the 613 Yes results are currently on the haplotree.

R.Rocca
02-28-2014, 09:06 PM
I have results!

However, I was surprised with the number of undefined results.
36,566 tested.
613 Yes
25,046 No
10,907 Undefined.

Unfortunately, Z367, Z49, and Z35 all came in as undefined. But I think I'm still L2* anyway, since Z34, Z142 and Z258 all came up No.

It says i have to wait a few days before I can download the raw results, but once I do, is anyone keen on collecting/seeing them?

You have definitely shed your L2* status and are now L2+FGC4183+ along with a German sample. Please read here:

http://www.anthrogenica.com/showthread.php?1472-New-Group-U152-gt-L2-gt-13685121-(C-T)-gt-21885515-(C-T)&p=32313&viewfull=1#post32313

tbartold
02-28-2014, 09:21 PM
You have definitely shed your L2* status and are now L2+FGC4183+ along with a German sample. Please read here:

http://www.anthrogenica.com/showthread.php?1472-New-Group-U152-gt-L2-gt-13685121-(C-T)-gt-21885515-(C-T)&p=32313&viewfull=1#post32313

Thank you for figuring that out Richard. Unforunately it probably means I'm not as closely related to you as I hoped. In any case, I can now go back and try and figure out how you figured that out. I like learning new things!

mafe
03-01-2014, 02:03 PM
I am slightly worried that I won't be able to find important SNPs without comparison to others. Are important U152* SNPs like PF6658 and CTS11993 reported as such? or should we look for positions?

R.Rocca
03-01-2014, 02:19 PM
I am slightly worried that I won't be able to find important SNPs without comparison to others. Are important U152* SNPs like PF6658 and CTS11993 reported as such? or should we look for positions?

PF and CTS SNPs are reported in Big-Y, but I don't know where the cutoff is as some of these were made public at different. I would say that if you don't find the PF or CTS SNP, you should look for the position.

Tonsa71
03-02-2014, 04:41 PM
Hi !
New here at this forum and waiting for my big-Y results. Interesting to read your posts here and I looking forward to see how my results fit in to yours.
But I have to wait until late march.

tbartold
03-07-2014, 01:03 AM
I am slightly worried that I won't be able to find important SNPs without comparison to others. Are important U152* SNPs like PF6658 and CTS11993 reported as such? or should we look for positions?

If it helps any, I see PF7648 and CTS13035 as the highest numbers tested in my results (I have No for both of the ones you asked about).

mafe
03-07-2014, 03:28 PM
If it helps any, I see PF7648 and CTS13035 as the highest numbers tested in my results (I have No for both of the ones you asked about).

Thank you for checking, searching SNP names is much easier than searching locations when results come in so I'm glad PF6658 and CTS11993 are listed.

Rathna
03-07-2014, 04:28 PM
Thank you for checking, searching SNP names is much easier than searching locations when results come in so I'm glad PF6658 and CTS11993 are listed.


PF6658 20850039 22440651 no no no no no A -> G
CTS11993 21817322 23407934 no no no no no C -> G

Kwheaton
03-09-2014, 03:35 PM
Hi !
New here at this forum and waiting for my big-Y results. Interesting to read your posts here and I looking forward to see how my results fit in to yours.
But I have to wait until late march.

Welcome Tonsa71. Are you already a member of FTDNA U152? If so do you mind sharing your kit number?
I am waiting for the WHEATON group results end of March or thereabouts from Full Genomes. We are also L2.
Kelly

Tonsa71
03-09-2014, 05:04 PM
Yes I am a member of FTDNA U152. Kit number : 203953

Kwheaton
03-09-2014, 08:09 PM
Yes I am a member of FTDNA U152. Kit number : 203953

Thanks. Hubby kit 199087

haleaton
03-20-2014, 08:55 AM
My BigY results were available today though there was no e-mail sent (which is usual).
Of the "named" SNPs they report my L2 status was "?", buy they did report U152+.

I am L2* with 45 High Quality Private SNPs from my FGC results that have yet to be known to be shared by another L2* test results.

79 Novel Variant BigY SNPs were reported (70 High Confidence, 9 Medium Confidence). No Indels were reported.

54 of these were classified as "shared" by my FGC results based on last years reports. I have not requested the updated reports from Full Genomes, yet.

Of the remaining 25 assumed Private and Novel BigY SNPS, 15 Matched 95%-99% Confidence FGC Private SNPs and 6 matched 40% Confidence FGC Private SNPS.

BigY found 4 High Confidence Novel SNPs that were not reported by Full Genomes at all, but the bam file has not been checked for no-call.


So at first look, Big Y may have missed over 50% of the Private SNPs that FGC reported for my case of a heavily tested L2*.

Big Y did find many of the FGC Private SNPs and found 4 that it may have missed.

emmental
03-20-2014, 09:13 AM
I have not requested the updated reports from Full Genomes, yet.


Big Y did find many of the FGC Private SNPs and found 4 that it may have missed.

I don't think you need to request the updated reports from FGC. They should be loaded onto your private FGC page. The 4 private SNPs, or some of them, may have been reported in the updates.

haleaton
03-20-2014, 10:04 AM
I don't think you need to request the updated reports from FGC. They should be loaded onto your private FGC page. The 4 private SNPs, or some of them, may have been reported in the updates.

No, not yet. My private FGC page still has my kit being processed unless I am not looking at the right place. I was going to request it from GregM after Rocca's results are added. I did not know there were big differences. [Edit 3/20/2014 -- GregM sent me updated reports a few seconds after I e-mailed him]

Below is the comparison for what I have now. Notice the sequential SNPs in the BigY Novel data usually for low confidence shared SNPs. I don't know if this is a bug or a feature . . .



Position Reference Genotype BigY Novel FGC SNP FGC Type
6985619 G A High FGC5296+ Private 99%
7115859 T C High FGC5299+ Private 99%
7321330 A C High Shared 99%
7832161 T C Medium FGC5300+ Private 95%
7899592 C T High FGC5301+ Private 95%
8320779 A C High FGC5303+ Private 95%
8805525 A G High Shared 95%
9034891 C T High Shared 40%
9156208 T C High FGC5304+ Private 95%
9227801 A T High Shared 40%
9296025 G A High Shared 40%
9316833 A G High Shared 40%
9937995 A T High Shared 40%
13142597 G T High Shared 40%
13271933 T A High N/R
13677424 G A Medium Private 40%
13677425 A T Medium Private 40%
13687378 A T High Shared 40%
13820260 G A High N/R
14071348 A T High Shared 40%
14367269 C A High Shared 40%
14398980 A G High Shared 40%
14399063 A G High Shared 40%
14399074 A G High Shared 40%
14399077 G A High Shared 40%
14399105 G A High Shared 40%
14644698 C T High Shared 40%
14644742 C T High Share 40%
14709276 A T High Shared 40%
14709277 C G High Shared 40%
14865182 A C High FGC5308+ Private 99%
16267644 C G High FGC5311+ Private 99%
16338151 C T High FGC5312+ Private 99%
17008323 A C High FGC5313+ Private 99%
17794885 G A High FGC5315+ Private 99%
18825164 G A High FGC5316+ Private 99%
18964422 T C High FGC5317+ Private 99%
19842035 G T High N/R
21654553 A G High FGC5321+ Private 99%
21853779 A T High N/R
21952388 T C High Shared 99%
22229722 T A High Shared 40%
22229913 C G High Shared 40%
22233732 C G High Shared 40%
22235226 C T High Shared 40%
22246045 C G High Shared 95%
22246199 G A High Shared 95%
22259729 T C High Shared 40%
22262889 A T High Shared 40%
22269664 C G High Shared 40%
22269796 T A High Shared 40%
22293981 C G High Shared 95%
22302537 C T High Shared 40%
22318641 A C High Shared 40%
22318642 G A High Shared 40%
22318643 A C High Shared 40%
22318978 T C High Shared 40%
22319065 T C Medium Shared 40%
22319066 A T Medium Shared 40%
22319170 A T High Shared 40%
22319171 G T High Shared 40%
22319362 A T High Shared 40%
22319363 T A High Shared 40%
22346168 A T High Shared 40%
22422202 T C High Shared 40%
22432368 G C High Shared 40%
22436300 A C High Shared 40%
22444659 A T High Shared 40%
22467805 G T Medium Private 40%
22467806 A G Medium Private 40%
22489310 G T High FGC5323+ Private 95%
22562625 G A Medium Private 40%
22562626 T A Medium Private 40%
23354909 A C High Shared 40%
24447989 A C High Shared 99%
24453842 G T High Shared 40%
28787127 G A High Shared 40%
28787141 C G High Shared 40%
28788695 T A High Shared 40%

haleaton
03-20-2014, 06:08 PM
As for my Big Y named SNPs here is a break out from my results. Interesting that 30% named SNPs were "?" including L2+ which is my terminal named SNP from multiple testing including Deep Clade & WTY.

Seems kind of high to me and I don't think this is a coverage issue. I was also "?" for Z49 & Z36 so there is a question if BigY would even predict my Haplogroup correctly though I have not checked duplicate SNP names.

It would be interesting to find out for somebody without other testing except Y-STR 37 which (I think) is the minimum to participate in BigY how well it determines Haplogroup with so many "?" SNPs particularly when FTDNA goes to a more modern Y Tree.

Unlike SNP chip tests, I would assume that "?" results for stable SNPs are a random thing for each test being run not a systematic problem for NGS Sequencing, but I don't know for sure.

Geno 2.0 failed L2, but was supplemented by other testing. Deep Clade testing they repeated the Sanger Sequencing until they got it. WTY did two Sanger sequencies (L&R) only and also had some no calls.



Confidence
Named SNPs Number Percent High Medium Low
On Y Tree - Yes(+) 90 0.2% 90 0 0
On Y Tree - No(-) 657 1.8% 657 0 0
On Y Tree - ? 36 0.1% 0 0 36
Not on Y Tree - Yes(+) 514 1.4% 509 0 5
Not on Y Tree - No(-) 24108 65.9% 24056 11 41
Not on Y Tree - ? 11157 30.5% 0 0 11157
Total 36562 100.0% 25312 11 11239

haleaton
03-20-2014, 07:23 PM
Quick response from FGC again a few minutes after I sent info.

GregM of FGC:

"I looked at those 4 cases you've identified.

13271933: This is included in the new reports as a shared *** SNP

13820260: This is seen in your raw Full Genomes results but doesn't meet our current reporting criteria due to apparent mapping/homology issues in this region. This seems to be unique to you, but I would consider it to be somewhat speculative. It might be interesting to investigate this one by talking with Thomas Krahn of YSEQ and seeing if he thinks it might be confirmed by Sanger sequencing.

19842035: Again, this is seen in your raw Full Genomes results, but doesn't meet our current reporting criteria. This one seems to have some clear warning flags, and I would consider it to be very speculative due to issues with sequence homology. In any case, if it is genuine, it seems to be very widely shared so won't be of phylogenetic interest

21853779: This is included in the new reports as a shared *** SNP"




No, not yet. My private FGC page still has my kit being processed unless I am not looking at the right place. I was going to request it from GregM after Rocca's results are added. I did not know there were big differences. [Edit 3/20/2014 -- GregM sent me updated reports a few seconds after I e-mailed him]

Below is the comparison for what I have now. Notice the sequential SNPs in the BigY Novel data usually for low confidence shared SNPs. I don't know if this is a bug or a feature . . .



Position Reference Genotype BigY Novel FGC SNP FGC Type
6985619 G A High FGC5296+ Private 99%
7115859 T C High FGC5299+ Private 99%
7321330 A C High Shared 99%
7832161 T C Medium FGC5300+ Private 95%
7899592 C T High FGC5301+ Private 95%
8320779 A C High FGC5303+ Private 95%
8805525 A G High Shared 95%
9034891 C T High Shared 40%
9156208 T C High FGC5304+ Private 95%
9227801 A T High Shared 40%
9296025 G A High Shared 40%
9316833 A G High Shared 40%
9937995 A T High Shared 40%
13142597 G T High Shared 40%
13271933 T A High N/R
13677424 G A Medium Private 40%
13677425 A T Medium Private 40%
13687378 A T High Shared 40%
13820260 G A High N/R
14071348 A T High Shared 40%
14367269 C A High Shared 40%
14398980 A G High Shared 40%
14399063 A G High Shared 40%
14399074 A G High Shared 40%
14399077 G A High Shared 40%
14399105 G A High Shared 40%
14644698 C T High Shared 40%
14644742 C T High Share 40%
14709276 A T High Shared 40%
14709277 C G High Shared 40%
14865182 A C High FGC5308+ Private 99%
16267644 C G High FGC5311+ Private 99%
16338151 C T High FGC5312+ Private 99%
17008323 A C High FGC5313+ Private 99%
17794885 G A High FGC5315+ Private 99%
18825164 G A High FGC5316+ Private 99%
18964422 T C High FGC5317+ Private 99%
19842035 G T High N/R
21654553 A G High FGC5321+ Private 99%
21853779 A T High N/R
21952388 T C High Shared 99%
22229722 T A High Shared 40%
22229913 C G High Shared 40%
22233732 C G High Shared 40%
22235226 C T High Shared 40%
22246045 C G High Shared 95%
22246199 G A High Shared 95%
22259729 T C High Shared 40%
22262889 A T High Shared 40%
22269664 C G High Shared 40%
22269796 T A High Shared 40%
22293981 C G High Shared 95%
22302537 C T High Shared 40%
22318641 A C High Shared 40%
22318642 G A High Shared 40%
22318643 A C High Shared 40%
22318978 T C High Shared 40%
22319065 T C Medium Shared 40%
22319066 A T Medium Shared 40%
22319170 A T High Shared 40%
22319171 G T High Shared 40%
22319362 A T High Shared 40%
22319363 T A High Shared 40%
22346168 A T High Shared 40%
22422202 T C High Shared 40%
22432368 G C High Shared 40%
22436300 A C High Shared 40%
22444659 A T High Shared 40%
22467805 G T Medium Private 40%
22467806 A G Medium Private 40%
22489310 G T High FGC5323+ Private 95%
22562625 G A Medium Private 40%
22562626 T A Medium Private 40%
23354909 A C High Shared 40%
24447989 A C High Shared 99%
24453842 G T High Shared 40%
28787127 G A High Shared 40%
28787141 C G High Shared 40%
28788695 T A High Shared 40%

CelticGerman
03-25-2014, 11:43 PM
My results just came in. First point I can underline is that CTS188, CTS4333 and CTS7958, found by Geno, are confirmed here.

emmental
03-26-2014, 12:22 AM
My results just came in. First point I can underline is that CTS188, CTS4333 and CTS7958, found by Geno, are confirmed here.

We anxiously await your results!

CelticGerman
03-26-2014, 08:27 AM
My results indicate 625 entries (filtered from 36,564 total entries), of which 93 on Y-tree.
U152 is there.
Z36 is strange : They indicate "Derived ?", "On Y-Tree No", "Reference A", "Genotype ?", "Confidence unknown". Well, Z36 was tested "+" before by FTDNA and GENO 2.0 already.
CTS188, CTS4333 and CTS7958 (all tested "+" by GENO 2.0) are confirmed here, as indicated in an earlier post.
Novel variants 136 (please let me know what to do with it).

emmental
03-26-2014, 10:33 AM
My results indicate 625 entries (filtered from 36,564 total entries), of which 93 on Y-tree.
U152 is there.
Z36 is strange : They indicate "Derived ?", "On Y-Tree No", "Reference A", "Genotype ?", "Confidence unknown". Well, Z36 was tested "+" before by FTDNA and GENO 2.0 already.
CTS188, CTS4333 and CTS7958 (all tested "+" by GENO 2.0) are confirmed here, as indicated in an earlier post.
Novel variants 136 (please let me know what to do with it).

If you paste and post your novel variants (most will be above Z36) we can help to sort them out and compare them to Kees' and my FGC results and see if there are any shared SNPs. It is strange that they had trouble picking up the Z36. It will be interesting to see if that problem continues with the rest of our group.

CelticGerman
03-26-2014, 10:57 AM
If you paste and post your novel variants (most will be above Z36) we can help to sort them out and compare them to Kees' and my FGC results and see if there are any shared SNPs. It is strange that they had trouble picking up the Z36. It will be interesting to see if that problem continues with the rest of our group.

13271933 T A High
13672823 C T High
13687378 A T High
14367269 C A High
14398980 A G High
14399063 A G High
14399074 A G High
14399077 G A High
14399105 G A High
14644698 C T High
14644742 C T High
14647641 T A High
14709276 A T High
14709277 C G High
14744185 T C High
15540519 T C High
15858877 G A High
16357373 T C High
16441973 A C High
16494396 T G High
16731274 A G High
16911488 T C High
16992269 A T High
17178479 G T High
18354280 A G High
18638789 A G High
19311810 C G High
19842035 G T High
21404728 G A High
21569454 G T High
21952388 T C High
22229722 T A High
22229913 C G High
22233732 C G High
22235226 C T High
22240888 A T High
22246045 C G High
22246199 G A High
22259729 T C High
22262889 A T High
22269664 C G High
22269796 T A High
22293981 C G High
22302537 C T High
22316451 C G High
22318641 A C High
22318642 G A High
22318643 A C High
22318978 T C High
22319170 A T High
22319171 G T High
22319362 A T High
22319363 T A High
22346168 A T High
22422202 T C High
22432368 G C High
22436300 A C High
22444659 A T High
22459019 T G High
22459048 C A High
22459098 G T High
22459121 T A High
22459127 G T High
22461490 A C High
22461574 G A High
22462549 A T High
22462651 A G High
22464001 T G High
22464007 A T High
22464022 A G High
22464030 C A High
22467097 G T High
22467126 A T High
22469869 A G High
22473179 C T High
22473287 G T High
22474534 G T High
22474565 A G High
22474572 A C High
22474589 G T High
22474638 G T High
22474721 A C High
22474730 A G High
22475479 A T High
22475524 A C High
22476329 T G High
22476381 A T High
22476393 G T High
22476404 A T High
22476419 T A High
22476914 G A High
22476922 G C High
22513335 T C High
22898224 A C High
22920241 G A High
23354909 A C High
23457952 C A High
24008094 T C High
24382845 G A High
24447989 A C High
24453842 G T High
28787127 G A High
28787141 C G High
28788643 G T High
28788695 T A High
6898366 T C High
7321330 A C High
8725633 A G High
8805525 A G High
9227801 A T High
9231864 G C High
9296025 G A High
9316833 A G High
9350171 A G High
9392243 C T High
9992071 A C High

emmental
03-26-2014, 11:53 AM
Thanks for posting. At first glance, I don't see anything that Kees, you and/or I share under Z36. Bummer :(

CelticGerman
03-26-2014, 12:34 PM
Thanks for posting. At first glance, I don't see anything that Kees, you and/or I share under Z36. Bummer :(

Not surprising, I think, as you don't have the three CTS mutations I have. We need patience and much more people doing the test.

emmental
03-26-2014, 04:13 PM
OK, I took your list and compared it to others who have posted on the forum. I marked the SNPs which are shared outside our haplogroup:

13271933 T A High shared
13672823 C T High
13687378 A T High shared
14367269 C A High shared
14398980 A G High shared
14399063 A G High shared
14399074 A G High shared
14399077 G A High shared
14399105 G A High shared
14644698 C T High shared
14644742 C T High shared
14647641 T A High
14709276 A T High shared
14709277 C G High shared
14744185 T C High
15540519 T C High
15858877 G A High
16357373 T C High
16441973 A C High
16494396 T G High
16731274 A G High
16911488 T C High
16992269 A T High
17178479 G T High
18354280 A G High
18638789 A G High
19311810 C G High
19842035 G T High shared
21404728 G A High
21569454 G T High
21952388 T C High shared
22229722 T A High shared
22229913 C G High shared
22233732 C G High shared
22235226 C T High shared
22240888 A T High
22246045 C G High shared
22246199 G A High shared
22259729 T C High shared
22262889 A T High shared
22269664 C G High shared
22269796 T A High shared
22293981 C G High shared
22302537 C T High shared
22316451 C G High shared
22318641 A C High shared
22318642 G A High shared
22318643 A C High shared
22318978 T C High shared
22319170 A T High shared
22319171 G T High shared
22319362 A T High shared
22319363 T A High shared
22346168 A T High shared
22422202 T C High shared
22432368 G C High shared
22436300 A C High shared
22444659 A T High shared
22459019 T G High
22459048 C A High
22459098 G T High
22459121 T A High
22459127 G T High
22461490 A C High
22461574 G A High
22462549 A T High
22462651 A G High
22464001 T G High
22464007 A T High
22464022 A G High
22464030 C A High
22467097 G T High
22467126 A T High
22469869 A G High
22473179 C T High
22473287 G T High
22474534 G T High
22474565 A G High
22474572 A C High
22474589 G T High
22474638 G T High
22474721 A C High
22474730 A G High
22475479 A T High
22475524 A C High
22476329 T G High
22476381 A T High
22476393 G T High
22476404 A T High
22476419 T A High
22476914 G A High
22476922 G C High
22513335 T C High
22898224 A C High
22920241 G A High
23354909 A C High shared
23457952 C A High
24008094 T C High
24382845 G A High
24447989 A C High shared
24453842 G T High shared
28787127 G A High shared
28787141 C G High shared
28788643 G T High shared
28788695 T A High shared
6898366 T C High
7321330 A C High shared
8725633 A G High
8805525 A G High shared
9227801 A T High
9231864 G C High
9296025 G A High shared
9316833 A G High shared
9350171 A G High
9392243 C T High
9992071 A C High shared


There seems to be a of of SNPs in that one short section.

Belgae
03-26-2014, 10:50 PM
Posted by Emmental: "Thanks for posting. At first glance, I don't see anything that Kees, you and/or I share under Z36."


Indeed, I agree: no apparent matches. I find it difficult to determine which variants are above or below Z36. But you are making a good effort Jim! Possibly Richard may also assist here.

emmental
03-28-2014, 03:09 AM
Posted by Emmental: "Thanks for posting. At first glance, I don't see anything that Kees, you and/or I share under Z36."


Indeed, I agree: no apparent matches. I find it difficult to determine which variants are above or below Z36. But you are making a good effort Jim! Possibly Richard may also assist here.

OK, I went through the list again comparing to my variant compare file from FGC. I matched on all the shared SNPs, but most of them were lower confidence (either ** or ***). The quality matches are marked with FGC numbers.

Then I went through Kees' variant compare and found that there were three matches to Konther's novel SNPs!!!! All three were lower confidence calls, but the fact that they are matches should raise the confidence level.

Here is the list with revised labels:

13271933 T A High shared
13672823 C T High
13687378 A T High shared
14367269 C A High shared
14398980 A G High shared
14399063 A G High shared
14399074 A G High shared
14399077 G A High shared
14399105 G A High shared
14644698 C T High shared
14644742 C T High shared
14647641 T A High
14709276 A T High shared
14709277 C G High shared
14744185 T C High
15540519 T C High
15858877 G A High
16357373 T C High
16441973 A C High
16494396 T G High MATCH Recourt ***
16731274 A G High
16911488 T C High
16992269 A T High
17178479 G T High
18354280 A G High
18638789 A G High
19311810 C G High
19842035 G T High shared
21404728 G A High
21569454 G T High
21952388 T C High shared FGC26
22229722 T A High shared
22229913 C G High shared
22233732 C G High shared FGC1558
22235226 C T High shared
22240888 A T High MATCH Recourt **
22246045 C G High shared
22246199 G A High shared FGC1556
22259729 T C High shared
22262889 A T High shared
22269664 C G High shared
22269796 T A High shared
22293981 C G High shared
22302537 C T High shared
22316451 C G High shared
22318641 A C High shared
22318642 G A High shared
22318643 A C High shared
22318978 T C High shared
22319170 A T High shared
22319171 G T High shared
22319362 A T High shared
22319363 T A High shared
22346168 A T High shared
22422202 T C High shared
22432368 G C High shared
22436300 A C High shared
22444659 A T High shared
22459019 T G High
22459048 C A High
22459098 G T High
22459121 T A High
22459127 G T High
22461490 A C High
22461574 G A High
22462549 A T High
22462651 A G High
22464001 T G High
22464007 A T High
22464022 A G High
22464030 C A High
22467097 G T High
22467126 A T High
22469869 A G High
22473179 C T High
22473287 G T High
22474534 G T High
22474565 A G High
22474572 A C High
22474589 G T High
22474638 G T High
22474721 A C High
22474730 A G High
22475479 A T High
22475524 A C High
22476329 T G High
22476381 A T High
22476393 G T High
22476404 A T High
22476419 T A High
22476914 G A High
22476922 G C High
22513335 T C High
22898224 A C High
22920241 G A High
23354909 A C High shared FGC7450
23457952 C A High
24008094 T C High
24382845 G A High
24447989 A C High shared FGC15
24453842 G T High shared
28787127 G A High shared
28787141 C G High shared
28788643 G T High shared
28788695 T A High shared
6898366 T C High
7321330 A C High shared FGC21
8725633 A G High
8805525 A G High shared FGC22
9227801 A T High shared
9231864 G C High
9296025 G A High shared
9316833 A G High shared
9350171 A G High MATCH Recourt ***
9392243 C T High
9992071 A C High shared


Edit Note: In the variant compare file all the matches to Recourt also had matches outside the hg. Frustrating and confusing.

R.Rocca
03-28-2014, 05:46 AM
OK, I went through the list again comparing to my variant compare file from FGC. I matched on all the shared SNPs, but most of them were lower confidence (either ** or ***). The quality matches are marked with FGC numbers.

Then I went through Kees' variant compare and found that there were three matches to Konther's novel SNPs!!!! All three were lower confidence calls, but the fact that they are matches should raise the confidence level.

Here is the list with revised labels:

13271933 T A High shared
13672823 C T High
13687378 A T High shared
14367269 C A High shared
14398980 A G High shared
14399063 A G High shared
14399074 A G High shared
14399077 G A High shared
14399105 G A High shared
14644698 C T High shared
14644742 C T High shared
14647641 T A High
14709276 A T High shared
14709277 C G High shared
14744185 T C High
15540519 T C High
15858877 G A High
16357373 T C High
16441973 A C High
16494396 T G High MATCH Recourt ***
16731274 A G High
16911488 T C High
16992269 A T High
17178479 G T High
18354280 A G High
18638789 A G High
19311810 C G High
19842035 G T High shared
21404728 G A High
21569454 G T High
21952388 T C High shared FGC26
22229722 T A High shared
22229913 C G High shared
22233732 C G High shared FGC1558
22235226 C T High shared
22240888 A T High MATCH Recourt **
22246045 C G High shared
22246199 G A High shared FGC1556
22259729 T C High shared
22262889 A T High shared
22269664 C G High shared
22269796 T A High shared
22293981 C G High shared
22302537 C T High shared
22316451 C G High shared
22318641 A C High shared
22318642 G A High shared
22318643 A C High shared
22318978 T C High shared
22319170 A T High shared
22319171 G T High shared
22319362 A T High shared
22319363 T A High shared
22346168 A T High shared
22422202 T C High shared
22432368 G C High shared
22436300 A C High shared
22444659 A T High shared
22459019 T G High
22459048 C A High
22459098 G T High
22459121 T A High
22459127 G T High
22461490 A C High
22461574 G A High
22462549 A T High
22462651 A G High
22464001 T G High
22464007 A T High
22464022 A G High
22464030 C A High
22467097 G T High
22467126 A T High
22469869 A G High
22473179 C T High
22473287 G T High
22474534 G T High
22474565 A G High
22474572 A C High
22474589 G T High
22474638 G T High
22474721 A C High
22474730 A G High
22475479 A T High
22475524 A C High
22476329 T G High
22476381 A T High
22476393 G T High
22476404 A T High
22476419 T A High
22476914 G A High
22476922 G C High
22513335 T C High
22898224 A C High
22920241 G A High
23354909 A C High shared FGC7450
23457952 C A High
24008094 T C High
24382845 G A High
24447989 A C High shared FGC15
24453842 G T High shared
28787127 G A High shared
28787141 C G High shared
28788643 G T High shared
28788695 T A High shared
6898366 T C High
7321330 A C High shared FGC21
8725633 A G High
8805525 A G High shared FGC22
9227801 A T High shared
9231864 G C High
9296025 G A High shared
9316833 A G High shared
9350171 A G High MATCH Recourt ***
9392243 C T High
9992071 A C High shared


Edit Note: In the variant compare file all the matches to Recourt also had matches outside the hg. Frustrating and confusing.

I am flying back from Switzerland today and will check this weekend. No doubt I was with many of our U152 brethren all week without knowing it :)

Belgae
03-28-2014, 12:14 PM
OK, I went through the list again comparing to my variant compare file from FGC. I matched on all the shared SNPs, but most of them were lower confidence (either ** or ***). The quality matches are marked with FGC numbers.

Then I went through Kees' variant compare and found that there were three matches to Konther's novel SNPs!!!! All three were lower confidence calls, but the fact that they are matches should raise the confidence level.

Edit Note: In the variant compare file all the matches to Recourt also had matches outside the hg. Frustrating and confusing.

Thanks for the good work Jim, I did not look at the lower confidence level yet. With respect to your edit, indeed confusing.... I do not know the answer to that. Apparently above Z36?

Rathna
03-28-2014, 12:23 PM
I am flying back from Switzerland today and will check this weekend. No doubt I was with many of our U152 brethren all week without knowing it :)

Perhaps also a glance Southwards wouldn't have been out of place! lol

R.Rocca
03-28-2014, 04:57 PM
Perhaps also a glance Southwards wouldn't have been out of place! lol

Would have been nice, but unfortunately it was a business trip with no time for a long overdue visit to Italy.

Rathna
03-28-2014, 05:38 PM
Would have been nice, but unfortunately it was a business trip with no time for a long overdue visit to Italy.

I did mean with the spirit, not with the body. Unfortunately is the spirit which lacks.

MitchellSince1893
03-29-2014, 02:29 AM
Got my results today. According to the FTDNA filters I've got a question mark for Z150. So no clue on that one.

MitchellSince1893
03-29-2014, 04:06 AM
13271933 T A High
13672823 C T High
etc.

Not sure if this is helpful, but I compared your list to mine and we shared these below.
So I assume these would be higher up the tree than your Z36+ and my L2+.
That leaves me with 46 novel high confidence snps at or below L2.
Assuming 82.5 years per snp (one every 3 generations or 75-90 years is one estimate). That would put the age of L2 at around 3800ybp...assuming BigY didn't miss many snps.

13271933
13687378
14367269
14398980
14399063
14399074
14399077
14399105
14644698
14644742
14709276
14709277
19842035
21952388
22229722
22229913
22233732
22235226
22240888
22246045
22246199
22259729
22262889
22269664
22269796
22293981
22302537
22318641
22318642
22318643
22318978
22319170
22319171
22319362
22319363
22346168
22422202
22432368
22436300
22444659
23354909
24447989
24453842
28787127
28787141
28788643
28788695
7321330
8805525
9227801
9296025
9316833
9992071

R.Rocca
03-29-2014, 04:36 AM
Got my results today. According to the FTDNA filters I've got a question mark for Z150. So no clue on that one.

It is showing you as 8413680 (A>G) which is Z12222 and you are also 22867545 (A>T). Both of these look like they are the same subclade level as Z150. Unfortunately no read at CTS9490 and negative for CTS7970.

R.Rocca
03-29-2014, 12:53 PM
Thanks for the good work Jim, I did not look at the lower confidence level yet. With respect to your edit, indeed confusing.... I do not know the answer to that. Apparently above Z36?

It looks like those three SNPs are very common outside of U152.

MitchellSince1893
03-29-2014, 02:51 PM
Here are what my results look like on the Experimental Tree view (available once you get your BigY results). I'm officially U152 now (tested positive for P312 and L2 before but not previously tested for U152)

Green is positive for, red is negative for listed snp. Although I show as a no call for Z150, as discussed above, Rich confirmed I was positive for both Z12222 and 22867545, both are approximate of Z150.

1660

Pigmon
03-29-2014, 03:20 PM
Congratulations! You finally got your Big Y results. As far as the Z150 SNP - I am considering the Geno 2.0 test because I am still waiting for FTDNA to offer the test a la carte. Hopefully there will be another sale for Geno 2.0!


Here are what my results look like on the Experimental Tree view (available once you get your BigY results). I'm officially U152 now (tested positive for P312 and L2 before but not previously tested for U152)

Green is positive for, red is negative for listed snp. Although I show as a no call for Z150, as discussed above, Rich confirmed I was positive for both Z12222 and 22867545, both are approximate of Z150.

1660

MitchellSince1893
03-29-2014, 04:28 PM
Congratulations! You finally got your Big Y results. As far as the Z150 SNP - I am considering the Geno 2.0 test because I am still waiting for FTDNA to offer the test a la carte. Hopefully there will be another sale for Geno 2.0!

Why don't you go with Thomas Krahn's company YSEQ DNA? http://shop.yseq.net/

You can order the snp Z12222 (approximate to Z150) http://shop.yseq.net/advanced_search_result.php?keywords=z150&search_in_description=1&osCsid=ddac15e2332f6be9483d274304f30887&x=8&y=12

It's only $35.00.

haleaton
03-29-2014, 06:11 PM
Here are what my results look like on the Experimental Tree view (available once you get your BigY results). I'm officially U152 now (tested positive for P312 and L2 before but not previously tested for U152)

Green is positive for, red is negative for listed snp. Although I show as a no call for Z150, as discussed above, Rich confirmed I was positive for both Z12222 and 22867545, both are approximate of Z150.

1660

Interesting, for my Big Y, there is no new "Experimental Tree" just the four or five year old one based on my Deep Clade and Z196- single SNP test. They may have been unable to determine my Haplogroup by Big Y and relied on old results since I was a no call for L2 and Z49 in the Big Y Test though have other tests to verify I am L2* plus private SNPS found by Fullgenomes, and about half those show up in Big Y.

Perhaps they published their Experimental Y tree elsewhere? Thanks.

MitchellSince1893
03-29-2014, 07:37 PM
Interesting, for my Big Y, there is no new "Experimental Tree" just the four or five year old one based on my Deep Clade and Z196- single SNP test. They may have been unable to determine my Haplogroup by Big Y and relied on old results since I was a no call for L2 and Z49 in the Big Y Test though have other tests to verify I am L2* plus private SNPS found by Fullgenomes, and about half those show up in Big Y.

Perhaps they published their Experimental Y tree elsewhere? Thanks.
Try viewing your BigY results in google chrome with the BigY Addon https://chrome.google.com/webstore/detail/big-y-addon/efblkbamlmgongbfkddoediffhcdfdmj

Pigmon
03-29-2014, 07:47 PM
Why don't you go with Thomas Krahn's company YSEQ DNA? http://shop.yseq.net/

You can order the snp Z12222 (approximate to Z150) http://shop.yseq.net/advanced_search_result.php?keywords=z150&search_in_description=1&osCsid=ddac15e2332f6be9483d274304f30887&x=8&y=12

It's only $35.00.

I was not aware of this company. Thanks for the info - I will check it out and consider it!

In the meantime I will keep checking the records for ancestors!

Curtis Pigman/Pigmon/Pygmon/Pimond/Piemont/Piemonte/Piedmont, etc.

haleaton
03-29-2014, 10:27 PM
Try viewing your BigY results in google chrome with the BigY Addon https://chrome.google.com/webstore/detail/big-y-addon/efblkbamlmgongbfkddoediffhcdfdmj

Thanks, there were multiple issues but when add in working in Chrome there is still no updated tree for FTDNA though links to ISOGG tree.

Added successfully to Chrome. Cleared Caches et cetera (this was needed) Then add-in worked with add on features . . . Thanks!

HOWEVER when I go to the FTDNA Tree, It is still the same 2010 Tree from Deep Clade.

I sent them a message and will wait for response. It might be due to L2 no call which must just be random thing, I hope. However since L2 is pretty standard on old trees for a new tester they should repeat BIG Y (at their expense) until the haplogroup is determined--In my case there are no downstream public SNPs so they would have to.

Hopefully the other L2 -Z49 -Z367 Big Y samples are not L2 no call. Rich will let us know. Waiting to get my BAM file from FTDNA.

This also happened to me with L2 in Chromo2 due to a defect when creating the Chip but they had a very updated tree for U152 and Britains DNA performed additional testing to determine my haplogroup at their own expense. This was not a random thing, but would be fixed on next chip if there is one.

Interested in FTDNA Big Y. no calls are randomly distributed and as long as you get >25K ones (useless or not) you pass Q/A.

haleaton
03-30-2014, 12:06 AM
1662

Here is comparison of my Big Y, I am L2+ Z367- Z49- based on other testing, against the Chromo2 tree. "No Call" means it was "?". N/A was not reported.

I was also L196- No(-) correctly so based on the FTDNA 2010 tree they have determined my haplogroup to knowledge at that time.

Others Big Y results hopefully will be different.

MitchellSince1893
03-30-2014, 12:29 AM
Thanks, there were multiple issues but when add in working in Chrome there is still no updated tree for FTDNA though links to ISOGG tree.

Added successfully to Chrome. Cleared Caches et cetera (this was needed) Then add-in worked with add on features . . . Thanks!

HOWEVER when I go to the FTDNA Tree, It is still the same 2010 Tree from Deep Clade.

I sent them a message and will wait for response. It might be due to L2 no call which must just be random thing, I hope. However since L2 is pretty standard on old trees for a new tester they should repeat BIG Y (at their expense) until the haplogroup is determined--In my case there are no downstream public SNPs so they would have to.

Hopefully the other L2 -Z49 -Z367 Big Y samples are not L2 no call. Rich will let us know. Waiting to get my BAM file from FTDNA.

This also happened to me with L2 in Chromo2 due to a defect when creating the Chip but they had a very updated tree for U152 and Britains DNA performed additional testing to determine my haplogroup at their own expense. This was not a random thing, but would be fixed on next chip if there is one.

Interested in FTDNA Big Y. no calls are randomly distributed and as long as you get >25K ones (useless or not) you pass Q/A.

It's called Moreley DNA. See the circled area on the picture below (taken with BigY addon in google chrome)
1663

haleaton
03-30-2014, 06:31 AM
It's called Moreley DNA. See the circled area on the picture below (taken with BigY addon in google chrome)
1663

Oh I did look at this. I thought this was a third party thing not connected to FTDNA. Could not determine my haplogroup at all unless the tree established by by comparing 1K Genomes data is broken. Similar results with ISOGG tree.

Is this really FTNDNA's new tree?

[Edit. I manually added L2+, Z36-, Z49- and the ISOGG comparison almost determined my haplogroup but needed Z56- and the Experimental tree was unable to determine my haplogroup at really. At least what I believe to be my haplogroup based on Sanger and Fullgenomes and Chromo2. ] I was also L2+ at 23andme five years ago.

Solothurn
03-30-2014, 12:44 PM
Not one Big Y U152* result in >:(

I wonder how many have received new kits?

emmental
03-30-2014, 07:31 PM
I'm going through Konther's SNP list recently posted on the R-U152 SNP page. Apparently he tested Z47+ in the Big Y. Can this be?

CelticGerman
03-30-2014, 07:45 PM
I'm going through Konther's SNP list recently posted on the R-U152 SNP page. Apparently he tested Z47+ in the Big Y. Can this be?

It's indicated with "Confidence high". If you find anything else, let us know. I hope Monnier will have his results shortly, for he was somehow "close" to me.

I quickly had a look on FTDNA project's SNP lists. In fact, Z47+ exists in a few U152, L2 and L20 people.

R.Rocca
03-30-2014, 08:37 PM
Not one Big Y U152* result in >:(

I wonder how many have received new kits?

Presley, kit no. 40733, (CTS7193+ L2- Z36- Z56- Z192- F1493- PF4363-) is showing as completed, but is throwing an error when I try to look at his results. I sent FTDNA a note. The hope is that CTS7193 is a downstream marker and there are other hidden ones above it. On a positive note, there are two Chromo 2.0 U152* samples that have tested S20550+ and Genome of the Netherlands shows an additional two S20550+ samples.

Kwheaton
03-31-2014, 01:03 AM
1662

Here is comparison of my Big Y, I am L2+ Z367- Z49- based on other testing, against the Chromo2 tree. "No Call" means it was "?". N/A was not reported.

I was also L196- No(-) correctly so based on the FTDNA 2010 tree they have determined my haplogroup to knowledge at that time.

Others Big Y results hopefully will be different.
Hal,

I want to thank you for sharing the comparisons and for testing on both platforms. And it is confirmation for me that we made the right choice in going for the Full Y. This does not surprise me.

I imagine some folks will hit most of the important marks with Big Y but some as you show will not.

MitchellSince1893
03-31-2014, 01:29 AM
I'm going through Konther's SNP list recently posted on the R-U152 SNP page. Apparently he tested Z47+ in the Big Y. Can this be?

I also did BigY and have Z47+. Looking at the FTDNA U152 SNP page, https://www.familytreedna.com/public/R1b-U152/default.aspx?section=ysnp
there are 10 kits that are Z47+.

R.Rocca
03-31-2014, 02:23 AM
I also did BigY and have Z47+. Looking at the FTDNA U152 SNP page, https://www.familytreedna.com/public/R1b-U152/default.aspx?section=ysnp
there are 10 kits that are Z47+.

Perhaps something is wrong with what is being represented on the FTDNA U152 SNP page, because your raw data file is showing you as ancestral (0 value) in the Z47 position 15487097. However, Z47 is actually a deletion and may be a bit "unreliable".

MitchellSince1893
03-31-2014, 04:54 AM
I have seen some minor inconsistencies in the SNPs reported for my kit on the U152 SNP page, vs my BigY results and within the BigY results themselves when comparing the table results to the downloadable results.

For example PF1396 shows up as derived in the table form but it's not in the downloadable data.

CTS1795 shows up in both the table and downloadable data, but isn't listed for me on the U152 SNP page.

haleaton
03-31-2014, 05:03 AM
Perhaps something is wrong with what is being represented on the FTDNA U152 SNP page, because your raw data file is showing you as ancestral (0 value) in the Z47 position 15487097. However, Z47 is actually a deletion and may be a bit "unreliable".

Big Y me has me as Z47(+) Reference:G Genotype:G
Full Genomes has me as Z47- Consensus Sample Allele:G Reference Sample Allele:G

So I think it may be definition thing in comparing with reference? Or just an error.

haleaton
03-31-2014, 06:30 AM
Hal,

I want to thank you for sharing the comparisons and for testing on both platforms. And it is confirmation for me that we made the right choice in going for the Full Y. This does not surprise me.

I imagine some folks will hit most of the important marks with Big Y but some as you show will not.

I think we will learn new things about U152 from Big Y but it will just take some time. A random no call is better than a true false call you cannot predict.

Solothurn
03-31-2014, 03:51 PM
Has Presley done the Big Y or was his CTS7193+ from Geno 2.0?

I only ask as on U152 his group says 'CTS7193 (L2- Z36- Z56- Z192- F1493- PF4363-, Please order BigY'



Presley, kit no. 40733, (CTS7193+ L2- Z36- Z56- Z192- F1493- PF4363-) is showing as completed, but is throwing an error when I try to look at his results. I sent FTDNA a note. The hope is that CTS7193 is a downstream marker and there are other hidden ones above it. On a positive note, there are two Chromo 2.0 U152* samples that have tested S20550+ and Genome of the Netherlands shows an additional two S20550+ samples.

tbartold
03-31-2014, 04:32 PM
Perhaps something is wrong with what is being represented on the FTDNA U152 SNP page, because your raw data file is showing you as ancestral (0 value) in the Z47 position 15487097. However, Z47 is actually a deletion and may be a bit "unreliable".

My BigY results show Z47+ at FTDNA, but I sent the BigY BAM file to both FGC and YFull. YFull lists Z47/15487097 as negative with 66 reads. FGC does not list that position.

So it looks like FTDNA is interpreting it wrong?

It does not occur on my listing from the U152 SNP page, since not all of my results from BigY are included.

I have to wonder if it only occurs on the U152 SNP page for BigY participants whose results were transferred starting March 25?

R.Rocca
03-31-2014, 05:20 PM
Has Presley done the Big Y or was his CTS7193+ from Geno 2.0?

I only ask as on U152 his group says 'CTS7193 (L2- Z36- Z56- Z192- F1493- PF4363-, Please order BigY'

He ordered both, but his Big-Y results are not displaying.

Solothurn
03-31-2014, 06:31 PM
Thanks Rich



He ordered both, but his Big-Y results are not displaying.

Barellalee
04-01-2014, 06:10 AM
What is the presenc, if any, of U152 in more eeastern locales, like Greece and the Balkans? Not much I imagine, as I see it strongly represented as a quite western and central European "Italic" or "Celtic" Branch.

Armenis
04-01-2014, 08:00 AM
What is the presenc, if any, of U152 in more eeastern locales, like Greece and the Balkans? Not much I imagine, as I see it strongly represented as a quite western and central European "Italic" or "Celtic" Branch.

I am the person from Greece who has ordered the Big Y and is R1b-L2* thus far. Should be interesting to see if there are any common markers downstream of L2.

Sinclar
04-01-2014, 10:13 AM
I received my Big Y late last evening. I'm 216196 ancestor Charles St Clair.
I had an initial hiccup looking for known SNPs downstream of U152*. I'm negative for two I was looking for: Z193- (PF6658-) and CTS11933-. But I do have 85 novel variants of high confidence. :)
I'll have to wait to see if the U152 guys (Richard or Steve) can find anything in my raw data for known SNPs downstream of U152*. The problem with downloading my raw data is now fixed.

MitchellSince1893
04-01-2014, 12:06 PM
Congrats to you!

Barellalee
04-01-2014, 03:31 PM
That is very interesting, where abouts in Greece is your Paternal side from. Im not the most educated on R1b, but learning. I don't know yet any of the other Y Haplogroups of my family either, apart from mine, I2a1c L233. My Maternal Uncle is testing now, so we shall know that soon. His result will be reflective of my Maternal Great-Grandfather who was from Abruzzo in South Italy. Latest work by Brisighelli, seems to indicate that R1b and J2 are close runners up in Abruzzo, and other Haplogroups are pretty minor, but we shall see.

Armenis
04-01-2014, 04:15 PM
That is very interesting, where abouts in Greece is your Paternal side from. Im not the most educated on R1b, but learning. I don't know yet any of the other Y Haplogroups of my family either, apart from mine, I2a1c L233. My Maternal Uncle is testing now, so we shall know that soon. His result will be reflective of my Maternal Great-Grandfather who was from Abruzzo in South Italy. Latest work by Brisighelli, seems to indicate that R1b and J2 are close runners up in Abruzzo, and other Haplogroups are pretty minor, but we shall see.

We are from the island of Corfu. I have tested a number of men with the same surname from Corfu and they are all R1b-L2*. I'm hoping the Big Y result will enlighten us as to where our L2* came from before establishing themselves on Corfu i.e. Angevin (Maine-et-Loire, Provence or Burgundy), Venetian (Treviso), Dolomites (Cadore), Genoan (Liguria), Gallatian, Dorian etc.

R.Rocca
04-01-2014, 04:44 PM
I received my Big Y late last evening. I'm 216196 ancestor Charles St Clair.
I had an initial hiccup looking for known SNPs downstream of U152*. I'm negative for two I was looking for: Z193- (PF6658-) and CTS11933-. But I do have 85 novel variants of high confidence. :)
I'll have to wait to see if the U152 guys (Richard or Steve) can find anything in my raw data for known SNPs downstream of U152*. The problem with downloading my raw data is now fixed.

Good news...you share three SNPs with two unrelated/anonymous males from the UK. The SNPs are as follows:

16515046(A>G)
22478765(G>C)
23059272(C>A)

No name for these SNPs yet, but you definitely form a new branch below U152. Congratulations!

Technically the two other samples are one level below you because they share 15797586(A>G) with each other.

Sinclar
04-01-2014, 05:28 PM
That's fantastic news, Richard.

Really appreciate your efforts... It feels great to contribute to the U152 study.

It was well worth doing the Big Y.

Kwheaton
04-01-2014, 06:23 PM
That's fantastic news, Richard.

Really appreciate your efforts... It feels great to contribute to the U152 study.

It was well worth doing the Big Y.

Congrats Sinclir and Tha ks to Rich for his tireless efforts.
Kelly

MitchellSince1893
04-01-2014, 06:47 PM
Corfu was occupied by both romans and normans so that could be a source for the U152.

Armenis
04-01-2014, 10:40 PM
Corfu was occupied by both romans and normans so that could be a source for the U152.

True, the Romans and Normans left their mark on Corfu. Both Italy (Sicily & Southern Italy 'Naples') and Corfu were ruled by the Normans for a period of time. The Angevins followed immediately afterwards. The Romans were a diverse group ... it could be Roman but I'm hoping my results suggest a specific population group or region. Corfu was an Angevin stronghold (1267-1401) and a Venetian stronghold for almost 400 years (1401-1797). I found a document in the archives that predates the Venetian period where my family name is mentioned, ruling out Venetian origin?

MitchellSince1893
04-02-2014, 02:22 AM
Now that I've got my BigY results I anxiously waiting for kit#s 7181 (Davenport) and N115212 (Brace) to come out to see if we share any novel SNPs. Right now I'm all alone in the
U152> L2> Z49/Z68> Z142> Z150/Z12222/22867545 group on the U152 project page.

In less than 2 weeks I should have my BAM file, so I can send it for further analysis.

A cursory look at other publically posted U152 results on this site narrows my novel SNP list down to these currently unique (to me) SNPs. Let me know if you match any of these:

Position Reference Genotype Confidence
6754788 G C High
6833853 C T High
7224581 G C High
7881772 C G High
8194117 T G High
8290583 T C High
9795464 C G High
9852155 C T High
9862775 G A High
13142597 G T Medium
13302072 C T High
13713820 T C High
14071348 A T Medium
14497774 A C High
15607220 G C High
15878557 C T High
15971853 G A High
16185253 G A High
16692081 C A High
16692088 C A High
16692095 C A High
17003970 T C High
17299391 C T High
19436291 G A High
21290212 A G High
21690021 G T High
22240008 T C High
22242681 C G High
22242700 T C High
22242777 A T High
22242910 T C High
22242922 C A High
22242951 G A High
22242957 A C High
22242963 G C High
22243012 A C Medium
22244165 A G High
22244750 G T High
22244761 C A High
22244785 C G Medium
22244786 T C Medium
22244804 A T High
22244848 T G Medium
22244849 A T Medium
22319065 T C Medium
22319066 A T Medium
22476861 G A High
22486450 G A High
22771081 G A High
22941997 G A High
23415300 G A High
23969601 G A High
24991713 G C High

LUKE33
04-02-2014, 12:34 PM
.... and a Venetian stronghold for almost 400 years 1401-1797. I found a document in the archives that predates the Venetian period where my family name is mentioned, ruling out Venetian origin?

Hello ,

Don't forget, that there were two periods of Venetian rule - Corfu/kerkyra :

1) The first period 1204 - 1214

2) The Second Period 1386 – 1797

Here is the distribution of the Armeni surname Italy :

http://www.cognomix.it/mappe-dei-cognomi-italiani/ARMENI


http://whc.unesco.org/en/list/978

For those individuals wishing to know a little more about " the old town Corfu/Kerkyra".

Solothurn
04-02-2014, 02:55 PM
Congratulations :)

I am anxiously awaiting Steve's results, kit 133986. Then again he may have received a new kit instead :(

Zafonte and Aulicino's results may also be interesting, being from Sicily and Campania!


I received my Big Y late last evening. I'm 216196 ancestor Charles St Clair.
I had an initial hiccup looking for known SNPs downstream of U152*. I'm negative for two I was looking for: Z193- (PF6658-) and CTS11933-. But I do have 85 novel variants of high confidence. :)
I'll have to wait to see if the U152 guys (Richard or Steve) can find anything in my raw data for known SNPs downstream of U152*. The problem with downloading my raw data is now fixed.

R.Rocca
04-02-2014, 03:15 PM
Now that I've got my BigY results I anxiously waiting for kit#s 7181 (Davenport) and N115212 (Brace) to come out to see if we share any novel SNPs. Right now I'm all alone in the
U152> L2> Z49/Z68> Z142> Z150/Z12222/22867545 group on the U152 project page.

In less than 2 weeks I should have my BAM file, so I can send it for further analysis.

A cursory look at other publically posted U152 results on this site narrows my novel SNP list down to these currently unique (to me) SNPs. Let me know if you match any of these:

Don't forget that there are other groups with Z150/Z12222 kits in them that show private SNPs that may not be very relevant in the grand scheme of things....point being, you are not alone.

Barellalee
04-02-2014, 07:11 PM
Do you think it is actually possible it was Dorian? I don't know, I'm just seeing your opinion. From what I know, the Dorians were Indo-European migrants from the northeast of where Greece is, though could be slightly off there. Not positive, but I would guess Italian links would be a more likely explanation.

MitchellSince1893
04-03-2014, 02:23 AM
...A cursory look at other publically posted U152 results on this site narrows my novel SNP list down to these currently unique (to me) SNPs. Let me know if you match any of these:

Position Reference Genotype Confidence
...
22242951 G A High S3077 BritainsDNA
22242957 A C High S27780 BritainsDNA
...

Checked the snps listed in post 139 above against the BritainsDNA snps list. https://www.dropbox.com/s/46ubi9qntb2un03/BritainsDNAchromo2positions.xlsx

These 2 two SNPs I previously listed above are also on Britain's DNA SNP list as:
22242951 = S3077
22242957 = S27780

Relevance? Significance? Not sure at this point.

Armenis
04-03-2014, 09:34 AM
Do you think it is actually possible it was Dorian? I don't know, I'm just seeing your opinion. From what I know, the Dorians were Indo-European migrants from the northeast of where Greece is, though could be slightly off there. Not positive, but I would guess Italian links would be a more likely explanation.

It's possible, and if it was then what SNP should I be looking for lol. I'll settle for anything really, I have decided to let my DNA do the talking. In my STR matches I have 1 Greek and 2 Montenegrins at 23/25 ... they are all R1b-L2*. The other 4 matches at 23/25 are coincidental - all are British and not even positive for R1b-U152. No Italian matches unfortunately ...

Rathna
04-03-2014, 10:13 AM
It's possible, and if it was then what SNP should I be looking for lol. I'll settle for anything really, I have decided to let my DNA do the talking. In my STR matches I have 1 Greek and 2 Montenegrins at 23/25 ... they are all R1b-L2*. The other 4 matches at 23/25 are coincidental - all are British and not even positive for R1b-U152. No Italian matches unfortunately ...

Of course the link you have with this person from Montenegro is very close: within a few centuries, and that he has translittered his Serbian/Montenegran surname of Konjevic in Cognevich demonstrates, I think, an Italian link, because only in Italian "gn" translitters "nj".
Thus I think to a link with the Venetian Republik. About the genetic origin only a SNP deep test will say something definitive, but R-U152 is very strong in Italy till Central Europe, much less in Slav countries, but we know that above all in Ex-Yugoslavia the presence of not Slav genetics is very huge.
XJHU9 Armenis Corfu, South Africa
13 24 14 11 11 15 12 12 12 14 13 30 17 9 10 11 11 23 15 19 31 15 16 17 17 11 11 19 23 16 14 17 18 35 36 12 12 12 12 13 11 9 15 16 8 10 10 8 10 11 23 23 16 10 12 12 14 8 23 20 12 11 13 11 11 12 12
GGE54 Cognevich Montenegro
13 24 14 11 11 14 12 12 12 14 13 30 17 9 9 11 11 23 15 19 31 15 16 17 17 11 11 19 23 16 14 17 17 36 36 12 12 12 12 13 11 9 15 16 8 10 10 8 10 11 23 23 16 10 12 12 14 8 22 20 12 11 13 11 11 12 12

vettor
04-03-2014, 10:47 AM
Do you think it is actually possible it was Dorian? I don't know, I'm just seeing your opinion. From what I know, the Dorians were Indo-European migrants from the northeast of where Greece is, though could be slightly off there. Not positive, but I would guess Italian links would be a more likely explanation.

Dorians where from North-west of Greece around ~1100BC, currently they where from lands of Albania and Epirus

vettor
04-03-2014, 10:51 AM
Of course the link you have with this person from Montenegro is very close: within a few centuries, and that he has translittered his Serbian/Montenegran surname of Konjevic in Cognevich demonstrates, I think, an Italian link, because only in Italian "gn" translitters "nj".
Thus I think to a link with the Venetian Republik. About the genetic origin only a SNP deep test will say something definitive, but R-U152 is very strong in Italy till Central Europe, much less in Slav countries, but we know that above all in Ex-Yugoslavia the presence of not Slav genetics is very huge.
XJHU9 Armenis Corfu, South Africa
13 24 14 11 11 15 12 12 12 14 13 30 17 9 10 11 11 23 15 19 31 15 16 17 17 11 11 19 23 16 14 17 18 35 36 12 12 12 12 13 11 9 15 16 8 10 10 8 10 11 23 23 16 10 12 12 14 8 23 20 12 11 13 11 11 12 12
GGE54 Cognevich Montenegro
13 24 14 11 11 14 12 12 12 14 13 30 17 9 9 11 11 23 15 19 31 15 16 17 17 11 11 19 23 16 14 17 17 36 36 12 12 12 12 13 11 9 15 16 8 10 10 8 10 11 23 23 16 10 12 12 14 8 22 20 12 11 13 11 11 12 12

My Wife has a 3rd cousin from Friuli with the surname Velcovich ........there are a lot of these "carnico" ....vich ( i was told it means something like son of ) endings in Friuli and especially in the town of Cadore di Piave

Rathna
04-03-2014, 12:47 PM
My Wife has a 3rd cousin from Friuli with the surname Velcovich ........there are a lot of these "carnico" ....vich ( i was told it means something like son of ) endings in Friuli and especially in the town of Cadore di Piave

No doubt that these are Slav surnames, but about Velcovich I'd be curious to know what did mean that Velco-, which is in many languages the name of Latins as to others (in origin Volcae were a Celt people opposed to German ones), see Welsh in Great Britain etc. Also to day in Hungary Italy is Olasz(orszag).
Of course in these zones surnames changed frequently from one language to another: in your Trentino/Alto Adige we know that many Italian surnames were Germanized, and genetics is still here to demonstrate the origin of that people. Of course in other times many surnames were Italianized etc. But every hypothesis has to be verified deeply. As to Konjevic we don't know if it was a Slavization of Italian Cavallini or from other not Slav languages. For that I said that only a deep SNP test will be able to answer this question.
I wouldn't be surprised if this R-U152 were from Balkans before the arrival of Slavs.

Armenis
04-03-2014, 03:34 PM
Of course the link you have with this person from Montenegro is very close: within a few centuries, and that he has translittered his Serbian/Montenegran surname of Konjevic in Cognevich demonstrates, I think, an Italian link, because only in Italian "gn" translitters "nj".
Thus I think to a link with the Venetian Republik. About the genetic origin only a SNP deep test will say something definitive, but R-U152 is very strong in Italy till Central Europe, much less in Slav countries, but we know that above all in Ex-Yugoslavia the presence of not Slav genetics is very huge.

This Cognevich family now live in the USA and are originally from the area of Kotor. They have no Y DNA matches with other Konjevic from Montenegro and are confused about their ancestral origins. My family from Corfu traded with Kotor and the islands of Korcula, Brac etc. (Dalmatia) during the Venetian period. The Italian encyclopedia of family names for Yugoslavia gives the name Arneri from Korcula with Armeni alongside it as the Italian equivalent. My family name is also spelt Darmer (d'Armer) in old archive documents on Corfu and the Angevin barony on Corfu named Darmer was where the Armenis family are from (Armenades, Rachtades). The d'Armer were an old Venetian family apparently from Cadore? But other Venetian sources state that the Armeni family in Venice was from Istria (Ossero) and was also known as Arminio (Arminii) and Armadio (Amadii). Apparently Armadio = Armer in the Venetian dialect. Venetian, Istrian or Angevin (French) ... perhaps ancient Dorian in the historical sense (Sea people)?

Rathna
04-03-2014, 04:08 PM
This Cognevich family now live in the USA and are originally from the area of Kotor. They have no Y DNA matches with other Konjevic from Montenegro and are confused about their ancestral origins. My family from Corfu traded with Kotor and the islands of Korcula, Brac etc. (Dalmatia) during the Venetian period. The Italian encyclopedia of family names for Yugoslavia gives the name Arneri from Korcula with Armeni alongside it as the Italian equivalent. My family name is also spelt Darmer (d'Armer) in old archive documents on Corfu and the Angevin barony on Corfu named Darmer was where the Armenis family are from (Armenades, Rachtades). The d'Armer were an old Venetian family apparently from Cadore? But other Venetian sources state that the Armeni family in Venice was from Istria (Ossero) and was also known as Arminio (Arminii) and Armadio (Amadii). Apparently Amadio = Armer in Venetian/French lexicons. Venetian, Istrian or Angevin (French) ... perhaps ancient Dorian in the historical sense (Sea people)?

"I d'Armer (talvolta anche Darmer, Dalmario o Armeri) furono una famiglia patrizia veneziana, annoverata fra le cosiddette Case Nuove [...]Questa famiglia si estinse probabilmente nel 1553 con Giacomo di Alvise d'Armer".

Also the "del Badia" of Castelfiorentino, after having had illustrious people like Bonaventura Neri Badia and above all his son Pompeo Neri Badia and having mixed with noble families, went extinct. No one takes the surname "del Badia" after the historian Iodoco del Badia, but from "Antonio del Badia" and his two sons Piero and Michelagnolo of the late 15th century came the Tognoni, the Togni, and probably many others, if my haplotype has been found in one anonymous Brazilian etc.
Nobles and riches went extinct, often, and poor people survived. Perhaps you are one of the "D'Armer" descendants, but only genetics will be able to demonstrate that.

Armenis
04-03-2014, 06:13 PM
"Perhaps you are one of the "D'Armer" descendants, but only genetics will be able to demonstrate that.

If the D'Armer name is no more and survives as Armenis on Corfu how can we determine if I am indeed a descendant of the d'Armer family utilizing DNA testing? Venetian genealogists claimed that the d'Armer family were from Cadore in Belluno ... any L2* people from this region please raise your hand!

vettor
04-03-2014, 06:41 PM
No doubt that these are Slav surnames, but about Velcovich I'd be curious to know what did mean that Velco-, which is in many languages the name of Latins as to others (in origin Volcae were a Celt people opposed to German ones), see Welsh in Great Britain etc. Also to day in Hungary Italy is Olasz(orszag).
Of course in these zones surnames changed frequently from one language to another: in your Trentino/Alto Adige we know that many Italian surnames were Germanized, and genetics is still here to demonstrate the origin of that people. Of course in other times many surnames were Italianized etc. But every hypothesis has to be verified deeply. As to Konjevic we don't know if it was a Slavization of Italian Cavallini or from other not Slav languages. For that I said that only a deep SNP test will be able to answer this question.
I wouldn't be surprised if this R-U152 were from Balkans before the arrival of Slavs.

As you know, the Volcae commenced in southern France ( gallic people) and moved eastwards

R.Rocca
04-03-2014, 07:46 PM
Guys, please stay on topic as folks are here to look for Big-Y results.

vettor
04-03-2014, 07:53 PM
No doubt that these are Slav surnames, but about Velcovich I'd be curious to know what did mean that Velco-, which is in many languages the name of Latins as to others (in origin Volcae were a Celt people opposed to German ones), see Welsh in Great Britain etc. Also to day in Hungary Italy is Olasz(orszag).
Of course in these zones surnames changed frequently from one language to another: in your Trentino/Alto Adige we know that many Italian surnames were Germanized, and genetics is still here to demonstrate the origin of that people. Of course in other times many surnames were Italianized etc. But every hypothesis has to be verified deeply. As to Konjevic we don't know if it was a Slavization of Italian Cavallini or from other not Slav languages. For that I said that only a deep SNP test will be able to answer this question.
I wouldn't be surprised if this R-U152 were from Balkans before the arrival of Slavs.

My wife corrected me, it was vencovich ..........venci means wickers in Venetian. The name was what was given by slav authorities to Italian authorities for the children.

But the surname was maybe fabricated as the children ( her cousins ) where separated from the parents and where part of the 250000 Italians that exited ( forced) from istria, Dalmatia, croatia after WWII . They settled in Concordia Friuli then moved to Caorle Veneto..........but you would know the majority of these displaced people settled in Asiago

vettor
04-03-2014, 08:01 PM
If the D'Armer name is no more and survives as Armenis on Corfu how can we determine if I am indeed a descendant of the d'Armer family utilizing DNA testing? Venetian genealogists claimed that the d'Armer family were from Cadore in Belluno ... any L2* people from this region please raise your hand!

2013 paper has


Adige-valley [56 samples] is Rovereto and Trento which is the Venetian part of Welsch Tyrol;

Fiemme-valley [41 samples] is Venetian part of Welsch Tyrol;

Primiero-valley [41 samples] is Venetian part of Welsch Tyrol;

Fersina-valley [25 samples] is the German (Fersental) part of Welsch Tyrol;

Cimbrians (Luserna/Lissinia) [total 49 samples] is the German isolates of Welsch Tyrol;

Giudicarie-valley [51 samples] is the Lombard part of Welsch Tyrol;

Non-valley [48 samples] is Lombard/Ladiner part of Welsch Tyrol;

Sole-valley [66 samples] is Lombard/Ladiner part of Welsch Tyrol;

Badia/Fassa/Gardena [total 142 samples] all Ladiner valleys of South & Welsch Tyrol;

Timau/Sappada/Sauris [91 samples] all German isolate valleys in the Karnian Alps;


Ladiners are heavy in R1b-U152 L2+
23.9% of the 142 samples are L2+ alone (U152 total = 26.0% 142 samples)
37 samples are R1b-U152 with 34 L2+ & 3 U152* (91.8% of all U152 in Ladiners is L2)

Ladiners in Gardena are also heavy in R1b-L21;


Coia et al 2013 -
http://www.plosone.org/article/info%...l.pone.0081704

142 samples of three Ladiner valleys (Badia/Fassa/Gardena)

10.5% K-M9 [15 samples] ( 4 are L marker and 11 are T marker)

0.7% R1b-M269 [1 samples]
8.4% R1b-L51 [12 samples]
0.7% R1b-L11 [1 samples]
28.1% R1b-U152 [40 samples]
10.5% R1b-L21 [15 samples]
4.2% R1b-U106 [6 samples]

1.4% R1a [2 samples]

0.7% I-M170 [1 samples]
4.9% I1-M253 [7samples]
0.7% I2-P37.2 [1 samples]

5.6% G-M201 [8 samples]

0.7% E-M35 [1 samples]
2.8% E-V13 [4 samples]

4.9% J1-M267 [7samples]
0.7% J2-M172 [1 samples]
10.5% J2a [15 samples]
3.5% J2b [5 samples]

Highlights are
The 28.1% R1b-U152 [2.1% U152* / 26.0% L2] meaning 92.5% of all U152 in Ladiner folks is L2;
And 10.5% R1b-L21 (reaching 24.4% in Gardena-valley 12/49 samples);
4.9% J1-M267 (only in Fassa-valley 14.8% 7/47 samples);

The R1b-U152 is no surprise - the overwhelming amount of U152/L2+ however is;
(26.0% of the total pop. and 92.5% within U152 / 142 samples);
R1b-U152 is most def. due to all the Indo-European Keltic (Vennones/Carni) and Venetic folks mingling with/within the East Alpine Raetic realms (as attested by Historic and Linguistic inscriptions); prob. also the Indo-European Symrbi (Umbrians);


J2a is not that surprising as its well common all across Italy and also other Alpine regions;
J-M304 is 8.8% in East Tyrol (270 samples - Niederstätter et al 2012)
J2-M172 is 6.8% in Bavaria (218 samples - Rebala et al 2013)


The 10.5% of R1b-L21 is the real sensation (whats the Brythonic Keltic link?);
Bavaria = 1.3% R1b-L21 (218 samples - Rebala et al 2013)
East Tyrol = 0.0% R1b-L21 (270 samples - Niederstätter et al 2012)
Venetia = 0.0% R1b-L21 (73 samples - Boattini et al 2013)

And yet right in middle of all these regions (0-1.3%) there is a Ladiner valley (Grödner/Gardena) with 24.4% and a certain volk-group (Ladiner/Raeto-Romanic) with 10.5% R1b-L21 overall 142 sampels;
Obviously an isolated pan-Keltic phenomenan;
Im waiting for a study with Romansch samples (the other Raeto-Romanic people);
Maybe R1b-L21 is an Alpine isolate in addition to a pan-Keltic phenomanan with R1b-U152 stuffing the center of this pan-Keltic phenomenan;

138 samples from the Venetian areas/valleys (Adige/Primiero/Fiemme)

3.6% K-M9 [5 samples] ( 2 are L marker and 3 are T marker )

9.4% R1b-M269 [13 samples]
2.1% R1b-L51 [3 samples]
0.7% R1b-L11 [1 samples]
4.3% R1b-P312 [6 samples]
1.4% R1b-SRY2627 [2 samples]
0.7% R1b-L21 [1 samples]
26.0% R1b-U152 [36 samples]
6.5% R1b-U106 [9 samples]

5.0% R1a-M17 [7 samples]

18.1% G-M201 [25 samples]

4.3% I1-M253 [6 samples]
0.7% I2-M223 [1 samples]
2.1% I2-M423 [3 samples]

5.7% E-V13 [8 samples]
0.7% E-V22 [1 samples]

1.4% J1-M267 [2 samples]
2.1% J2a [3 samples]
2.8% J2b [4 samples]

[2 samples n.a.]

vettor
04-03-2014, 08:12 PM
This Cognevich family now live in the USA and are originally from the area of Kotor. They have no Y DNA matches with other Konjevic from Montenegro and are confused about their ancestral origins. My family from Corfu traded with Kotor and the islands of Korcula, Brac etc. (Dalmatia) during the Venetian period. The Italian encyclopedia of family names for Yugoslavia gives the name Arneri from Korcula with Armeni alongside it as the Italian equivalent. My family name is also spelt Darmer (d'Armer) in old archive documents on Corfu and the Angevin barony on Corfu named Darmer was where the Armenis family are from (Armenades, Rachtades). The d'Armer were an old Venetian family apparently from Cadore? But other Venetian sources state that the Armeni family in Venice was from Istria (Ossero) and was also known as Arminio (Arminii) and Armadio (Amadii). Apparently Amadio = Armer in Venetian/French lexicons. Venetian, Istrian or Angevin (French) ... perhaps ancient Dorian in the historical sense (Sea people)?

Where did you see that Amadio = Armer..........I ask because my great grand mother is a Amadio

also Alvise is Venetian for Luis in English or Luigi in Italian

Solothurn
04-04-2014, 12:31 PM
I just tried to see if Weir and Auliciano were in the SNP page for BigY results! They have been removed or my eyes are deceiving me! Can somebody please search for them?

emmental
04-04-2014, 12:57 PM
I just tried to see if Weir and Auliciano were in the SNP page for BigY results! They have been removed or my eyes are deceiving me! Can somebody please search for them?

They are both listed, but it looks like no results yet. I am interested in Mollestad's (Z36) results. It appears that his came in the other day. I'd like to see his novel SNPs to compare to mine, but they don't post them and he doesn't seem to be a member of this forum. :(

Sinclar
04-04-2014, 01:54 PM
I have an interesting novel variant clash (23059272) which I'm sure will get more clarification when the U152 Big Y workload eases a bit.
I'm (216196 - Charles St Clair) A1 U152> 16515046(A>G) / 22478765(G>C) / 23059272(C>A)
Duncan is A1 U152> 193 / PF6658 (Z192-) 23059272 (C>A)

Solothurn
04-04-2014, 02:53 PM
Thanks :)

My phone's search was too tired. Or I am too impatient :)


They are both listed, but it looks like no results yet. I am interested in Mollestad's (Z36) results. It appears that his came in the other day. I'd like to see his novel SNPs to compare to mine, but they don't post them and he doesn't seem to be a member of this forum. :(

mafe
04-04-2014, 08:46 PM
My Big-Y results just came in. 81 novel variants, 62 high confidence.
Negative for the known SNPs: PF6658, Z193, CTS11993, S20550, 16515046, 22478765, 23059272 and 23119461.

This is one for the U152 experts!

MitchellSince1893
04-04-2014, 08:54 PM
Congrats Mafe! Now the fun begins.

Sinclar
04-04-2014, 09:39 PM
Congratulations on your results, Mafe. It's just the beginning...

Solothurn
04-04-2014, 11:23 PM
Congratulations mafe :)

Andereggen's are in too!

MitchellSince1893
04-05-2014, 03:25 AM
Got my bam file link today...quicker than I thought...took 5 business days. Already sent it to Yfull.com and FGC for further analysis.

Excited about getting this analysis back.

Also began downloading my bam zip file at 6:30 tonight. 5 hours later I've downloaded 15%! 1GB in size.

mafe
04-05-2014, 09:42 AM
My BIG-Y stats:

Known SNPs

Total: 36281
Derived: 503
Ancestral: 24380
?: 11398

Novel variants

Total: 81
High: 62
Medium: 19
Unknown: 0


Of the 81 novel variants, 45 are reported in other results, so that leaves me with 36 novel variants that could be downstream of U152*.

mafe
04-06-2014, 07:57 AM
Now that I've got my BigY results I anxiously waiting for kit#s 7181 (Davenport) and N115212 (Brace) to come out to see if we share any novel SNPs. Right now I'm all alone in the
U152> L2> Z49/Z68> Z142> Z150/Z12222/22867545 group on the U152 project page.

In less than 2 weeks I should have my BAM file, so I can send it for further analysis.

A cursory look at other publically posted U152 results on this site narrows my novel SNP list down to these currently unique (to me) SNPs. Let me know if you match any of these:

Position Reference Genotype Confidence
6754788 G C High
6833853 C T High
7224581 G C High
7881772 C G High
8194117 T G High
8290583 T C High
9795464 C G High
9852155 C T High
9862775 G A High
13142597 G T Medium
13302072 C T High
13713820 T C High
14071348 A T Medium
14497774 A C High
15607220 G C High
15878557 C T High
15971853 G A High
16185253 G A High
16692081 C A High
16692088 C A High
16692095 C A High
17003970 T C High
17299391 C T High
19436291 G A High
21290212 A G High
21690021 G T High
22240008 T C High
22242681 C G High
22242700 T C High
22242777 A T High
22242910 T C High
22242922 C A High
22242951 G A High
22242957 A C High
22242963 G C High
22243012 A C Medium
22244165 A G High
22244750 G T High
22244761 C A High
22244785 C G Medium
22244786 T C Medium
22244804 A T High
22244848 T G Medium
22244849 A T Medium
22319065 T C Medium
22319066 A T Medium
22476861 G A High
22486450 G A High
22771081 G A High
22941997 G A High
23415300 G A High
23969601 G A High
24991713 G C High

16692081 and 16692088 are also in my list, but are also reported in R2.

Rathna
04-06-2014, 08:17 AM
16692081 and 16692088 are also in my list, but are also reported in R2.

The fact that a mutation has happened independently in another haplogroup (more if rarely as it seems in this case) shouldn't prevent from considering it valid, as I think your case is.

P.S. Perhaps there is a link in these two mutations: they are close (only 8 bp of difference) and the same C to A.

mafe
04-06-2014, 08:24 AM
The fact that a mutation has happened independently in another haplogroup (even if rarely as it seems in this case) shouldn't prevent from considering it valid, as I think your case is.

MitchellSince1893 is L2+. I am L2-. If these SNPs aren't in other L2+ lists, it likely is upstream of U152. I haven't seen them in other U152+ lists.

Rathna
04-06-2014, 08:31 AM
MitchellSince1893 is L2+. I am L2-. If these SNPs aren't in other L2+ lists, it likely is upstream of U152. I haven't seen them in other U152+ lists.

I apologize. I thought you were in the same subclade. If not, something doesn't fit. It is unlikely that they are in U152, otherwise all the others would have had them. Probably they are independent also in L2+ and in L2-. I think it would be important to understand the nature of this mutation, because it could be only one mutation and not two independent ones.

mafe
04-06-2014, 08:36 AM
I apologize. I thought you were in the same subclade. If not, something doesn't fit. It is unlikely that they are in U152, otherwise all the others would have had them. Probably they are independent also in L2+ and in L2-. I think it would be important to understand the nature of this mutation, because it could be only one mutation and not two independent ones.

No worries, 9981785 is a third one I share with the reported R2 list, they are all medium confidence, perhaps a barcoding issue?

MitchellSince1893
04-07-2014, 04:07 AM
16692081 and 16692088 are also in my list, but are also reported in R2.

Thanks. That leaves me with 44 novel snps that dont' match other haplogroups so far.

May I ask where you are accessing the R2 snps? I would like to see if any of these 44 match any r2 snps.
Edit: Found it here http://www.anthrogenica.com/showthread.php?2245-Family-Tree-DNA-Product-Launch-Big-Y&p=34514&viewfull=1#post34514

Found another snp I share with R2 individual: 16692095

So now I'm down to 43 novel snps.

mafe
04-07-2014, 01:07 PM
I entered my 36 "non-shared" novel variants into Ybrowse and I found three known point mutations, two from BritainsDNA and one from FGC. Two are high confidence variants, the other is medium and doesn't report the same derived allele.

S19861 (T to A)
S24831 (G to T) mine is (G to C) Medium confidence.
FGC6232 (G to A)

MitchellSince1893
04-07-2014, 02:53 PM
I'll have to try out ybrowse on my remaining snps tonight.

MitchellSince1893
04-07-2014, 10:54 PM
Mafe, (or anyone else in the know) could you walk me through how you are using ybrowse?

I went to the ybrowse browser and entered 50 below and 50 above my snp e.g. for novel snp 6833853 I entered "ChrY:6,833,803..6,833,903"

Is this what you are doing? If so what do I do next? What am I looking for?

Forgive my ignorance on this. Not that intuitive for a humanities/social sciences guy :)

EDIT: Figured it out...just enter your snp in the browser in following format:
"ChrY: 8413680..8413680" At the bottom you will see any named snps. In this case you would see S7402 and Z12222. If you don't see anything listed then it doesn't have a name yet.

Went through all 43....no named snps on ybrowse.

mafe
04-08-2014, 02:38 PM
Mafe, (or anyone else in the know) could you walk me through how you are using ybrowse?

I went to the ybrowse browser and entered 50 below and 50 above my snp e.g. for novel snp 6833853 I entered "ChrY:6,833,803..6,833,903"

Is this what you are doing? If so what do I do next? What am I looking for?

Forgive my ignorance on this. Not that intuitive for a humanities/social sciences guy :)

EDIT: Figured it out...just enter your snp in the browser in following format:
"ChrY: 8413680..8413680" At the bottom you will see any named snps. In this case you would see S7402 and Z12222. If you don't see anything listed then it doesn't have a name yet.

Went through all 43....no named snps on ybrowse.

It is easier than it looks :)

mafe
04-08-2014, 08:09 PM
I have serious concerns about the number of total entries and the number of unclear/no-call values in my Big-Y results.

My number of total entries (known variants): 36281
My number of ' ? ' values (known variants): 11398

Please post your number of total entries and ' ? ' values in this thread so we can compare them and see if there are big differences between kits.

Biloo
04-08-2014, 08:13 PM
My number of total entries (known variants): 36278
My number of ' ? ' values (known variants): 10367

Sinclar
04-08-2014, 09:17 PM
36,552 in total
567 (Yes)
25,521 (No)
10,464 (?)

MitchellSince1893
04-09-2014, 12:04 AM
36551 total
552 (Yes) Used to be 612 but dropped for some reason
24930 (No)
11069(?)

MitchellSince1893
04-09-2014, 02:27 AM
After googling my remaining 43 novel snps, I'm now down to 36.

I had 6 that matched L21 DF41 snps (anthrogenica thread) and 1 that matched a J haplogroup tester.

Here are the remaining novel snps:
6754788 6833853 7224581 7881772 8194117 8290583 9795464 9852155 9862775 13713820 14497774 15607220 15878557 15971853 16185253 17003970 17299391 19436291
21290212 21690021 22240008 22242777 22242910 22242922 22242963 22244165 22244750 22244785 22244786 22244804 22476861 22486450 22771081 22941997 23415300 23969601 24991713

tbartold
04-09-2014, 02:38 AM
I have results!

However, I was surprised with the number of undefined results.
36,566 tested.
613 Yes
25,046 No
10,907 Undefined.

One more interesting number, is that it says that only 91 of the 613 Yes results are currently on the haplotree.

Obviously I posted results a while back, but decided to check again, and yes, they've changed!

36,557 total
563 Yes
25,087 No
10,907 Undefined.

89 of the Yes results are on the Y-Tree.

Curious that so many Yes turned in No, and some disppeared from the Total.

At least, the Undefined number remained the same.

Also, the numbers on the Novel Variants tab remained the same: 99 High + 33 Medium.

haleaton
04-09-2014, 05:57 AM
Mine also changed. Unfortunately, at that time I was unable to capture the named SNP list due to web browser issue. I don't know if the Y-tree changed but probably not unless it is not the same as the 2010 Y-tree they provide. Maybe the BED file changed? Also only the High confidence SNPs changed.


Confidence
Named SNPs Number Update Change
On Y Tree - Yes(+) 90 88 -2
On Y Tree - No(-) 657 655 -2
On Y Tree - ? 36 36 0
Not on Y Tree - Yes(+) 514 459 -55
Not on Y Tree - No(-) 24108 24185 77
Not on Y Tree - ? 11157 11157 0
Total 36562 36553 -9

haleaton
04-09-2014, 01:52 PM
Mine also changed. Unfortunately, at that time I was unable to capture the named SNP list due to web browser issue. I don't know if the Y-tree changed but probably not unless it is not the same as the 2010 Y-tree they provide. Maybe the BED file changed? Also only the High confidence SNPs changed.


Confidence
Named SNPs Number Update Change
On Y Tree - Yes(+) 90 88 -2
On Y Tree - No(-) 657 655 -2
On Y Tree - ? 36 36 0
Not on Y Tree - Yes(+) 514 459 -55
Not on Y Tree - No(-) 24108 24185 77
Not on Y Tree - ? 11157 11157 0
Total 36562 36553 -9



It may just be a FTDNA web page math issue counting the number of SNPs that changed, as if I do a fresh download (using the Chrome Add-in) and count the SNPs in Excel I get the old numbers in my chart. Nothing seems to have changed in the data.

MitchellSince1893
04-12-2014, 03:46 PM
Got my FGC analysis of my BigY results today...took 5 business days. Reviewing it now.

One cool thing about doing this is that your unnamed novel snps get names. e.g FGC#####.

I will give a more detailed post once I go through it all but I've already learned they've determined I share 6 snps with HG01777...the individual with me on the latest U152 tree, at the Z150/Z12222 position.

21690021 G T FGC12378+ (also shared with HG02977)
7224581 G C FGC12379+
6833853 C T FGC12380+
9852155 C T FGC12381+
6754788 G C FGC12382+
7733015 T G FGC12383+

MitchellSince1893
04-12-2014, 07:09 PM
After googling my remaining 43 novel snps, I'm now down to 36.

I had 6 that matched L21 DF41 snps (anthrogenica thread) and 1 that matched a J haplogroup tester.

Here are the remaining novel snps:
6754788 6833853 7224581 7881772 8194117 8290583 9795464 9852155 9862775 13713820 14497774 15607220 15878557 15971853 16185253 17003970 17299391 19436291
21290212 21690021 22240008 22242777 22242910 22242922 22242963 22244165 22244750 22244785 22244786 22244804 22476861 22486450 22771081 22941997 23415300 23969601 24991713

FGC analysis of my BigY results:
As I mentioned in above post, I share 6 SNPs with 1KG-HG01777 (Spanish male participate of the 1000 Genome project), but one of these is also shared with a 3rd kit which doesn't appear to be in our Haplogroup.

FGC report lists 23 novel SNPs with 95% or higher confidence
7547230 C T FGC12384+
7881772 C G FGC12385+
8173636 G A FGC12386+
8194117 T G FGC12387+
8290583 T C FGC12388+
9795464 C G FGC12389+
9862775 G A FGC12390+
10024162 T A FGC12391+
13713820 T C FGC12392+
14497774 A C FGC12393+
15129680 A C FGC12394+
15607220 G C FGC12395+
15878557 C T FGC12396+
15971853 G A FGC12397+
16185253 G A FGC12398+
17003970 T C FGC12399+
17299391 C T FGC12400+
19436291 G A FGC12401+
21290212 A G FGC12402+
22476861 G A FGC12403+
22771081 G A FGC12404+
22941997 G A FGC12405+
23969601 G A FGC12406+

So according to FGC I may have approximately 28 SNPs below Z150/Z12222.

FWIW, I've seen a couple of estimates for number of years between SNPs for BigY, 110 years and 150.

150 years 28 SNPs = 4200 years ago for age of Z150
110 years x 28 SNPs = 3080 years ago for age of Z150

Based on the above and playing with the TMRCA tool for Z142+ folks I would lean toward 125 years/SNP.

R.Rocca
04-13-2014, 10:32 AM
Got my FGC analysis of my BigY results today...took 5 business days. Reviewing it now.

One cool thing about doing this is that your unnamed novel snps get names. e.g FGC#####.

I will give a more detailed post once I go through it all but I've already learned they've determined I share 6 snps with HG01777...the individual with me on the latest U152 tree, at the Z150/Z12222 position.

21690021 G T FGC12378+ (also shared with HG02977)
7224581 G C FGC12379+
6833853 C T FGC12380+
9852155 C T FGC12381+
6754788 G C FGC12382+
7733015 T G FGC12383+

Thanks for the update, I have added them to the tree and they will appear in the next version. I also checked the Genome of the Netherlands project, and each of these SNPs is shared with two of their samples, so they seem to have a pretty good distribution.

Armenis
04-14-2014, 09:27 PM
My Big Y results have been posted.

I have removed as many common SNPs as possible from my novel SNP list, this is what remains (novel SNPs = 47):

13883832
14174464
14580291
15555018
15663417
15719954
16441973
16608728
16790178
16865442
16924999
17253641
17793926
17870616
19049873
19159079
21202753
22271629
22319065
22319066
22466255
22661359
22759013
22786678
23141463
23195831
23302793
23581721
23755998
23780213
23780861
23817063
2796841
6864498
7388811
7717741
7810808
7981457
8528995
8617548
8823984
9227801
9311383
9316833
9476463
9786712
9852985

Please let me know if you recognize any of these SNPs.
These I got from the MyFTDNA page, there are probably a few more in the data files that I haven't managed to pick up yet.

R.Rocca
04-16-2014, 12:21 AM
And then there was one...only kit no. 577 (Adam Kerchner b.c. 1704 Germany d. 1768 PA) has remained in the U152* group after doing FullGenomes and/or Big-Y testing.

haleaton
04-16-2014, 01:02 AM
And then there was one...only kit no. 577 (Adam Kerchner b.c. 1704 Germany d. 1768 PA) has remained in the U152* group after doing FullGenomes and/or Big-Y testing.

Is this the same Kerchner line that first tested positive for U-152?

R.Rocca
04-16-2014, 01:09 AM
Is this the same Kerchner line that first tested positive for U-152?

Indeed, and he first tested his Y-DNA in 2001! He was also the long time administrator of the U152 project.

Solothurn
04-16-2014, 06:24 AM
There appears to be very few SNPs for him in the results. Are all his BigY's on there?

mafe
04-16-2014, 10:46 AM
Is he U152*, as in, no novel SNPs downstream of U152?

R.Rocca
04-16-2014, 11:44 AM
Is he U152*, as in, no novel SNPs downstream of U152?

No, all kits have downstream SNPs. He is U152* because his downstream SNPs do not match that of others.

R.Rocca
04-16-2014, 11:46 AM
There appears to be very few SNPs for him in the results. Are all his BigY's on there?

I don't check the public SNP results page, just the raw data files from each kit's home page.

mafe
04-16-2014, 11:50 AM
No, all kits have downstream SNPs. He is U152* because his downstream SNPs do not match that of others.

Ok thanks, Do I share any SNPs with others? I was under the impression that I was a U152* aswell.

Biloo
04-16-2014, 12:13 PM
My Big Y results have been posted.

I have removed as many common SNPs as possible from my novel SNP list, this is what remains (novel SNPs = 47):

13883832
14174464
14580291
15555018
15663417
15719954
16441973
16608728
16790178
16865442
16924999
17253641
17793926
17870616
19049873
19159079
21202753
22271629
22319065
22319066
22466255
22661359
22759013
22786678
23141463
23195831
23302793
23581721
23755998
23780213
23780861
23817063
2796841
6864498
7388811
7717741
7810808
7981457
8528995
8617548
8823984
9227801
9311383
9316833
9476463
9786712
9852985

Please let me know if you recognize any of these SNPs.
These I got from the MyFTDNA page, there are probably a few more in the data files that I haven't managed to pick up yet.

We share 9227801 A>T . If other L2 (Z49- Z367-) don't have this mutation. It would mean that 9227801 A>T is downstream L2 and upstream DF90 since you are DF90-

R.Rocca
04-16-2014, 12:16 PM
We share 9227801 A>T . If other L2 (Z49- Z367-) don't have this mutation. It would mean that 9227801 A>T is downstream L2 and upstream DF90 since you are DF90-

9227801 is found in many other L2, Z36, Z56 etc. samples and is likely upstream of R1a and R1b.

R.Rocca
04-16-2014, 12:23 PM
Ok thanks, Do I share any SNPs with others? I was under the impression that I was a U152* aswell.

I was hoping to send you an email with the good news today, but here goes...you lost your star last night!!! You share 13668489(T>C) with 1000 Genomes Sample NA19720 from Mexico. Congratulations!

Biloo
04-16-2014, 12:26 PM
9227801 is found in many other L2, Z36,
Z56 etc. samples and is likely upstream of R1a and R1b.
Too bad...but thanks for the info !

Kwheaton
04-16-2014, 01:49 PM
Slightly off the current discussion but has anyone heard what has happened to the BIG Y that have not yet returned. Results page says March 28. That has obviously past. Of 12 Big Ys in my 2 groups 5 are still not returned. No explanation, no replacement kits sent anyone know whats up?
Thanks Kelly

mafe
04-16-2014, 03:01 PM
I was hoping to send you an email with the good news today, but here goes...you lost your star last night!!! You share 13668489(T>C) with 1000 Genomes Sample NA19720 from Mexico. Congratulations!

Great news Richard! Is this a confirmed / stable SNP? or is additional testing needed? Please send me all the info you have on this SNP, I need a good story to convince my distant matches that this might also be their downstream SNP.

R.Rocca
04-16-2014, 03:14 PM
Great news Richard! Is this a confirmed / stable SNP? or is additional testing needed? Please send me all the info you have on this SNP, I need a good story to convince my distant matches that this might also be their downstream SNP.

I checked samples across many haplogroups across different projects and the only two samples that share that SNP are yours and the 1KG sample which was also U152*. So to answer your question, it does indeed seem like a stable SNP.

mafe
04-16-2014, 03:38 PM
I checked samples across many haplogroups across different projects and the only two samples that share that SNP are yours and the 1KG sample which was also U152*. So to answer your question, it does indeed seem like a stable SNP.

Thanks, I'll see what I can do to get this SNP confirmed.

R.Rocca
04-16-2014, 06:38 PM
Thanks, I'll see what I can do to get this SNP confirmed.

By the way, I am still investigating another SNP that you, NA19720 and an anonymous English sample share. The SNP is 21387964(C>T) and, if confirmed, would bump down 13668489(T>C) one level, since the English sample does not have 13668489(T>C).

mafe
04-16-2014, 07:52 PM
By the way, I am still investigating another SNP that you, NA19720 and an anonymous English sample share. The SNP is 21387964(C>T) and, if confirmed, would bump down 13668489(T>C) one level, since the English sample does not have 13668489(T>C).

Thanks, This is great news! Is there anything I can do to help confirm these SNPs? I could contact my matches and ask them if they are willing to test with YSEQ.

Armenis
04-16-2014, 08:11 PM
How does one know whether a novel SNP is downstream from another SNP?

R.Rocca
04-16-2014, 08:25 PM
How does one know whether a novel SNP is downstream from another SNP?

If we take U152 for example, we know it is above L2 because more people have it. Same with these novel SNPs, as we see who has them and who doesn't, we can place them in the proper level of the tree.

Biloo
04-17-2014, 09:04 PM
This afternoon, FTDNA sent me the link to the .bam file of my big Y data. Do I need to upload the data to my computer before ordering the Yfull or can I just put this link directely in the order process of YFull.com ?

Thanks

MitchellSince1893
04-17-2014, 09:12 PM
No you just paste the link into the yfull.com order form.

Biloo
04-17-2014, 09:28 PM
No you just paste the link into the email you send them.

So if I understand well, I just have to copy and paste the link I got from FTDNA here : http://www.yfull.com/order/r/

MitchellSince1893
04-17-2014, 09:36 PM
So if I understand well, I just have to copy and paste the link I got from FTDNA here : http://www.yfull.com/order/r/

Sorry, bad memory on the email part...you will receive an email notification after you send in the order which includes your link.

Go to yfull.com and click the "order now" button (I chose the researcher one). In the window that opens there will be a field to paste your url. "Link to a raw data file (.BAM or .FASTQ)"

Biloo
04-18-2014, 02:14 PM
Starting from today, Yfull charges 49$ for an interpretation of a Y seq data. I feel so lucky. FTDNA sent me the bam file just in time:)

MitchellSince1893
04-18-2014, 02:45 PM
I'm suppose to get my yfull analysis results tomorrow.

Armenis
04-18-2014, 07:36 PM
I'm suppose to get my yfull analysis results tomorrow.

Unfortunately, I didn't make it in time. I asked Greg Magoon about the analysis Full Genomes Corp. is offering and he asked me to donate my BAM file for cross-kit referencing in their database. Any ideas as to which company (YFull or Full Genomes Corp.) has the largest U152 database for comparisons. I would like to compare my results with other similar U152-L2* kits.

haleaton
04-18-2014, 07:47 PM
Unfortunately, I didn't make it in time. I asked Greg Magoon about the analysis Full Genomes Corp. is offering and he asked me to donate my BAM file for cross-kit referencing in their database. Any ideas as to which company (YFull or Full Genomes Corp.) has the largest U152 database for comparisons. I would like to compare my results with other similar U152-L2* kits.

I think depends on Haplogroup, but Rich Rocca has the U152 largest database and goes to BAM file for analysis. I had FGC BGI testing and analysis and also got them to analyze my Big Y BAM. I think for analysis (and data) FGC is clearly the best.

I have had Y-Full analysis on my FGC BGI BAM file and was also good, but not as good with statistical analysis and transparency. Y-Full does do a good job comparing against known databases like 1K Genomes and probably for some Haplogroups is fantastic. Nice thing about FGC is they pretty tell you everything they did to determine whether a SNP is reliable.

I think it is worth it to pay for NGC Analysis of their Big Y data for the small fee and also consider the value of having a Full Genomes BGI test, though it is currently too much for many people.

Armenis
04-18-2014, 09:40 PM
I think depends on Haplogroup, but Rich Rocca has the U152 largest database and goes to BAM file for analysis. I had FGC BGI testing and analysis and also got them to analyze my Big Y BAM. I think for analysis (and data) FGC is clearly the best.

I have had Y-Full analysis on my FGC BGI BAM file and was also good, but not as good with statistical analysis and transparency. Y-Full does do a good job comparing against known databases like 1K Genomes and probably for some Haplogroups is fantastic. Nice thing about FGC is they pretty tell you everything they did to determine whether a SNP is reliable.

I think it is worth it to pay for NGC Analysis of their Big Y data for the small fee and also consider the value of having a Full Genomes BGI test, though it is currently too much for many people.

I have gone with FGC for my BAM file analysis.

MitchellSince1893
04-19-2014, 01:56 AM
Got my YFull results today...Still going through it all.

They identified 72 Private SNPs broken into 3 Quality levels:
Best=13, Acceptable=10, Unreliable=48, Low=1.

There is also a qual column. I'm not sure what the difference is as you see some unreliable snps with Qual=100

Some of these overlap FTDNA and FGC identified SNPs and some are unique. Here is the whole list.

Pos / Ref / Derived / Qual / Quality / Name
4063930 A G 100 Unreliable YFS084607
4542586 C A 100 Unreliable YFS084613
4810743 C A 100 Unreliable YFS084615
5201725 C A 100 Unreliable YFS084616
5248865 C A 100 Unreliable YFS084617
5358646 C A 100 Unreliable YFS084618
5513547 G T 100 Unreliable YFS084619
5829007 A T 100 Unreliable YFS084620
7081090 C A 100 Unreliable YFS084628
7174416 C A 100 Unreliable YFS084629
7174512 G T 100 Unreliable YFS084630
7360081 A G 100 Unreliable YFS084635
7547230 C T 100 Best YFS084636
7861289 A G 100 Unreliable YFS084638
7881772 C G 100 Best YFS084639
7897468 T C 100 Acceptable YFS084640
7897945 G T 100 Unreliable YFS084641
8173636 G A 100 Best YFS084645
8194117 T G 100 Best YFS084647
8290583 T C 100 Best YFS084648
9517035 G T 100 Unreliable YFS084659
9795464 C G 92 Acceptable YFS084674
9862775 G A 98 Acceptable YFS084676
13871171 G A 100 Acceptable YFS084856
14073023 C A 100 Unreliable YFS084857
14161683 A G 100 Unreliable YFS084858
14308214 A T 100 Unreliable YFS084860
14490470 T C 100 Unreliable YFS084863
14497774 A C 95 Acceptable YFS084864
14740194 C A 100 Unreliable YFS084866
14742100 C T 100 Unreliable YFS084867
15129680 A C 100 Best YFS084871
15607220 G C 99 Acceptable YFS084878
15857668 C A 100 Unreliable YFS084883
15878557 C T 100 Best YFS084885
15971853 G A 100 Best YFS084886
16003872 C A 100 Unreliable YFS084887
16185253 G A 100 Best YFS084911
17003970 T C 100 Best YFS084936
17071118 A G 100 Unreliable YFS084937
17203264 G A 100 Unreliable YFS084938
17299391 C T 100 Best YFS084939
17502862 A G 100 Unreliable YFS084940
17839588 C A 100 Unreliable YFS084941
17883247 G T 100 Unreliable YFS084943
18242103 C A 100 Unreliable YFS084951
19040635 C A 100 Unreliable YFS084979
19385801 C T 100 Unreliable YFS084981
19436291 G A 98 Acceptable YFS084982
19523409 C A 100 Unreliable YFS084983
20408815 C T 93 Acceptable YFS085012
21110030 G T 100 Unreliable YFS085047
21262590 G T 100 Unreliable YFS085063
21290212 A G 90 Unreliable YFS085064
21311488 G A 100 Unreliable YFS085065
21525003 C A 100 Unreliable YFS085109
21775341 G T 100 Unreliable YFS085113
22318347 T A 81 Low YFS085114
22476861 G A 95 Acceptable YFS085125
22532960 C T 100 Unreliable YFS085127
22545702 T C 100 Unreliable YFS085128
22628337 C A 100 Unreliable YFS085129
22771081 G A 94 Acceptable YFS085130
22941997 G A 100 Best YFS085162
23101990 G T 100 Unreliable YFS085163
23190765 C A 100 Unreliable YFS085164
23514489 C A 100 Unreliable YFS085166
23969601 G A 100 Best YFS085169
28503826 G T 100 Unreliable YFS085295
28514033 C A 100 Unreliable YFS085296
28560402 C A 100 Unreliable YFS085298
28638490 A G 100 Unreliable YFS085300

MitchellSince1893
04-20-2014, 03:54 AM
The 5 SNPs below, previously mentioned from the FGC analysis of my BigY; were also identified by the YFull analysis of my BigY.

Here are both their FGC and YFull names.

Position FGC/YFULL Name
6754788 FGC12382/Y3144
6833853 FGC12380/Y3143
7224581 FGC12379/Y3142
7733015 FGC12383/Y3141
9852155 FGC12381/Y3140

On YFull they aren't listed with my private SNPs, but rather are shown as "new" terminal SNPs in the "Hg and SNP" section. They are shown as being R1b1a2a1a2b1c1* aka below Z142.

Based on Richard Rocca's earlier comments, all of these are shared with a 1000 Genome participant from Valencia, Spain (HG01777), and 2 individuals from the Genome of the Netherlands project.

The next U152 tree update may include these SNPs.

MitchellSince1893
04-20-2014, 04:16 AM
My Big Y results have been posted.

I have removed as many common SNPs as possible from my novel SNP list, this is what remains (novel SNPs = 47):

13883832
14174464
14580291
15555018
15663417
15719954
16441973
16608728
16790178
16865442
16924999
17253641
17793926
17870616
19049873
19159079
21202753
22271629
22319065 YFC003458
22319066 YFC003459
22466255
22661359
22759013
22786678
23141463
23195831
23302793
23581721
23755998
23780213
23780861
23817063
2796841
6864498
7388811
7717741
7810808
7981457
8528995
8617548
8823984
9227801 Not yet named by YFull
9311383 Not yet named by YFull
9316833 Not yet named by YFull
9476463
9786712
9852985

Please let me know if you recognize any of these SNPs.
These I got from the MyFTDNA page, there are probably a few more in the data files that I haven't managed to pick up yet.

I share the 5 ones in bold.

R.Rocca
04-20-2014, 02:45 PM
I share the 5 ones in bold.

All are found across different subclades of U152 and other haplogroups.

MitchellSince1893
04-23-2014, 03:12 AM
Checked the snps listed in post 139 above against the BritainsDNA snps list. https://www.dropbox.com/s/46ubi9qntb2un03/BritainsDNAchromo2positions.xlsx

These 2 two SNPs I previously listed above are also on Britain's DNA SNP list as:
22242951 = S3077
22242957 = S27780

Relevance? Significance? Not sure at this point.
1. To partially answer my own question. It doesn't appear that S3077 is relevant/significant as two Chinese individuals in Haplogroup O have this SNP


Got my FGC analysis of my BigY results today...took 5 business days. Reviewing it now.

One cool thing about doing this is that your unnamed novel snps get names. e.g FGC#####.

I will give a more detailed post once I go through it all but I've already learned they've determined I share 6 snps with HG01777...the individual with me on the latest U152 tree, at the Z150/Z12222 position.

21690021 G T FGC12378+ (also shared with HG02977)
7224581 G C FGC12379+
6833853 C T FGC12380+
9852155 C T FGC12381+
6754788 G C FGC12382+
7733015 T G FGC12383+
2. According to YFull experimental tree, HG02977 is from Haplogroup E1b1; http://www.yfull.com/tree/E1b1a1a1f1a1d-Z1704*/
So obviously that wouldn't be downstream of Z150/Z12222

3. Not sure if it's significant, but FGC has a Chinese individual (Sample # NA18549) that is positive for position 22867545 (approximate to Z150 and Z12222 on Richard's U152 tree). According to the YFUll experimental tree this individual is from Haplogroup G3 http://www.yfull.com/tree/G2a2b2a1c1/

Biloo
05-06-2014, 07:43 PM
In the yfull.com analysis of my big Y data, DF90 is not listed under Private SNPs. Does that mean someone else is also DF90+ in the yfull database ?

R.Rocca
05-08-2014, 12:32 PM
In the yfull.com analysis of my big Y data, DF90 is not listed under Private SNPs. Does that mean someone else is also DF90+ in the yfull database ?

Were you able to get a response to this question from the YFull folks?

Biloo
05-08-2014, 02:57 PM
Were you able to get a response to this question from the YFull folks?
Not yet. DF90 has been put under Known SNP.

MitchellSince1893
05-13-2014, 10:29 PM
Anybody have any insight as to when the 9 outstanding U152 BigY tests will be complete or what the hold up is? Inquiring minds want to know.

I'm assuming Rich is holding off on an update to the U152 tree until these 9 are complete.

Solothurn
05-16-2014, 07:27 AM
I had a reply from Steve Wear and his 'pending' BigY results. Nothing, not even an email from FTDNA to apologise for the delay.

Very poor service from a very big company >:(

alan
05-22-2014, 11:15 PM
What sort of number of SNPs are people from U152 testing the full y finding between U152 and now

haleaton
05-23-2014, 04:12 AM
What sort of number of SNPs are people from U152 testing the full y finding between U152 and now

I am U152-L2* with Full Y BGI data which found 42 Private SNPs & 6 Private IDELs (high reliability). Two other SNPs were found to be invalid due to complex issue though it was found through comparison with Big Y test. Another two, so far, were found to valid by Sanger Sequencing but considered only ** reliability. They were flagged by YFull--there may be a few more like this. Number also include a few matches with one other person of a distant halplogroup.

Significant percentage of SNPs are not "amenable" Sanger sequencing, though probably perfectly good. Hope to have comparison with very distant paternal cousin in a few months, however it would be interesting to see a Full Y BGI NGS comparison of two brothers down to the *** reliability.

emmental
05-23-2014, 12:27 PM
What sort of number of SNPs are people from U152 testing the full y finding between U152 and now

I have 50 new SNPs under Z36 which FGC and YFull agree are quality matches. I share 27 of them with a 1KG sample and 23 are private.

R.Rocca
05-23-2014, 01:42 PM
What sort of number of SNPs are people from U152 testing the full y finding between U152 and now

55 high probability SNPs and 2 high probability INDELS in my kit below L2 which is one level down from U152. Three are known in a low quality sequence of a Sardinian male, so I may match many more with him.

MitchellSince1893
05-23-2014, 04:17 PM
I didn't do full genome but based on current stats that BiGY is averaging 47.8% of the novel SNPs compared to FGC:

I have 10-11 shared snps below u152. FGC Analysis of my BigY found 24 private SNPs. 24/.478= approx 50 private SNPs if I had done full genome test; for a total of ~60. Of course the 47.8% could be off for my particular test, but the actual number is probably between 46 and 67.

mafe
06-10-2014, 02:47 PM
Perhaps the U152 admins could notify members about the Big-Y coupon? I'm sure some Big-Y participants are willing to donate their coupons to other project members.

Armenis
06-10-2014, 09:12 PM
Perhaps the U152 admins could notify members about the Big-Y coupon? I'm sure some Big-Y participants are willing to donate their coupons to other project members.

I have been contacted by a L2* man who would like to purchase the Big Y and I want to give my $100 coupon to him. Where does one look for the coupon?

Thanks in advance

R.Rocca
06-11-2014, 12:07 PM
I have been contacted by a L2* man who would like to purchase the Big Y and I want to give my $100 coupon to him. Where does one look for the coupon?

Thanks in advance

You should have received it via the email.

Armenis
06-11-2014, 06:10 PM
You should have received it via the email.

I do not have it so I've asked the helpdesk to send me a coupon. It shouldn't be a problem ..

R.Rocca
06-11-2014, 06:38 PM
I do not have it so I've asked the helpdesk to send me a coupon. It shouldn't be a problem ..

Many folks are finding it in their "bulk" or "junk" folder. Since the FTDNA helpdesk has such a large backlog, let me know if you do not get a response as we may have others that are willing to share their coupon. I'd hate to see someone not take advantage of the sale.

Bolgeris
06-11-2014, 09:48 PM
For others people.. L20+ ..
i should like to share my coupon..
ciao.

mafe
06-12-2014, 03:20 PM
If I don't hear back from my U152 contacts I will donate my coupon to the project.

I've got a feeling alot of people don't know about these coupons, and a fair amount of coupons will go to waste.

R.Rocca
06-12-2014, 07:04 PM
If I don't hear back from my U152 contacts I will donate my coupon to the project.

I've got a feeling alot of people don't know about these coupons, and a fair amount of coupons will go to waste.

Fortunately we've had a coupon available for each U152+ that has requested one.

Solothurn
06-14-2014, 12:44 PM
Steve is now S20550+

So I ordered it at Yseq and await the result. I also contacted all my former U152 19, 22 and 27 matches and 'suggested they order it.

Nobody replied, either they're all away, passed on or just completely fed up with me pestering them :)

Hopefully we will have more luck when S20550 becomes available at FTDNA. I asked the helpdesk and they said they don't know, maybe months! :(




I had a reply from Steve Wear and his 'pending' BigY results. Nothing, not even an email from FTDNA to apologise for the delay.

Very poor service from a very big company >:(

R.Rocca
06-14-2014, 01:01 PM
Steve is now S20550+

So I ordered it at Yseq and await the result. I also contacted all my former U152 19, 22 and 27 matches and 'suggested they order it.

Nobody replied, either they're all away, passed on or just completely fed up with me pestering them :)

Hopefully we will have more luck when S20550 becomes available at FTDNA. I asked the helpdesk and they said they don't know, maybe months! :(

For those who don't know, Weir is also PF6658/Z193+.

glamberson
07-24-2014, 11:11 AM
Hello,

I am proxy for my mother's brother's results at FTDNA (kit#232800 Henderson). He was predicted L21 (which seemed dubious to me to begin with), but today his BigY results came in showing U152+L2+Z49+Z150+CTS7970+ .

I'm very active with my own L21+ and DF41+ groups, and now that I have my uncle's results, I'm hoping to jump in here.

Also, I joined U152 and P312 on FTDNA. Please advise what else I can do to get my uncle's results to the right people to further the development of the U152 tree.

Thanks,

Greg Lamberson

R.Rocca
07-24-2014, 12:29 PM
Hello,

I am proxy for my mother's brother's results at FTDNA (kit#232800 Henderson). He was predicted L21 (which seemed dubious to me to begin with), but today his BigY results came in showing U152+L2+Z49+Z150+CTS7970+ .

I'm very active with my own L21+ and DF41+ groups, and now that I have my uncle's results, I'm hoping to jump in here.

Also, I joined U152 and P312 on FTDNA. Please advise what else I can do to get my uncle's results to the right people to further the development of the U152 tree.

Thanks,

Greg Lamberson

Hello Greg. I will check your results tonight against my tree. Regards.

Pigmon
07-24-2014, 01:43 PM
Greg,

Does your Uncle have a ysearch ID? I looked at Henderson in there but there are a lot of them.

Curtis


Hello,

I am proxy for my mother's brother's results at FTDNA (kit#232800 Henderson). He was predicted L21 (which seemed dubious to me to begin with), but today his BigY results came in showing U152+L2+Z49+Z150+CTS7970+ .

I'm very active with my own L21+ and DF41+ groups, and now that I have my uncle's results, I'm hoping to jump in here.

Also, I joined U152 and P312 on FTDNA. Please advise what else I can do to get my uncle's results to the right people to further the development of the U152 tree.

Thanks,

Greg Lamberson

glamberson
07-24-2014, 02:00 PM
Hi Richard, Thanks. I look forward to hearing what you think. When I get a BAM file I'll run his kit through YFull as well. He doesn't look too close to hardly anyone so I'm guessing you'll see some useful data.

glamberson
07-24-2014, 02:02 PM
Hi Curtis, I just uploaded his STR results to YSEARCH. In addition to today's BigY results he has 67 STR markers. His YSearch I'D is EHBHA.

Pigmon
07-24-2014, 08:44 PM
Thanks Greg,

I will check it out!


Hi Curtis, I just uploaded his STR results to YSEARCH. In addition to today's BigY results he has 67 STR markers. His YSearch I'D is EHBHA.

Pigmon
07-24-2014, 09:09 PM
I am a genetic distance of 17 out of 67 from him. Thought I would be closer!

Curtis