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Hg38 to T2T upgrate
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YFull is? offering a Hg38 to T2T upgrade for €23. What is the benefit of doing this???
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Kevin Terry
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Hi Kevin,
The hg38 genome, and earlier published human genomes, contained regions of DNA that were very difficult or impossible to sequence using short read "Next Generation" sequencers.? In short reads only the first 150 or so nucleotides are sequenced at either end of the DNA fragments.? I understand that the sequencing difficulty was caused by those parts of the human genome that are very repetitious.? The T2T reference genome, which was released in March 2022, used more recent "long read" sequencing technology to determine the nucleotide sequence for all regions of the genome, filling in all of the unsequenced gaps that existed in the hg38 genome.? Long read sequencers are able to recover sequences containing many thousands of nucleotides, but usually with a higher density of sequencing errors.
Will there be any great benefit to genetic genealogists to use realign their short read datasets against the gapless T2T genome?? I suspect that there would be relatively little benefit since the gaps that that are now covered in T2T probably didn't contain much useful information for genetic genealogy purposes.? But perhaps the T2T made corrections to other genealogically significant parts of the genome, sections that were not correctly sequenced in hg38, such as in the notoriously repetitious Y chromosome.? The upgrade cost of
€23 is modest, and so I would encourage you to give it a try and then report on any interesting changes that you obtained.
Bruce
[Edited Message Follows]
[Reason: Hg 38 to T2T upgrade!!]
YFull is? offering a Hg38 to T2T upgrade for €23. What is the benefit of doing this???
--
Kevin Terry
|
Hi Kevin, all, Brian or others might be able to correct my description of the technology but, as Bruce mentions, the T2T consortium has published the first complete sequence of the Y chromosome, unlocking the remaining 60% of our Y chromosomes that could not be sequenced until now. This is possible because of the longer chunks of DNA that these new technologies (HiFi, ultra-nanopone) can read. Previous efforts (hg38, a.k.a. GRCh38) used shorter read technology, like the BigY itself, which cuts up the DNA into chunks of about 150 base pairs at a time. If you only have a small chunk, it's like only having small pieces in a jigsaw puzzle - you can't always be sure you are putting the jigsaw piece in the right part of the chromosome. Having a complete map of the chromosome from T2T is like being given the box the jigsaw came in: you can more clearly see what can go where, and where potential duplications might lie. This makes the mapping exercise of fitting the jigsaw pieces together a little simpler. Aligning to T2T instead of hg38 therefore will let you correctly map more of your Y chromosome, but the differences aren't huge. They represent an extra few percent more on the size of the BigY test. Some SNPs can and have come out of this (the FTT series at FTDNA, including the FTT8 SNP that most of us have). You can pay the fee and have these SNPs tested in your own DNA for the sake of personal interest. However, the question remains what you do with these SNPs once you've discovered them. Unless the people around you upgrade, you have no idea whether they are positive or negative for most of these SNPs, so finding them becomes an increasingly academic exercise. Some people will be happy to pay a small fee for these SNPs that (currently) have fairly limited use, some will not. The early adopters may encourage others to do so, or spur FTDNA to perform the realignment faster (they have already done some kits, hence the FTT SNPs). Most likely, the first tangible benefit that they'll see from this is that any new SNPs that may or may not be found will either remain private or become shared with others. In rare circumstances where SNPs are found and found to be shared where no other defining SNP occurs, this could lead to a new haplogroup at YFull, but would still take quite some time to end up in the Family Tree DNA system, Discover, etc. By that time, it's likely that FTDNA will have realigned more kits to the T2T reference anyway. In the longer term, we're going to see more of this: more reference sequences that we could align to. The huge structural variations in the Y chromosome that appear to occur between different haplogroups could have a significant benefit if you align to a sequence close to your own haplogroup. For us, that would mean getting a T2T reference sequence within R-U106. That will likely happen eventually, and eventually we can hope that these tests become affordable for us consumers to get a T2T sequence of our own DNA. Until then, it's a gamble of what you get. Upgrading to a T2T alignment for €23 is a good way for YFull to make money - for consumers it's a long-odds gamble as to whether you'll get anything useful, but maybe that shouldn't stop some of us doing it for the curiosity or the fun. Cheers, Iain.
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Dante offers an alignment of results to T2T for $20.? ? - FASTQ data aligned to the T2T-CHM13 v2.0 assembly
- T2T is the most complete reference genome
- Receive BAM files and VCFs aligned to the T2T via download, with the possibility to access your data from anywhere?
Guess I will have to wipe the dust off of the other cousin genomes and get them refreshed with T2T alignments.? ?Note that I have an interest in non-Y genealogically relevant sequences.? The Y is just one item in the toolbox.? Specific copy number variants (CNV) should be quite useful. - Wayne K.
On Sunday, March 3, 2024 at 04:42:11 PM EST, Iain via groups.io <gubbins@...> wrote:
Hi Kevin, all, Brian or others might be able to correct my description of the technology but, as Bruce mentions, the T2T consortium has published the first complete sequence of the Y chromosome, unlocking the remaining 60% of our Y chromosomes that could not be sequenced until now. This is possible because of the longer chunks of DNA that these new technologies (HiFi, ultra-nanopone) can read. Previous efforts (hg38, a.k.a. GRCh38) used shorter read technology, like the BigY itself, which cuts up the DNA into chunks of about 150 base pairs at a time. If you only have a small chunk, it's like only having small pieces in a jigsaw puzzle - you can't always be sure you are putting the jigsaw piece in the right part of the chromosome. Having a complete map of the chromosome from T2T is like being given the box the jigsaw came in: you can more clearly see what can go where, and where potential duplications might lie. This makes the mapping exercise of fitting the jigsaw pieces together a little simpler. Aligning to T2T instead of hg38 therefore will let you correctly map more of your Y chromosome, but the differences aren't huge. They represent an extra few percent more on the size of the BigY test. Some SNPs can and have come out of this (the FTT series at FTDNA, including the FTT8 SNP that most of us have). You can pay the fee and have these SNPs tested in your own DNA for the sake of personal interest. However, the question remains what you do with these SNPs once you've discovered them. Unless the people around you upgrade, you have no idea whether they are positive or negative for most of these SNPs, so finding them becomes an increasingly academic exercise. Some people will be happy to pay a small fee for these SNPs that (currently) have fairly limited use, some will not. The early adopters may encourage others to do so, or spur FTDNA to perform the realignment faster (they have already done some kits, hence the FTT SNPs). Most likely, the first tangible benefit that they'll see from this is that any new SNPs that may or may not be found will either remain private or become shared with others. In rare circumstances where SNPs are found and found to be shared where no other defining SNP occurs, this could lead to a new haplogroup at YFull, but would still take quite some time to end up in the Family Tree DNA system, Discover, etc. By that time, it's likely that FTDNA will have realigned more kits to the T2T reference anyway. In the longer term, we're going to see more of this: more reference sequences that we could align to. The huge structural variations in the Y chromosome that appear to occur between different haplogroups could have a significant benefit if you align to a sequence close to your own haplogroup. For us, that would mean getting a T2T reference sequence within R-U106. That will likely happen eventually, and eventually we can hope that these tests become affordable for us consumers to get a T2T sequence of our own DNA. Until then, it's a gamble of what you get. Upgrading to a T2T alignment for €23 is a good way for YFull to make money - for consumers it's a long-odds gamble as to whether you'll get anything useful, but maybe that shouldn't stop some of us doing it for the curiosity or the fun. Cheers, Iain.
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? Iain is right on all accounts. Several in my group decided to play around with it.?
I can only see a benefit if a SNP splits a block somewhere or ties two or more ancestral ?blocks together. I believe FTDNA is doing this, as I am a beneficiary of FTT8, FTT32 and FTT33.?
?We have upgraded a test in at least one kit in each of the main branches of FGC11696 at Yfull. (This is FGC11674 at FTDNA) and it¡¯s parent FGC11665.?
www.yfull.com/tree/R-FGC11696/
This has been a mix of Big Y and WGS tests that were upgraded. As such, there are several SNPs not in the coverage area of other tests that are somewhere between FGC11696/FGC11674 and S5520 or S264 that cannot be placed without further testing.?
In my own branch, FGC11677 there are a few new SNPs. This is me and my father.?
If one is interested in what they can get from such upgrades, you can go to the tree | |
And click the ¡°info¡± tab> SNPs and look at the Y5xxxxx SNPs on the branches FGC11696, FGC11685, R-A5406 and FGC11677 branches. Each of these particular branches have had more than one upgrade.?
I should say we did all of this for ¡°entertainment purposes¡±. That includes comparing WGS to Big Y and WGS between other providers.?
Hi All
?
I would agree with most of what Iain says here.
?
I am a big fan of Oxford Nanopore Technology ¨C they have devoted so much time over the past dozen or more years to make all this long-read sequencing technology become viable. Their stated aim is to be able
to sequence DNA or RNA on a desktop set-up anywhere ¨C even in rural Africa ¨C wherever this type of approach can be viable.
?
You gradually learn with science as applied to medicine that many if not most advances occur because new analytical or imaging technologies become available.
?
There are diseases where miscounting of these long repetitive sequences of DNA can seemingly give rise to some types of human disease.? The ones that have the best provenance that I am aware of are Huntington¡¯s
Disease and Amyotrophic Lateral Sclerosis.
?
I think the T2T consortium data only unlocks the remaining 11% of the human genome ¨C but about 50+% of the Y chromosome specifically.
?
What remains to be tackled, as far as I am aware, is how is the Y-Chromosome is stored and packaged around specific histones and the role of chromatin in all that 3-D organisation.? Ultimately, this gets you
into how the DNA is unwound and copied for real ¨C and thus when do the mutations we are working off actually occur in the overall copying process.
?
-------------
?
I always love the videos produced by the Walter and Eliza Hall Institute (WEHI) in Australia, specifically the work of Drew Berry and his small team of graphic animation artists there from about 2003-2021
and beyond on many aspects of complex but fundamental cell biochemistry.
?
?
Instead of posting a link to the copying of the Y Chromosome ¨C let me post one talking about X-Chromosome Inactivation and Epigenetics.
?
?
X inactivation is a vital process that occurs in all DNA-containing cells of the female body. It is also an important research model and tool for studying epigenetics.
?
Epigenetics refers to processes that tell our cells how, and when, to read the DNA blueprint. The epigenetic regulation of DNA is critical in both normal development and disease.
?
X inactivation is a type of gene dosage compensation. In humans, the sex chromosomes X and Y determine the sex of an individual ¨C females have two X chromosomes (XX), males have one X and one Y chromosome
(XY). All of the genes on the Y chromosome are required in male development, while the genes on the X chromosome are needed for both male and female development. Because females receive two X chromosomes, they inherit two copies of many of the genes that are
needed for normal function. Extra copies of genes or chromosomes can affect normal development. An example is Down¡¯s syndrome, which is caused by an extra copy of part or all of chromosome 21. In female mammals, a process called X inactivation has evolved
to compensate for the extra X chromosome. In X inactivation, each cell ¡®switches off¡¯ one of its X chromosomes, chosen at random, to ensure the correct number of genes are expressed, and to prevent abnormal development.
?
?
Trust this helps ¨C and I must confess that some of this does get a bit difficult to understand if you do not have an organic chemistry background, in my experience. But the graphics are amazing.
?
Brian
?
toggle quoted message
Show quoted text
From: [email protected] <[email protected]>
On Behalf Of Iain via groups.io
Sent: Sunday, March 3, 2024 9:42 PM
To: [email protected]
Subject: Re: [R1b-U106] Hg38 to T2T upgrate
?
Hi Kevin, all,
Brian or others might be able to correct my description of the technology but, as Bruce mentions, the T2T consortium has published the first complete sequence of the Y chromosome, unlocking the remaining 60% of our Y chromosomes that could not be sequenced
until now. This is possible because of the longer chunks of DNA that these new technologies (HiFi, ultra-nanopore) can read.
Previous efforts (hg38, a.k.a. GRCh38) used shorter read technology, like the BigY itself, which cuts up the DNA into chunks of about 150 base pairs at a time. If you only have a small chunk, it's like only having small pieces in a jigsaw puzzle - you can't
always be sure you are putting the jigsaw piece in the right part of the chromosome. Having a complete map of the chromosome from T2T is like being given the box the jigsaw came in: you can more clearly see what can go where, and where potential duplications
might lie. This makes the mapping exercise of fitting the jigsaw pieces together a little simpler.
Aligning to T2T instead of hg38 therefore will let you correctly map more of your Y chromosome, but the differences aren't huge. They represent an extra few percent more on the size of the BigY test. Some SNPs can and have come out of this (the FTT series
at FTDNA, including the FTT8 SNP that most of us have). You can pay the fee and have these SNPs tested in your own DNA for the sake of personal interest. However, the question remains what you do with these SNPs once you've discovered them. Unless the people
around you upgrade, you have no idea whether they are positive or negative for most of these SNPs, so finding them becomes an increasingly academic exercise.
Some people will be happy to pay a small fee for these SNPs that (currently) have fairly limited use, some will not. The early adopters may encourage others to do so, or spur FTDNA to perform the realignment faster (they have already done some kits, hence
the FTT SNPs). Most likely, the first tangible benefit that they'll see from this is that any new SNPs that may or may not be found will either remain private or become shared with others. In rare circumstances where SNPs are found and found to be shared where
no other defining SNP occurs, this could lead to a new haplogroup at YFull, but would still take quite some time to end up in the Family Tree DNA system, Discover, etc. By that time, it's likely that FTDNA will have realigned more kits to the T2T reference
anyway.
In the longer term, we're going to see more of this: more reference sequences that we could align to. The huge structural variations in the Y chromosome that appear to occur between different haplogroups could have a significant benefit if you align to a
sequence close to your own haplogroup. For us, that would mean getting a T2T reference sequence within R-U106. That will likely happen eventually, and eventually we can hope that these tests become affordable for us consumers to get a T2T sequence of our own
DNA. Until then, it's a gamble of what you get. Upgrading to a T2T alignment for €23 is a good way for YFull to make money - for consumers it's a long-odds gamble as to whether you'll get anything useful, but maybe that shouldn't stop some of us doing it for
the curiosity or the fun.
Cheers,
Iain.
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Thanks to all for all the advice. I have ordered the T2T analysis & will share any relevant information. Interestingly what drew my attention to the T2T analysis was a new SNP match on YFull, who tested T2T with Nebula Genomics. Don't know who that person is!
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Kevin Terry
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I received my T2T results today. Attached shows the difference with the upgrade. It will take me some time to digest this!?
--
Kevin Terry
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Hello Kevin I am interested in this upgrade. Have you learned anything? Is it worth it?
°ä¾±²¹°ù¨¢²Ô
On Friday, March 8, 2024 at 07:19:56 PM UTC, Kevin Terry <kevintyrry@...> wrote:
I received my T2T results today. Attached shows the difference with the upgrade. It will take me some time to digest this!?
--
Kevin Terry
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Hi °ä¾±²¹°ù¨¢²Ô
Before the upgrade I had two SNP matches at the level Y128031. With one, a BigY500, I had 34 shared SNPs and 20 assumed shared SNPs. With the other, a T2T Nebula Genomics test I had 43 shared SNPs and 5 assumed shared SNPs. After the T2T upgrade with the Big Y500 match I? had 29 shared SNPs and 18 assumed shared SNPs. With the Nebula Genomics test I had 51 shared SNPs and 3 assumed shared SNPs. It would seem that the T2T test brings more certainty to matches, with fewer assumed matches. YFull are revising age estimates.
Because the Nebula Genomics tester only recently uploaded to YFull, I expect the next version of the YTree will show some more branching for me and my two SNP matches.?
Kevin Terry
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On Saturday, March 9, 2024 at 03:32:16 PM UTC, Kevin Terry <kevintyrry@...> wrote:
Hi °ä¾±²¹°ù¨¢²Ô
Before the upgrade I had two SNP matches at the level Y128031. With one, a BigY500, I had 34 shared SNPs and 20 assumed shared SNPs. With the other, a T2T Nebula Genomics test I had 43 shared SNPs and 5 assumed shared SNPs. After the T2T upgrade with the Big Y500 match I? had 29 shared SNPs and 18 assumed shared SNPs. With the Nebula Genomics test I had 51 shared SNPs and 3 assumed shared SNPs. It would seem that the T2T test brings more certainty to matches, with fewer assumed matches. YFull are revising age estimates.
Because the Nebula Genomics tester only recently uploaded to YFull, I expect the next version of the YTree will show some more branching for me and my two SNP matches.?
Kevin Terry
|
Kevin I have seven more private YSNPs from the upgrade. That's a total of 12 YSNPs that are specific to my Y line. I will have to wait until Yfull updates their tree to see if it makes a difference to the TMRCA of my main branch.
°ä¾±²¹°ù¨¢²Ô
On Saturday, March 9, 2024 at 03:32:16 PM UTC, Kevin Terry <kevintyrry@...> wrote:
Hi °ä¾±²¹°ù¨¢²Ô
Before the upgrade I had two SNP matches at the level Y128031. With one, a BigY500, I had 34 shared SNPs and 20 assumed shared SNPs. With the other, a T2T Nebula Genomics test I had 43 shared SNPs and 5 assumed shared SNPs. After the T2T upgrade with the Big Y500 match I? had 29 shared SNPs and 18 assumed shared SNPs. With the Nebula Genomics test I had 51 shared SNPs and 3 assumed shared SNPs. It would seem that the T2T test brings more certainty to matches, with fewer assumed matches. YFull are revising age estimates.
Because the Nebula Genomics tester only recently uploaded to YFull, I expect the next version of the YTree will show some more branching for me and my two SNP matches.?
Kevin Terry
|
| SNPs (all): | 403261 | | | Positive: | 2246?(0.56%) | | | Negative: | 14766?(3.66%) | | | Ambiguous: | 15?(0.00%) | | | No call: | 3843?(0.95%) |
This is from my T2T upgrade | SNPs (all): | 403261 | | | Positive: | 2865?(0.71%) | | | Negative: | 14350?(3.56%) | | | Ambiguous: | 38?(0.01%) | | | No call: | 1725?(0.43%) |
On Saturday, March 9, 2024 at 03:32:16 PM UTC, Kevin Terry <kevintyrry@...> wrote:
Hi °ä¾±²¹°ù¨¢²Ô
Before the upgrade I had two SNP matches at the level Y128031. With one, a BigY500, I had 34 shared SNPs and 20 assumed shared SNPs. With the other, a T2T Nebula Genomics test I had 43 shared SNPs and 5 assumed shared SNPs. After the T2T upgrade with the Big Y500 match I? had 29 shared SNPs and 18 assumed shared SNPs. With the Nebula Genomics test I had 51 shared SNPs and 3 assumed shared SNPs. It would seem that the T2T test brings more certainty to matches, with fewer assumed matches. YFull are revising age estimates.
Because the Nebula Genomics tester only recently uploaded to YFull, I expect the next version of the YTree will show some more branching for me and my two SNP matches.?
Kevin Terry
|
There are no more matches on my kit at YFull probably because the terminal snp is at Y7378 (above what FTdna has as the final), but it's interesting to see the number of snps that are now 'positive' which previously were marked as 'no call' or 'negative'.
On Wednesday, March 13, 2024 at 05:33:43 PM CDT, C.B. via groups.io <irishz156@...> wrote:
| SNPs (all): | 403261 | | | Positive: | 2246?(0.56%) | | | Negative: | 14766?(3.66%) | | | Ambiguous: | 15?(0.00%) | | | No call: | 3843?(0.95%) |
This is from my T2T upgrade | SNPs (all): | 403261 | | | Positive: | 2865?(0.71%) | | | Negative: | 14350?(3.56%) | | | Ambiguous: | 38?(0.01%) | | | No call: | 1725?(0.43%) |
On Saturday, March 9, 2024 at 03:32:16 PM UTC, Kevin Terry <kevintyrry@...> wrote:
Hi °ä¾±²¹°ù¨¢²Ô
Before the upgrade I had two SNP matches at the level Y128031. With one, a BigY500, I had 34 shared SNPs and 20 assumed shared SNPs. With the other, a T2T Nebula Genomics test I had 43 shared SNPs and 5 assumed shared SNPs. After the T2T upgrade with the Big Y500 match I? had 29 shared SNPs and 18 assumed shared SNPs. With the Nebula Genomics test I had 51 shared SNPs and 3 assumed shared SNPs. It would seem that the T2T test brings more certainty to matches, with fewer assumed matches. YFull are revising age estimates.
Because the Nebula Genomics tester only recently uploaded to YFull, I expect the next version of the YTree will show some more branching for me and my two SNP matches.?
Kevin Terry
|
Hi °ä¾±²¹°ù¨¢²Ô and all.? I too have done the upgrade and am under S5520. Not just me, but 9 or 10 McMillans under FGC11674/FGC11696 and its parent FGC11665. While I agree with Dr McDonald's views on this, we have a large family under FGC11674/FGC11696 and several of us did this for entertainment purposes. I have notes on several new SNPs and the branches the fit somewhere on below FGC11696/FGC11674. I am going to continue to chase these despite knowing better.? Previous to a recent upgrade, we are the only ones I know of under S5520 that have done the upgrade. Now I see two. A recent Big Y that I assume has been discussed here and a Nebula sample that is coming in. 3 of the McMillan samples that were upgraded are WGS samples, and the best I can tell, have several SNPs not in the Big Y coverage area. I am glad to see the Nebula Sample coming in under S5520 that may clear it up a little and this will help the Big Y sample recently upgraded not too far from each other on the yfull tree.? The new SNPs above FGC11665 are of little interest to me because they are outside a genealogical timeframe, and we already have large unbroken blocks of SNPs there, I would still be interested to know if a S5520 sample is positive for any of them, so I can update my notes. I guess I will see when the tree is updated. My understanding is the "T2T" upgrade Y full is using is the CP086569.2 alignment. I believe this is based off a man from the J1 haplogroup. I wish for R1b people they used the CM034974.1 which was constructed from a R1b person. One day I am sure we will have a better test and a R-U106 reference. My thoughts are until we have long read tests this is all just for fun and perhaps we can gain a couple of SNPs that are useful to split branches or tie a few branches together along the way. I am not going to campaign for people to run out and do this upgrade, but I welcome it. For most people at Yfull, you will just get some more SNPs. As more do it, those will be placed as time goes on.? I think my situation is slightly different. We have around 125/130 Big Y and WGS results in our surname with 75 or so branches. Because we have several results and tested multiple branches of FGC11674, we now have several CP086569.2 SNPs we have identified to those branches. I tried to order a few SNPs to be available for testing at Yseq, and received a reply that they are only currently developing primers for the Hg38 SNPs at this time. All of this may sound a little crazy (and it probably is) but again, we have around 130 Big Y and WGS tests in the family. I am sure at some point there will be a better upgrade, and when worthwhile FTDNA will probably change references in the future. I have already received 3 SNPs from FTDNA's work on this. FTT8, and the more recent FTT32 and FTT33.? That being said our testing has identified several new SNPs between FGC11665 and R-S5520<>z156/S264. Maybe they will help someone.? Here are some notes I have for FGC11665-R-S5520. I have also included 3 SNPs found on my FGC11677 branch where I previously had no private variants. Through tests of known cousins, I know FGC11677 is either my 4th or 5th great grandfather. People that decend from my 4th great grandfather have FGC11677, and a gentleman that comes from my 6th great grandfather does not. We have WGS tests from 2 more branches of FGC11674 that I will probably get around to realigning at WGS Extract in the future and uploading.? Notes on new S5520 SNPs:
?
?
Big Y
Y516411? ? level R-FGC11696<->R-S5520
Y516412? ? level R-FGC11696<->R-S5520
Y508519? ? level R-FGC11665<->R-S5520
Y508520? ? level R-FGC11665<->R-S5520
Y508521? ? level R-FGC11665<->R-S5520
Y508522? ? level R-FGC11665<->R-S5520
?
WGS
Y516414? ? level R-FGC11677<->R-S264
Y502956? ? level R-FGC11677<->R-S264
Y516413? ? level R-FGC11677<->R-S264
Y502955? ? level R-FGC11677<->R-S264
Y502957? ? level R-FGC11677<->R-S264
Y516408? ? level R-FGC11677<->R-S5520 My branch new SNPs:
Y516407? ? level R-FGC11677<->R-FGC11685
Y516410? ? level R-FGC11677<->R-FGC11685
Y516409? ? level R-FGC11677<->R-FGC11685
?
FGC11677 Private
Y491152 level R-FGC11677
Y491150 level R-FGC11677
Y491229 level R-FGC11677
?
?
-Robert McMillan
|
Yfull has put up their latest Ytree TMRCA's probably linked to the T2T results!
On Thursday, March 14, 2024 at 05:18:11 PM UTC, Robert McMillan via groups.io <tensawmac@...> wrote:
Hi °ä¾±²¹°ù¨¢²Ô and all.? I too have done the upgrade and am under S5520. Not just me, but 9 or 10 McMillans under FGC11674/FGC11696 and its parent FGC11665. While I agree with Dr McDonald's views on this, we have a large family under FGC11674/FGC11696 and several of us did this for entertainment purposes. I have notes on several new SNPs and the branches the fit somewhere on below FGC11696/FGC11674. I am going to continue to chase these despite knowing better.? Previous to a recent upgrade, we are the only ones I know of under S5520 that have done the upgrade. Now I see two. A recent Big Y that I assume has been discussed here and a Nebula sample that is coming in. 3 of the McMillan samples that were upgraded are WGS samples, and the best I can tell, have several SNPs not in the Big Y coverage area. I am glad to see the Nebula Sample coming in under S5520 that may clear it up a little and this will help the Big Y sample recently upgraded not too far from each other on the yfull tree.? The new SNPs above FGC11665 are of little interest to me because they are outside a genealogical timeframe, and we already have large unbroken blocks of SNPs there, I would still be interested to know if a S5520 sample is positive for any of them, so I can update my notes. I guess I will see when the tree is updated. My understanding is the "T2T" upgrade Y full is using is the CP086569.2 alignment. I believe this is based off a man from the J1 haplogroup. I wish for R1b people they used the CM034974.1 which was constructed from a R1b person. One day I am sure we will have a better test and a R-U106 reference. My thoughts are until we have long read tests this is all just for fun and perhaps we can gain a couple of SNPs that are useful to split branches or tie a few branches together along the way. I am not going to campaign for people to run out and do this upgrade, but I welcome it. For most people at Yfull, you will just get some more SNPs. As more do it, those will be placed as time goes on.? I think my situation is slightly different. We have around 125/130 Big Y and WGS results in our surname with 75 or so branches. Because we have several results and tested multiple branches of FGC11674, we now have several CP086569.2 SNPs we have identified to those branches. I tried to order a few SNPs to be available for testing at Yseq, and received a reply that they are only currently developing primers for the Hg38 SNPs at this time. All of this may sound a little crazy (and it probably is) but again, we have around 130 Big Y and WGS tests in the family. I am sure at some point there will be a better upgrade, and when worthwhile FTDNA will probably change references in the future. I have already received 3 SNPs from FTDNA's work on this. FTT8, and the more recent FTT32 and FTT33.? That being said our testing has identified several new SNPs between FGC11665 and R-S5520<>z156/S264. Maybe they will help someone.? Here are some notes I have for FGC11665-R-S5520. I have also included 3 SNPs found on my FGC11677 branch where I previously had no private variants. Through tests of known cousins, I know FGC11677 is either my 4th or 5th great grandfather. People that decend from my 4th great grandfather have FGC11677, and a gentleman that comes from my 6th great grandfather does not. We have WGS tests from 2 more branches of FGC11674 that I will probably get around to realigning at WGS Extract in the future and uploading.? Notes on new S5520 SNPs:
?
?
Big Y
Y516411? ? level R-FGC11696<->R-S5520
Y516412? ? level R-FGC11696<->R-S5520
Y508519? ? level R-FGC11665<->R-S5520
Y508520? ? level R-FGC11665<->R-S5520
Y508521? ? level R-FGC11665<->R-S5520
Y508522? ? level R-FGC11665<->R-S5520
?
WGS
Y516414? ? level R-FGC11677<->R-S264
Y502956? ? level R-FGC11677<->R-S264
Y516413? ? level R-FGC11677<->R-S264
Y502955? ? level R-FGC11677<->R-S264
Y502957? ? level R-FGC11677<->R-S264
Y516408? ? level R-FGC11677<->R-S5520 My branch new SNPs:
Y516407? ? level R-FGC11677<->R-FGC11685
Y516410? ? level R-FGC11677<->R-FGC11685
Y516409? ? level R-FGC11677<->R-FGC11685
?
FGC11677 Private
Y491152 level R-FGC11677
Y491150 level R-FGC11677
Y491229 level R-FGC11677
?
?
-Robert McMillan
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Hi Iain, I was quite surprised to see B move backward from R-BY39679 > R-Y31448.? The top tester L still has not finished the STR sorting.? When completed I will see if he also moves backwards.? There was no change in the other 7 T2T completed.? I have not asked Tatiana why the change backwards yet.
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I would check the latest updates. I had an individual (a new closest match outside of my known genealogy) upload their bam, and it created the FGC11686 block on the yfull tree. It listed a few new terminal T2T SNPs for that newly formed branch that were either no call or negative. In other words, not terminal SNPs for that new branch.?
?I wrote yfull and it¡¯s fixed in the live view now. Switching between the regular view and live view you can see the couple I¡¯m talking about.?
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On Apr 29, 2024, at 7:54?AM, genesweetser via groups.io <genesweetser@...> wrote:
? Hi Iain, I was quite surprised to see B move backward from R-BY39679 > R-Y31448.? The top tester L still has not finished the STR sorting.? When completed I will see if he also moves backwards.? There was no change in the other 7 T2T completed.? I have not asked Tatiana why the change backwards yet.
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Hi Gene, ? I don't have much time to dig deep into the details tonight, but have you got the order right? R-Y31448 layers above R-BY39679, so a move from R-Y31448 to R-BY39679 would actually be a refinement of the haplogroup. ? Cheers, ? Iain.
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Just the opposite Iain? My last two tester at FTDNA are R-BY39679.? I did the Yfull T2T upgrade for Brandon and they moved him from R-BY39679 to R-Y31448.? I have not upgraded Larry to T2T at Yfull since they have not completed the STR process.? Larry is still R-BY39679 at both Yfull and FTDNA.? ?The other 7 upgrades to T2T did not change their Haplogroup.? Brandon is still listed at FTDNA at R-BY39678
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Kevin Terry
Wayne
