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Thread: I-A12974 Branch

  1. #11
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    Quote Originally Posted by deadly77 View Post
    This is largely where I am with these, and very much agree with the strategy of concentrating on the reliable SNP candidates first and then looking at the more questionable ones later that Thomas Krahn outlined in the presentation linked in #4. And for sure, A12974 and FGC74335 don't have any recent genealogical influence. The I-Y33691 folks have between 17 and 20 SNPs on the YFull tree that are suitable for age estimation (plus several more on the YFull tree) that track their descent from I-L338 while I have 17 different ones in the same category so we can chart our divergence from each other without including A12974 or FGC74335 as a stepping stone. Although I must admit that I'm interested if this I-A12974 is reliable in a phylogenetic sense in terms of the architecture of the tree. More curious than practical for genealogy and it may be chasing ghosts that may not be real.
    Although to add to that, I'm very intrigued by the one individual on the FTDNA public haplotree that is on I-A12974 branch but not on either of the two downstream branches (I-A2006 and I-S24090) and if he is on my branch. Would have to be a Big Y since A12974 or FGC74335 aren't in any SNP packs or offered individually. He's not in either of the FTDNA projects for I1 or I1-Z140 and it's unlikely he'll be on the I-S24090 folks Big Y match list since that branch has 32 SNPs on the I-S24090 branch that would take him past the 30 non-matching variants that FTDNA uses as their matching threshold. Hope this individual makes his way to the FTDNA project or YFull. Although knowing my luck, our common ancestor will be at I-L338 and he'll have in own separate string of 17+ novel SNPs downstream of that...
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  3. #12
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    Quote Originally Posted by deadly77 View Post
    Although to add to that, I'm very intrigued by the one individual on the FTDNA public haplotree that is on I-A12974 branch but not on either of the two downstream branches (I-A2006 and I-S24090) and if he is on my branch. Would have to be a Big Y since A12974 or FGC74335 aren't in any SNP packs or offered individually. He's not in either of the FTDNA projects for I1 or I1-Z140 and it's unlikely he'll be on the I-S24090 folks Big Y match list since that branch has 32 SNPs on the I-S24090 branch that would take him past the 30 non-matching variants that FTDNA uses as their matching threshold. Hope this individual makes his way to the FTDNA project or YFull. Although knowing my luck, our common ancestor will be at I-L338 and he'll have in own separate string of 17+ novel SNPs downstream of that...
    If I’m reading it correctly, it looks like he has 16 Novel Variants:

    “I-A12974

    On average 16 Private Variants in 1 Big Y participant”.


    He’s the only one I can see who’s still carrying I-A12974 in the group coming out of the same.
    Unfortunately, the Big Block Tree is a little clunky & unmanageable, so it’s hard to get a reduced shot of it, that includes all of the pertinent subclades.

    On the other hand, it may be my iPad that’s the culprit.
    Last edited by JMcB; 01-24-2020 at 04:06 AM.
    Paper Trail: 43.8% English, 29.7% Scottish, 12.5% Irish, 6.25% German, 6.25% Italian & 1.5% French. Or: 86% British Isles, 6.25% German, 6.25% Italian & 1.5% French.
    LDNA(c): 86.3% British Isles (48.6% English, 37.7% Scottish & Irish), 7.8% NW Germanic, 5.9% Europe South (Aegian 3.4%, Tuscany 1.3%, Sardinia 1.1%)
    BigY 700: I1-Z140 >I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 620 AD) >A13242/YSEQ (circa 765 AD) >FT80854 (circa 1650 AD).

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  5. #13
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    Quote Originally Posted by JMcB View Post
    If I’m reading it correctly, it looks like he has 16 Novel Variants:

    “I-A12974

    On average 16 Private Variants in 1 Big Y participant”.


    He’s the only one I can see who’s still carrying I-A12974 in the group coming out of the same.
    Unfortunately, the Big Block Tree is a little clunky & unmanageable, so it’s hard to get a reduced shot of it, that includes all of the pertinent subclades.

    On the other hand, it may be my iPad that’s the culprit.
    Well that at least confirms a Big Y - I must admit to not being too familiar with the Big Y Block Tree (since I don't have Big Y). I've seen screenshots that others have posted which show how many matches that each kit has. Does that show in the Block Tree that you can see for the I-A12974 individual or just that just apply to your own matches on the Block Tree? My guess it is the latter.

    Not sure if Mr I-A12974 will appear on anyone's Big Y match list as I'm guessing that he has more than 30 non matching variants with the others downstream. There are 16 SNPs on the I-A2006 branch level, so adding Mr I-A12974's 16 private variants gets to 32 without even considering the SNPs on downstream branches below I-A2006 or private variants. Ditto for I-S24090 branch's 32 SNPs.

    Looks like there are 13 individuals at I-A12974 branch or downstream, with 10 of them in the FTDNA I1-Z140 project. Missing one from I-S24090, one from I-A2051 (Denmark) and Mr I-A12974.

    I checked my STR matches and I don't match most of these at any level. The only example is one of the I-A1972 folks at Y12, GD1. Looking at the project it looks like I have GD2-3 with most of the rest of these folks at Y12, so outside the threshold.
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  7. #14
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    Quote Originally Posted by deadly77 View Post
    Well that at least confirms a Big Y - I must admit to not being too familiar with the Big Y Block Tree (since I don't have Big Y). I've seen screenshots that others have posted which show how many matches that each kit has. Does that show in the Block Tree that you can see for the I-A12974 individual or just that just apply to your own matches on the Block Tree? My guess it is the latter.

    Not sure if Mr I-A12974 will appear on anyone's Big Y match list as I'm guessing that he has more than 30 non matching variants with the others downstream. There are 16 SNPs on the I-A2006 branch level, so adding Mr I-A12974's 16 private variants gets to 32 without even considering the SNPs on downstream branches below I-A2006 or private variants. Ditto for I-S24090 branch's 32 SNPs.

    Looks like there are 13 individuals at I-A12974 branch or downstream, with 10 of them in the FTDNA I1-Z140 project. Missing one from I-S24090, one from I-A2051 (Denmark) and Mr I-A12974.

    I checked my STR matches and I don't match most of these at any level. The only example is one of the I-A1972 folks at Y12, GD1. Looking at the project it looks like I have GD2-3 with most of the rest of these folks at Y12, so outside the threshold.
    He doesn’t appear to have any matches. I managed to cobble together two screen shots for his area. Unfortunately, the way the Big Block Tree is design you have to scroll back and forth to see everything you want. So I couldn’t fit everything in

    At any rate here it is:

    Attachment 36000
    Paper Trail: 43.8% English, 29.7% Scottish, 12.5% Irish, 6.25% German, 6.25% Italian & 1.5% French. Or: 86% British Isles, 6.25% German, 6.25% Italian & 1.5% French.
    LDNA(c): 86.3% British Isles (48.6% English, 37.7% Scottish & Irish), 7.8% NW Germanic, 5.9% Europe South (Aegian 3.4%, Tuscany 1.3%, Sardinia 1.1%)
    BigY 700: I1-Z140 >I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 620 AD) >A13242/YSEQ (circa 765 AD) >FT80854 (circa 1650 AD).

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  9. #15
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    Quote Originally Posted by JMcB View Post
    He doesn’t appear to have any matches. I managed to cobble together two screen shots for his area. Unfortunately, the way the Big Block Tree is design you have to scroll back and forth to see everything you want. So I couldn’t fit everything in

    At any rate here it is:

    Attachment 36000
    Yep, looks that way - and that appears to be the case for all of the individuals in that screenshot. Thanks for the screenshot. I hope this individual makes it over to the FTDNA Z140 project or YFull of his own accord. Even if A12974 turns out not to be reliable or he doesn't share any of my currently private SNPs, it's a new branch of I-L338.
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  11. #16
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    Well, YFull say they are confident in A12974 - they said they analyze BAM files manually and take into account not only this mutation but the whole situation in different samples in this region regarding potential pseudo SNPs from other chromosomes. They think my ambiguous A12974 result is actually positive. They say they don't trust FGC74335 due to homology with the X chromosome though.
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  13. #17
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    Quote Originally Posted by deadly77 View Post
    Well, YFull say they are confident in A12974 - they said they analyze BAM files manually and take into account not only this mutation but the whole situation in different samples in this region regarding potential pseudo SNPs from other chromosomes. They think my ambiguous A12974 result is actually positive. They say they don't trust FGC74335 due to homology with the X chromosome though.

    There is another SNP on YFull that received a 5 star rating and is located in the “questionable” centromeric region. The SNP / subclade branch is I-Y2170. So it does appear that there are many factors that go into judging the suitability of a SNP and that we should not simply discount these “questionable” SNPs based solely on their locations.
    I1 > DF29 > Z58 > Z59 > Z2041 > Z2040 >
    Z382 > S26361 > S16414 > FGC24354 > FGC24357 >
    FGC24356 > S10350 > FGC75802 > Y125947 >
    S21197 Netherlands >
    BY149414 Scotland >
    BY188003 Belgium >
    BY188570 Belgium

    YFull id: YF68407

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  15. #18
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    Quote Originally Posted by mwauthy View Post
    There is another SNP on YFull that received a 5 star rating and is located in the “questionable” centromeric region. The SNP / subclade branch is I-Y2170. So it does appear that there are many factors that go into judging the suitability of a SNP and that we should not simply discount these “questionable” SNPs based solely on their locations.
    Yeah, I'm just looking for a bit more understanding about why some of the SNPs in the centromere are ok, and some are not so I can apply it to candidate SNPs in this region in the future. If I look at my WGS, there are differences at 44 positions in the centromere region and 65 positions in the DYZ19 region compared to the reference sequence. Obviously not all of these will be reliable, but I'd like to have a better understanding of which ones are worth considering and which to ignore, and how to assess that. Comparing by BLAT to reference genome for high identity? Phylogenetic consistency across Y-DNA branches? Statistically predicting potential recombination events? Just not sure how to evaluate that at my current level of understanding.

    Of course, not all these 109 differences in the centromere and DYZ19 will be real "derived" since the hg38 reference is R1b, some of the positions in the reference sequence represent derived mutations from the ancestral state for R1b rather than for other haplogroups.

    I've sent FTDNA a query regarding their view of A12974 and if they'd consider making it available for single SNP testing, but they have yet to reply to either yet. Might ask FGC as well.

    I asked a few people on this branch who had kits uploaded to YFull to join the YFull I1-Z140 group and most of them have. It gives a bit of a clearer picture of what YFull is looking at from a phylogenetic consistency perspective. This is especially for those who have done Big Y Y700 and added that to an earlier Big Y Y500, in which the later test reads A12974 much better.
    Groups view Z140 tree position A12974 012920.png
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  17. #19
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    Quote Originally Posted by deadly77 View Post
    Yeah, I'm just looking for a bit more understanding about why some of the SNPs in the centromere are ok, and some are not so I can apply it to candidate SNPs in this region in the future. If I look at my WGS, there are differences at 44 positions in the centromere region and 65 positions in the DYZ19 region compared to the reference sequence. Obviously not all of these will be reliable, but I'd like to have a better understanding of which ones are worth considering and which to ignore, and how to assess that. Comparing by BLAT to reference genome for high identity? Phylogenetic consistency across Y-DNA branches? Statistically predicting potential recombination events? Just not sure how to evaluate that at my current level of understanding.

    Of course, not all these 109 differences in the centromere and DYZ19 will be real "derived" since the hg38 reference is R1b, some of the positions in the reference sequence represent derived mutations from the ancestral state for R1b rather than for other haplogroups.

    I've sent FTDNA a query regarding their view of A12974 and if they'd consider making it available for single SNP testing, but they have yet to reply to either yet. Might ask FGC as well.

    I asked a few people on this branch who had kits uploaded to YFull to join the YFull I1-Z140 group and most of them have. It gives a bit of a clearer picture of what YFull is looking at from a phylogenetic consistency perspective. This is especially for those who have done Big Y Y700 and added that to an earlier Big Y Y500, in which the later test reads A12974 much better.
    Groups view Z140 tree position A12974 012920.png

    I’m in the same boat as you are. I’d like to have a better understanding of the criteria for differences in quality as well.

    I recently learned that some SNPs in the combBED regions are not suitable for analysis either so I quit trying to do rough age estimates for people’s private SNPs that were in the combBED regions.

    Another question I have is why are some of the novel SNPs with the red “H” next to them because they are homologous listed in the “Acceptable” category? My first cousin had one of those. When I uploaded my Big Y-700 results to YFull that homologous novel SNP disappeared from his novel section but it wasn’t added to the Haplotree either. Not sure why it was considered acceptable at the beginning and then not afterwards?
    I1 > DF29 > Z58 > Z59 > Z2041 > Z2040 >
    Z382 > S26361 > S16414 > FGC24354 > FGC24357 >
    FGC24356 > S10350 > FGC75802 > Y125947 >
    S21197 Netherlands >
    BY149414 Scotland >
    BY188003 Belgium >
    BY188570 Belgium

    YFull id: YF68407

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  19. #20
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    Quote Originally Posted by mwauthy View Post
    I’m in the same boat as you are. I’d like to have a better understanding of the criteria for differences in quality as well.

    I recently learned that some SNPs in the combBED regions are not suitable for analysis either so I quit trying to do rough age estimates for people’s private SNPs that were in the combBED regions.

    Another question I have is why are some of the novel SNPs with the red “H” next to them because they are homologous listed in the “Acceptable” category? My first cousin had one of those. When I uploaded my Big Y-700 results to YFull that homologous novel SNP disappeared from his novel section but it wasn’t added to the Haplotree either. Not sure why it was considered acceptable at the beginning and then not afterwards?
    Yes, I have some of those too. It seems being in the combBED region alone is not the only qualification that YFull uses to determine if suitable for age estimation. The "x Known SNPs" and "x Novels" tabs under "age estimation are helpful. From there, I can see several SNPs that YFull list as phyloequivalent with I-Z58 branch, but they're not included because of more than five different localizations - ie, S10311 in the combBED region but also found in 349 haplogroups/subclades different from mine, so too many examples of recurrence. Another one (Y125444) is classed as an INDEL.

    For the SNPs tagged as homologous (the novel SNPs with the red “H” next to them), I believe that YFull once said that they use "soft reject" for these cases - they report them in novel SNPs but don't add them to the tree, use them for age estimation or use them for phylogeny. I think the situation with your cousin's SNP is similar to what I saw with FGC74335 in post #2 - initially reported in my novel SNPs as position read in my test but not in any of the other Big Y Y500 tests on I-Y33691 or I-Y12329. I can see that since two of the kits upgraded to Y700, they are now showing positive result for FGC74335. So FGC74335 has disappeared from my novel SNPs because it's not found only in my sample. But not added to YFull tree because it's homologous. FTDNA is listing FGC74335 on their haplotree, though.
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