Re: FamilyTreeDNA provides Y-DNA haplogroups from Family Finder autosomal tests
Hi,
This is indeed excellent news. We should in theory see the number of testers positive for certain R-U106 subclades increase quite significantly. I guess the available SNPs depend on the chip version (V1 to V3) used for autosomal testing. I don't know if it will be possible for us to know the list of SNPs supported by these different chip versions.
Cheers,
Ewenn
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FamilyTreeDNA provides Y-DNA haplogroups from Family Finder autosomal tests
Sorry folks. Didn't know where else to post this but its good news.
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"Big News!?FamilyTreeDNA?is delivering holiday gifts early!
Y DNA?haplogroups are beginning to be delivered as a free benefit to men who took the?Family Finder?test at?FamilyTreeDNA. This is the first wave of a staggered rollout. Haplogroup results will be delivered to several thousand people at a time, in batches, beginning today.
This is no trivial gift and includes LOTS of information that can be used in various ways for your genealogy. Please feel free to share this article. The new?Family Finder?haplogroups are another reason to take a?Family Finder?test and to encourage other family members to do so as well."
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Re: Match on block tree but not listed as Big Y Match
In addition, the deletion of FT354122 was not linked to the upgrade from a bigY500 test to a bigY700. This was, it seems to me, more linked to its detection on a certain number of aDNAs which did not however belong to this branch.
Hi Iain,?
Thank you for your reply.
Yes, that¡¯s what I observe in my match. Ultimately, when the number of bigY tests will have increased considerably, the number of resilient PVs should drop considerably, and undoubtedly lose their interest.
Aren't some recurring SNPs also likely to one day be deleted from NMV lists? I suppose, given the imperfection of the GRCh38 reference, that some of these may be somehow "puppets", and not actually imply a valid mutation between 2 tests. If we were to one day move to a new comprehensive reference, taking into account the entire Y chromosome (and the rest of the human genome), as well as all its variations (also including all the existing, sometimes very long, indels), I presume that certain current results would ultimately be invalidated (bad alignments for example - this should in particular be even more true as we move away, in the Y tree, from the person who served as the basis for the development of the GRCh38 reference).
Cheers,
Ewenn
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Re: Match on block tree but not listed as Big Y Match
Hi Iain,?
Thank you for your reply.
Yes, that¡¯s what I observe in my match. Ultimately, when the number of bigY tests will have increased considerably, the number of resilient PVs should drop considerably, and undoubtedly lose their interest.
Aren't some recurring SNPs also likely to one day be deleted from NMV lists? I suppose, given the imperfection of the GRCh38 reference, that some of these may be somehow "puppets", and not actually imply a valid mutation between 2 tests. If we were to one day move to a new comprehensive reference, taking into account the entire Y chromosome (and the rest of the human genome), as well as all its variations (also including all the existing, sometimes very long, indels), I presume that certain current results would ultimately be invalidated (bad alignments for example - this should in particular be even more true as we move away, in the Y tree, from the person who served as the basis for the development of the GRCh38 reference).
Cheers,
Ewenn
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Re: Match on block tree but not listed as Big Y Match
Hi Ewenn,
The private variants list is essentially stripped straight out of the VCF file, from what I can tell. Private variants will gradually get replaced with named SNPs, which will lead to changes over time. Is this what you are seeing? Alternatively, SNPs can appear and disappear if a tester upgrades from BigY-500 to BigY-700.
For realignment, remember that we have already had a realignment from hg19/GRCh37 to h38/GRCh38. A realignment to T2T has certainly been tried for a few tests (hence the FTT series of SNPs), but I don't know if they are planning a wider roll-out.
Cheers,
Iain.
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Re: Match on block tree but not listed as Big Y Match
Hi John,
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Indeed, the cohabitation between bigY500 and bigY700 tests does not seem very ideal. Imagine if we had to move to a T2T reference and long reads tests...
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Coming back to the Private Variants deletions, I¡¯ve done a ??shortcut??.
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My personal test initially (end of 2021) had 12 PVs, and that of my only match 10. Towards the end of 2022, or perhaps the beginning of 2023, I only had 10 PVs and 8 (it seems to me) for this match. In my case, it's not actually deletion. In reality, these variants went from being PVs, presented only by their position on the Y chromosome, to being NMVs with a defined name. For example, 19 363 847 became FTA36935 (which is also associated with R-BY40294), or 25 614 603 became BY237271 (SNP which does not seems to appear on the Y Tree).
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I also observed at the same time that the average number of PVs of other terminal haplogroups close to mine had also been revised downwards. No new kit had appeared on these branches, which could potentially explain these changes.
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In conclusion, the list of PVs associated with a kit can be reviewed without a new test appearing close to its terminal haplogroup, or forming a new haplogroup with it.
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Another "curiosity", but which seems more logical to me, following the appearance of a bigY700 tester on a branch initially formed from a mix between bigY500 and Y700 tests, SNPs initially associated with a haplogroup were moved upwards to an upstream haplogroup of this branch.
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However, it effectively very rarely happens that certain ¡°established¡± SNPs, and associated as equivalent to a haplogroup, are ultimately simply deleted from the Haplotree. An example with FT354122 (I seem to remember having found a few other deleted SNPs in the past, but I can't get my hands on it), registered in 2020 by FTDNA with ISOGG, initially associated with the R-FT253286 block (3 testers positive to date). This one was finally deleted by FTDNA at the end of 2022 (without the appearance of any new tester). I suppose that FTDNA had reached the conclusion that this SNP was invalid, without knowing precisely why (linked to the imperfection of the GRCh38 reference?). So I suppose (that's where I made my shortcut) that some PVs could also ultimately prove inconsistent.
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I'm not really convinced that this could be the correct explanation for the issue Mary is having. As I said, this is only a very uncertain hypothesis... To be plausible, the first condition to be fulfilled would be that the list of NMVs associated with matches (and therefore non-matches) in the big Y Results is not re-evaluated following modifications, for old tests (which I would find rather annoying by the way). I would lean more towards the explanation presented by Ray Wings.
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It seems to me that to this day there are still gray areas on how FTDNA interprets test results, considers a mutation as valid (or reassess it later), sets certain criteria or limits (sometimes differently from one tool / list to another), constructs its Y-DNA Haplotree, etc. This sometimes seems to lead to misunderstanding among testers.
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An example, for a long-established haplogroup, such as R-M269 (among others), the Y-DNA Haplotree indicates 97 equivalent SNPs, compared to 112 for Discover¡ Why these 15 additional SNPs are not part of the Y-DNA Haplotree??
Kind regards,
Ewenn
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Re: Match on block tree but not listed as Big Y Match
Hello Ewen <mutations can sometimes be deleted from the list of PVs associated with a
kit, without this being reflected on the associated bigY match(es)
If I am reading your post correctly, this is something I have never seen/noticed. That presumes that your PVs are what ISOGG refers to as singletons, and not the other PV (Public Variants). Unless you are suggesting that Kit A has singleton 9 deleted, while it remains on the Kit B singleton Private Variant list; which would be much stranger again. What I do notice is that men with only Big Y-500 results typically have more/many NMVs than men with Big Y-700 results. If I remember correctly Iain has previously advised us to ignore them (in the main), as they are typically inconsistent. Working with a mixture of Y500 and Y700 results, obviously presents many problems. So much so, that FTDNA have offered (in the current sale) the chance to get a new Big Y-700 for a true bargain basement price. We should encourage everyone with Big Y-500 to get (on average) 50% more singletons (and other SNPs too) by jumping into Big Y-700 while it is so cheap (about 1/4 usual price).
FTDNA's recent blog might be of interest to some too.
Kind regards John
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Re: Match on block tree but not listed as Big Y Match
Hi, all!
Thank you, John and Iain, for the information you've shared with me!??
John - if I understand correctly, the X in the non matching variants column means the two kits have greater than 30 non matching variants.??
My follow up question is - what is the cutoff for being shown as a match on the block tree?? The match that has X in the NMV column shows up as a match in the block tree.? It's confusing to me that the match is considered a match one place - in the block tree, but not in another - the match list. So the two reports must have different cutoff thresholds?
Iain - I so appreciate your offer, but I don't want to trouble you unnecessarily?with looking at the kit - I have a query in to FTDNA, and hopefully they can clear up the analysis of this kit compared to the Big Y match.
With much appreciation,?
Mary
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On Tuesday, November 28, 2023 at 10:40:40 PM EST, John T via groups.io <z343snp@...> wrote:
Hello Mary It is not often (in fact a first) that I can elucidate in respect of an Iain McDonald answer. An x in the NMV column always means more than 30 NMVs, and is only ever shown where you have Y37/67/111 matches with someone with Big Y results. Hello Iain It is not the first time we have seen shading below Big Y blocks. I am hoping that as on other occasions it will revert back to what we usually see. Probably hoping a bit too much that it might herald some enhancement. Maybe the display of academic and other 'hidden' results. Kind regards John
On Wednesday, 29 November 2023 at 08:43:39 am ACDT, Iain via groups.io <gubbins@...> wrote:
Hi all - apparently FTDNA have taken away the average number of private variants from each haplogroup on the Block Tree. The teal-coloured blocks that used to denote these have been replaced throughout by hashed-out boxes.
Mary - happy to look into your kits, but I'll need the kit numbers - feel free to send me them privately. The "x" either means there are no mis-matching variants (say, if you have a match within your immediate family) or that data is absent due to some error. If you've already written to FTDNA, they'll be able to give you a more authoritative answer than I can.
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Re: Match on block tree but not listed as Big Y Match
Hi Mary,
Several answers have already been provided to you by other members, more competent than I am, and FTDNA should shed more light on the issue you are having with these kits. Therefore, what follows will probably provide you with little useful information.
It indeed seems to me (almost) impossible to know the list of NMVs between two kits if it exceeds the number of 30. The PV average indicated in the block tree corresponds to the average of Private Variants of the set of kits attached to a particular haplogroup (excepted some of them if they fall into specific parts of the Y chromosome, it seems to me). These have not yet been given a name (in fact, most of them have, if you search on YBrowse based on their position on the Y chromosome - FTDNA has pre-registered these with ISOGG). However, in the list of NMVs between 2 kits, a number of mutations have already been observed elsewhere in the Y tree, and are therefore named. In the example you give to us (with the X), the NMVs with the kit above indicate a single PV and 16 NMVs already named (most starting with BY18...). My personal experience has shown me that mutations can sometimes be deleted from the list of PVs associated with a kit, without this being reflected on the associated bigY match(es) (I don't know if this list of NMVs between 2 kits is likely to be updated). Perhaps similar circumstances could give the following situation: initial list of NMVs > 30 => deletion of certain irrelevant variants bringing this number below this threshold => refresh in the Block Tree without refresh in the list of bigY matches. .. This is just a very uncertain hypothesis.
Since the two kits you are interested in are quite old, I assume that TMRCA have been estimated for the corresponding haplogroup(s). In this case, a TMRCA rather distant from the present (~1950) should be associated with a fairly high number of NMVs between those kits. Conversely, if the number of NMVs is relatively small, the corresponding TMRCA should be more recent (however the calculation of TMRCA, with other parameters which are not all known at the moment, also takes into account STR distances, and does not in principle take into account certain NMVs).
Cheers,?
Ewenn
Thanks John - that's what comes of not reading the original post carefully enough! :)
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Re: Match on block tree but not listed as Big Y Match
Thanks John - that's what comes of not reading the original post carefully enough! :)
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Re: Match on block tree but not listed as Big Y Match
Hello Mary It is not often (in fact a first) that I can elucidate in respect of an Iain McDonald answer. An x in the NMV column always means more than 30 NMVs, and is only ever shown where you have Y37/67/111 matches with someone with Big Y results. Hello Iain It is not the first time we have seen shading below Big Y blocks. I am hoping that as on other occasions it will revert back to what we usually see. Probably hoping a bit too much that it might herald some enhancement. Maybe the display of academic and other 'hidden' results. Kind regards John
On Wednesday, 29 November 2023 at 08:43:39 am ACDT, Iain via groups.io <gubbins@...> wrote:
Hi all - apparently FTDNA have taken away the average number of private variants from each haplogroup on the Block Tree. The teal-coloured blocks that used to denote these have been replaced throughout by hashed-out boxes.
Mary - happy to look into your kits, but I'll need the kit numbers - feel free to send me them privately. The "x" either means there are no mis-matching variants (say, if you have a match within your immediate family) or that data is absent due to some error. If you've already written to FTDNA, they'll be able to give you a more authoritative answer than I can.
Cheers,
Iain.
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Re: Match on block tree but not listed as Big Y Match
Hi all - apparently FTDNA have taken away the average number of private variants from each haplogroup on the Block Tree. The teal-coloured blocks that used to denote these have been replaced throughout by hashed-out boxes.
Mary - happy to look into your kits, but I'll need the kit numbers - feel free to send me them privately. The "x" either means there are no mis-matching variants (say, if you have a match within your immediate family) or that data is absent due to some error. If you've already written to FTDNA, they'll be able to give you a more authoritative answer than I can.
Cheers,
Iain.
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Re: Match on block tree but not listed as Big Y Match
Hi, all!
Thank you, Iain, for your reply and suggestions - and for your offer to look at the kit.??
Both kits are old - a few years old.??
There are no Big Y matches at all, which makes it easy to tell that the match on the Block Tree isn't in the match list.
I took °ä¾±²¹°ù¨¢²Ô's suggestion, and?I have a query in to FTDNA.
I appreciate all the suggestions and help from this group's members.??
Side question:? when I click on the block in the Block Tree to get the Branch Information Card, why does an X show up for one of the two matches below under the non matching variants column?? It's filled in for one match, but has an X for the other.? This is a different kit than the one I was asking about.? The detail for that kit, which has only one Block Tree match, also has an X in that column.? So I looked at another kit - below - to see what usually shows up there, but I don't know what the X means for one of the two matches.
Thank you!
Mary
On Tuesday, November 28, 2023 at 12:31:23 PM EST, Iain via groups.io <gubbins@...> wrote:
Hi Mary,
If the match isn't shown on your list of BigY match, you can't check the number of mis-matching variants.
Overall, this is an issue that doesn't look like it should occur, but which we've seen before and was then (IIRC) related to a hiccup in quality control whereby parts of results are released either piecemeal or prematurely. If this is a new match, it could be that the test has had a haplogroup assigned, but that the matching algorithm has not yet been run - your best bet then is to wait a little while for the database to be recomputed (this may be an overnight or weekend job).
If they don't show up by then or disappear from your Block Tree, you'd need to contact FTDNA for the specifics. Before you do, you might want to do the usual sanity checks - make sure their name hasn't been abbreviated to fit on the Block Tree, that they're not simply on a second page of results, and that all the pages have recently been refreshed. I can have a look myself if you like, though I'm not sure of the kit number.
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Re: Match on block tree but not listed as Big Y Match
Hi Mary,
If the match isn't shown on your list of BigY match, you can't check the number of mis-matching variants.
Overall, this is an issue that doesn't look like it should occur, but which we've seen before and was then (IIRC) related to a hiccup in quality control whereby parts of results are released either piecemeal or prematurely. If this is a new match, it could be that the test has had a haplogroup assigned, but that the matching algorithm has not yet been run - your best bet then is to wait a little while for the database to be recomputed (this may be an overnight or weekend job).
If they don't show up by then or disappear from your Block Tree, you'd need to contact FTDNA for the specifics. Before you do, you might want to do the usual sanity checks - make sure their name hasn't been abbreviated to fit on the Block Tree, that they're not simply on a second page of results, and that all the pages have recently been refreshed. I can have a look myself if you like, though I'm not sure of the kit number.
Cheers,
Iain.
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Re: Match on block tree but not listed as Big Y Match
Hi, all!
Thank you for your reply, John!? What I find conflicting is that the match shows up - by name - in the block tree, but isn't listed in the Big Y matches.? I would think that if they are mismatched on more than 30 variants the match wouldn't show up in the block tree, either.??
Questions: - There are only an average of 4 private variants between the tester and the match.? Is there a correlation between private variants for two matches and the total number of variants on which the two testers don't match?? Four private variants seems like a pretty low number, which makes me question whether or not the two have different results on more than 30 locations.
- How can I double check how many variants the two have a mismatch on, please?? Three csv files can be downloaded for the Big Y results - Derived SNPs, Ancestral SNPs and No Call SNPs.? I would think the way to determine how many variants the two don't match on would be to compare the Derived SNPs files - and however many SNPs have a different value would tell me whether they are a mismatch on more, or less, than 30.? Is that correct?
Thank you!
Mary
On Monday, November 27, 2023 at 08:39:10 PM EST, John T via groups.io <z343snp@...> wrote:
Hello Mary
Big Y matches are restricted to those with 30 or less non matching variants.
Blocktree matches start with Y37/67/111 matches that do not make the cut, followed by the Big Y matches.
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Re: Match on block tree but not listed as Big Y Match
Hello Mary Big Y matches are restricted to those with 30 or less non matching variants. Blocktree matches start with Y37/67/111 matches that do not make the cut, followed by the Big Y matches. You might like to write to the match, and compare. Kind regards John
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Re: Match on block tree but not listed as Big Y Match
Hi!
Thank you for your response, °ä¾±²¹°ù¨¢²Ô and?Raymond!? The match shows up in the list of STR matches, and has provided a family tree and earliest known ancestor.? And they show up on the block tree.? (And they are a member of the surname group) Is it possible for a match to opt in to sharing that information, but not sharing that they are a Big Y-700 match (and sharing the information for matching, non-matching and private variants)?? Can a match piecemeal what they share in that fashion?? I'm thinking I should take °ä¾±²¹°ù¨¢²Ô'²õ?advice and email FTDNA to make sure everything is reflected properly on the account.
Mary?
On Monday, November 27, 2023 at 04:31:12 PM EST, Raymond Wing <wing.genealogist@...> wrote:
I believe the issue may be that the other tester has opted NOT to share his results.
Hi!
I have a question, please.? Why is there one match in the same block on the Big Y Block Tree, but that match is not listed under Big Y Matches - Big Y Matches says "Currently no matches"?? Both kits were processed years ago, so that's not the issue.??
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Re: Match on block tree but not listed as Big Y Match
I believe the issue may be that the other tester has opted NOT to share his results.
Hi!
I have a question, please.? Why is there one match in the same block on the Big Y Block Tree, but that match is not listed under Big Y Matches - Big Y Matches says "Currently no matches"?? Both kits were processed years ago, so that's not the issue.? Both kits did the Big Y-700 test and under the Y-match list it says the Big Y STR Differences are 5 of 605 but the match does not show up under the Big Y Matches.
Thank you!
Mary
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Re: Match on block tree but not listed as Big Y Match
Hi Mary, You should email FTDNA about this. It doesn't seem right.?
°ä¾±²¹°ù¨¢²Ô
On Monday, November 27, 2023 at 07:14:38 PM UTC, mlh via groups.io <mhendersona2@...> wrote:
Thank you for your response!? How do I determine if they meet the 30 SNP variation threshold, please?? The average number of private variants between the two testers is only 4.? How would I determine how many other variants are non-matching between the two kits?
Mary
On Monday, November 27, 2023 at 01:30:39 PM EST, C.B. via groups.io <irishz156@...> wrote:
FTDNA's Big Y match threshold is 30 YSNPs between two testers. The Big Y tester is still a valuable match though even if they are outside the threshold. I have some in my block tree page that are not in my Big Y matches list.?
°ä¾±²¹°ù¨¢²Ô
On Monday, November 27, 2023 at 05:42:49 PM UTC, mlh via groups.io <mhendersona2@...> wrote:
Hi!
I have a question, please.? Why is there one match in the same block on the Big Y Block Tree, but that match is not listed under Big Y Matches - Big Y Matches says "Currently no matches"???
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Re: Match on block tree but not listed as Big Y Match
Thank you for your response!? How do I determine if they meet the 30 SNP variation threshold, please?? The average number of private variants between the two testers is only 4.? How would I determine how many other variants are non-matching between the two kits?
Mary
On Monday, November 27, 2023 at 01:30:39 PM EST, C.B. via groups.io <irishz156@...> wrote:
FTDNA's Big Y match threshold is 30 YSNPs between two testers. The Big Y tester is still a valuable match though even if they are outside the threshold. I have some in my block tree page that are not in my Big Y matches list.?
°ä¾±²¹°ù¨¢²Ô
On Monday, November 27, 2023 at 05:42:49 PM UTC, mlh via groups.io <mhendersona2@...> wrote:
Hi!
I have a question, please.? Why is there one match in the same block on the Big Y Block Tree, but that match is not listed under Big Y Matches - Big Y Matches says "Currently no matches"???
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Ewenn