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R.Rocca
04-06-2014, 12:34 PM
Here is my updated U152 tree based on data from Full Genomes Corp, Big-Y, BritainsDNA etc. The tree might still change as more data is available for cross-comparison. If a Big-Y kit does not appear there, they either do not share any new SNPs with other kits or I haven't been able to get to them yet. If you see any errors/omissions, etc. please let me know. Also, the 1KG, BritainsDNA and some UK samples are anonymous, so I cannot help anyone with deciphering who they are.

http://r1b.org/imgs/U152_Tree_v001.pdf

Sinclar
04-06-2014, 01:51 PM
Thank you for all you work, Rich.

Pigmon
04-06-2014, 02:58 PM
Rich,

Thank you for putting all of this together! Trying to not take up your time but I have a quick question.

Do you know if the Z12222 test with YSEQ will transfer to the FTDNA data?

If it will I think I will test it but I don't really want to have to re-test when and if FTDNA adds Z150 to the a-la-carte menu.

Thanks,
Curtis

MitchellSince1893
04-06-2014, 03:27 PM
Rich,

On the FTDNA U152 project page it lists kit# 1370 and 1620 under CTS 7970 but on your tree 1620 isn't shown and 1370 isn't shown under CTS7970 but only under generic Z150/Z12222.

Also kit# 256287 is shown in Z150>L654 on U152 project while 7735 is shown in Z150/Z12222>L654>S42. On your tree they are both listed twice. Once under generic Z150/Z12222 and once under 19477303(G/C), 20815008(C/T).

Based on your tree I see why you said "you're not alone" but based on the U152 project page I'm the only one currently listed as Z150/Z12222/22867545. Just confused by the differences.

Thank you for your work on this tree.

Kwheaton
04-06-2014, 05:04 PM
Rich,
Awesome work. Is 2QAKU Fowler included? I couldn't tell whether I was going blind or just not there?

I know you are busy.....so in due time....just we have a vested interest.
Thanks again for all your thousands of hours of work,
Kelly

haleaton
04-06-2014, 05:13 PM
Here is my updated U152 tree based on data from Full Genomes Corp, Big-Y, BritainsDNA etc. The tree might still change as more data is available for cross-comparison. If a Big-Y kit does not appear there, they either do not share any new SNPs with other kits or I haven't been able to get to them yet. If you see any errors/omissions, etc. please let me know. Also, the 1KG, BritainsDNA and some UK samples are anonymous, so I cannot help anyone with deciphering who they are.

http://r1b.org/imgs/U152_Tree_v001.pdf

Rich, Congrats on FGC10543! Others results from Britain's DNA was a pleasant surprise as you indicated earlier. I was curious about the BDNA numbers, if that was something they provided--maybe I missed it. I was wondering if it was something we could get from them and make public or was it your own accounting system. I assume nothing came out of our mutual FGC BAM vs BAM and I am happy still being R-L2* with FGC Private.

One of the many nice things about FGC is now I can sit back and look for matches even with the limited Big Y data coming in while waiting for my Big Y Bam file to finish downloading . . . :pop2:

Kwheaton
04-06-2014, 07:06 PM
Rich, Congrats on FGC10543! Others results from Britain's DNA was a pleasant surprise as you indicated earlier. I was curious about the BDNA numbers, if that was something they provided--maybe I missed it. I was wondering if it was something we could get from them and make public or was it your own accounting system. I assume nothing came out of our mutual FGC BAM vs BAM and I am happy still being R-L2* with FGC Private.

One of the many nice things about FGC is now I can sit back and look for matches even with the limited Big Y data coming in while waiting for my Big Y Bam file to finish downloading . . . :pop2:

Hal I will join you eating popcorn:pop2:

It looks like there is some geographical clustering in the L2 downstream---Hal you stand alone on top of the mountain---still!
DF103 (or downstream)Germany and UK BARTOLD, CRAUSS
FGC5336 etc Italy PONTONARLIS
FGC10543 Italy ROCCA !!!!
CTS5689 Slovakia? ROKRUT
DF110 Germany and UK FINCKE, BARTON
DF90 Algeria, HANNI
7426675 (A/C) etc N.England or Scotland? ARMSTRONG
6707762(G/A) etc W. or N England TAYLOR, JOHNSON
*203243 (C/G) Scotland VANCE, HAY

Some of these surname locales are based on frequency in the Isles. I've got to do something while I am waiting....

R.Rocca
04-06-2014, 09:43 PM
Rich,

On the FTDNA U152 project page it lists kit# 1370 and 1620 under CTS 7970 but on your tree 1620 isn't shown and 1370 isn't shown under CTS7970 but only under generic Z150/Z12222.

Also kit# 256287 is shown in Z150>L654 on U152 project while 7735 is shown in Z150/Z12222>L654>S42. On your tree they are both listed twice. Once under generic Z150/Z12222 and once under 19477303(G/C), 20815008(C/T).

Based on your tree I see why you said "you're not alone" but based on the U152 project page I'm the only one currently listed as Z150/Z12222/22867545. Just confused by the differences.

Thank you for your work on this tree.

Thanks for the updates. I will not add S42 as it seems to be a private or family SNP at this time. Now I know what you meant by being alone, but hopefully with more tests coming in weekly it won't last too long.

R.Rocca
04-06-2014, 09:50 PM
Rich,
Awesome work. Is 2QAKU Fowler included? I couldn't tell whether I was going blind or just not there?

I know you are busy.....so in due time....just we have a vested interest.
Thanks again for all your thousands of hours of work,
Kelly

I'm still going through the Fowler data now. Since there are a lot less FGC samples, it is tougher to rule out which matching SNPs are just "noise".

R.Rocca
04-06-2014, 09:58 PM
Rich, Congrats on FGC10543! Others results from Britain's DNA was a pleasant surprise as you indicated earlier. I was curious about the BDNA numbers, if that was something they provided--maybe I missed it. I was wondering if it was something we could get from them and make public or was it your own accounting system. I assume nothing came out of our mutual FGC BAM vs BAM and I am happy still being R-L2* with FGC Private.

One of the many nice things about FGC is now I can sit back and look for matches even with the limited Big Y data coming in while waiting for my Big Y Bam file to finish downloading . . . :pop2:

Thanks Hal. I noticed FGC10543 was also found in an L2+ Sardinian sample, but I sent it over to Dr. Francalacci to confirm it, as the published samples were only "low pass" sequenced.

Osiris
04-07-2014, 02:06 AM
Wow! Thank you for all your hard work Richard.

I'm FTDNA 4818 and while I love the ancestry of this all I can't help but also fall in love with the math of all this. So cool!

R.Rocca
04-07-2014, 02:31 AM
Thanks Osiris, it looks like you belong to an important new subclade of L2 defined by 6707762(G/A) and 8126625(G/C).

Rathna
04-07-2014, 02:53 AM
Thanks Hal. I noticed FGC10543 was also found in an L2+ Sardinian sample, but I sent it over to Dr. Francalacci to confirm it, as the published samples were only "low pass" sequenced.

The link between Sardinia and Sicily wouldn't be strange. If you remember I hypothesized a link between LoPiccolo (R-M269*) and one Sardinian sample from YHRD. This should exclude a recent link with North Italy, the colonizations of the Lombards (not Langobards, Lombards from Lombardia) in Sicily etc. We should think to a maritime link between these two isles which could be also very ancient.
I supposed also a link between Amato (Sicily) and my friend Malvolti from Tuscany, tested by SMGF and with not all the values released. If I remember well Amato has DYS492=14. Also in this case many spoke of Gallo-Italic colonies in Sicily.

Kwheaton
04-07-2014, 03:15 AM
I'm still going through the Fowler data now. Since there are a lot less FGC samples, it is tougher to rule out which matching SNPs are just "noise".

Rich,
Thanks for letting me know. If proximity means anything (and who knows if it does) but I would think our WHEATON might have the highest chance of sharing some downstream SNPs with FOWLER even though we are something like 20/37.

Again thanks for your efforts.

Feels like an archeological dig......sifting, sifting, sifting looking for that bone fragment....

In any event you deserve the following awards!

:first::first::first:

R.Rocca
04-07-2014, 12:40 PM
Rich, Congrats on FGC10543! Others results from Britain's DNA was a pleasant surprise as you indicated earlier. I was curious about the BDNA numbers, if that was something they provided--maybe I missed it. I was wondering if it was something we could get from them and make public or was it your own accounting system. I assume nothing came out of our mutual FGC BAM vs BAM and I am happy still being R-L2* with FGC Private.

One of the many nice things about FGC is now I can sit back and look for matches even with the limited Big Y data coming in while waiting for my Big Y Bam file to finish downloading . . . :pop2:

I realized this morning I did not answer your question about BritainsDNA data.

I used the anonymous 2,000 client file they made available here:

https://www.britainsdna.com/download/C2_2000.zip

...then, CeCe Moore was able to get the associated position data and she uploaded it here:

https://www.dropbox.com/s/46ubi9qntb2un03/BritainsDNAchromo2positions.xlsx

haleaton
04-07-2014, 03:47 PM
Thanks again, Rich. Interesting how much of the new U152 draft tree can be based on NGS and and bead chip sequencing technology only based on samples that folks have agreed to make public to varying degrees.

R.Rocca
04-09-2014, 06:24 PM
Here is the latest version of the U152 tree as per all of the FGC and Big-Y results that have come in to date. Please note that it does not include SNPs that were previously found in only one person as per WTY, Geno 2.0, etc.

http://r1b.org/imgs/U152_Tree_v002.png

mafe
04-09-2014, 06:43 PM
Richard, I share novel variant 9316833 with kit 216196, does kit 231195 have this variant aswell? I'm kit 255498.

R.Rocca
04-09-2014, 06:51 PM
Richard, I share novel variant 9316833 with kit 216196, does kit 231195 have this variant aswell? I'm kit 255498.

9316833 appears in roughly 30 kits across all of the different U152 subclades, so it is not phylogenetically stable.

mafe
04-09-2014, 06:58 PM
9316833 appears in roughly 30 kits across all of the different U152 subclades, so it is not phylogenetically stable.

Thank you. I'm hoping for at least one shared SNP downstream of U152 that I can use for my genealogical research.

Agamemnon
04-09-2014, 07:00 PM
What's the most common subclade in East Anglia?

R.Rocca
04-09-2014, 07:14 PM
What's the most common subclade in East Anglia?

There are important amounts of L20 and Z49 there.

Agamemnon
04-09-2014, 07:17 PM
There are important amounts of L20 and Z49 there.

How did Z49 come to the Isles? Where is it most commonly found?
Are there also Z36 cases in East Anglia? Just curious.

emmental
04-09-2014, 07:50 PM
Thanks Rich,

Are the two guys you have listed under Z36>Z54 as 1KG-283310??? and 1KG-231111??? the two guys who tested Z54+ in our U152 Project at FTDNA? Those are their kit numbers.

The tree is really growing. I think there will be even more shoots spouting this Spring!

Thank-you Rich, for making sense of all this.

Elly
04-09-2014, 07:59 PM
I realized this morning I did not answer your question about BritainsDNA data.

I used the anonymous 2,000 client file they made available here:

https://www.britainsdna.com/download/C2_2000.zip

...then, CeCe Moore was able to get the associated position data and she uploaded it here:

https://www.dropbox.com/s/46ubi9qntb2un03/BritainsDNAchromo2positions.xlsx


Hi Rich, I'll be sure to email you my Britainsdna results when they arrive. My sample was stored and Chromo 2 was ordered on 2014-03-01.

R.Rocca
04-09-2014, 08:01 PM
Thanks Rich,

Are the two guys you have listed under Z36>Z54 as 1KG-283310??? and 1KG-231111??? the two guys who tested Z54+ in our U152 Project at FTDNA? Those are their kit numbers.

The tree is really growing. I think there will be even more shoots spouting this Spring!

Thank-you Rich, for making sense of all this.

Yes, I changed their prefixes to "FTDNA-" and they'll appear like that in the next tree. Thanks!

MitchellSince1893
04-09-2014, 11:17 PM
So now it just me (249822) and my Iberian brother from another mother at Z150/Z12222* (1KG-HG01777).

Thanks again Rich for all your work on this. :)


On a related note, I did find my two previously mentioned BritainsDNA snps that I share (S3077 and S227780) mentioned in a ScotlandsDNA spreadsheet. I would love to know where these two snps fit into the tree e.g. above U152? below Z142?

I did email Britainsdna about these snps and got a response, asking for my BritainsDNA account number. Haven't heard anything back since I informed them I didn't have one :(

Hopefully some kind person at BritainsDNA will provide whatever information they are allowed to share.

R.Rocca
04-09-2014, 11:20 PM
So now it just me and my Iberian brother from another mother at Z150/Z12222* (1KG-HG01777).

Thanks again Rich for all your work on this. :)


On a related note, I did find my two previously mentioned BritainsDNA snps that I share (S3077 and S227780) mentioned in a ScotlandsDNA spreadsheet. I would love to know where these two snps fit into the tree e.g. above U152? below Z142?

I did email Britainsdna about these snps and got a response, asking for my BritainsDNA account number. Haven't heard anything back since I informed them I didn't have one :(

Hopefully some kind person at BritainsDNA will provide whatever information they are allowed to share.

Neither of these SNPs were shared between U152 samples in the spreadsheet BritainsDNA released, so for the time being, we don't know if they are in other haplogroups or not. If any of them wind up repeating within L2>Z142>Z150, then I'll add it. Thanks.

Agamemnon
04-09-2014, 11:22 PM
I checked 23&Me and my maternal grandfather's lineage is negative for L20, however L2 is a "no call" so I suspect my grandfather was actually positive to L2...
I'll have to gear up for a transfer to FTDNA.

Rathna
04-09-2014, 11:39 PM
@ Richard Rocca

How can you be sure that this sample is R-U152*?


293471 William James Harrison R1b1a2a1a1b3 R-U152
M269+, M294+, M299+, M306+, M343+, M42+, M45+, M526+, M74+, M89+, M9+, M94+, P108+, P128+, P131+, P132+, P133+, P134+, P135+, P136+, P138+, P139+, P14+, P140+, P141+, P143+, P145+, P146+, P148+, P149+, P151+, P157+, P158+, P159+, P160+, P161+, P163+, P166+, P187+, P207+, P224+, P226+, P228+, P229+, P230+, P232+, P233+, P234+, P235+, P236+, P237+, P238+, P239+, P242+, P243+, P244+, P245+, P280+, P281+, P282+, P283+, P284+, P285+, P286+, P294+, P295+, P297+, P305+, P310+, P311+, P312+, P316+, P9.1+, P97+, PK1+, SRY10831.1+, U152+, L11+, L138+, L141+, L15+, L150+, L151+, L16+, L51+, L52+, M168+, M173+, M207+, M213+, L23+, L4-, M228.2-, M126-, M160-, L196-, L20-

Sinclar
04-10-2014, 12:14 AM
Thank you once again, Rich

I now share five SNPs downstream of U152 with someone with a genetic distance from me of 24 for 67 markers. I'm guessing that means the last of the five SNPs is pretty old.

MitchellSince1893
04-10-2014, 12:59 AM
Neither of these SNPs were shared between U152 samples in the spreadsheet BritainsDNA released, so for the time being, we don't know if they are in other haplogroups or not. If any of them wind up repeating within L2>Z142>Z150, then I'll add it. Thanks.

Thanks for that response...it made my "clue" light come on....I went to that link you provided previously to the chromo2 snp spreadsheet (C2_2000) and searched through it.

None of the 2000 anonymous individuals in any of the haplogroups had either the S3077 nor the S27780 snp mutations. I guess in a way that's a good sign...if they had been in another haplgroup it would have ruled them out from being downstream of Z150.

R.Rocca
04-10-2014, 02:40 AM
@ Richard Rocca

How can you be sure that this sample is R-U152*?


293471 William James Harrison R1b1a2a1a1b3 R-U152
M269+, M294+, M299+, M306+, M343+, M42+, M45+, M526+, M74+, M89+, M9+, M94+, P108+, P128+, P131+, P132+, P133+, P134+, P135+, P136+, P138+, P139+, P14+, P140+, P141+, P143+, P145+, P146+, P148+, P149+, P151+, P157+, P158+, P159+, P160+, P161+, P163+, P166+, P187+, P207+, P224+, P226+, P228+, P229+, P230+, P232+, P233+, P234+, P235+, P236+, P237+, P238+, P239+, P242+, P243+, P244+, P245+, P280+, P281+, P282+, P283+, P284+, P285+, P286+, P294+, P295+, P297+, P305+, P310+, P311+, P312+, P316+, P9.1+, P97+, PK1+, SRY10831.1+, U152+, L11+, L138+, L141+, L15+, L150+, L151+, L16+, L51+, L52+, M168+, M173+, M207+, M213+, L23+, L4-, M228.2-, M126-, M160-, L196-, L20-

He is U152* as per his Big-Y raw data file.

Rathna
04-10-2014, 03:00 AM
He is U152* as per his Big-Y raw data file.

Thanks. From the SNPs published didn't seem a Big Y, but of course, as it happens for the mt, he will have many singletons which, when they match just one singleton of another sample, he will have his own subclade under U152* which of course doesn't exist.

As your SNP demonstrates that you are linked to Sardinia, we'll see then whom this English/Scandinavian person is linked to.

CelticGerman
04-10-2014, 08:43 AM
Results Monnier have arrived. I have not seen the results, but according to a first feed back from him, he has some of the new positions between Z36 and CTS188, but not all. Seems interesting. I asked him to send results to one of the experts ......

Tonsa71
04-10-2014, 03:27 PM
Got my Big Y results today.
As I can se on Richard Roccas U152 tree on first page I am L2+, Z367+, Z33+ (and same level Z259+, Z276+, CTS 9044), Z34+.
But downstream from that I can not se any common who is listed on U152 tree.

How can I sort out if there is more downstream from here ??

FTDNA kit: 203953

R.Rocca
04-10-2014, 04:25 PM
Got my Big Y results today.
As I can se on Richard Roccas U152 tree on first page I am L2+, Z367+, Z33+ (and same level Z259+, Z276+, CTS 9044), Z34+.
But downstream from that I can not se any common who is listed on U152 tree.

How can I sort out if there is more downstream from here ??

FTDNA kit: 203953

You do have more SNPs below the ones on the tree, but none of them matched against that of others. You can check your SNPs in the "Novel SNPs" tab of your Big-Y results page.

Sinclar
04-10-2014, 06:18 PM
I now match a chap on five SNPs downstream of U152, but we have a genetic distance of 24 for 67 markers. Would anyone hazard a guess of the date of our most recent common ancestor? I'm thinking perhaps 2500-2000 years ago.

MitchellSince1893
04-11-2014, 12:17 AM
I now match a chap on five SNPs downstream of U152, but we have a genetic distance of 24 for 67 markers. Would anyone hazard a guess of the date of our most recent common ancestor? I'm thinking perhaps 2500-2000 years ago.

Have you entered your data into this tool? http://www.mymcgee.com/tools/yutility.html?mode=ftdna_mode


Out of curiosity:

1. What is the GD between you and the R1b-U152 all subclades modal aka QM4ES?
2. What is the GD between your match and QM4ES?

Sinclar
04-11-2014, 09:30 AM
Thanks for the reply. I haven't used that tool, but will give it a go.

For 67 markers, I've got a GD of 9 off U152 (QM4ES) and my downstream SNP match is 18.


Have you entered your data into this tool? http://www.mymcgee.com/tools/yutility.html?mode=ftdna_mode


Out of curiosity:

1. What is the GD between you and the R1b-U152 all subclades modal aka QM4ES?
2. What is the GD between your match and QM4ES?

Pigmon
04-11-2014, 12:45 PM
Hey guys,

I am a GD of 12 from the U152 modal.

Curtis


Thanks for the reply. I haven't used that tool, but will give it a go.

For 67 markers, I've got a GD of 9 off U152 (QM4ES) and my downstream SNP match is 18.

R.Rocca
04-11-2014, 01:39 PM
Thanks. From the SNPs published didn't seem a Big Y, but of course, as it happens for the mt, he will have many singletons which, when they match just one singleton of another sample, he will have his own subclade under U152* which of course doesn't exist.

As your SNP demonstrates that you are linked to Sardinia, we'll see then whom this English/Scandinavian person is linked to.

Now that the results have slowed down a bit, I'm doing another sweep of the data and 293471 is Z367+. Since the man that was used as the reference for all DNA study was Z367, those values are reversed in Z367 samples (ancestral is derived and derived is ancestral). Good catch Gioiello, and thanks for bringing it to my attention. I'll publish a new tree shortly.

R.Rocca
04-11-2014, 02:19 PM
OK guys, here is the Friday edition of the U152 tree. Roughly 90% of the U152+ Big-Y results are in, so the pipeline is winding down. Corrections/comments are appreciated. I will do a second round of QA checks once they are all in.

http://r1b.org/imgs/U152_Tree_v003.png

Biloo
04-11-2014, 02:36 PM
What is the position of the snp S18462 on the Chr Y ? What do you think of 1KGHG02436 being S18462+ and DF90+ ?

R.Rocca
04-11-2014, 02:47 PM
What is the position of the snp S18462 on the Chr Y ? What do you think of 1KGHG02436 being S18462+ and DF90+ ?

Since BritainsDNA does not test for DF90, it could be that their sample BDNA-1323 is also DF90+ and S18462 is downstream of DF90. Don't forget that BritainsDNA is not a full genome test and only tests individual known SNPs. The other possibility is that S18462 is unstable. We'll only know when we have more samples to compare.

CelticGerman
04-11-2014, 02:54 PM
Great Richard,
Thanks for your work!!! Just a question. Is FTDNA 5825 (Z36 level) still without BigY results? It would be the last one, which could be interesting for my branch (CTS188 etc.), I think. Any idea (approximately) when the CTS188 branch and the branch of FTDNA 199556 and N21533 started? I really hope other Z36 people will be motivated now to do the BigY or another test as well.

R.Rocca
04-11-2014, 03:15 PM
Great Richard,
Thanks for your work!!! Just a question. Is FTDNA 5825 (Z36 level) still without BigY results? It would be the last one, which could be interesting for my branch (CTS188 etc.), I think. Any idea (approximately) when the CTS188 branch and the branch of FTDNA 199556 and N21533 started? I really hope other Z36 people will be motivated now to do the BigY or another test as well.

Yes, he is on the tree at the Z36* level as FTDNA-5825. If a kit is on the tree, I've already taken a look at the FG and/or Big-Y data.

Tonsa71
04-11-2014, 09:15 PM
I have some "Z-snp" in my Big Y results and I wonder were these could be placed on the U152 tree . Could these be downstreams to Z33 or is it unknown places.
I am L2+, Z367+, Z33+.
I wonder about Z34 and Z258. And I have some with higher numbers Z1331, Z1918, Z5997, Z6030, Z6032
FTDNA kit :203953

Ravai
04-12-2014, 01:53 PM
Hi Richard, my FTDNA kit is N119885. Know you tell me which of the following subclasses have most likely belong? Z367, L196, L408 or Z49. Other?

Regards

Thanks

MitchellSince1893
04-12-2014, 02:15 PM
Rich,

Just wanted to give you a heads up that I mentioned your tree on an FTDNA thread asking what've learned so far from BigY.

http://forums.familytreedna.com/showthread.php?t=34776

tbartold
04-13-2014, 05:02 PM
OK guys, here is the Friday edition of the U152 tree. Roughly 90% of the U152+ Big-Y results are in, so the pipeline is winding down. Corrections/comments are appreciated. I will do a second round of QA checks once they are all in.


Richard -

14927800 was labeled FGC8158 and 23891656 was labeled FGC8178 by FGC. 23098660 was labeled YFS053413 by YFull.

But, I'm curious, why did you list those particular variants?

R.Rocca
04-14-2014, 12:03 AM
Richard -

14927800 was labeled FGC8158 and 23891656 was labeled FGC8178 by FGC. 23098660 was labeled YFS053413 by YFull.

But, I'm curious, why did you list those particular variants?

Those are the SNP that you share with two anonymous UK kits, and therefor are the only ones that are phylogenetically relevant (so far).

lamahorse
04-15-2014, 01:16 AM
I'm quite jealous of all you big Y DNA spenders.

After a momentary loss of sanity concerning my father's results and my outdated 23andme haplogroup; it seems that our terminal SNP is U152/S28 (I'm positive for it and P312, FTDNA has put him in this direction). I've recently upgraded my father's Y-67 test to a Y-111. A quick skype call to FTDNA confirms I didn't order a new test (was quite confusing upgrading) but the guy says that the results will updated very soon.

I don't have any of the markers for any further subclades so it seems at this moment in time; I'm just U152!

Mudgeeclarke
04-23-2014, 10:09 AM
I'm quite jealous of all you big Y DNA spenders ... .... .... !

I'm jealous of all those Big Y spenders who understand their results !! I have my Big Y results, and being almost 10% Neanderthal/Denisovan, all I see are rows of numbers !

I salute Rich Rocca for his excellent work and feedback here. At least I see my FTDNA number on his latest tree, so that's a good thing.

Like many with Paternal NPE a couple of generations back, I'm waiting (not so patiently) for someone to tell me they have totally matched my results and have put their published family tree in the mail, with my GGF shown quite prominently therein.

Ummm, probably not going to happen, right.

Still, I love the science and I'm glad to contribute to the growing database. Please feel free, anyone, to delve into my results. My only grouch about all of this is that I am an all Apple OS family at home and the office, and sometimes, I can't join the fun of fumbling around with my data and some of the excellent tools which appear as links.

Happy number crunching, everyone.

:beerchug:

mafe
04-26-2014, 08:33 AM
Does YSEQ also design primers for unnamed SNPs?

haleaton
04-26-2014, 09:57 AM
Does YSEQ also design primers for unnamed SNPs?

Yes, but they give them "A" names (with number) and always define them and their primers in YBrowse.

mafe
04-27-2014, 08:18 AM
EDIT:

I have ordered YSEQ primer design for the following SNPs:

Name: N/A
Position: 21387964
allele_anc: C
allele_der: T

Found downstream of R-U152*. (1000 Genomes NA19720 and BIG-Y 255498)

Name: N/A
Position: 13668489
allele_anc: T
allele_der: C

Found downstream of R-U152* > 21387964. (1000 Genomes NA19720 and BIG-Y 255498)

R.Rocca
04-27-2014, 05:01 PM
EDIT:

I have ordered YSEQ primer design for the following SNPs:

Name: N/A
Position: 21387964
allele_anc: C
allele_der: T

Found downstream of R-U152*. (1000 Genomes NA19720 and BIG-Y 255498)

Name: N/A
Position: 13668489
allele_anc: T
allele_der: C

Found downstream of R-U152* > 21387964. (1000 Genomes NA19720 and BIG-Y 255498)

Excellent. Please let me know when they become available and when they show up on the ISOGG browser.

MitchellSince1893
04-27-2014, 06:45 PM
To Richard Rocca:

I tried to send the following to you via PM but got an error message saying
Richard A. Rocca has exceeded their stored private messages quota and cannot accept further messages until they clear some space.

Anyway the PM I tried to send asked:


Richard,

Looking at the last version of your tree, it looks as though HG01777 is negative for CTS9490. Is this a correct interpretation?

Also are the 2 GoNL samples you said were positive for the SNPSs mentioned at link below, positive or negative for CTS9490?
http://www.anthrogenica.com/showthread.php?1567-U152-FTDNA-BIG-Y-DNA-test&p=37016&viewfull=1#post37016

Just trying to determine if it would be wise for me to order CTS9490; or you are already able to determine that I would be negative for CTS9490 based on the answers to the above.

Thanks,

Mark

R.Rocca
04-27-2014, 07:05 PM
To Richard Rocca:

I tried to send the following to you via PM but got an error message saying

Anyway the PM I tried to send asked:

Your kit and HG01777 are negative for CTS9490. There were no CTS9490+ samples in the GoNL data.

MitchellSince1893
04-27-2014, 07:06 PM
Ok thanks...saves me $25.

mafe
04-28-2014, 09:18 AM
Excellent. Please let me know when they become available and when they show up on the ISOGG browser.

Will do, I'm hoping to test at least two of my distant matches for these SNPs.

MitchellSince1893
04-29-2014, 02:42 AM
On the U152 Project page N115212 Stephen Brace, d. 1692, b. 1644 England has just joined me in the U152> L2> Z49/Z68> Z142> Z150/Z12222/22867545> FGC12379 et al. branch.

If I've added correctly, that makes 5 individuals now on this branch.

It will be interesting to see if we share any novel SNPs.

mafe
05-01-2014, 03:54 PM
Excellent. Please let me know when they become available and when they show up on the ISOGG browser.



Email from YSEQ:

We have added the following markers to our database:
A274 ChrY:21387964 C to T
A275 ChrY:13668489 T to C
PCR primers have been designed and will be ordered from our supplier.

A274 is predicted to be a stable marker however A275 is in the centromeric GGAAT repeat region. We have found unique primers but since this region is highly repetitive we may have difficulties with the Sanger sequencing reads. If you want to substitute A275 against an alternative marker then please let us know before we place the order for the primers.



Richard, what do you suggest regarding A275/13668489 ?

R.Rocca
05-01-2014, 03:59 PM
Email from YSEQ:

We have added the following markers to our database:
A274 ChrY:21387964 C to T
A275 ChrY:13668489 T to C
PCR primers have been designed and will be ordered from our supplier.

A274 is predicted to be a stable marker however A275 is in the centromeric GGAAT repeat region. We have found unique primers but since this region is highly repetitive we may have difficulties with the Sanger sequencing reads. If you want to substitute A275 against an alternative marker then please let us know before we place the order for the primers.

Richard, what do you suggest regarding A275/13668489 ?

Those are the only two SNPs in your group, so I can't think of anything else to do but to try to see if the A275/13668489 primer works or not.

mafe
05-01-2014, 04:15 PM
Those are the only two SNPs in your group, so I can't think of anything else to do but to try to see if the A275/13668489 primer works or not.

Ok, I'll confirm the order. If this primer works, will it work for every single test, or could there be false negatives because of the difficult region?

R.Rocca
05-01-2014, 04:20 PM
Ok, I'll confirm the order. If this primer works, will it work for every single test, or could there be false negatives because of the difficult region?

Good question...you should ask Thomas as he knows the ins and outs of sanger testing results.

mafe
05-01-2014, 05:00 PM
Good question...you should ask Thomas as he knows the ins and outs of sanger testing results.

Reply:

Dear Martijn,

If the PCR assay for A275 works then we'll report a clear ancestral or derived allele. However if the assay fails we'll report a Null allele and notify the customer that we can't determine his ancestral or derived state. We'll take down the marker from the shop if this happens too often. We may be lucky and A275 works just fine, but we can't give any warranties. Therefore if you have alternatives, let me have a look at them. If there are no alternatives we'll simply try A275. However I recommend to check it out for a single sample first, before you suggest it to others for testing.

I hope this helps,

Thomas

pasquale
05-01-2014, 07:41 PM
So, I don't do anything with my DNA education for awhile then come back to my research the day after FTDNA made some "minor" changes. I was lost before, now I am drowing.
I went from R1b1a2a1a1b3 to R1b1a1a1a1a4. I cannot find any reference to "name". With all the new information, I haven't the faintest idea where I should test.
And what is the story behind SEMARGL SNP MAPS http://www.semargl.me/en/dna/? What is the conflict? I found that site very useful.
And thank you for any words of wisdom/guidance/

mafe
05-02-2014, 04:22 PM
A274 and A275 are added to ISOGG YBrowse.

MitchellSince1893
05-02-2014, 10:35 PM
FYI, YFULL updated their experimental tree yesterday. Here is the U152 section. http://www.yfull.com/tree/R1b1a2a1a2b/

Just click on the top row of white boxes to expand the tree.

The branch labeled R-Y3140 Y3140 * Y3141 * Y3142 * Y3143 * Y3144 is the same as these FGC names

Y3140 = FGC12381
Y3141 = FGC12383
Y3142 = FGC12379
Y3143 = FGC12380
Y3144 = FGC12382

This is the same branch that is listed on the FTDNA U152 proeject page as: U152> L2> Z49/Z68> Z142> Z150/Z12222/22867545> FGC12379 et al.

R.Rocca
05-13-2014, 11:15 PM
All, Dr. Francalacci was generous enough to share some of his U152 data with me. So, I created a new tree that includes his findings and some others. The PF6658/Z193 part of the tree was so large that I had to split it into its own tree. I guess that's the benefit of whole sequencing over 100 U152+ samples from one region. Imagine what that would mean if we can get it from high frequency ares like northern Italy and Switzerland!

Anyway, here is the non-PF6658/Z193 part of the tree...

http://r1b.org/imgs/U152_Tree_v004_Part_I.png

R.Rocca
05-13-2014, 11:17 PM
...and the PF6658/Z193 part of the tree (see the non-PF6658/Z193 part of the tree in the post prior to this one)...

http://r1b.org/imgs/U152_Tree_v004_Part_II.png

MitchellSince1893
05-13-2014, 11:46 PM
That's awesome work Rich!

I feel like Steve Martin in the movie "The Jerk" yelling "The new phonebooks are here! The new phonebooks are here!" :)

https://www.youtube.com/watch?v=-7aIf1YnbbU

R.Rocca
05-13-2014, 11:57 PM
That's awesome work Rich!

I feel like Steve Martin in the movie "The Jerk" yelling "The new phonebooks are here! The new phonebooks are here!" :)

https://www.youtube.com/watch?v=-7aIf1YnbbU

Wow, I had completely forgotten that scene. Thanks for the link.

MitchellSince1893
05-14-2014, 01:46 AM
So 4 subclades down from Z142, on the the L562 branch we see Sardinians appear, but they are currently absent on the other branches of Z142.

I wonder if this is related to the time of the arrival of Bell Beaker to Sardinia. If so it could help date the age of these SNPs and the SNPs above it e.g. Z142, Z49, L2, and U152.

haleaton
05-14-2014, 02:28 AM
Wow, I had completely forgotten that scene. Thanks for the link.

Rich, any thoughts on eventual inclusion of the branches added in the FTDNA Haplotrees said to be from the tens of thousands of GENO data, or was that incorporated? What would it take to make it useful?

R.Rocca
05-14-2014, 11:40 AM
Rich, any thoughts on eventual inclusion of the branches added in the FTDNA Haplotrees said to be from the tens of thousands of GENO data, or was that incorporated? What would it take to make it useful?

Unfortunately, I have very little confidence in their tree. I suspect that the great majority of their SNPs are found across multiple haplogroups, and therefore, we cannot be sure if the SNPs occurred even within U152 subclades as one time events. Also, since Geno 2.0 is not anywhere near full genome testing, there is no way of knowing where to place some of these SNPs on a tree as they may be part of SNP subclade groups that have the misfortune of being in positions of the Y that primers cannot be developed for. A good example is PF6658/Z193.

R.Rocca
05-14-2014, 02:01 PM
So 4 subclades down from Z142, on the the L562 branch we see Sardinians appear, but they are currently absent on the other branches of Z142.

I wonder if this is related to the time of the arrival of Bell Beaker to Sardinia. If so it could help date the age of these SNPs and the SNPs above it e.g. Z142, Z49, L2, and U152.

Sardinian Bell Beakers are derived from the Tyrrhenian Group. The Tyrrhenian BB Group is most similar to the Rhone-Rhine BB Group and has been dated to about 2500 BC.

haleaton
05-14-2014, 02:27 PM
Unfortunately, I have very little confidence in their tree. I suspect that the great majority of their SNPs are found across multiple haplogroups, and therefore, we cannot be sure if the SNPs occurred even within U152 subclades as one time events. Also, since Geno 2.0 is not anywhere near full genome testing, there is no way of knowing where to place some of these SNPs on a tree as they may be part of SNP subclade groups that have the misfortune of being in positions of the Y that primers cannot be developed for. A good example is PF6658/Z193.


I mean the ones at the bottom of their tree, such as it is with all its faults, as shown below for L2+ Z49- Z367-. If GENO 2.0 did provide the same type of documentation (without identification) that Britain's DNA did for Chromo2 then they might be ripe for inclusion. Your comment also applies to inclusion of Chromo2 data or a new SNP chip test that may come out this year.




L2+ Z49- Z367- Downstream FTDNA Order
CTS667 6933008 ( G > C )
Y
CTS1166 7248487 ( G > T ) aka Z1744
N

F4205 16331432 ( A > G )
Y
F1643 9902395 ( G > A )
N
PF7610 13658168 ( G > A )
N
F3916 14348251 ( G > A )
Y
PF4367 14481150 ( C > T )
N
CTS5153 16040682 ( A > G ) in N113573
N
PF6610 16504649 ( C > T )
N

~PF70 3966485 ( C > T )
N
CTS6942 17203952 ( G > T )
N
CTS7010 17233286 ( C > T ) in N117716, N123359
Y
CTS7491 17506937 ( C > T )
N
CTS10009 19207382 ( G > C ) aka S1582 in BDNA-1870
N

CTS3080 14648041 ( G > A ) aka S1565
N
M126 21930258 ( AATA > del ) aka S27477
Y

R.Rocca
05-15-2014, 12:14 PM
I mean the ones at the bottom of their tree, such as it is with all its faults, as shown below for L2+ Z49- Z367-. If GENO 2.0 did provide the same type of documentation (without identification) that Britain's DNA did for Chromo2 then they might be ripe for inclusion. Your comment also applies to inclusion of Chromo2 data or a new SNP chip test that may come out this year.




L2+ Z49- Z367- Downstream FTDNA Order
CTS667 6933008 ( G > C )
Y
CTS1166 7248487 ( G > T ) aka Z1744
N

F4205 16331432 ( A > G )
Y
F1643 9902395 ( G > A )
N
PF7610 13658168 ( G > A )
N
F3916 14348251 ( G > A )
Y
PF4367 14481150 ( C > T )
N
CTS5153 16040682 ( A > G ) in N113573
N
PF6610 16504649 ( C > T )
N

~PF70 3966485 ( C > T )
N
CTS6942 17203952 ( G > T )
N
CTS7010 17233286 ( C > T ) in N117716, N123359
Y
CTS7491 17506937 ( C > T )
N
CTS10009 19207382 ( G > C ) aka S1582 in BDNA-1870
N

CTS3080 14648041 ( G > A ) aka S1565
N
M126 21930258 ( AATA > del ) aka S27477
Y


I added CTS10009 and CTS3080 to the tree since 1KG-NA07357 is also positive for both and we can get a good idea of their tree positioning. The rest are still very much a question mark. Take for example CTS7010... it is found in N123359 who is L2- and in N117716 that is L2+.

Solothurn
05-21-2014, 03:00 AM
Thanks for the update Rich :)

Steve Wear came in as PF6658+ and Z193?. Do you think his Z193? is actually Z193+ based on the results of other PF6658s ?

R.Rocca
05-23-2014, 01:13 PM
Thanks for the update Rich :)

Steve Wear came in as PF6658+ and Z193?. Do you think his Z193? is actually Z193+ based on the results of other PF6658s ?

Kit 133986 is now PF6658+S20550+ and assumed to be Z193+ as no PF6658+ in full genome samples have been Z193-. Also S20550+ are Britain'sDNA kits 1318 and 1324. Two Genomes of the Netherlands kits are also S20550+. This now moves the S20550 tree from the U152* tree to the PF6658+ tree.

Solothurn
05-23-2014, 04:33 PM
Thanks Rich

That is excellent news :)

Do you think S20550 would be a more 'stable' SNP to look for in kit's 133986 close STR matches?



Kit 133986 is now PF6658+S20550+ and assumed to be Z193+ as no PF6658+ in full genome samples have been Z193-. Also S20550+ are Britain'sDNA kits 1318 and 1324. Two Genomes of the Netherlands kits are also S20550+. This now moves the S20550 tree from the U152* tree to the PF6658+ tree.

R.Rocca
05-23-2014, 04:35 PM
Thanks Rich

That is excellent news :)

Do you think S20550 would be a more 'stable' SNP to look for in kit's 133986 close STR matches?

Since Britain'sDNA tests for it, then it is likely stable enough for Sanger sequencing.

Solothurn
05-23-2014, 05:44 PM
Thanks Rich

Thomas at Yseq is ordering the primers :)

Is there a possible 'age' for PF6658/Z193 yet?




Since Britain'sDNA tests for it, then it is likely stable enough for Sanger sequencing.

jbarry6899
05-24-2014, 03:00 PM
Just received positive result for S8183; FTDNA kit number 240232. Anglo-Norman-Irish ancestry; some genealogical sources suggest 10th century ancestors in Flanders. I plan to request S12993, S8172, S20782 and S22778 from YSeq and then test sequentially. Any other suggestions welcome.

Jim

R.Rocca
05-24-2014, 04:54 PM
Just received positive result for S8183; FTDNA kit number 240232. Anglo-Norman-Irish ancestry; some genealogical sources suggest 10th century ancestors in Flanders. I plan to request S12993, S8172, S20782 and S22778 from YSeq and then test sequentially. Any other suggestions welcome.

Jim

Did you test S8183+ with BritainsDNA?

jbarry6899
05-24-2014, 05:16 PM
Did you test S8183+ with BritainsDNA?

No, tested with YSeq

R.Rocca
05-24-2014, 08:27 PM
No, tested with YSeq

OK, I changed your kit's grouping.

jbarry6899
05-24-2014, 11:59 PM
Thanks, Richard. We have a cluster of men in the Barry Surname Project who have Cork ancestry and are Z49+/Z142-. I will do some further testing downstream and then try to get several of them to test as well. Hopefully we will have a few order BigY in due course.

Jim

MitchellSince1893
05-25-2014, 02:03 AM
Just received positive result for S8183; FTDNA kit number 240232. Anglo-Norman-Irish ancestry; some genealogical sources suggest 10th century ancestors in Flanders. I plan to request S12993, S8172, S20782 and S22778 from YSeq and then test sequentially. Any other suggestions welcome.

Jim

Congrats Jim!

jbarry6899
05-25-2014, 03:07 PM
For what it's worth, I did an STR comparison of the FTDNA kits that are S8183+ and found a GD of 6-23 at 67 markers. The geographic distribution of MDKA, 17th-18th century, is Czech (1), Italy (2), Ireland (1-mine), Sweden (2). GD within geographic groups was Italy 7, Sweden 6. Among groups it was Ireland-Sweden 17, Ireland-Italy 20-21, Ireland-Czech 23, Sweden-Czech 11-15, Sweden-Italy 13-20, Italy-Czech 17-21. Sample size is very small so it will be interesting to see what turns up as more results come in.

Jim

Solothurn
05-27-2014, 03:05 PM
Rich

Do you know any background of the kits from Britain'sDNA or the ones from the Netherlands?

Thanks


Kit 133986 is now PF6658+S20550+ and assumed to be Z193+ as no PF6658+ in full genome samples have been Z193-. Also S20550+ are Britain'sDNA kits 1318 and 1324. Two Genomes of the Netherlands kits are also S20550+. This now moves the S20550 tree from the U152* tree to the PF6658+ tree.

R.Rocca
05-27-2014, 05:17 PM
Rich

Do you know any background of the kits from Britain'sDNA or the ones from the Netherlands?

Thanks

Neither GoNL nor BritainsDNA provided sample information.

MitchellSince1893
05-31-2014, 04:21 AM
Neither GoNL nor BritainsDNA provided sample information.

Rich,

Can you tell me if anyone else on my branch of your tree beside HG017777, matches me at position 22258595? i.e N115212 and the 2xGoNLs

R.Rocca
06-03-2014, 06:51 PM
Rich,

Can you tell me if anyone else on my branch of your tree beside HG017777, matches me at position 22258595? i.e N115212 and the 2xGoNLs

HG01777 has a 'T' value at that position. GoNL did not list that as one of their derived SNPs. N115212 I no longer have the csv file for, since admins no longer have access to them.

MitchellSince1893
06-07-2014, 04:38 AM
Wanted to give a heads up I got a notification from Yfull about a change to the section below Z142 at the Z150 branch; and that they were going to do a major update to the whole yfull tree in less than 2 weeks.

On the branch below Z142, they're using the name S7402 for Z12222 at position 8413680.

Unlike Rich's tree, they aren't yet showing Z150 and position 22867545 which yfull is calling YFC013199. Maybe they will appear in the big update.

Also they've added 3 new kits to the tree...most likely BigY or FGC results they recently analyzed. Their positions can be seen here where you see "new"
http://www.yfull.com/tree/R1b1a2a1a2b/

There are now 6 individual samples being shown in the U152 group (in addition to the 44 samples from major studies such as 1000 genome project).

MitchellSince1893
06-19-2014, 01:31 AM
FYI: One of my previous Yfull private SNPs is now a named SNP, Y4272. It was a "Best" rated private SNP.

ChrY position: 22941997 (+strand)
Reads: 79
Position data: 79A
Weight for A: 1.0
Probability of error: 0.0 (0<->1)
Consensus allele: A
Reference allele: G
Known SNPs: Y4272

Does any other U152 folks have this SNP with a nucelotide value of "A"

Just trying to figure out where this SNP fits into the haplotree.

I'm assuming that now that it's named that some one else has this SNP.

Armenis
06-20-2014, 09:31 AM
Wanted to give a heads up I got a notification from Yfull about a change to the section below Z142 at the Z150 branch; and that they were going to do a major update to the whole yfull tree in less than 2 weeks.

On the branch below Z142, they're using the name S7402 for Z12222 at position 8413680.

Unlike Rich's tree, they aren't yet showing Z150 and position 22867545 which yfull is calling YFC013199. Maybe they will appear in the big update.

Also they've added 3 new kits to the tree...most likely BigY or FGC results they recently analyzed. Their positions can be seen here where you see "new"
http://www.yfull.com/tree/R1b1a2a1a2b/

There are now 6 individual samples being shown in the U152 group (in addition to the 44 samples from major studies such as 1000 genome project).

Is there any info regarding YF01706 that I see as a 'new' SNP. I sent my BAM file to Yfull for them to add to their U152 database ... would like to know if this is one of my private SNPs.

MitchellSince1893
06-20-2014, 12:26 PM
YF01706 isn't a snp. It's an individual that recently had their data added to the yfull tree. It may be you. I asked them to confirm that my kit was yf01489 but never heard anything back.

By process of elimination I confirmed it.

Osiris
06-20-2014, 09:09 PM
You can also get it by logging into yfull.com. Click settings. Click change account settings. Then it will display your value.

I'm YF01527

haleaton
06-20-2014, 09:43 PM
YF01706 isn't a snp. It's an individual that recently had their data added to the yfull tree. It may be you. I asked them to confirm that my kit was yf01489 but never heard anything back.

My process of elimination I confirmed it.

In my case when I log into my YFull account my YF number is there though on the tree they added an extra forward zero.

MitchellSince1893
06-20-2014, 11:38 PM
You can also get it by logging into yfull.com. Click settings. Click change account settings. Then it will display your value.

I'm YF01527

Thanks. I forgot about that

MitchellSince1893
06-29-2014, 03:03 AM
FYI the Yfull tree has just announced these changes below my branch of Z142. I assume they made other changes throughout the tree, but my notification seems to be limited to my subclade.

Y-Tree changing:
at subclade R1b1a2a1a2b1c1a added SNPs S369/Z51, Z55
subclade R-Z57 added to R1b1a2a1a2b1c1a as parent of R-CTS6554 with SNP S1468/Z57
subclade R-CTS6554 added to R-Z57 with SNPs CTS6554, S214/Z53, S489/Z148, S490/Z149, Z147, Z52
at subclade R-S7402 added SNP S257/Z150
subclade R-CTS9490 added to R-S7402 with SNP CTS9490

http://www.yfull.com/tree/R1b1a2a1a2b/

jbarry6899
06-29-2014, 08:56 PM
Also some new SNPs below my subclade Z49>S8183.

Alessio B. Bedini
07-30-2014, 03:38 PM
Looking through the results of the "FTDNA project U152" I saw that the SNPs 7426675 (A / C) and 6707762 (G / A) are as yet unnamed.

Solothurn
08-02-2014, 10:36 AM
Hi Rich

On the Full Y experimental tree Z193 is now shown downstream of PF6658. How sure are we that S20550 is Z193+?

Thanks

S.


Here is my updated U152 tree based on data from Full Genomes Corp, Big-Y, BritainsDNA etc. The tree might still change as more data is available for cross-comparison. If a Big-Y kit does not appear there, they either do not share any new SNPs with other kits or I haven't been able to get to them yet. If you see any errors/omissions, etc. please let me know. Also, the 1KG, BritainsDNA and some UK samples are anonymous, so I cannot help anyone with deciphering who they are.

http://r1b.org/imgs/U152_Tree_v001.pdf

R.Rocca
08-02-2014, 01:12 PM
Kit 133986 is now PF6658+S20550+ and assumed to be Z193+ as no PF6658+ in full genome samples have been Z193-. Also S20550+ are Britain'sDNA kits 1318 and 1324. Two Genomes of the Netherlands kits are also S20550+. This now moves the S20550 tree from the U152* tree to the PF6658+ tree.

Since writing the above, FTDNA re-ran a lot of the Big-Y data and the PF6658+S20550+ kit 133986 now shows as Z193- (before it was Z193?). So, I will re-do the tree and re-post it. @Solothurn, thanks for bringing it to my attention.

Solothurn
08-03-2014, 09:41 AM
Thanks Rich

So is this the only PF6658+ Z193- in the U152 project that you know of, or are there others after the re-runs?

S.



Since writing the above, FTDNA re-ran a lot of the Big-Y data and the PF6658+S20550+ kit 133986 now shows as Z193- (before it was Z193?). So, I will re-do the tree and re-post it. @Solothurn, thanks for bringing it to my attention.

Armenis
08-03-2014, 11:59 AM
You can also get it by logging into yfull.com. Click settings. Click change account settings. Then it will display your value.

I'm YF01527

I donated my BAM file to YFull on the 17th May specifically so that they could add my results to their database. From their reply it is clear that language is an issue for YFull and there is not much in terms of value in donating your BAM file after the cut-off date. I donated my BAM file after the free interpretation service was available and therefore in order for me to identify my value on the YFull experimental tree I need to purchase their interpretation service, which I do not want or need.

I inquired about my 'value' and received the following reply on 2nd August:

Hello.
May be our automatic email at May 17, 2014 has misled you. Sorry we hadn't a different text for "bam donation".
You ordered our interpretation for your sample with comment "BAM donation for database comparisons".
For us it means: [lol]
1. The interpretation are free.
2. The interpretation processes with low priority.
3. We can use your sample for database comparisons and divided private and common SNPs of other samples. We can use results of interpretation for changing YTree.
4. You will have no access to results of the interpretation.
5. The sample will shown on YTree by our decision.

We didn't complete a interpretation yet because it processes with low priority.

In short, I am not expecting some form of 'identity' and placement on the YFull experimental tree, if and when they decide to finally process my BAM file and incorporate my private snp values in their U152 database. I am hopeful that other YFull customers who have access will be able to identify my kit somehow, perhaps my kit will have GR for Greek ancestry?

R.Rocca
08-03-2014, 12:42 PM
Thanks Rich

So is this the only PF6658+ Z193- in the U152 project that you know of, or are there others after the re-runs?

S.

I have to go back and check all of them.

Solothurn
08-03-2014, 01:21 PM
Thanks Rich

On full Y are they also showing Z192 as 'above' Z193?

PF6658 * Z192/PF6660

R-PF6658*
id:NA20754TSI
R-Z193

http://www.yfull.com/tree/R-PF6658/


I have to go back and check all of them.

R.Rocca
08-03-2014, 01:35 PM
Thanks Rich

On full Y are they also showing Z192 as 'above' Z193?

PF6658 * Z192/PF6660

R-PF6658*
id:NA20754TSI
R-Z193

http://www.yfull.com/tree/R-PF6658/

Actually, if you could, please send me your BAM file. If you recall, Z193 displays both positive and negative values even in positive samples. It may be that Z193 is positive in your sample, but below YFull's threshold.

Solothurn
08-03-2014, 03:43 PM
Rich

Yes I do recall. It is Steve Wear who did the BigY, will he have a BAM file from BigY to send you?

S.



Actually, if you could, please send me your BAM file. If you recall, Z193 displays both positive and negative values even in positive samples. It may be that Z193 is positive in your sample, but below YFull's threshold.

Armenis
08-03-2014, 07:19 PM
Vadim Urasin of YFull sent me an email confirming that I'm YF01706. That was nice of him, thank-you Mr Urasin!

jbarry6899
09-09-2014, 09:49 PM
Just received the following from YSeq:

S20782 was running 4 times with your DNA sample. We've used two different sets of primers to improve the assay. Unfortunately it didn't work with your sample. Our internal control sample worked fine with S20782. We think you have a null allele at S20782.

I've previously tested positive for S8183. I recently ordered BigY so we will see if there is a different result in that test.

Jim Barry
FTDNA 230232

R.Rocca
09-13-2014, 12:21 AM
Below is the latest U152+ tree. And to think that just a few years back, you could count the known U152 SNPs on one hand!

Enjoy...

http://www.r1b.org/imgs/U152_Tree_2014-09-12.png

Solothurn
09-13-2014, 09:58 AM
Thanks Rich

Do you have the link to the PF6658 tree?


Below is the latest U152+ tree. And to think that just a few years back, you could count the known U152 SNPs on one hand!

Enjoy...

http://www.r1b.org/imgs/U152_Tree_2014-09-12.png

MitchellSince1893
09-13-2014, 12:13 PM
The Graves cluster is informative. 23 BigY identified SNPs below Z150/Z12222 to common ancestor in 1665 or later.

On my Z150/Z12222 branch BigY, Yfull, and FGC, have identified ~36 SNPs to the mid 20th century.

beaugrandjacques
09-13-2014, 01:02 PM
R: according to my recent ad hoc test at YSEQ, FTDNA-31300 whose path is R-U152>L2>Z49>Z142>Z150 would be ancestral on CTS9490. It is shown derived on your tree.
Best regards
Jacques Beaugrand-Champagne

Sample Id=840

CTS9490 ChrY 18928795 18928795 C-

Pigmon
09-13-2014, 03:35 PM
I just ordered CTS9490 from YSEQ. This is my first order from them so I will await the swab test kit.

Regards,
Curtis

R.Rocca
09-13-2014, 04:45 PM
R: according to my recent ad hoc test at YSEQ, FTDNA-31300 whose path is R-U152>L2>Z49>Z142>Z150 would be ancestral on CTS9490. It is shown derived on your tree.
Best regards
Jacques Beaugrand-Champagne

Sample Id=840

CTS9490 ChrY 18928795 18928795 C-

Thanks Jacques. I have fixed it and the image above should reflect it (you may have to refresh the page to see the new version). There are still a few inconsistencies with some of the Big-Y results below Z150, and for that reason I have question marks after some of them. Regards.

R.Rocca
09-13-2014, 04:48 PM
Thanks Rich

Do you have the link to the PF6658 tree?

Here you go Solothurn... (by the way, I'm still awaiting Weir's BAM file)...

http://r1b.org/imgs/PF6658_Tree_2014-09-12.png

Solothurn
09-13-2014, 04:52 PM
Thanks Rich

He did ask for it but nobody replied. He thinks he contacted the wrong person. Any ideas who he should ask that will actually act on his request? :)


Here you go Solothurn... (by the way, I'm still awaiting Weir's BAM file)...

http://r1b.org/imgs/PF6658_Tree_2014-09-12.png

Solothurn
09-13-2014, 04:54 PM
I actually submitted with the UK10K, so if a sample comes in that is S20550+ it could well be mine :)

beaugrandjacques
09-13-2014, 05:21 PM
Merci beaucoup Richard. Excellent travail!

Jacques Beaugrand-Champagne

R.Rocca
09-13-2014, 07:53 PM
Thanks Rich

He did ask for it but nobody replied. He thinks he contacted the wrong person. Any ideas who he should ask that will actually act on his request? :)

Should have been the FTDNA Help Desk... [email protected]

pasquale
09-15-2014, 03:59 PM
Richard Rocca
Note, I tested positive for L2. However, I have not spent much time with this project (anything else) because of knee replacement surgery. I will be back to normal soon (not soon enough) and will continue my DNA education
Thanks for you advice and help

R.Rocca
09-15-2014, 04:14 PM
Richard Rocca
Note, I tested positive for L2. However, I have not spent much time with this project (anything else) because of knee replacement surgery. I will be back to normal soon (not soon enough) and will continue my DNA education
Thanks for you advice and help

Hope you have a quick recovery Pasquale.

Petr
09-25-2014, 06:52 AM
Dear Richard,

In Z49-S8183 branch, I see a duplicity for 2 SNPs, 8356636(T/C) and S12993=10025720(C/T) are both in "FTDNA-195364, FTDNA-309846" line and in "UK10K_ALS5085251, UK10K_ALS5085486" line.

(BTW, FTDNA-195364 is mine)

Petr

R.Rocca
10-03-2014, 08:32 PM
Thanks Rich

So is this the only PF6658+ Z193- in the U152 project that you know of, or are there others after the re-runs?

S.

I was finally able to download Weir's Big-Y bam file and it was just as I expected, he is Z193+.

Weir:
PF6658: 112 total reads of which 104 reads = derived G (93%) and 8 reads = ancestral A (7%)
Z193: 90 total reads of which 62 reads = derived T (69%) and 28 reads = ancestral G (31%)

For comparison, here are my Full Genomes results:

Rocca
PF6658: 325 total reads, 321 = ancestral A (99%)
Z193: 318 total reads, 316 = ancestral G (99%)

So, whatever threshold FTDNA has for determining a positive result was not met, so it was showing as Z193-.

Solothurn
10-04-2014, 03:51 AM
Thanks Rich

So in your opinion, did Z193 occur soon after U152 and in a similar location?




I was finally able to download Weir's Big-Y bam file and it was just as I expected, he is Z193+.

Weir:
PF6658: 112 total reads of which 104 reads = derived G (93%) and 8 reads = ancestral A (7%)
Z193: 90 total reads of which 62 reads = derived T (69%) and 28 reads = ancestral G (31%)

For comparison, here are my Full Genomes results:

Rocca
PF6658: 325 total reads, 321 = ancestral A (99%)
Z193: 318 total reads, 316 = ancestral G (99%)

So, whatever threshold FTDNA has for determining a positive result was not met, so it was showing as Z193-.

R.Rocca
10-04-2014, 11:28 AM
Thanks Rich

So in your opinion, did Z193 occur soon after U152 and in a similar location?

Yes. I think Z56 is the only one of the larger U152 subclades that occurred later. And for what it's worth, U152, DF27, L21, P312 all likely happened within a few generations of each other as part of the initial Bell Beaker expansions with L2, Z36 and PF6658/Z193 happening just a few generations after that.

jdean
10-04-2014, 01:42 PM
Yes. I think Z56 is the only one of the larger U152 subclades that occurred later. And for what it's worth, U152, DF27, L21, P312 all likely happened within a few generations of each other as part of the initial Bell Beaker expansions with L2, Z36 and PF6658/Z193 happening just a few generations after that.

Whilst this is likely true of P312, U152 & U152, L21 has anouther four SNPs that stubbornly remain equivalent suggesting L21's expansion may have been delayed a while ?

rms2
10-04-2014, 01:46 PM
Probably L21 was born amongst the early Beakers, as Rich said, but perhaps its big expansion awaited its arrival in the Isles? (Sorry for dragging a good U152 thread off topic.)

jdean
10-04-2014, 04:40 PM
Probably L21 was born amongst the early Beakers, as Rich said, but perhaps its big expansion awaited its arrival in the Isles? (Sorry for dragging a good U152 thread off topic.)

I think L21 expanding out of the Isles not so likely, remember we are talking L21 pre DF63 & DF13 here, but as you say this is not the best place to discuss this.

rms2
10-04-2014, 11:10 PM
I think L21 expanding out of the Isles not so likely, remember we are talking L21 pre DF63 & DF13 here, but as you say this is not the best place to discuss this.

I did not mean for it to sound like I was talking about L21 expanding out of the Isles. I think it got to the Isles from the Continent. I was just thinking that its big population boom occurred in the Isles after it got there from the Continent.

Gray Fox
10-08-2014, 08:41 PM
Just incase any of you missed this..

https://groups.yahoo.com/neo/groups/R1b-DF27-Project/conversations/messages/1986

P312 > ZZ11 > DF27,U152????

MitchellSince1893
10-09-2014, 04:40 AM
Just incase any of you missed this..

https://groups.yahoo.com/neo/groups/R1b-DF27-Project/conversations/messages/1986

P312 > ZZ11 > DF27,U152????

At position 22286799 I have the following report from YFull

ChrY position: 22286799 (+strand)
Reads: 323
Position data: 257C 66G
Weight for C: 0.793926959376
Weight for G: 0.206073040624
Probability of error: 0.29143128889 (0<->1)
Sample allele: C
Reference (hg19) allele: C

According to the author of the link you posted you are positive for SNP Z11 if you have
a collection of both 'C' and 'G' reads at position 22286799.

So I guess I'm positive for SNP ZZ11

haleaton
10-09-2014, 05:55 AM
At position 22286799 I have the following report from YFull

ChrY position: 22286799 (+strand)
Reads: 323
Position data: 257C 66G
Weight for C: 0.793926959376
Weight for G: 0.206073040624
Probability of error: 0.29143128889 (0<->1)
Sample allele: C
Reference (hg19) allele: C

According to the author of the link you posted you are positive for SNP Z11 if you have

So I guess I'm positive for SNP ZZ11

Me too (or three) as I have results from Big Y and FGC BGI:
Sample: NGC BGI Bam
ChrY position: 22286799 (+strand)
Reads: 1217
Position data: 2T 929C 286G
Weight for T: 0.000494862166332
Weight for C: 0.762728146013
Weight for G: 0.23677699182
Probability of error: 0.335203701409 (0<->1)
Sample allele: C
Reference (hg19) allele: C

Sample: #FTDNA Big Y Bam
ChrY position: 22286799 (+strand)
Reads: 409
Position data: 2A 294C 113G
Weight for A: 0.0027386541471
Weight for C: 0.720657276995
Weight for G: 0.276604068858
Probability of error: 0.314010949122 (0<->1)
Sample allele: S (C or G)
Reference (hg19) allele: C

Could the referenced author from Yahoo groups mean that if you are ZZ11- then you have unambiguous ancestral results though have to linked with another location with connected ambiguity? Unfortunately, many of the public samples are low read and heterozygous results can swing either way. My Big Y and NGC BGI results do differ (+ vs -) on a number of squirrely snps . . .

Petr
10-09-2014, 06:25 AM
This is interesting, I have reading:

Sample: #YF01551 (R-Y4355)
ChrY position: 22286799 (+strand)
Reads: 492
Position data: 370C 122G
Weight for C: 0.752546989921
Weight for G: 0.247453010079
Probability of error: 0.349951402904 (0<->1)
Sample allele: C
Reference (hg19) allele: C

Does it mean that BigY test has 122 wrong readings on this position or it is correct that 25 % alleles are G and 75 % C?

Petr

R.Rocca
10-13-2014, 07:57 PM
For those that are U152* and have not done Big-Y or Full Genomes testing...(and since PF6658/Z193 aren't available), S20550 is now available for single SNP orders at FTDNA.

Solothurn
10-14-2014, 02:38 AM
Thanks Rich

I will spread the word :)



For those that are U152* and have not done Big-Y or Full Genomes testing...(and since PF6658/Z193 aren't available), S20550 is now available for single SNP orders at FTDNA.

haleaton
10-14-2014, 03:05 AM
This is interesting, I have reading:

Sample: #YF01551 (R-Y4355)
ChrY position: 22286799 (+strand)
Reads: 492
Position data: 370C 122G
Weight for C: 0.752546989921
Weight for G: 0.247453010079
Probability of error: 0.349951402904 (0<->1)
Sample allele: C
Reference (hg19) allele: C

Does it mean that BigY test has 122 wrong readings on this position or it is correct that 25 % alleles are G and 75 % C?

Petr

On ZZ11 I don't think there is anything there but need further understanding how maybe this concept has meaning for the Little Scottish Cluster.

I am far from an expert, but my understanding is that in order to sequence your Y-DNA they have to chop it up in much tinier pieces called the read length. All of these pieces include other DNA that gets chopped up too. In some cases the regions are very similar to other regions particularly on the Y that when they compare against the reference sequence they overlap each other and cause perhaps accurate reads but of unknown DNA. I would think this a chemical a hydroynamic process which varies a lot leading to heterozygous SNPs. These are often ones found in multiple Haplogroups. The hard part is when there are low number of reads this can swing either way and may not look heterozygous. All data has noise.

So for example for several SNP I get different results + or - with Big Y or FGC. These tend to be SNPs that are inconsistent and do not have phylogenetical (sp?) value to the tree and can just be ignored until some future date when read lengths get bigger.

The other factor is a heterozygous postive read is likely more accurate if places you the tree consistent with multiple other measurements. Similar to Y-STR matches with people with very uncommon surnames are more likely to truly be matches.

kw5368
10-17-2014, 05:23 PM
Hello,

This probably has been answered many times before and I hope it is ok to bring it up in this thread. Thanks for your patience with my lack of knowledge.

I have a question about how haplogroups are grouped on FTDNA projects. If you have been found to be L2 for example, why are you still grouped with others that are for example L552 or Z49?

Thanks for your help!

Kwheaton
10-17-2014, 05:52 PM
Hello,

This probably has been answered many times before and I hope it is ok to bring it up in this thread. Thanks for your patience with my lack of knowledge.

I have a question about how haplogroups are grouped on FTDNA projects. If you have been found to be L2 for example, why are you still grouped with others that are for example L552 or Z49?

Thanks for your help!

Unfortunately the Haplogroup designations that populate the results pages are a terrible mess and many not updated. FTDNA is aware of the problem but no date has been announced for a fix. Your actual FTDNA page at FTDNA should be the correct Haplogroup assignment. Work with Rich Rocca. He is the L2 guru within the U152 project.
Kelly

jbarry6899
10-17-2014, 08:49 PM
Hello,

This probably has been answered many times before and I hope it is ok to bring it up in this thread. Thanks for your patience with my lack of knowledge.

I have a question about how haplogroups are grouped on FTDNA projects. If you have been found to be L2 for example, why are you still grouped with others that are for example L552 or Z49?

Thanks for your help!

L552 and Z49 are subclades (subgroups) of L2. If you are L2+ and your haplotype (STR pattern) closely matches others who have tested positive for L552 or Z49 that would account for your placement there. As Kelly said, Richard or Steve Gilbert could help you.

I have found that the subclade groupings for U152 are generally sound and up to date.

Jim

Kwheaton
10-17-2014, 09:05 PM
L552 and Z49 are subclades (subgroups) of L2. If you are L2+ and your haplotype (STR pattern) closely matches others who have tested positive for L552 or Z49 that would account for your placement there. As Kelly said, Richard or Steve Gilbert could help you.

I have found that the subclade groupings for U152 are generally sound and up to date.

Jim

Jim,

The subclades are fine for those with Big Y results. For those who ordered individual SNP tests they do not populate to the Project result pages. Arrggh! For example a cousin (R-L21) whose kit I manage is listed in red as M222 although he is positive for 3 downstream SNPS at FTDNA so his terminal SNP should be populating the pages as DF97. So yes Big Y results seem to populate okay but individual results not so much....
Kelly

Petr
10-17-2014, 09:46 PM
AFAIK it is caused by the fact that FTDNA uses Geno 2.0 haplotree https://my.familytreedna.com/y-dna-haplotree/ and therefore SNPs not tested by Geno 2.0 are not taken into consideration. DF97 is not on this tree.

Kwheaton
10-17-2014, 09:59 PM
AFAIK it is caused by the fact that FTDNA uses Geno 2.0 haplotree https://my.familytreedna.com/y-dna-haplotree/ and therefore SNPs not tested by Geno 2.0 are not taken into consideration. DF97 is not on this tree.
Yes but what about the upstream ones like DF105 and DF85 are those also not tested in Geno2.0---In any event it makes no sense that they only go by GENO 2.0 SNPs

Petr
10-17-2014, 10:07 PM
I fully agree, I just described how it - probably - works. Apparently some SNPs not tested by Geno 2.0 were later added, e.g. DF99. IIRC group administrator may ask for addition of new SNP to the tree?

Kwheaton
10-17-2014, 10:25 PM
As I wrote to FTDNA its bad fr business for people to test SNPS and not see them reflected properly. And I do not know what their commitment to GENO 2.0 is but it looks like it has hamstrung them right and left.

MitchellSince1893
10-17-2014, 11:49 PM
I'm in the same boat...3 levels below Z49 but still shown at z49...even though my Z142 test was done at ftdna.

kw5368
10-18-2014, 12:21 AM
Unfortunately the Haplogroup designations that populate the results pages are a terrible mess and many not updated. FTDNA is aware of the problem but no date has been announced for a fix. Your actual FTDNA page at FTDNA should be the correct Haplogroup assignment. Work with Rich Rocca. He is the L2 guru within the U152 project.
Kelly

Thank you all for your answers to my question. This is exactly what I feared was happening. I am trying to track possible relatives but it is hard to do if their haplogroup has not been updated.

I'm sure I will have many more questions once I receive my results.

Thank you all again!

Kwheaton
10-18-2014, 12:35 AM
You are quite welcome!

jbarry6899
10-18-2014, 12:39 AM
Jim,

The subclades are fine for those with Big Y results. For those who ordered individual SNP tests they do not populate to the Project result pages. Arrggh! For example a cousin (R-L21) whose kit I manage is listed in red as M222 although he is positive for 3 downstream SNPS at FTDNA so his terminal SNP should be populating the pages as DF97. So yes Big Y results seem to populate okay but individual results not so much....
Kelly

I agree, although I think Richard and Steve do a pretty good job of sorting and grouping despite those challenges.

Kwheaton
10-18-2014, 12:56 AM
Jim,
Indeed they do! I think what is probleatic is when people look at their match lists (lots who don't belong to Haplogroup projects) and try to make sense of thier matches. Or within surname projects and you ahv agroup of men with a common ancestor and they all show different Halogroup designations....hopefully FTDNA wil get it sorted before hell feeezes over :P

kw5368
10-24-2014, 10:27 PM
Hello everyone,

I have another question for you experts. I have been waiting to receive my results for my Y111 testing and I was notified on the 22nd that my results were complete. The problem is that they are releasing the STR values one panel at a time. I have only received two panels in the last two days. Is this normal?

Thanks for any help!

Kwheaton
10-24-2014, 10:57 PM
Hello everyone,

I have another question for you experts. I have been waiting to receive my results for my Y111 testing and I was notified on the 22nd that my results were complete. The problem is that they are releasing the STR values one panel at a time. I have only received two panels in the last two days. Is this normal?

Thanks for any help!

Yes that is very normal (typical). Nothing to worry about.
Kelly

razyn
12-05-2014, 03:19 AM
Just incase any of you missed this..

https://groups.yahoo.com/neo/groups/R1b-DF27-Project/conversations/messages/1986

P312 > ZZ11 > DF27,U152????

I didn't miss the original assertions by Alex Williamson (inasmuch as we discussed them some, in the DF27 Yahoo group); but I did miss the fact that you had asked whether the U152 group had missed it.

Seems to me, ZZ11 can separate the sheep (i.e. us, U152 and DF27) from the goats (i.e. the several other haplogroups under P312). If true -- and I'm not sure whether proving it takes science, or just rhetoric -- it also seems to me that these new ZZs need to get onto the ISOGG and YFull trees, etc.

By the way, another ZZ seems to distinguish Z195/Z196 (and its fairly well-described progeny) from all the other clades and subclades under DF27 -- most of them still far less well-described, and (perhaps for that reason) not yet heavily populated in our project subgroups. That one isn't going to tousle the heads of any U152 guys; but it might shorten the testing path for our Z195- guys, especially if we can get separate chips designed for their "terminal SNP" search.

R.Rocca
12-05-2014, 03:59 AM
I didn't miss the original assertions by Alex Williamson (inasmuch as we discussed them some, in the DF27 Yahoo group); but I did miss the fact that you had asked whether the U152 group had missed it.

Seems to me, ZZ11 can separate the sheep (i.e. us, U152 and DF27) from the goats (i.e. the several other haplogroups under P312). If true -- and I'm not sure whether proving it takes science, or just rhetoric -- it also seems to me that these new ZZs need to get onto the ISOGG and YFull trees, etc.

By the way, another ZZ seems to distinguish Z195/Z196 (and its fairly well-described progeny) from all the other clades and subclades under DF27 -- most of them still far less well-described, and (perhaps for that reason) not yet heavily populated in our project subgroups. That one isn't going to tousle the heads of any U152 guys; but it might shorten the testing path for our Z195- guys, especially if we can get separate chips designed for their "terminal SNP" search.

Indeed, ZZ11 is quite interesting and may have a great tale to tell. Regarding its inclusion on the ISOGG tree, I doubt it will (or should) be included given its somewhat inconsistent nature.

haleaton
12-05-2014, 04:56 AM
Indeed, ZZ11 is quite interesting and may have a great tale to tell. Regarding its inclusion on the ISOGG tree, I doubt it will (or should) be included given its somewhat inconsistent nature.

Noticed ZZ11_1 on YBrowse, but no ZZ11_2. Cannot determine whether my own inability to understand or others very dry humor.

MitchellSince1893
12-07-2014, 09:25 PM
WOOHOO! The U152 tree has been updated under the "Essentials" section at this link

https://www.familytreedna.com/public/R1b-U152/default.aspx?section=results

MitchellSince1893
12-14-2014, 01:15 AM
I created this graphic to illustrate how much U152 has exploded, just 2 levels down from U152 thanks to the "SNP Tsunumi"...the results from this year's BigY and FGC test participants.

It was developed from Richard Rocca's early December U152 tree. In some places Richard's tree drills down 13 levels.

3217

Higher resolution version at this link
http://media-cache-ak0.pinimg.com/originals/5c/b7/45/5cb7458cb65ffc33eea353eff4c22406.jpg

For comparison here is an Aug 2013 U152 tree from Eupedia


From 4 to 8 branches one level below U152.

From 4 to 18 branches one level below L2.

If you are on the fence, take the plunge and order BigY or the FGC tests. Do your part to expand our knowledge of the tree.\

Solothurn
12-14-2014, 04:22 AM
Wow great graphic, thanks :)

In the early tree Z192 was 'considered' Italo-Roman.
Does anybody know what PF6658/Z193 is considered as?




I created this graphic to illustrate how much U152 has exploded, just 2 levels down from U152 thanks to the "SNP Tsunumi"...the results from this year's BigY and FGC test participants.

It was developed from Richard Rocca's early December U152 tree. In some places Richard's tree drills down 13 levels.

3202

Higher resolution version at this link
http://media-cache-ak0.pinimg.com/originals/b0/eb/4a/b0eb4a92afd481d6c63a677f49d16775.jpg

For comparison here is an Aug 2013 U152 tree from Eupedia
3203

From 4 to 8 branches one level below U152.

From 4 to 18 branches one level below L2.

If you are on the fence, take the plunge and order BigY or the FGC tests. Do your part to expand our knowledge of the tree.

MitchellSince1893
12-14-2014, 05:49 AM
Wow great graphic, thanks :)

In the early tree Z192 was 'considered' Italo-Roman.
Does anybody know what PF6658/Z193 is considered as?

I see participants from Switzerland, Italy, Sweden, Belgium, possibly Ireland, Ukraine, Germany, and Spain. About the best you could say it's concentrated in Western Europe.

I think you will need to go down a few more levels before you start seeing more geographically concentrated results.

For example, on my particular branch of L2, which is 4 levels lower than PF6658/Z193 (U152>L2>Z49>Z142>Z150>FGC12378/79/80/81/82), it's still at the Western European level with participants from Spain, The Netherlands, and England.

Also due to it's age (based on various SNP dating methodologies), I believe PF6658/Z193, along with all the other branches right below U152, are pre proto-Italic, pre Italo-Celtic and pre Italo-Roman for that matter.

One level below U152 would be anywhere between ~3800 to 6100 years ago, depending on the SNP dating method used. Earliest mention of Italic languages I could find was around 2600 years ago. while the earliest mention of Italic tribes was 3200 years ago.

Acque agitate
12-14-2014, 10:48 PM
Hello everyone,
when I study our group R-U152 and its interactions with the other groups, I use a history chart based on the number of snp.
I am attaching a simple chart that I have worked with Excel, exclusively for R-L2 (of course you can do everything by entering R-U152, but the page became too great).
The data are based on those provided by our friend Riccardo Rocca.
I put in the time factor associated with each mutation snp.
I made two assumptions:
1) in the first, L2 was born about the year 3450 BC and the mutation rate of each snp is 100 years (my favorite hypothesis);
2) in the second hypothesis L2 was born about the year 2750 BC and the mutation rate of each snp is equal to 90 years;
Having used Excel I can change the year of birth of L2 and the mutation rate as I wish.
What seems to me more interesting is that this graph is able to detect if some explosions of some traits coincide. It is obvious that in case of coincidence there may be some correlation between different strokes occurred in some specific ages.
To me it was very useful to understand if certain explosions could be related to certain historical events (Bronze Age and earlier)


I believe also helpful to look at the chart to avoid thinking to the people, at least now. In this state of depth, it seems very premature to assign a subgroup to a people (entities much more recent).

I apologize for English but for me the translation is not very simple (thankfully that exists google).

Obviously if someone is interested in the excel file let me know.


3216

Kwheaton
12-14-2014, 11:00 PM
I created this graphic to illustrate how much U152 has exploded, just 2 levels down from U152 thanks to the "SNP Tsunumi"...the results from this year's BigY and FGC test participants.

It was developed from Richard Rocca's early December U152 tree. In some places Richard's tree drills down 13 levels.

3207



Higher resolution version at this link
http://media-cache-ec0.pinimg.com/originals/27/b7/14/27b714d4f93f75bb300098257265c10b.jpg

For comparison here is an Aug 2013 U152 tree from Eupedia


From 4 to 8 branches one level below U152.

From 4 to 18 branches one level below L2.

If you are on the fence, take the plunge and order BigY or the FGC tests. Do your part to expand our knowledge of the tree.\


These are really gorgeous thank you so much for your work. And Rich and all the testers for making it all possible!!!! I agree if you are on the fence JUMP!

Il PapÓ
12-14-2014, 11:27 PM
I created this graphic to illustrate how much U152 has exploded, just 2 levels down from U152 thanks to the "SNP Tsunumi"...the results from this year's BigY and FGC test participants.

It was developed from Richard Rocca's early December U152 tree. In some places Richard's tree drills down 13 levels.

3207

Higher resolution version at this link
http://media-cache-ec0.pinimg.com/originals/27/b7/14/27b714d4f93f75bb300098257265c10b.jpg

For comparison here is an Aug 2013 U152 tree from Eupedia


From 4 to 8 branches one level below U152.

From 4 to 18 branches one level below L2.

If you are on the fence, take the plunge and order BigY or the FGC tests. Do your part to expand our knowledge of the tree.\

Being a 7959751(G/C) et al positive (under z56), I just noticed that you missed one of the five mutation : 19279266(C/G) but you still did a great work ! :). We also need more sample to break those closely related subclade who share an enormous amount of snps.

MitchellSince1893
12-14-2014, 11:44 PM
Being a 7959751(G/C) et al positive (under z56), I just noticed that you missed one of the five mutation : 19279266(C/G) but you still did a great work ! :). We also need more sample to break those closely related subclade who share an enormous amount of snps.

You are correct. It's there, I just need to pull the box down so it shows up. The comma after the last line means there's more below it.
Sorry about that. If anyone else see's any errors, let me know.

EDIT: It's updated

MitchellSince1893
12-15-2014, 03:46 AM
I created this graphic to illustrate how much U152 has exploded, just 2 levels down from U152 thanks to the "SNP Tsunumi"...the results from this year's BigY and FGC test participants.

3220

It was developed from Richard Rocca's early December U152 tree. In some places Richard's tree drills down 13 levels.

Higher resolution version at this link
http://media-cache-ak0.pinimg.com/originals/83/f2/5e/83f25eef978c9edb95f240f3b19bdacf.jpg
...
I can no longer update/edit the original post, but I did update the graphic and link in the section above to resolve a minor issue with the appearance.

None of the actual data was changed.

MitchellSince1893
12-20-2014, 11:35 PM
FYI: One of my previous Yfull private SNPs is now a named SNP, Y4272. It was a "Best" rated private SNP.

ChrY position: 22941997 (+strand)
Reads: 79
Position data: 79A
Weight for A: 1.0
Probability of error: 0.0 (0<->1)
Consensus allele: A
Reference allele: G
Known SNPs: Y4272

Does any other U152 folks have this SNP with a nucelotide value of "A"

Just trying to figure out where this SNP fits into the haplotree.

I'm assuming that now that it's named that some one else has this SNP.

I asked this back in June.

My new match Horatio Sylvanus Roberts shares this SNP with me.

lamahorse
12-23-2014, 11:05 AM
My Big Y results are in. :)

Solothurn
12-23-2014, 01:07 PM
Any surprises?


My Big Y results are in. :)

lamahorse
12-24-2014, 06:36 AM
Any surprises?

I'm not that sure about that. Appears the testing for various U152 subclades have come back as 'Unknown'.

Big Y matches are bizarre. I share unique SNPs with four other fellows but they don't show up on the other Y-111 etc lists as genetically related to me.

Within the McCarthy surname project, I have been linked with another branch of McCartys from North America. I don't think it's coincidental that we both share the same surname despite my side of the family having no paper trail prior to 1807. The American McCartys have two common ancestors (who were most likely brothers) who were both born around 1765 in the Thirteen Colonies. Y testing proved the relation between these two parts of that family but I've yet to determine how or when our distant common ancestor was born or how our distant cousin got over that side of the Atlantic.

I'm speculating from the regular Y matches that we're related to the Irish Noonan family as my closest matches are all with Newmans and Noonans. Newman is an Anglicisation of Noonan and it seems there are a whole tranch of fellows who are unaware of their Irish ancestry. This fact seems caught up with Newman being a surname in places like Germany and the UK.

I'm not sure what one can do with my Big Y. I say the most important thing is to see how myself and my distant McCarty American cousin match up with other U152 branches. Doesn't it take a few days for them to upload the BAM file?

Petr
12-24-2014, 08:01 AM
I'd say that the first thing would be to determine the real private (novel) mutations, FTDNA determines them by very strange way causing many false positives and false negatives and useless matches as well. Sou you can use BigY and/or FGC service. You can try to analyze the BM file yourselves: http://www.y-str.org/2014/04/bam-analysis-kit.html - but I'm afraid the results of that process are almost useless.

Do those McCartys from North America have BigY test results? And Irish Noonan family?

lgmayka
12-24-2014, 09:04 AM
Doesn't it take a few days for them to upload the BAM file?
Yes, but you need to ask [email protected] for it.

MitchellSince1893
12-24-2014, 01:11 PM
I'm not sure what one can do with my Big Y.
One thing you can do is go to "BigY Matches" and use the "Shared Novel Variants" filter:

1. Make a list of those matches that have (1)...towards the bottom, and then do the same thing (2), and maybe (3).

2. Use the U152 project STR pages to see if you can find your match names on a certain branch https://www.familytreedna.com/public/R1b-U152/default.aspx?section=ycolorized. Use the find feature...e.g. control "F" to look for surnames...sometimes the names listed on the BigY match may have a different first names listed on the STR page.


Not every name found in step 1 above is necessarily on your branch. You may share a false positive SNP or a unstable SNP (i.e. it's in multiple haplogroups)

It's not quick, but it may allow you to identify what branch you are on while you are waiting for more detailed analysis.

For example, when I do the above steps, I have 8 matches at (1). 5 are in fact to my closest match. On the STR page he's listed by his MRCA as Horatio Roberts. On the BigY match he's listed by the actual test taker, Stephen Roberts. However, I also have 3 (1) matches to a Gary Burkhart. The SNP matches to Burkart are either false positive SNPs or unstable. This will be evident as I go to the next levels of matches.

When I go to (2) matches I see all false positive matches...so it's not helping. This won't be evident to you at this point in time.

When I go to (3) matches I again see 3 matches that have Stephen Roberts, and I also see 3 matches to Charles Lincoln and Stephen Brace. This is encouraging because I'm seeing Roberts again.

Comparing these names to the FTDNA U152 project STR pages, I can see a branch containing Brace and Lincoln. 2 levels down I see Roberts. This is a good indication that I've found my branch.

Further analysis from Richard Rocca and/or Yfull or FGC will confirm this.

Also, my closest match via BigY is a GD of 24 at 111 markers, so don't worry if you don't have any close 111 marker matches.

lamahorse
12-24-2014, 06:04 PM
Aha, I see now. The page has been frequently updated throughout the day.

Billy Leonard McCarty
89 0 26,782 23/12/2014

My biggest match is expectedly with the same McCarty from the other side of the Atlantic. I'll continue to run through the suggestions Michell lists when I have a little more time later. This is all new to me! I hope to identify what branch that we fit as it would be nice to see how we shape up to other U152 branches.

Yes, Petr; we discovered the link through the McCarthy Y DNA project. The lady who was administrating all her side of the McCarty family kits hadn't any idea whether they were actual McCartys until we matched with them. Our common ancestor roughly lived maybe around 12-16 generations from my father/the closest match. So speculating that it was around the 1500s that we branched off. It's an encouraging sign that both our common ancestor was styling himself as a McCarthy but compared to the other 100 or so McCarthys in that surname study; we don't match any of them. We're the only U152+ McCarthys compared to the rest who are mainly the common two Irish hapolgroups (which fits the narrative of two leading McCarthy Septs).

Y-67 wise, my closest matches are Noonans/Newmans each who have no common relation over their paper trails. Genitically, our surnames come from the same general area but we are slightly closer related to those Noonans than the McCarthys over 67 markers.

Searching family history, I discovered an unknown Sept of McCarthy 'Naghey' in the same townland as my ggg grandfather 22 years after his supposided birth. The man is a candidate for his father (of three who's names each run in my family) so this Sept and the lack of any written history about it, intrigues me to say the least. I think Nagehy means Na Gaoithe or Storm/Windy.

Anyway, early days.

Merry Christmas fellow U152ers!

mafe
12-24-2014, 06:18 PM
lamahorse, you could look up PF6658 and Z193 in your Known SNPs-list to see if you are positive for these two SNPs.

lamahorse
12-24-2014, 07:56 PM
lamahorse, you could look up PF6658 and Z193 in your Known SNPs-list to see if you are positive for these two SNPs.

PF6658 No(-) No A A High

Z193 No(-) No G G High
Z1936 No(-) No C C High

For L2, I get.

L2 ? Yes T ? Unknown

Z36

Z36 ? Yes A ? Unknown

mafe
12-24-2014, 08:26 PM
PF6658 No(-) No A A High

Z193 No(-) No G G High
Z1936 No(-) No C C High

For L2, I get.

L2 ? Yes T ? Unknown

Z36

Z36 ? Yes A ? Unknown

Unfortunately the results for L2, Z36 and Z56(PF6601) are all very ambiguous in Big-Y.

Il PapÓ
12-24-2014, 11:53 PM
PF6658 No(-) No A A High

Z193 No(-) No G G High
Z1936 No(-) No C C High

For L2, I get.

L2 ? Yes T ? Unknown

Z36

Z36 ? Yes A ? Unknown

What about Z43 ? (it's apparently the same as Z56)

lamahorse
12-26-2014, 12:25 AM
Z43 No(-) No G G High

I will look for my bam file, I'm sure we'll fit in somewhere.

MitchellSince1893
01-14-2015, 02:58 AM
I created this graphic to illustrate how much U152 has exploded, just 2 levels down from U152 thanks to the "SNP Tsunumi"...the results from this year's BigY and FGC test participants.

It was developed from Richard Rocca's early December U152 tree. In some places Richard's tree drills down 13 levels.
...

Updated U152 organization chart based on Richard Rocca's Jan 2015 U152 Tree.
Biggest changes I noted were expansion of branches under L2

3381

High resolution version here http://media-cache-ak0.pinimg.com/originals/a6/85/2c/a6852cd1e6e603444691643abe4f22bc.jpg

razyn
01-27-2015, 01:10 AM
Indeed, ZZ11 is quite interesting and may have a great tale to tell. Regarding its inclusion on the ISOGG tree, I doubt it will (or should) be included given its somewhat inconsistent nature.

I don't want to drop this conversation entirely, it still needs resolution. My recent correspondence with Alex Williamson leaves me with the understanding that ZZ11_1 is phylogenetically consistent. Its more-apparent-than-real "inconsistency" is a function of testing methods, and choices made by people who set the parameters to be investigated in labs, or on chips, etc. (If they aren't looking where it is, they won't see it -- but that does not mean they couldn't detect it, or that it's not there.) So, it is not consistently detected; not found in the academic literature, nor in the raw data on which those have been based -- yet it's a consistent mutation. It happened to a person, and therefore in a time and place. And it has phylogenetic consequences for its descendants -- some of whom are U152+ and some DF27+, but none of whom are L21+, nor U106+. It's ancient, and forms a branching point below P312 that we probably should be attempting to date, and map -- just as we have for several years been attempting to map the differential distributions of L21, U106, U152, and latterly DF27. And, of course, the subclades of all of the above.

An alternative explanation, that would save me a good bit of work I'm about to undertake (primarily because of ZZ12 -- which doesn't affect U152, but does reorganize DF27 pretty substantially) is that Alex is mistaken. I'd like to believe that -- but I don't.

Petr
01-27-2015, 10:25 PM
Just if there is anybody with S12993 subclade. The current U152 tree shows one subclade with 3252488(G/A), 6404480(T/C), 10006576(T/C), 13218678(C/T), 13611363(G/A), 13611386(T/C)?, 59025293(C/A)? with UK10K_ALS5085486 and with additional SNP S8172 1KG-HG00736, UK10K_ALS5085251, BDNA-1354, BDNA-1545, BDNA-1615.

So I tried to check my results for these mutations.

3252488 G -> A: My Yfull results just 1 A reading, i.e. positive but unreliable
6404480 T -> C: YFull no call, so I ordered it from YSEQ, it was named A1168 and it is positive
10006576 T -> C: YFull 23 T readings, i.e. negative
13218678 C -> T: YFull no call
13611363 G -> A: YFull no call
13611386 T -> C: YFull no call
59025293 C -> A: YFull no call
23595215 A -> G (S8172): YFull 53 A readings, i.e. negative

I compared my results with results of 1KG-HG00736.
3252488 G -> A: 3G - negative
6404480 T -> C: 7C - positive
10006576 T -> C: 4T - negative
13218678 C -> T: 3T - positive
13611363 G -> A: 1G - negative
13611386 T -> C: 2T - negative
59025293 C -> A: 9A 12C - unstable negative
23595215 A -> G (S8172): positive

It seems to me quite confusing.

I tried to order other SNPs from YSEQ but received the reply that I don't understand well:
Unfortunately many of those markers have been left out from the BigY enrichment process for a reason:

3252488 G -> A 99.3% X + 88980954 88981953
13218678 C -> T 95.1% 11 + 70848858 70850055
13611363 G -> A 96.0% 2 + 92203880 92204879
13611386 T -> C 96.1% 2 + 92203903 92204902
59025293 C -> A Pseudo Autosomal Region (PAR)

Most of them are highly identical with other regions in the genome and therefore prone to recombination events. This goes normally hand in hand with inconsistent phylogenies due to parallel and back mutations.

Does anybody know how to get UK10K and BDNA values for these mutations?

Now I'm awaiting FGC Elite results, I will see if these SNPs will be there or not.

I'm not sure what does all this mean so I wrote it here.

Petr

Petr
01-27-2015, 10:42 PM
Just if anybody is interested, I compared all mutations in U152 tree with YBrowse and added (alternate) names if they exist, see the attached spreadsheet. There are names for 86 unnamed SNPs and many alternate names, esp. FGC - Y.

Two named SNPs in the U152 tree are missing from ISOGG Ybrowse database, DF90 (8688682 T/C) and DF103, I have no idea why.

On the forum I have found your post that DF103 = 9020396 (TAGA/-)

But if I check hg19 data, on 9020396 position I see gtagata... So maybe the mutation is 9020396(GTAGA/G) or 9020397(TAGA/-)?

Petr

R.Rocca
01-28-2015, 06:22 PM
I don't want to drop this conversation entirely, it still needs resolution. My recent correspondence with Alex Williamson leaves me with the understanding that ZZ11_1 is phylogenetically consistent. Its more-apparent-than-real "inconsistency" is a function of testing methods, and choices made by people who set the parameters to be investigated in labs, or on chips, etc. (If they aren't looking where it is, they won't see it -- but that does not mean they couldn't detect it, or that it's not there.) So, it is not consistently detected; not found in the academic literature, nor in the raw data on which those have been based -- yet it's a consistent mutation. It happened to a person, and therefore in a time and place. And it has phylogenetic consequences for its descendants -- some of whom are U152+ and some DF27+, but none of whom are L21+, nor U106+. It's ancient, and forms a branching point below P312 that we probably should be attempting to date, and map -- just as we have for several years been attempting to map the differential distributions of L21, U106, U152, and latterly DF27. And, of course, the subclades of all of the above.

An alternative explanation, that would save me a good bit of work I'm about to undertake (primarily because of ZZ12 -- which doesn't affect U152, but does reorganize DF27 pretty substantially) is that Alex is mistaken. I'd like to believe that -- but I don't.

@razyn, it is a topic worth continuing IMO. So is Alex Williamson saying that all DF27 and U152 folks are heterozygous at this position and that nobody that is DF27 or U152 has been ancestral to date? Perhaps you can ask Alex to post here as well?

razyn
01-28-2015, 11:33 PM
I think it's more that the founders were whatchamacallit; there have been subsequent back mutations or additional mutations in a couple of branches of DF27. But the "ancestral" from which they were mutating was the mutated ancestor (who was already long since DF27, by then). It's more of a problem when the ZZ mutation is on a palindrome arm than when it isn't. But the phylogeny as such ultimately has to do with "who's your daddy," not "what's the reference sequence value." And at some point in time and space, he was ZZ11. For both U152 and DF27.

R.Rocca
01-29-2015, 01:26 AM
I think it's more that the founders were whatchamacallit; there have been subsequent back mutations or additional mutations in a couple of branches of DF27. But the "ancestral" from which they were mutating was the mutated ancestor (who was already long since DF27, by then). It's more of a problem when the ZZ mutation is on a palindrome arm than when it isn't. But the phylogeny as such ultimately has to do with "who's your daddy," not "what's the reference sequence value." And at some point in time and space, he was ZZ11. For both U152 and DF27.

That's the problem...if there have been back mutations in several mutations of DF27...and maybe some in U152, then maybe it exists in other haplogroups.

razyn
01-29-2015, 03:34 AM
I don't know of any back mutations in ZZ11_1, do you? Most people haven't tested for it, anyhow -- but it was found in people who matched, and they were all DF27 or U152. I was speaking more generally. We have a ZZ12_1 that's on a palindrome, and is more or less all the people in DF27 who aren't Z195... except there's been one additional mutation; so the bunch that is now ZZ12 in both directions -- though more mutated -- is the easiest to see. And one family (Plant) appears to have had a back-mutation, and lost it. But that doesn't mean the Plants go back to being Z195+ (which they never were); or that lacking ZZ12_1 and Z195, they are now DF27- (a different mutation is involved).

Petr
01-29-2015, 03:45 PM
So is Alex Williamson saying that all DF27 and U152 folks are heterozygous at this position and that nobody that is DF27 or U152 has been ancestral to date? Perhaps you can ask Alex to post here as well?I've checked the YFull U152 group and it seems there is one kit with ancestral ZZ11_1 results, YF02497 = FTDNA-64890 (Dyrek). It has clear "C", 396 readings. All other BigY/FGC results have in average 23 % readings "G" and 77 % readings "C".

R.Rocca
01-29-2015, 05:39 PM
I've checked the YFull U152 group and it seems there is one kit with ancestral ZZ11_1 results, YF02497 = FTDNA-64890 (Dyrek). It has clear "C", 396 readings. All other BigY/FGC results have in average 23 % readings "G" and 77 % readings "C".

Thanks Petr...can you tell me out of how many samples? Also, is the data viewable for those that are not YFull clients?

Petr
01-29-2015, 07:52 PM
YFull U152 group has 64 members, 43 of them are from 1000 Geomes project and 21 of them are real BigY (and maybe FGC) results. Here are the results:
YF02458 R1b1a2a1a2b* 5A 303C 5T 80G
YF02497 R1b1a2a1a2b1 396C
YF02170 R1b1a2a1a2b1 2A 294C 113G
YF01555 R1b1a2a1a2b1 4A 275C 2T 85G
YF02311 R1b1a2a1a2b1 319C 124G
YF01527 R1b1a2a1a2b1 3A 268C 68G
YF01461 R1b1a2a1a2b1* 929C 2T 286G
YF01754 R-CTS9733 3A 485C 148G
YF02125 R-Y6789 1A 323C 94G
YF02435 R1b1a2a1a2b1c1* 1A 562C 149G
YF01926 R-S7404 221C 70G
YF02596 R-Y9080 426C 127G
YF01489 R-Y9080 257C 66G
YF01733 R-S8183* 337C 87G
YF02229 R-Y4356* 294C 92G
YF01551 R-Y4355 370C 122G
YF01647 R-Y3960 2A 357C 84G
YF02345 R-PF6577 143C 73G
YF01743 R-Z36* 3A 1216C 1T 362G
YF02052 R-Z36* 389C 101G
YF01575 R-Y3577 1A 1254C 1T 379G

There are some pure ancestral results among 1000KG samples too but it may be caused by low count of reads:


HG00152 R1b1a2a1a2b 1C
NA19649 R-Z291 2C
HG02219 R1b1a2a1a2b3* 2C
NA20754 R-Z192* 1C
NA19685 R-CTS10676 4C
NA19661 R-CTS10676 1C
HG01060 R-Z36* 6C
HG01383 R-Z36* 6C
All others are mixed C and G.

The administrator of YFull U152 group is Tony Wilson <[email protected]>. I have no idea if there is a possibility to be a member of a group without being a member of YFull.

Now I applied for a membership in YFull P312 group too, it has 211 members and administrators are Stephen Parrish, Rodney Jewett and Didier Vernade.

R.Rocca
01-29-2015, 07:59 PM
YFull U152 group has 64 members, 43 of them are from 1000 Geomes project and 21 of them are real BigY (and maybe FGC) results. Here are the results:
YF02458 R1b1a2a1a2b* 5A 303C 5T 80G
YF02497 R1b1a2a1a2b1 396C
YF02170 R1b1a2a1a2b1 2A 294C 113G
YF01555 R1b1a2a1a2b1 4A 275C 2T 85G
YF02311 R1b1a2a1a2b1 319C 124G
YF01527 R1b1a2a1a2b1 3A 268C 68G
YF01461 R1b1a2a1a2b1* 929C 2T 286G
YF01754 R-CTS9733 3A 485C 148G
YF02125 R-Y6789 1A 323C 94G
YF02435 R1b1a2a1a2b1c1* 1A 562C 149G
YF01926 R-S7404 221C 70G
YF02596 R-Y9080 426C 127G
YF01489 R-Y9080 257C 66G
YF01733 R-S8183* 337C 87G
YF02229 R-Y4356* 294C 92G
YF01551 R-Y4355 370C 122G
YF01647 R-Y3960 2A 357C 84G
YF02345 R-PF6577 143C 73G
YF01743 R-Z36* 3A 1216C 1T 362G
YF02052 R-Z36* 389C 101G
YF01575 R-Y3577 1A 1254C 1T 379G

There are some pure ancestral results among 1000KG samples too but it may be caused by low count of reads:


HG00152 R1b1a2a1a2b 1C
NA19649 R-Z291 2C
HG02219 R1b1a2a1a2b3* 2C
NA20754 R-Z192* 1C
NA19685 R-CTS10676 4C
NA19661 R-CTS10676 1C
HG01060 R-Z36* 6C
HG01383 R-Z36* 6C
All others are mixed C and G.

The administrator of YFull U152 group is Tony Wilson <[email protected]>. I have no idea if there is a possibility to be a member of a group without being a member of YFull.

Now I applied for a membership in YFull P312 group too, it has 211 members and administrators are Stephen Parrish, Rodney Jewett and Didier Vernade.

Thanks Peter. The only way of knowing the full value of ZZ11 is if it is ancestral in all groups outside of U152 and DF27, so it you can confirm it with the P312 that would be great.

Petr
01-29-2015, 09:32 PM
So I merged P312 and U152 group results and there are 46 BigY (and maybe FGC) results, of which:

DF27: 7, all have about 25 % G reads
U152: 21, 20 have about 25 % G reads, one is pure ancestral
L21: 12, all are ancestral
DF99: 1, ancestral
undetermined: 5, all have about 25 % G reads, it means thea are ZZ11_1 positive

The undetermined are:
YF02078 GBR R1b1a2a1a2 168C 1T 43G
YF01643 R1b1a2a1a2 371C 123G
YF01729 R1b1a2a1a2 2A 250C 86G
YF01626 R1b1a2a1a2 2A 202C 73G
YF02376 SCT R1b1a2a1a2 2A 372C 117G
I don't know how to assign them to FTDNA kit numbers.

I noticed that all of them have no call for DF27, so maybe all these undetermined are DF27.

I don't count 1KG samples because of low number of readings and therefore big risk of error.

Hope it helps.

R.Rocca
01-30-2015, 01:50 AM
So I merged P312 and U152 group results and there are 46 BigY (and maybe FGC) results, of which:

DF27: 7, all have about 25 % G reads
U152: 21, 20 have about 25 % G reads, one is pure ancestral
L21: 12, all are ancestral
DF99: 1, ancestral
undetermined: 5, all have about 25 % G reads, it means thea are ZZ11_1 positive

The undetermined are:
YF02078 GBR R1b1a2a1a2 168C 1T 43G
YF01643 R1b1a2a1a2 371C 123G
YF01729 R1b1a2a1a2 2A 250C 86G
YF01626 R1b1a2a1a2 2A 202C 73G
YF02376 SCT R1b1a2a1a2 2A 372C 117G
I don't know how to assign them to FTDNA kit numbers.

I noticed that all of them have no call for DF27, so maybe all these undetermined are DF27.

I don't count 1KG samples because of low number of readings and therefore big risk of error.

Hope it helps.

Either way, are there any 1KG samples (across any haplogroups) that have the G reads?

Petr
01-30-2015, 08:14 AM
Yes, most 1KG samples from DF27 and U152 have G reads and none from other HG have G reads.
DF27: 92 1KG samples, 67 have G reads, 25 don't have G reads (5x1C, 5x2C, 2x3C, 3x4C, 2x5C, 2x6C, 3x7C, 3x8C).
U152: 44 1KG samples, 35 have G reads, 9 don't have G reads (3x1C, 2x2C, 1x4C, 1x5C, 1x6C, 1x7C)
L21, DF99, Z2244: 40 samples, no G reads

lamahorse
01-30-2015, 01:21 PM
Sorry to interrupt but I have downloaded a tool from http://www.y-str.org/p/tools-utilities.html to analyse my Big Y.

It doesn't look like I can locate L2 in the out folder. Are there any markers associated with L2 that I can check for? I seem to be negative for the markers downstream of it.

Also is there anything else interesting one can try themselves with their BAM file?

Petr
01-30-2015, 02:41 PM
I am not sure why but it looks like this tool is not able to detect L2 SNP. It seems that even FTDNA is not able to detect it. YFull and FGC detect it with no problem, have you ordered any of these services? As for at least some downstream markers, like Z49 and Z68, BigY does not test them at all, see my experience here: http://www.anthrogenica.com/showthread.php?3277-Low-quality-of-Z49-Z68-SNPs

Petr
01-31-2015, 11:20 PM
Do I remember correctly that you are FTDNA-B6821? Then according to http://www.r1b.org/docs/FTDNA_U152_Project_Tree.xlsx you are placed to R-L2*. Are you confirmed Z49-? I looked at U152 project, there are 13 L2+ BigY samples, of which:
- 2 are Z49+
- 1 is Z49-
- 10 are Z49 no call

lamahorse
02-01-2015, 02:17 AM
Z49 ? Yes G ? Unknown

That's the result from Big Y. That's the kit number of my father.

After Billy Leonard McCarty (who is a distance of 8 from my father y-111), you are the next match on the Big Y list for me. Under 'Non Matching SNPs', CTS5150 is listed. What is the significance of that as it's listed under SNPs that we differ on. Is there much significance in that?

Does it mean that paternally we have some closer ancestry? Or does it mean that we are just blessed with the same series of poker hands?

Edit: Had a few too many beers tonight but 23andme also failed for rs2566671 (L2), is there a point for z49 I can look for from 23andme?

Petr
02-01-2015, 09:15 AM
So from your result you don't know if you are Z49+ or Z49-? Maybe you could look at ZZ11_1, in your FTDNA variants.vcf you should see line like
chrY 22286799 . C G 1484.13 REJECTED . GT 0/1
I would order YFull interpretation, it can give you better answer to L2, ZZ11 and private markers. As of Z49, maybe you could order Z49 SNP from FTDNA, with 15for15 coupon just for $24 (http://forums.familytreedna.com/showthread.php?p=398892). Maybe Richard Rocca will have better recommendation?

BigY matches are almost useless. My best match with 0 differences is with Mr. Stuart Baillie Strong (kit# 5825) who is R-Z36, i.e. far from me.

I see Mr. Connor David McCarthy (kit# B6821) with CTS5150 difference and Billy Leonard McCarty (kit# 115106) with differences in CTS5150 and CTS11841. CTS5150 is I-M170/PF3715 equivalent.

CTS5150 = PF3739 and within P312/U152 YFull projects I can see the following positive (T) results:
YF02322 I-Y4734* 52T
HG00129 R1b1a2a1a2b1* 1T

CTS11841, within P312/U152 YFull projects I can see the follwing positive (T) results:
HG01063 R1b1a2a1a2a* 1C 8T 1G
NA07347 R1b1a2a1a2b1a2a1 2T
NA20342 R-CTS9762* 1T
YF01489 R-Y9080 8C 24T
NA12874 R-Z216* 1C 3T
YF01387 R-Y5649* 1C 9T
YF02267 R-Y7845 2C 5T
and some others

It means just random results with no real significance.

lamahorse
02-01-2015, 03:21 PM
The 15 for 15 option seems like the best bet. Confirming whether we're L2+ and other markers is probably the best course of action.

Under what you asked to look for;

chrY 22286799 . C G 1484.13 REJECTED . GT 0/1


What kind of price range we looking at for YFull?

Petr
02-01-2015, 04:17 PM
YFull analysis costs $49: http://www.yfull.com/ I suppose L2 will be part of the analysis because the BigY BAM file usually contains it. (Z49 and Z68 not)

lamahorse
02-01-2015, 05:14 PM
If you think YFull is the best option to proceed, I'll go ahead with it.

Do they offer sales often or should I just go ahead and order it as soon as I can?

Petr
02-01-2015, 06:36 PM
The alternative is https://www.fullgenomes.com/ ($40) but I prefer YFull. I've never seen any sale yet. They will charge you when the analysis is is complete, i.e. approx 4-5 weeks after submitting the BAM file.

lamahorse
02-01-2015, 08:16 PM
They've received my BAM file. I suppose we'll find out in 4-5 weeks. Thanks Petr for you patience and help!

Petr
02-01-2015, 11:25 PM
And you could consider FTDNA Z49 SNP test.

lamahorse
02-13-2015, 03:28 AM
We have been placed on the L2+ tree so I guess that is my answer.

Once the YFull has completed, I'll see where to go next.

Petr
02-14-2015, 09:32 PM
OK. BigY does not test Z49 nor Z68 but maybe there will be other important SNPs.

Petr
02-14-2015, 09:42 PM
Just if there is anybody with S12993 subclade. The current U152 tree shows one subclade with 3252488(G/A), 6404480(T/C), 10006576(T/C), 13218678(C/T), 13611363(G/A), 13611386(T/C)?, 59025293(C/A)? with UK10K_ALS5085486 and with additional SNP S8172 1KG-HG00736, UK10K_ALS5085251, BDNA-1354, BDNA-1545, BDNA-1615.

So I tried to check my results for these mutations.

3252488 G -> A: My Yfull results just 1 A reading, i.e. positive but unreliable
6404480 T -> C: YFull no call, so I ordered it from YSEQ, it was named A1168 and it is positive
10006576 T -> C: YFull 23 T readings, i.e. negative
13218678 C -> T: YFull no call
13611363 G -> A: YFull no call
13611386 T -> C: YFull no call
59025293 C -> A: YFull no call
23595215 A -> G (S8172): YFull 53 A readings, i.e. negative

I compared my results with results of 1KG-HG00736.
3252488 G -> A: 3G - negative
6404480 T -> C: 7C - positive
10006576 T -> C: 4T - negative
13218678 C -> T: 3T - positive
13611363 G -> A: 1G - negative
13611386 T -> C: 2T - negative
59025293 C -> A: 9A 12C - unstable negative
23595215 A -> G (S8172): positive

It seems to me quite confusing.

I tried to order other SNPs from YSEQ but received the reply that I don't understand well:

Unfortunately many of those markers have been left out from the BigY enrichment process for a reason:

3252488 G -> A 99.3% X + 88980954 88981953
13218678 C -> T 95.1% 11 + 70848858 70850055
13611363 G -> A 96.0% 2 + 92203880 92204879
13611386 T -> C 96.1% 2 + 92203903 92204902
59025293 C -> A Pseudo Autosomal Region (PAR)

Most of them are highly identical with other regions in the genome and therefore prone to recombination events. This goes normally hand in hand with inconsistent phylogenies due to parallel and back mutations.
Does anybody know how to get UK10K and BDNA values for these mutations?

Now I'm awaiting FGC Elite results, I will see if these SNPs will be there or not.

I'm not sure what does all this mean so I wrote it here.

Petr

I have received results from FGC and they are:

3252488 G -> A: 24A 23G - unstable
6404480 T -> C: 26C - positive (A1168)
10006576 T -> C: 11T 1G - negative
13218678 C -> T: 61T - positive (FGC31475)
13611363 G -> A: 1A 12G - negative
13611386 T -> C: 6T 4C 2G - unstable
59025293 C -> A: 50A 123C - unstable negative
23595215 A -> G (S8172): 48A - negative

So my only difference to HG00736 is S8172.

And mutations 3252488, 13611386 and 59025293 should not be on the tree I think.

For completeness, ZZ11_1: 2A 1372C 382G

Petr
02-15-2015, 08:27 PM
lamahorse, I was not exact. Z49 is often not covered by BigY, but sometimes it is. You can verify by yourself by checking the regions.bed file from your BigY_RawData file, Z49 has position 28462237.


We have been placed on the L2+ tree so I guess that is my answer.

Once the YFull has completed, I'll see where to go next.

lamahorse
02-22-2015, 10:27 PM
I cannot find that position on that regions file.

By the by, Richard updated the U152 tree and removed us from the L2 branch. We are now located on the bottom. I have yet to hear back from Yfull about that test for L2. Well, they haven't asked me to pay yet.

Petr
02-22-2015, 11:00 PM
If you got the login name and password, you can see something like "Data is being processed... Expected date: 03/10/2015!". But you can browse the BAM file using "Browse raw data". L2 = 5755550, Z49 = 28462237. Then you will see: something like:

ChrY position: 5755550 (+strand)
Reads: 32
Position data: 32T
Weight for T: 1.0
Probability of error: 0.0 (0<->1)
Sample allele: T
Reference (hg19) allele: T
Known SNPs at this position: L2 • S139 (C->T)

What is your YFull ID? My IDs are YF01551 (BigY) and YF02970 (FGC).

MitchellSince1893
02-26-2015, 03:01 AM
Updated U152 Organization Chart, two levels down, based on Richard Rocca's "March 2015" U152 Tree.

https://s-media-cache-ak0.pinimg.com/originals/d3/ac/23/d3ac2311547291f9408cea6b6ad728a8.jpg

Higher resolution version located here https://s-media-cache-ak0.pinimg.com/originals/d3/ac/23/d3ac2311547291f9408cea6b6ad728a8.jpg

lamahorse
02-27-2015, 10:02 PM
Petr,

My YFull just came in today. My ID: YF02872 .

I'm just trying to get my head around this new interface. It gives me U152* but no further.

Edit: My father is working on having a Noonan/Newman or two get some Y-67 tests to see if they match up to the rest of us. Probably worth a look.

Nice table Mitchell, what's myself on the right. What does it really mean though? Does it just imply that our common ancestors parted ways earlier than with other groupings? Does it mean that we were isolated from each other from an earlier point? Is it speculative to say that we possibly arrived at a different point to other U152 entry to Ireland; or with them. (Norman, Vikings, English settlers). etc

Petr
02-27-2015, 10:30 PM
So you are L2-?

Have you requested the membership in U152 group http://www.yfull.com/groups/r-u152/ ?

lamahorse
02-27-2015, 10:40 PM
I have applied to join.

your request to join the "R-U152" group was successfully created. Please, wait for approval.

Yes, I am L2- when I browse SNPs.

Edit: Accepted already!

Petr
02-27-2015, 11:07 PM
Yes, it seems the Carthy cluster is rather unique.

It looks like these Carthy cluster SNPs are not very reliable:
22437910 C/A 76A 222C
22437962 A/G 199A 59G
22444385 G/A 108A 38G
22475271 T/C 62C 117T

lamahorse
02-27-2015, 11:20 PM
Is there anything I can do myself with this data?

Petr
02-28-2015, 12:09 AM
You can send the data to Richard Rocca.

You can check the private (novel) variants, they will differe significantly to novel variants shown by FTDNA because bogus variants are removed and variants with less than 10 reads added. You will se the quality of each of them.

You can check for any SNP and for any position how many reads were with specific results.

You can check ZZ11_1 marker, it is position 22286799. If I see this correctly in the U152 group, your result is 252C 84G, it means you are ZZ11_1 positive.

You can put your additional STR results (when they will be ready) to http://www.ysearch.org/

You can check your mtDNA haplogroup and if you want to know details, you can use the FASTA file and upload it to http://dna.jameslick.com/mthap-new/

Statistics show you the statistics of your data. For example, my 6 BigY samples have between 10.9 mil. and 12.4 mil bp raw data no calls, between 11500 and 16000 no calls for SNP, 46 to 63 N/A for STR and 0 to 1171 no calls for mtDNA. (FGC Elite: 59 SNP no calls, 19 mtDNA no calls)

In the group, you can compare results for specific SNPs or positions with other members and with reference samples from 1000 genomes project.

lamahorse
03-08-2015, 09:10 PM
On FTDNA, it has CTS5150 for you, Petr, under Non-Matching-SNPs.

However, if I search for CTS5150 in YFull, I'm positive for CTS5150.

ChrY position: 16039881 (+strand)
Reads: 20
Position data: 19T 1C
Weight for T: 0.946164199192
Weight for C: 0.0538358008075
Probability of error: 0.0761353196432 (0<->1)
Sample allele: T
Reference (hg19) allele: C
Known SNPs at this position: CTS5150 • PF3739 (C->T) Rating for known SNP (3 Stars)

Edit:

I take it the reason we were excluded from the z56, z42, z43 branch because we are negative for z43 which is associated with the other two markers (both no calls); it implies the other two associated markers are negative?

I am a big fan of the SNP search interface on YFull. It's very nicely set up.

Yes, we are positive for zz11_1. The STR data will be ready around the 25/3/2015 so I'll upload them as soon as I am able to do so.

lgmayka
03-08-2015, 09:56 PM
#111961 of Poland has tested
P312+, U152+, L2-, Z36-, P66-, SRY2627-, M126-, M153-, M160-, M222-, M37-, M65-
His 76-marker haplotype is Ysearch HXZBW (http://www.ysearch.org/search_view.asp?uid=HXZBW&viewuid=HXZBW&p=1).
The U152 project suggests Z193. Is there a realistic hope that he is Z193+ , or is this simply a low-probability last resort?

Petr
03-09-2015, 12:00 AM
This is my result for CTS5150:

Sample: #YF01551 (R-Y4355)
ChrY position: 16039881 (+strand)
Reads: 50
Position data: 50C
Weight for C: 1.0
Probability of error: 0.0 (0<->1)
Sample allele: C
Reference (hg19) allele: C
Known SNPs at this position: CTS5150 • PF3739 (C->T)

So while I'm CTS5150-, you are CTS5150+.

In the U152 YFull group you can see CTS5150+ for YF02872 and HG00129 only - but for HG00129 it is just one read, so it may be mistake. It looks like this is your private SNP, because CTS5150+ defines haplogroup I - and this is not your case. In FTDNA matches I see the second person with CTS5150+ - kit #115106, Billy Leonard McCarty, who is apparently not on YFull.

So I think CTS5150 should be added to the McCarthy Cluster.

R.Rocca
03-09-2015, 03:04 AM
#111961 of Poland has tested
P312+, U152+, L2-, Z36-, P66-, SRY2627-, M126-, M153-, M160-, M222-, M37-, M65-
His 76-marker haplotype is Ysearch HXZBW (http://www.ysearch.org/search_view.asp?uid=HXZBW&viewuid=HXZBW&p=1).
The U152 project suggests Z193. Is there a realistic hope that he is Z193+ , or is this simply a low-probability last resort?

@lgmayka...most L2+ Z36- DYS492=12 are indeed Z193+. However, the big problem is that Z193 and PF6658 (both share a subclade) are not testable by PCR due to their locations on the Y. The only way to currently test for them is either through Big-Y or Full Genome sequencing.

razyn
03-09-2015, 04:28 AM
Isn't PCR just the way to make the sample adequately large, rather than a test? These positions may not be amenable to Sanger sequencing, or chip testing, I don't know the actual problem. Lab people seem to be able to do what they have to do; but rather quick to say something is impossible to do with the means at hand... if they don't, in fact, have to. It's actually possible to read palindromes, make nested primers, find a SNP buried in an STR, tell a Y from and X, and so on. My impression is that the actual stumbling block is that more complex tests aren't cost-effective. Feel free to correct me, if that's a mistaken impression.

lgmayka
03-09-2015, 10:02 AM
@lgmayka...most L2+ Z36- DYS492=12 are indeed Z193+. However, the big problem is that Z193 and PF6658 (both share a subclade) are not testable by PCR due to their locations on the Y. The only way to currently test for them is either through Big-Y or Full Genome sequencing.
I see. So the project's recommendation to test one of them doesn't really make sense:
"Z1 U152 (L2- Z36- Z56- (dys492=12), Please order Z193 and/or PF6658 or BigY"

R.Rocca
03-09-2015, 11:55 AM
I see. So the project's recommendation to test one of them doesn't really make sense:
"Z1 U152 (L2- Z36- Z56- (dys492=12), Please order Z193 and/or PF6658 or BigY"

We can change the "or" to "through".

lamahorse
03-09-2015, 04:18 PM
Ok, I was reading the Big Y interface wrong.

I'll ask the owner of Billy's Kit to sign up for the YFull to check the quality of his novel SNPs.

What's the significance of us being CTS5150+? It's listed under http://www.isogg.org/tree/ISOGG_HapgrpI14.html but I imagine since it's popped up in both my father and Billy's kits; it's not specific to their haplogroup?

MitchellSince1893
03-17-2015, 02:19 AM
Hi Rich, I see on the project page a new SNP name "Z26720" which is at the same level as Z150 and Z12222. Is that the new name for position 22867545(A/T)?

Petr
03-17-2015, 07:50 AM
You can check it here: http://ybrowse.org/gb2/gbrowse/chrY/?name=Z26720 - and yes, it is ChrY:22867545 A->T.

lamahorse
04-07-2015, 11:02 PM
On YFull in the U152 group, there is now an L2* kit HG00129 that is also confirmed positive for CTS5150 along with myself (U152*) YF02872. The other L2* HG01941 gives a no call on CTS5150.

Would there be any merit in getting a specific L2 test or are we most likely L2-? Is there any other SNP worth testing for?

MitchellSince1893
04-08-2015, 01:25 AM
On YFull in the U152 group, there is now an L2* kit HG00129 that is also confirmed positive for CTS5150 along with myself (U152*) YF02872. The other L2* HG01941 gives a no call on CTS5150.

Would there be any merit in getting a specific L2 test or are we most likely L2-? Is there any other SNP worth testing for?

CTS5150, position 16039881, is also found in haplogroup I, so due to its appearance in different haplogroups it may be unstable.

Petr
04-08-2015, 07:23 AM
On YFull in the U152 group, there is now an L2* kit HG00129 that is also confirmed positive for CTS5150But it is just one reading.

lamahorse
05-07-2015, 10:47 PM
I see on the latest update of the U152 tree and on the results page;

U152> 23505791 .

Seems we have a provisional branch linking us to an Ignatious Butler kit. It feels nice to have some sniff of a terminal SNP that isn't U152*. Keep up the good work. :)

Solothurn
05-08-2015, 01:34 AM
IYO does this also apply to other SNPs that appear in different haplogroups?

I ask as two of my STR 'matches' are Y6354+ which is also found in I1. One of my matches is 107/111.

http://www.yseq.net/product_info.php?products_id=11343

BTW I wished it at Yseq and they have arranged the primers for it!
(Comments: Also found in R1b-U152. Flanking a homopolymer!)




CTS5150, position 16039881, is also found in haplogroup I, so due to its appearance in different haplogroups it may be unstable.

MitchellSince1893
05-08-2015, 03:34 AM
IYO does this also apply to other SNPs that appear in different haplogroups?

I ask as two of my STR 'matches' are Y6354+ which is also found in I1. One of my matches is 107/111.

http://www.yseq.net/product_info.php?products_id=11343

BTW I wished it at Yseq and they have arranged the primers for it!
(Comments: Also found in R1b-U152. Flanking a homopolymer!)

I would defer to Thomas Krahn at Yseq. ISOGG will not show/list SNPs that are found in multiple haplogroups, but now that I think about it, they may still be useful for genealogical research if they are stable in both haplogroups.

E.g. a SNP in two haplogroups doesn't meet the requirements to be on the tree, but it still may be of use if two kits in the same haplogroup have it and are both positive for another SNPs in that haplogroup.

Again I would seek the advise of those more knowledgeable than myself on this subject...I don't want to steer you wrong.

Solothurn
05-08-2015, 02:32 PM
Hi and thanks :)

Yes two tested BigY and are both positive for three SNPs:

S20550, FGC30121 and Y6354.

They are 60/67 and 107/111 with me. Searfoss is 48/67 and is S20550+ and FGC30121+, but does not have Y6354.

My 107/111 and I could have more shared SNPs but BigY is beyond us at present. I am just wishing and ordering at Yseq to confirm SNPs without the BigY $$$ :)



I would defer to Thomas Krahn at Yseq. ISOGG will not show/list SNPs that are found in multiple haplogroups, but now that I think about it, they may still be useful for genealogical research if they are stable in both haplogroups.

E.g. a SNP in two haplogroups doesn't meet the requirements to be on the tree, but it still may be of use if two kits in the same haplogroup have it and are both positive for another SNPs in that haplogroup.

Again I would seek the advise of those more knowledgeable than myself on this subject...I don't want to steer you wrong.

haleaton
08-06-2015, 04:07 PM
Unfortunately, I have very little confidence in their tree. I suspect that the great majority of their SNPs are found across multiple haplogroups, and therefore, we cannot be sure if the SNPs occurred even within U152 subclades as one time events. Also, since Geno 2.0 is not anywhere near full genome testing, there is no way of knowing where to place some of these SNPs on a tree as they may be part of SNP subclade groups that have the misfortune of being in positions of the Y that primers cannot be developed for. A good example is PF6658/Z193.


I mean the ones at the bottom of their tree, such as it is with all its faults, as shown below for L2+ Z49- Z367-. If GENO 2.0 did provide the same type of documentation (without identification) that Britain's DNA did for Chromo2 then they might be ripe for inclusion. Your comment also applies to inclusion of Chromo2 data or a new SNP chip test that may come out this year.




L2+ Z49- Z367- Downstream FTDNA Order
CTS667 6933008 ( G > C )
Y
CTS1166 7248487 ( G > T ) aka Z1744
N

F4205 16331432 ( A > G )
Y
F1643 9902395 ( G > A )
N
PF7610 13658168 ( G > A )
N
F3916 14348251 ( G > A )
Y
PF4367 14481150 ( C > T )
N
CTS5153 16040682 ( A > G ) in N113573
N
PF6610 16504649 ( C > T )
N

~PF70 3966485 ( C > T )
N
CTS6942 17203952 ( G > T )
N
CTS7010 17233286 ( C > T ) in N117716, N123359
Y
CTS7491 17506937 ( C > T )
N
CTS10009 19207382 ( G > C ) aka S1582 in BDNA-1870
N

CTS3080 14648041 ( G > A ) aka S1565
N
M126 21930258 ( AATA > del ) aka S27477
Y


With the PF7609, PF7610 branch of L2 now added to the tree, I went back and looked at the mystery SNPs on the current public FTDNA Tree under L2, mostly from GENO 2.0 data without any documentation. M126 dates back to the Faux days and may have been a singleton, though Jim Wilson also named the location with a different definition. There a two floating SNPs that could use additional testing. The rest are found in other Haplogroups. When something is found only once elsewhere I always wonder if it is and independent mutation.

So a few of the GENO 2.0 SNPs did turn out to be valid. In bold are the L2 SNPs on the R1b backbone SNP Pack test.


L2+ Z49- Z367- Downstream U152 & Subclades Tree Comments
CTS667
No Also in Haplogroup C
CTS1166
No Also in Haplogroup E

F4205
No Also in Haplogroups Y & N
F1643
No Also in Haplogroup O
PF7610
Yes PF7609, PF7610 branch
F3916
No Also in Haplogroup I
PF4367
No Also in Haplogroup I2a
CTS5153
No Floating SNP < L2 N113573 - Nicolas Gosselin (Gausselin)
PF6610
Yes PF6603 - PF6610 - PF6622, 4461443(T/C) branch

~PF70
No Also in Haplogroup A
CTS6942
No Also in R-L513 < L21
CTS7010
No Questionable, Also in L2+, L2-, & DF27+
CTS7491
No Floating SNP < DF110 - N128737 Stanislaus Torzyk
CTS10009
Yes < S1555, S1566 < S1567, S1569, S1570, S1573 branch

CTS3080
Yes < CTS10009
M126
No M126 4 bp del Underhill et (2000) U152, S27477 AATA > del Wilson(2014) Hap ?

haleaton
08-06-2015, 06:18 PM
Can someone eligible to order the R1b Backbone SNP Pack test post a screen shot of the updated U152 portion of the FTDNA tree, if it has changed?

Curious if they removed any of the SNPs in the previous post.

My SNP in the test should be on the new tree but I can't order the new test I guess because I tested positive for it. Go figure.

Kwheaton
08-07-2015, 10:07 PM
Hal,
I tried but even though it shows up to test---I get a blank white screen when I select purchase.

haleaton
08-07-2015, 11:00 PM
Hal,
I tried but even though it shows up to test---I get a blank white screen when I select purchase.

Thanks, Kelly. Maybe they have not updated U152, yet. For L21 you do see a new tree tree (just 21 portion) with a banner embedded under M343 in a L21 account which I don't in my U152 account. When you click buy on banner it takes you directly to a filled shopping cart in the L21 account. They are probably just working on it.

For my U152 account under Big Y it now shows 36,272 Known SNPs of which 5,927 on the tree. It was 36,076 total a few days ago.

Also in the Shared Novel Variants pull down menu under Big Y Matches now has along with mostly location numbers, my valid match FG35301 but three matches to L582 and L862 which were not locations previously. It says the three samples matching samples where added today. However I am negative for those two.

So they are probably just editing away like busy beavers gnawing away at trees. It will be fun to see what kind of dam they end with.

Solothurn
08-14-2015, 01:55 PM
On the YFull experimental page
http://www.yfull.com/tree/R-CTS10676/

Is this the same as my Z10676?

Petr
08-14-2015, 05:16 PM
http://ybrowse.org/gb2/gbrowse/chrY/?name=CTS10676 => pos. 22,699,106
http://ybrowse.org/gb2/gbrowse/chrY/?name=Z10676 => pos. 15,706,746

Solothurn
08-14-2015, 05:25 PM
Thanks Petr :)


http://ybrowse.org/gb2/gbrowse/chrY/?name=CTS10676 => pos. 22,699,106
http://ybrowse.org/gb2/gbrowse/chrY/?name=Z10676 => pos. 15,706,746

lamahorse
09-09-2015, 11:23 PM
Hi folks,

I've noticed a new feature on YFull for Estimating Age. Can anyone give me an idea what it does and how is it useful?


HAPLOGROUP SELECTED SNP KNOWN SNP NOVELS UNROUNDED
AGE (YBP) ROUNDED AGE (YBP) AGE BY ALL SAMPLES (YBP)
− R-U152 28 3 25 4331 4300 (2900-6200) 4500 (4000-5100)

What's this age of '4331' correspond to?

lgmayka
09-10-2015, 12:11 AM
What's this age of '4331' correspond to?
That is the TMRCA suggested by this sample alone. YFull's actual TMRCA estimates are based on averaging multiple samples, of course.