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I'll try to make this short(er). ;-)
I don't seem to have the skills to address all the topics we've recently be conversing about, but I do appreciate everyone's input. I haven't thought much about these things for a while, maybe because I tend to get consumed by them. But I'm glad I have, despite putting off other things I should get done.
One thing that others may have pointed out is the diversity -- genetics, and tribal -- in the Isles. I think perhaps historians? may play a role in some of our misunderstandings of the past, including linguistic interpretations of names, places, etc.. Sure, the victors can attempt to mold history to their liking, but the academics also may purposely or accidentally slant history slightly, which the average person may often fully accept as truth.
I'd like to spend some serious time with a room of linguistics and hash out some concerns. In the?meantime I may come up with my own theories.? Leake brought up Kenneth 'ugly head', if my memory serves me.? I've read of a few different interpretations of 'Cinaed' and it's various spellings, but I continue to believe that some interpretations may just be incorrect, or simple guesses, or linguistic misunderstandings.? I haven't come across theories/speculations similar to mine -- that I remember (lol) -- regarding the origins and true intended meaning of Cinaed(a) in Kenneth Alpin's name.? I think it's true origins may reflect back to the Cunedda Clan -- which was apparently quite large and powerful -- especially when one considers the similarities? of pronunciation with words like Cunedda, Cinaed(a), Kenned(a)y, Canada(y).?
Then there's labelling of people, but like Leake mentioned -- everything was all mixed together. So questions like "were they Picts, Scots, Irish, Dalriadans, Gaels, Britons, Saxons, Norse, etc.", naturally arise for those that demand clarity of distinctions. That's something we all want.
I was never much of a reader, for various excuses I could list, but since I came across subjects like family genealogies and genetics 12 years ago I've read much more than years previous -- even if sometimes to my physical detriment. ;-)
Ydna genetic testing forced me, and not reluctantly, to read more? -- especially about Isles history. Along the way I've met some great people I'd like to one day meet in person.
Recently I've been somewhat sellfishly consumed with my McLean heritage. But it too has forced me to try and look at the bigger historical and genetics pucture, and reminds me how little we know about our past. So, we're quite often left with speculation -- which can be enjoyable itself.
We will likely never be satisfied about the past, but through genetic testing I'm cautiously optimistic that genealogy tree of mine, and others I've met, will be satifactorily filled in. On that note, as a 193 person with lots of L193 and L513 cousins, I consider myself lucky.? Not all mysteries can be solved but it sure can be fun to try!
While I'm at it, and I know Mike gave an answer, but how can I get my hands on some of Mike's great Excel productions? It still mystifies me how government legislators can stifle desired collaboration amongst the overwhelming majority who want to share their personal genetic information, especially when it's already knowingly on hundreds of thousands of people's personal computers and? public websites. People who don't want to share can easily protect it if they want, so I don't believe governments or corporations, or anybody, should cater to the infinitesimally small percentage of people responsible for the birth of such shackling, fear-mongering, and stifling legislation. It's a big step backwards, and shamefully so in my opinion.?
Hmm, from calm and collected, to the opposite so quickly?? I hope I didn't ruin anyone's calm. ;-)
Best,
Daryl?
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On Fri, Aug 19, 2022 at 01:31 AM, Class1 Driver wrote:
It still mystifies me how government legislators can stifle desired collaboration amongst the overwhelming majority who want to share their personal genetic information, especially when it's already knowingly on hundreds of thousands of people's personal computers and? public websites.
My response.
The EU GDPR rules are that if a person changes their mind and decides to remove their data from public sharing then then their data must be removed in 30 days.? This is just a hobby for me, but I don't have time to worry about if I removed someone from a spreadsheet within 30 days of them leaving the R-L513 project or some other project I administer or what country they live in, etc. I don't have the inclination to even take a chance on needing to talk to a lawyer for help. I hate lawyers even though I have lawyer friends. I hate what they have to do.
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I've been sick all week, and still am, but I need some help per questions below.?
I wonder how many people have been charged, or threatened to be charged, under that European GDPR legislation. If it's zero, then it doesn't appear it has much teeth. That's about the most polite thing I can say about it/them. ;-)
I finally loosened those tight Scot purse strings and ordered the BigY upgrade last night. Does anybody know why it doesn't include the Bam file? I'd like to send it out for analysis to yfull. This way I can see exactly the results of the 'read' results on any SNP/variant. I couldn't find information on that wonderful FTDNA website about how much extra it will presumably cost to get a Bam file. Anybody know??
I also noticed that FTDNA has 23 SNPs listed as apparent L193(S5982) equivalents on their Haplotree. Why?? Yfull.com shows only 15 unique variants -- the other 8 were the same variants with different names. But still, with 15 equivalents that's at least 6 more than Alex's 'good' 9 equivalents, and 4 more than his 11 'good and iffy' (a very nice scientific description of the two, I think) equivalents. Obviously ftdna didn't mean to confuse us -- but they did.?
So, since Alex's Big Tree is not being used as much anymore, it kind of forced me to get the BigY 700 upgrade, so that maybe I can keep up with the latest -- but only if I can also see other people's private SNPs, which I doubt? FTDNA provides to BigY testees. Or do they? But the main reason for taking the BigY is because I'm hoping it might match other BigY 700 testees where BigY 500 didn't/couldn't. (No, Leake, not to confirm I'm A1067 like my Aussie Martin cousin. lol )
?Another important reason is that I've appointed the L513 Haplogroup Project Administration as beneficiary of my account -- should I someday go to Scot heaven.? That's the only reasonable choice, in my mind, to ensure that DNA testing results remain useful in the future -- as long as ftdna and/or it's database survives. I also don't want to assume that any family member or friend will zealously take up the/my/our cause.
It doesn't appear that 2 vaccines last spring of 2021, plus a preumed omicron infection last 24dec2021 is enough to protect one from COVID mutated strains. At least, per my present condition. Or, it could be just a summer cold/flu which I can't remember ever getting before. ;-)
Best,
Daryl?
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Good Lord Daryl!? ?I'm pretty sure that's called "from the top rope"!!
Having just learned my daughter, SIL, and two grandkids all have COVID... I feel your dilemma.
Get better brother! Brad?
I've been sick all week, and still am, but I need some help per questions below.?
I wonder how many people have been charged, or threatened to be charged, under that European GDPR legislation. If it's zero, then it doesn't appear it has much teeth. That's about the most polite thing I can say about it/them. ;-)
I finally loosened those tight Scot purse strings and ordered the BigY upgrade last night. Does anybody know why it doesn't include the Bam file? I'd like to send it out for analysis to yfull. This way I can see exactly the results of the 'read' results on any SNP/variant. I couldn't find information on that wonderful FTDNA website about how much extra it will presumably cost to get a Bam file. Anybody know??
I also noticed that FTDNA has 23 SNPs listed as apparent L193(S5982) equivalents on their Haplotree. Why?? Yfull.com shows only 15 unique variants -- the other 8 were the same variants with different names. But still, with 15 equivalents that's at least 6 more than Alex's 'good' 9 equivalents, and 4 more than his 11 'good and iffy' (a very nice scientific description of the two, I think) equivalents. Obviously ftdna didn't mean to confuse us -- but they did.?
So, since Alex's Big Tree is not being used as much anymore, it kind of forced me to get the BigY 700 upgrade, so that maybe I can keep up with the latest -- but only if I can also see other people's private SNPs, which I doubt? FTDNA provides to BigY testees. Or do they? But the main reason for taking the BigY is because I'm hoping it might match other BigY 700 testees where BigY 500 didn't/couldn't. (No, Leake, not to confirm I'm A1067 like my Aussie Martin cousin. lol )
?Another important reason is that I've appointed the L513 Haplogroup Project Administration as beneficiary of my account -- should I someday go to Scot heaven.? That's the only reasonable choice, in my mind, to ensure that DNA testing results remain useful in the future -- as long as ftdna and/or it's database survives. I also don't want to assume that any family member or friend will zealously take up the/my/our cause.
It doesn't appear that 2 vaccines last spring of 2021, plus a preumed omicron infection last 24dec2021 is enough to protect one from COVID mutated strains. At least, per my present condition. Or, it could be just a summer cold/flu which I can't remember ever getting before. ;-)
Best,
Daryl?
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Daryl, I am sorry you haven't felt well. We wish you a speedy and full recovery. I really appreciate your beneficiary action. You are truly thinking about posterity, but please, we also wish you a much longer and healthy life.
In terms of EU GDPR. I don't know about activities in the U.S. but here is a list of their top fines to-date thru May.
I doubt if I have much personal risk, but you never know. I detest courts and the need to hire lawyers. I just choose to be on the safe side.
When I get a chance I'll try to look at your other questions.
I've been sick all week, and still am, but I need some help per questions below.?
I wonder how many people have been charged, or threatened to be charged, under that European GDPR legislation. If it's zero, then it doesn't appear it has much teeth. That's about the most polite thing I can say about it/them. ;-)
I finally loosened those tight Scot purse strings and ordered the BigY upgrade last night. Does anybody know why it doesn't include the Bam file? I'd like to send it out for analysis to yfull. This way I can see exactly the results of the 'read' results on any SNP/variant. I couldn't find information on that wonderful FTDNA website about how much extra it will presumably cost to get a Bam file. Anybody know??
I also noticed that FTDNA has 23 SNPs listed as apparent L193(S5982) equivalents on their Haplotree. Why?? Yfull.com shows only 15 unique variants -- the other 8 were the same variants with different names. But still, with 15 equivalents that's at least 6 more than Alex's 'good' 9 equivalents, and 4 more than his 11 'good and iffy' (a very nice scientific description of the two, I think) equivalents. Obviously ftdna didn't mean to confuse us -- but they did.?
So, since Alex's Big Tree is not being used as much anymore, it kind of forced me to get the BigY 700 upgrade, so that maybe I can keep up with the latest -- but only if I can also see other people's private SNPs, which I doubt? FTDNA provides to BigY testees. Or do they? But the main reason for taking the BigY is because I'm hoping it might match other BigY 700 testees where BigY 500 didn't/couldn't. (No, Leake, not to confirm I'm A1067 like my Aussie Martin cousin. lol )
?Another important reason is that I've appointed the L513 Haplogroup Project Administration as beneficiary of my account -- should I someday go to Scot heaven.? That's the only reasonable choice, in my mind, to ensure that DNA testing results remain useful in the future -- as long as ftdna and/or it's database survives. I also don't want to assume that any family member or friend will zealously take up the/my/our cause.
It doesn't appear that 2 vaccines last spring of 2021, plus a preumed omicron infection last 24dec2021 is enough to protect one from COVID mutated strains. At least, per my present condition. Or, it could be just a summer cold/flu which I can't remember ever getting before. ;-)
Best,
Daryl?
-- For R1b Y DNA questions please post on one of the two forums:
R1b Y DNA Project Facebook Group -? R1b All Subclades Project Activity Feed -
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Thanks Mike and Brad.
I'm not dying, just not feeling good physically. I put on my mask and drove a few blocks to the corner store and bought some lotto tickets last night -- like I tend to do every Friday. I told the cash clerk my symptoms thinking he'd agree it was COVID, but he surprised me and said he thinks it's just the summer flu that's been going around.
To clarify some more: I named the Project Administrator my beneficiary years ago. I probably could have explained it better in my last post, so forgive me for unintentionally misleading you about the severity of my health or my mental state. I tend to joke around a lot -- likely too much -- and make light of serious topics. I'm not a depressed sourpuss, but the opposite personality who trys to look at the positive and bring up the mood of others around me. Life is too short, so I want to enjoy it and spread joy to others if possible. :-)?
I've been forward thinking for years about this DNA genealogy hobby of ours, hence making present and future Administrators the beneficiaries seems a more sure bet to me that my account will always be open and usable. Since I don't know/remember if my Aussie Martin BigY cousin has also named the administrator as beneficiary, it then becomes another good reason for me to take the BigY test.? Plus, who doesn't want to be remembered, even if it's just through DNA data! Lol
Best,
Daryl Martin 181420
On Sat, Aug 27, 2022, 11:31 AM Tiger Mike < mwwdna@...> wrote: Daryl, I am sorry you haven't felt well. We wish you a speedy and full recovery. I really appreciate your beneficiary action. You are truly thinking about posterity, but please, we also wish you a much longer and healthy life.
In terms of EU GDPR. I don't know about activities in the U.S. but here is a list of their top fines to-date thru May.
I doubt if I have much personal risk, but you never know. I detest courts and the need to hire lawyers. I just choose to be on the safe side.
When I get a chance I'll try to look at your other questions.
I've been sick all week, and still am, but I need some help per questions below.?
I wonder how many people have been charged, or threatened to be charged, under that European GDPR legislation. If it's zero, then it doesn't appear it has much teeth. That's about the most polite thing I can say about it/them. ;-)
I finally loosened those tight Scot purse strings and ordered the BigY upgrade last night. Does anybody know why it doesn't include the Bam file? I'd like to send it out for analysis to yfull. This way I can see exactly the results of the 'read' results on any SNP/variant. I couldn't find information on that wonderful FTDNA website about how much extra it will presumably cost to get a Bam file. Anybody know??
I also noticed that FTDNA has 23 SNPs listed as apparent L193(S5982) equivalents on their Haplotree. Why?? Yfull.com shows only 15 unique variants -- the other 8 were the same variants with different names. But still, with 15 equivalents that's at least 6 more than Alex's 'good' 9 equivalents, and 4 more than his 11 'good and iffy' (a very nice scientific description of the two, I think) equivalents. Obviously ftdna didn't mean to confuse us -- but they did.?
So, since Alex's Big Tree is not being used as much anymore, it kind of forced me to get the BigY 700 upgrade, so that maybe I can keep up with the latest -- but only if I can also see other people's private SNPs, which I doubt? FTDNA provides to BigY testees. Or do they? But the main reason for taking the BigY is because I'm hoping it might match other BigY 700 testees where BigY 500 didn't/couldn't. (No, Leake, not to confirm I'm A1067 like my Aussie Martin cousin. lol )
?Another important reason is that I've appointed the L513 Haplogroup Project Administration as beneficiary of my account -- should I someday go to Scot heaven.? That's the only reasonable choice, in my mind, to ensure that DNA testing results remain useful in the future -- as long as ftdna and/or it's database survives. I also don't want to assume that any family member or friend will zealously take up the/my/our cause.
It doesn't appear that 2 vaccines last spring of 2021, plus a preumed omicron infection last 24dec2021 is enough to protect one from COVID mutated strains. At least, per my present condition. Or, it could be just a summer cold/flu which I can't remember ever getting before. ;-)
Best,
Daryl?
--
For R1b Y DNA questions please post on one of the two forums:
R1b Y DNA Project Facebook Group -? R1b All Subclades Project Activity Feed -
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I compared the phylogenetic blocks for R-S5982/R-L193 for the FTDNA and Big trees.
FTDNA haplotree:
A4, A5, A6, BY208, FGC21246, FGC64743, FGC64757, FGC64758, FGC64765, FGC64766, FGC64767, FT4063, L193, M6420, S5982, S5989, S5990, S5992, S5994, S7128, Y20022, Y23047, Z16332
Big Tree:
A4, A5, A6, L193, S7123, S5982, S5990, S5992, Z17621(?), Z17622(?DYZ19), Z16332, Z16333(DYZ19)
The Big Tree details has three SNPs that are questionable. It doesn't look like FTDNA is including them.? I think what is going on is that the Big Tree is loaded with a ton of old Big Y data from VCF files. Therefore, Alex can't see or hasn't yet looked at the better coverage raw data from Big Y700 testing and possibly FGC and other NGS testing.?
The Big Tree is missing this block’s FGC and FT named SNPs.? I haven't logged into FGC for a while but they must have these SNPs in their phylogenetic block for R-S5982.?
You can see most of Alex lists are SNPs in Combed regions. Combed regions are a subset of old Big Y coverage sweet spots. They are to the Poznik gold regions which are what ols Big Y targeted.
Big Y700 coverage of the Y chromosome is about 50% more than Big Y500's. That’s what you see a lot of times in the FT and FGC names. FGC Elite 2.0 has similar coverage to Big Y700.
I've been sick all week, and still am, but I need some help per questions below.?
I wonder how many people have been charged, or threatened to be charged, under that European GDPR legislation. If it's zero, then it doesn't appear it has much teeth. That's about the most polite thing I can say about it/them. ;-)
I finally loosened those tight Scot purse strings and ordered the BigY upgrade last night. Does anybody know why it doesn't include the Bam file? I'd like to send it out for analysis to yfull. This way I can see exactly the results of the 'read' results on any SNP/variant. I couldn't find information on that wonderful FTDNA website about how much extra it will presumably cost to get a Bam file. Anybody know??
I also noticed that FTDNA has 23 SNPs listed as apparent L193(S5982) equivalents on their Haplotree. Why?? Yfull.com shows only 15 unique variants -- the other 8 were the same variants with different names. But still, with 15 equivalents that's at least 6 more than Alex's 'good' 9 equivalents, and 4 more than his 11 'good and iffy' (a very nice scientific description of the two, I think) equivalents. Obviously ftdna didn't mean to confuse us -- but they did.?
So, since Alex's Big Tree is not being used as much anymore, it kind of forced me to get the BigY 700 upgrade, so that maybe I can keep up with the latest -- but only if I can also see other people's private SNPs, which I doubt? FTDNA provides to BigY testees. Or do they? But the main reason for taking the BigY is because I'm hoping it might match other BigY 700 testees where BigY 500 didn't/couldn't. (No, Leake, not to confirm I'm A1067 like my Aussie Martin cousin. lol )
?Another important reason is that I've appointed the L513 Haplogroup Project Administration as beneficiary of my account -- should I someday go to Scot heaven.? That's the only reasonable choice, in my mind, to ensure that DNA testing results remain useful in the future -- as long as ftdna and/or it's database survives. I also don't want to assume that any family member or friend will zealously take up the/my/our cause.
It doesn't appear that 2 vaccines last spring of 2021, plus a preumed omicron infection last 24dec2021 is enough to protect one from COVID mutated strains. At least, per my present condition. Or, it could be just a summer cold/flu which I can't remember ever getting before. ;-)
Best,
Daryl? _._,_._,_
开云体育 Links:
-- For R1b Y DNA questions please post on one of the two forums:
R1b Y DNA Project Facebook Group -? R1b All Subclades Project Activity Feed -
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In terms of variant call analysis, the Big Y tool set includes Y chromosome browser and lists of private and non matching variants by location number. The chrome BAMsAway add-on can help.
The FTDNA VCF files are still free and YFull accepts them. If you want to use YFull I suggest sending them the VCF file and then waiting to see if there are close matches on the tree with you. At that point you may find variants you question and want a full BAM analysis from YFull.
I think the YFull charge is $49 and includes a free upgrade to BAM file analysis. The FTDNA charge for a BAM file is $99. When they started this with Big Y700 they lowered prices from $100 to $150 but then you add to pay for the BAM file if you wanted it. Few people actually order it.? People who already had Big Y500 always get their BAM files for free, regardless of whether they upgrade to Big Y700 or not.
Something to keep in mind is phylogenetic analysis. This impacts call variant analysis. The more samples analyzed the better. FTDNA (and I think YFull too) may change a call on a variant after comparing raw data from several different samples of the same subclade.
I've been sick all week, and still am, but I need some help per questions below.?
I wonder how many people have been charged, or threatened to be charged, under that European GDPR legislation. If it's zero, then it doesn't appear it has much teeth. That's about the most polite thing I can say about it/them. ;-)
I finally loosened those tight Scot purse strings and ordered the BigY upgrade last night. Does anybody know why it doesn't include the Bam file? I'd like to send it out for analysis to yfull. This way I can see exactly the results of the 'read' results on any SNP/variant. I couldn't find information on that wonderful FTDNA website about how much extra it will presumably cost to get a Bam file. Anybody know??
I also noticed that FTDNA has 23 SNPs listed as apparent L193(S5982) equivalents on their Haplotree. Why?? Yfull.com shows only 15 unique variants -- the other 8 were the same variants with different names. But still, with 15 equivalents that's at least 6 more than Alex's 'good' 9 equivalents, and 4 more than his 11 'good and iffy' (a very nice scientific description of the two, I think) equivalents. Obviously ftdna didn't mean to confuse us -- but they did.?
So, since Alex's Big Tree is not being used as much anymore, it kind of forced me to get the BigY 700 upgrade, so that maybe I can keep up with the latest -- but only if I can also see other people's private SNPs, which I doubt? FTDNA provides to BigY testees. Or do they? But the main reason for taking the BigY is because I'm hoping it might match other BigY 700 testees where BigY 500 didn't/couldn't. (No, Leake, not to confirm I'm A1067 like my Aussie Martin cousin. lol )
?Another important reason is that I've appointed the L513 Haplogroup Project Administration as beneficiary of my account -- should I someday go to Scot heaven.? That's the only reasonable choice, in my mind, to ensure that DNA testing results remain useful in the future -- as long as ftdna and/or it's database survives. I also don't want to assume that any family member or friend will zealously take up the/my/our cause.
It doesn't appear that 2 vaccines last spring of 2021, plus a preumed omicron infection last 24dec2021 is enough to protect one from COVID mutated strains. At least, per my present condition. Or, it could be just a summer cold/flu which I can't remember ever getting before. ;-)
Best,
Daryl?
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Thanks for that good information Mike. I haven't kept up on current events for a few years now (at least).
I like the idea of a BAM file, as one never knows when it might come in handy.? It's good to know that it can be ordered any time in the future. I'll probably order it at some point, even if it's to simply satisfy my natural curiosity, but even more so to preserve that data for as long as possible.
I'm hoping those private variants of others can be traced to specific people, like on the Big Tree, so that I can possibly recommend cheaper single variant testing methods like Thomas Krahn's Yseq company. It worked well in our A1067 Haplogroup.
Yes, definitely, more data is best, as variant selection can be very subjective.
Any new (easy) formulas/methods for SNP rates and the combination of old SNP tests and new that help people like me to make 'best guess' ages of SNP Births and TMRCA??
Thanks for all your efforts Mike, and for staying current for all of us.
Daryl
I might have to relearn how to do a Blat on my phone -- at some future time -- for those questionable variants where it's exact location can't be exactly pinpointed.? ;-)
On Sat, Aug 27, 2022, 4:35 PM Tiger Mike < mwwdna@...> wrote: In terms of variant call analysis, the Big Y tool set includes Y chromosome browser and lists of private and non matching variants by location number. The chrome BAMsAway add-on can help.
The FTDNA VCF files are still free and YFull accepts them. If you want to use YFull I suggest sending them the VCF file and then waiting to see if there are close matches on the tree with you. At that point you may find variants you question and want a full BAM analysis from YFull.
I think the YFull charge is $49 and includes a free upgrade to BAM file analysis. The FTDNA charge for a BAM file is $99. When they started this with Big Y700 they lowered prices from $100 to $150 but then you add to pay for the BAM file if you wanted it. Few people actually order it.? People who already had Big Y500 always get their BAM files for free, regardless of whether they upgrade to Big Y700 or not.
Something to keep in mind is phylogenetic analysis. This impacts call variant analysis. The more samples analyzed the better. FTDNA (and I think YFull too) may change a call on a variant after comparing raw data from several different samples of the same subclade.
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I went ahead and checked the R-A1067 subgrouping in the project and then broke out R-A1067 haplogroup people into two:
13060. ...? R-A1067* 13061. ...? R-A1067
The 13061 folks might fit better downstream but just haven’t tested further. Meanwhile, the R-A1067* Big Y tested guy has latent private SNPs waiting for a match to come along.
Targeted SNP testing before having each Earliest Known Ancestor’s terminal haplogroup is defined is premature. This results in pile-ups of “stuck” testers. Unfortunately, some don’t test further so the tree has parts incomplete.
Targeted SNP testing can’t discover a new SNP. It can rule people out of a true terminal haplogroup, but negative results don’t help the tester, himself.
Thanks for that good information Mike. I haven't kept up on current events for a few years now (at least).
I like the idea of a BAM file, as one never knows when it might come in handy.? It's good to know that it can be ordered any time in the future. I'll probably order it at some point, even if it's to simply satisfy my natural curiosity, but even more so to preserve that data for as long as possible.
I'm hoping those private variants of others can be traced to specific people, like on the Big Tree, so that I can possibly recommend cheaper single variant testing methods like Thomas Krahn's Yseq company. It worked well in our A1067 Haplogroup.
Yes, definitely, more data is best, as variant selection can be very subjective.
Any new (easy) formulas/methods for SNP rates and the combination of old SNP tests and new that help people like me to make 'best guess' ages of SNP Births and TMRCA??
Thanks for all your efforts Mike, and for staying current for all of us.
Daryl
I might have to relearn how to do a Blat on my phone -- at some future time -- for those questionable variants where it's exact location can't be exactly pinpointed.? ;-) On Sat, Aug 27, 2022, 4:35 PM Tiger Mike < mwwdna@...> wrote: In terms of variant call analysis, the Big Y tool set includes Y chromosome browser and lists of private and non matching variants by location number. The chrome BAMsAway add-on can help.
The FTDNA VCF files are still free and YFull accepts them. If you want to use YFull I suggest sending them the VCF file and then waiting to see if there are close matches on the tree with you. At that point you may find variants you question and want a full BAM analysis from YFull.
I think the YFull charge is $49 and includes a free upgrade to BAM file analysis. The FTDNA charge for a BAM file is $99. When they started this with Big Y700 they lowered prices from $100 to $150 but then you add to pay for the BAM file if you wanted it. Few people actually order it.? People who already had Big Y500 always get their BAM files for free, regardless of whether they upgrade to Big Y700 or not.
Something to keep in mind is phylogenetic analysis. This impacts call variant analysis. The more samples analyzed the better. FTDNA (and I think YFull too) may change a call on a variant after comparing raw data from several different samples of the same subclade.
-- For R1b Y DNA questions please post on one of the two forums:
R1b Y DNA Project Facebook Group -? R1b All Subclades Project Activity Feed -
-- For R1b Y DNA questions please post on one of the two forums:
R1b Y DNA Project Facebook Group -? R1b All Subclades Project Activity Feed -
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Mike:?
Thanks for posting that information.?
Yes, I think I have a chance of BigY matching with IN48416, but only genealogically before the 1700s and likely a few hundred years before that even. Of course I'm playing the fun game called guessing, because it really is fun to do so.? He has a possible 10 good SNPs on his Big Tree private page, most of them named by ftdna.?
?I see on the Big Tree that FTDNA is/has been naming private SNPs that don't seem very good --? good being a blank white box with only a + sign in the middle. Is that because they believe they are good SNPs, or some other reason??
I should match at least one SNP with my Aussie Martin cousin, #44265, who only has two 'good' private snps, FGC40169 and FGC40170.?
See my comments (coloured) below in your post.? Yes, BigY is the first best choice, but some people are still leary of any DNA testing. Fears and doubts are big obstacles, and a major cause of SNP* paragroups without a near present day terminal SNP -- in my opinion.? Many people want to be 'sold' on a concept first, before dishing out the money.? I think it's slowly happening, but just not as fast as we'd like. ;-)
Daryl? ? On Sat, Aug 27, 2022, 8:43 PM Tiger Mike < mwwdna@...> wrote: I went ahead and checked the R-A1067 subgrouping in the project and then broke out R-A1067 haplogroup people into two:
13060. ...? R-A1067* 13061. ...? R-A1067
The 13061 folks might fit better downstream but just haven’t tested further. Meanwhile, the R-A1067* Big Y tested guy has latent private SNPs waiting for a match to come along.
Targeted SNP testing before having each Earliest Known Ancestor’s terminal haplogroup is defined is premature. This results in pile-ups of “stuck” testers.
Are pileups a true negative outcome? At least in a pileup we can see which Son SNP they belong to, in the case of L193 men. I suspect that some people just need to dip their toe in the water to get a sense of what it feels like. This may induce an interest to walk in further.?
Unfortunately, some don’t test further so the tree has parts incomplete.
I've found that many people just need someone to help them further into the water.?
Targeted SNP testing can’t discover a new SNP. It can rule people out of a true terminal haplogroup, but negative results don’t help the tester, himself
Yes, negative results may not show any relatedness but the whole process may stir up an interest to know more and may even convert doubters into believers of more expensive tests like BigY.? For R1b Y DNA questions please post on one of the two forums:
R1b Y DNA Project Facebook Group -? R1b All Subclades Project Activity Feed -
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You had two inquiries. I'll answer below.
Daryl wrote:? ?I see on the Big Tree that FTDNA is/has been naming private SNPs that don't seem very good --? good being a blank white box with only a + sign in the middle. Is that because they believe they are good SNPs, or some other reason??
[[MW: Every service has their own criteria for variant call analysis. They also have different depths and quantities of data. For instance, much of the Big Tree was built on VCF files. VCF files, particularly old ones, have less information than BAM files. FTDNA has and uses all of the BAM file data, and can and will even go back to the lab for more info.
Importantly, FTDNA also has the most NGS BAM file samples. This aids in phylogenetic analysis, which validates and/or invalidates variant call analysis in many situations.Read Alex's intro to the Big Tree. He says "The most important property of these mutations (SNPs) is that they are phylogenetically consistent." ]]
On Sat, Aug 27, 2022, 8:43 PM Tiger Mike < mwwdna@...> wrote: I went ahead and checked the R-A1067 subgrouping in the project and then broke out R-A1067 haplogroup people into two:
13060. ...? R-A1067* 13061. ...? R-A1067
The 13061 folks might fit better downstream but just haven’t tested further. Meanwhile, the R-A1067* Big Y tested guy has latent private SNPs waiting for a match to come along.
Targeted SNP testing before having each Earliest Known Ancestor’s terminal haplogroup is defined is premature. This results in pile-ups of “stuck” testers.
Daryl wrote:? Are pileups a true negative outcome? At least in a pileup we can see which Son SNP they belong to, in the case of L193 men. I suspect that some people just need to dip their toe in the water to get a sense of what it feels like. This may induce an interest to walk in further.?
? [[MW: What I'm calling a pile-up is caused by limited of SNP testing downstream of the haplogroup label for those in the pile-up. These folks end up being stuck, when their more youthful terminal haplogroup could be known with additional testing. As the tree grows with more and more Big Y testers, new downstream haplogroups are defined. These SNPs are missed by any prior targeted testing. They are not negative SNP results.
However, I think what you are saying is that the individuals stuck at a pile-up level is not bad to know. I agree it is fine to know but only leaves more and more questions that ultimately will only be resolved when there is a terminal haplogroup for every Earliest Known (genealogically) Ancestor. The targetted SNP testing is wasted until then. The efficient method time-wise and ultimately cost-wise, I think and there are many who agree, is to go straight to the real solution of Y SNP discovery testing, that is Big Y.? Ironically, it is a better investment to max out on Y STR testing to Y111 if you are looking for interim solutions. At least your expense is credited to you in a reduced upgrade price to Big Y.]]
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YFull has moved their payment center to somewhere due to the war- France maybe. They now charge 45 Euros, and for us using $$, that goes up and down with the conversion rate. I've sent two kits recently and the PayPal amount was around $47 US.? ?Works fine. Just don't let the Euro's throw you.??
-Tom Little
Little Surname DNA Project
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Mike, and all:
A mere quest for knowledge below.?
I'd like to get a detailed definition of "phylogenetically consistent" as Alex W used it, if you know of one. I can't seem to grasp exactly what he is referring?to.
I know choosing a 'good' SNP can be subjective, and Mike has explained some of the reasons for that already, but when does "consistency" come into play, especially to include the phylogenetic part?
Also, per a Sinkler BigY2 test below, I'm wondering if it's okay to label mutations as "good" SNPs when they are found very close together. Ian McDonald, below, doesn't seem to think so, but I could be misinterpreting him.?
Ian McDonald's website link here:
The first paragraph at top of Ian's page: "Time to most-recent common ancestor (TMRCA) estimates for targetted pairs" Then >>> "How to use this chart:
- Look vertically for the number of SNPs the differ between two tests. >>>>> MNPs (e.g. SNPs at sequential positions, or positions very close to each other) should be ignored."
In light of Ian's instructions I'm wondering why FTDNA has named these 4 snps below where they're all found within 44 bases of each other, and especially the bottom 2 which are within 2 bases of each other -- (11,072,631 to 633). Are they just potential SNPs or 'good' SNPs that are "phylogenetically consistent"? I'm just trying to understand what is a good acceptable SNP according to FTDNA. Note Alex's ** and box coloring in the right column. They're not the usual white background with a + sign that I would assume is a 'good' SNP.
"Sinkler BigY2: 127262
| 13228351-C-T | 11072675-C-T | | FT271494 | | | | | ** | | 13228320-C-T | 11072644-C-T | | FT441381 | | | | | ** | | 13228312-C-A | 11072636-C-A | | FT441380 | | | | | ** | | 13228309-A-G | 11072633-A-G | | FT441379 | | | | | ** | | 13228307-C-T | 11072631-C-T | | FT441378 " |
Also, will BigY3 700 results give me similar private SNP information for others, like Alex does above?
Best,
Daryl?
On Sun, Aug 28, 2022, 6:44 AM Tiger Mike < mwwdna@...> wrote: You had two inquiries. I'll answer below.
Daryl wrote:? ?I see on the Big Tree that FTDNA is/has been naming private SNPs that don't seem very good --? good being a blank white box with only a + sign in the middle. Is that because they believe they are good SNPs, or some other reason??
[[MW: Every service has their own criteria for variant call analysis. They also have different depths and quantities of data. For instance, much of the Big Tree was built on VCF files. VCF files, particularly old ones, have less information than BAM files. FTDNA has and uses all of the BAM file data, and can and will even go back to the lab for more info.
Importantly, FTDNA also has the most NGS BAM file samples. This aids in phylogenetic analysis, which validates and/or invalidates variant call analysis in many situations.Read Alex's intro to the Big Tree. He says "The most important property of these mutations (SNPs) is that they are phylogenetically consistent." ]]
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Hi Daryl - to be fair to Iain I thought I would provide some of his contemporary comments on similar subject (time estimates and aging)... There are all sorts of nomenclature used in these discussions - I would hardly claim to understand the precise meaning of every term. Loved the way Bucky Fuller would make up words (geodesic dome, dymaxion car) as he went along! "phylogenetically" may be one of those terms but I hear a taxonomist's concern for some criteria consistency - whether that's by number or morphology I assume. Even 'homologous markers' are not what I would have expected by the term alone... position on the chromosome appears to have some heft in the equation. And here's Iain: "Calls of SNPs will vary between analyses of the same BAM file, whether it's done by FTDNA, YFull, FGC or anyone else. This is because different choices are made regarding what constitutes a high-quality SNP call: how many reads it needs, what base quality those reads need to be, what mapping quality those reads have, the repetitiveness and other features of the surrounding genome, etc. Each test contains many shades of grey between having no reads at a position and SNPs of unquestionable quality."
"For TMRCA estimates, there are two things that matter. Maximising data is important to improve precision: more tests, better tests, better reference comparisons to provide better coverage, and so on. However, precision is nothing without accuracy, and self-consistency is the key here. If you count SNPs based on one interpretation of a BAM file, you should also count the test coverage according to the number of base pairs with good-quality reads in that BAM-file interpretation. That should also overlap with the base pairs that you are using to define your mutation rate."
"The key to a good TMRCA calculation is to maximise precision without sacrificing accuracy, while maintaining a computation that can be done with reasonable effort in reasonable time. All TMRCA calculators work on similar principles, but make different balances between these three factors. YFull sacrifice precision to ensure accuracy, by restricting the portion of the test they use to a specific subset of base pairs. FTDNA's methods aren't announced yet, but the numbers they provide for the upper haplogroups in R-U106 suggest they trade accuracy to obtain the most precise numbers. The exact methodology I personally use these days tries to keep both precision and accuracy to obtain the best TMRCAs, but requires very in-depth analysis that could not easily be rolled out to an entire haplotree. What balance anyone else wants to take is up to them!"
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Something we need to consider about TMRCA statistically based methods is they have (and should have) error ranges. Oftentimes the 95% confidence interval is long range of time. We should try to focus on the range of dates and not the specific mean or median date.? That is not very satisfying but consider that R-L513 has 765 subclade. Therefore, there are probably around 40 subclades that have TMRCA estimates outside the 95% range. Yikes!? This is true of all the TMRCA math based methods I know of.
We do not know FTDNA's method as they have not published it. .
I have been told by FTDNA:
1) Their methodology uses both SNPs and STRs.
2) Their methodology uses regional definitions they will call FTBED regions.? (McDonald uses something he calls McDonaldBED regions. YFull uses something called ComBED regions as defined by Adamov.)
3) The FTBED regions are fairly restrictive but more expansive that ComBED. (This seems to contradict Iain's statement somewhat.)
4) The SNP counting does not count SNPs that have less than six reads in the supporting Big Y700 results.
5) The SNP counting excludes not pure SNPs.
6) They plan to add another statistical technique soon (like maybe next week) that may help address some concerns in older haplogroups
I don't know if the "not pure" SNPs means they are excluding the MNPs. I agree they should exclude those or count them differently.? We do need to wait for their white paper.
I personally think they are more focused on genealogical time estimates and want those to be the best possible. They position themselves as a genetic genealogy company, not a haplogroup research institution. That requires some precision since each branch has less data for a shorter time period than the huge ancient branches.
?
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Daryl requested, "I'd like to get a detailed definition of "phylogenetically consistent" as Alex W used it".
Here is a description of phylogenetic comparison methods.
For Y DNA, "consistency" is just a matter of following the reality that every son has a father, only one father, and that he is from whom each son gets his Y chromosome.
There is no mixing of Y chromosomes
like there is of autosomal DNA.
Consistency with Y DNA would mean things like:
- My brother and I have the same SNPs our father does although my brother or I each might have an additional SNP.
- My male line cousins would have the same SNPs that our paternal grandfather has.
An inconsistency would be an SNP that shows up on and off across multiple unrelated lineages. Something is going on that we don't understand and that particular SNP perhaps is unstable or the test is having a hard time reading that location.
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Please, please do not repost this - MNPs are excluded.?
We need to be patient and wait for the white paper.
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Thanks for that explaination Mike. I guess it was the inconsistent SNPs that I wasn't factoring in which made the term "phylogenetically consistent" difficult to grasp. A "SNP that shows up on and off across multiple unrelated lineages" is something I didn't know, or had forgotten. Probably the latter. I guess until now I had just presumed it was a machine misread, and didn't realize the many different characteristics of an "unstable" SNP. Perhaps "what constitutes an unstable SNP?" should have been my question to ask. I had assumed unstable SNPs would be easily spotted and excluded, but that assumption made the need for the creation of a terminology -- "phylogenetically consistent", which was an already understood concept -- confusing. ;-)
Switching topic back to the McIntosh, 281409, that showed as BigY700, about 13 days ago, on my personal account, and with a terminal SNP of L193: He's now in our L513 Project as BY138237 (thanks to Mike's invite). This is one of many times that FTDNA has fooled me. I wish they wouldn't label men as BigY until they've determined his terminal SNP.? It looks like he's breaking up Alex W's block of several equivalent SNPs under FGC32127 -- the one which includes the 2 Walker's terminal SNP of BY66304.
Mike: It's good to hear about FTDNA's plans. I like that STRs are being looked at also. Years ago they seemed to have big plans for STRs. I have always believed more STRs would help us pin down closer relatives.
Mike, I know you suggested I invite the 1067* McLean, B99182, in the McLean Project,?to our L513 Project, but I was thinking he might be more receptive to an invite from you -- as our Project Administrator. What do you think. ;-)
Thank you Leake for the post that included Ian McDonald quotes. I'd like to follow/read those conversations you mentioned if you can provide a link to them.
Best,
Daryl?
On Wed, Aug 31, 2022, 7:54 AM Tiger Mike < mwwdna@...> wrote:
Daryl requested, "I'd like to get a detailed definition of "phylogenetically consistent" as Alex W used it".
Here is a description of phylogenetic comparison methods.
For Y DNA, "consistency" is just a matter of following the reality that every son has a father, only one father, and that he is from whom each son gets his Y chromosome.
There is no mixing of Y chromosomes
like there is of autosomal DNA.
Consistency with Y DNA would mean things like:
- My brother and I have the same SNPs our father does although my brother or I each might have an additional SNP.
- My male line cousins would have the same SNPs that our paternal grandfather has.
An inconsistency would be an SNP that shows up on and off across multiple unrelated lineages. Something is going on that we don't understand and that particular SNP perhaps is unstable or the test is having a hard time reading that location.
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Scotland
MagUidhir6
T J Little
Leake Little