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Thread: Any members of the I-Z140 Project here?

  1. #171
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    Quote Originally Posted by JMcB View Post
    As always nice work on both of your parts!

    Is there a link to the Z140 portion of the tree? Unfortunately, his clickable link doesn’t seem to work on an iPad. Perhaps, because it’s clickable but not touchable. ;-)
    It worked on my cell phone by touching the "Z140" and not the X, whether that's uniform among OS's I don't know.

    Thanks for passing this along Deadly77, hopefully there can be amendments made to the Phylogeographer for the one error on the map. Nice to see some mapping of the ancient I1 so far!

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  3. #172
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    Quote Originally Posted by spruithean View Post
    It worked on my cell phone by touching the "Z140" and not the X, whether that's uniform among OS's I don't know.

    Thanks for passing this along Deadly77, hopefully there can be amendments made to the Phylogeographer for the one error on the map. Nice to see some mapping of the ancient I1 so far!
    There you go, that’s the trick!

    Thanks, spruithean!
    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: 88.1% British Isles (59.7% English, 27% Scottish & 1.3% Irish), 5.9% Europe South (Aegian 3.4%, Tuscany 1.3%, Sardinia 1.1%), 4.4% Europe NW (Scandinavia) & 1.6% Europe East, (Mordovia).
    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. #173
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    Quote Originally Posted by deadly77 View Post
    I added a few branches of the I-Z140 tree to the I-Z140 Coggle diagram - additional new branches at YFull, branches on the FTDNA haplotree that are not at YFull, shared branches at the I-Z140 project. It'll never be complete (nor would I want it to be) but it's at least got some structure that is a composite of the main ones out there with a bit of a different visualization. As a result, it's "public" and Darin Flansburg, who very kindly hosts the Coggle has linked it to an overall I-M253 Coggle that he has been working on where I-Z140 and I-P109 are clickable links to more detailed subclade Coggles. To view the I-M253 coggle go here https://coggle.it/diagram/XC0kaeCE6k...5YgkZkZH3mlCFo
    Thanks deadly77 and thanks too for the tip spruithean. This is great work and nice to see my own terminal SNP there. Much appreciated.
    Living DNA's former Cautious mode:
    Wales-related ancestry: 86.8%
    Cornwall: 8%
    North England-related ancestry: 5.2%
    Y line: Peak District, England. Big Y match: Scania, Sweden; TMRCA 1,280 ybp (YFull);
    mtDNA: traces to Glamorgan, Wales
    Mother's Y: traces to Llanvair Discoed, Wales

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  7. #174
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    Quote Originally Posted by deadly77 View Post
    JonikW - it appears that there is a new individual in your subgroup at I-Y98720 at the I1-Z140 project page at FTDNA. William says this is a new result and it's Big Y Y700. Not finished all processing yet so doesn't have the full list of novel SNPs, etc. but based on where FTDNA have him right now, looks closer to the other fellow from Cambridgeshire than yourself and your match from Sweden. Still, be interesting to see if he breaks up the block at I-A21901 further and might give us a better idea if Big Y Y700 is much of an improvement on Big Y Y500 compared to you and the other two once he's fully done.
    A week after this post I received an email from my Swedish match saying we now have a second new match at the I-Y98720 level in addition to this February one. So our small tree is growing fast. One of the new matches is going through the process on YFull, which is exciting and we're in contact with each other. I still don't see them on my Big Y matches list however. Is this because they've taken the BY700 test?
    Living DNA's former Cautious mode:
    Wales-related ancestry: 86.8%
    Cornwall: 8%
    North England-related ancestry: 5.2%
    Y line: Peak District, England. Big Y match: Scania, Sweden; TMRCA 1,280 ybp (YFull);
    mtDNA: traces to Glamorgan, Wales
    Mother's Y: traces to Llanvair Discoed, Wales

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  9. #175
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    Quote Originally Posted by JonikW View Post
    A week after this post I received an email from my Swedish match saying we now have a second new match at the I-Y98720 level in addition to this February one. So our small tree is growing fast. One of the new matches is going through the process on YFull, which is exciting and we're in contact with each other. I still don't see them on my Big Y matches list however. Is this because they've taken the BY700 test?
    Good to hear - some nice progress on your little twig on the tree, congrats - I saw this one in the I1-Z140 project.

    Yes, I think you're not seeing him in your Big Y match list because it's a Big Y Y700. From what I've read, FTDNA is currently sticking to their less than 30 non-matching variants threshold. The Big Y Y700 has coverage in regions that the Big Y Y500 doesn't cover, so there will be SNPs in those regions that you won't be able to match just because your test doesn't read those SNPs. Also, not all of his non-matching variants will be downstream of I-Y98720 - some may be upstream but weren't found in FTDNA tests before but they'll count towards the 30 threshold. Until FTDNA adjusts the threshold criteria for the match list to compensate for this (which I'm sure they will, but it may take a while) or adds the upstream SNPs to the correct positions on their haplotree, the matching for Y700 vs. Y500 kits is going to be a bit off kilter.

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  11. #176
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    I noticed recently that the YFull analysis of my FGC YElite BAM have added a new SNP in the "low quality' section of the novel SNP results, named FT35578 which isn't listed on the current YFull tree. My YElite has 16T reads (derived allele, 2A reads (ancestral allele) and 1 DEL, giving a quality score of 82, hence YFull's assignment of low quality.

    Interestingly, this doesn't appear in the results for my YSEQ 30x WGS, but if I look for that position in the BAM file, that shows 9A reads and 13T reads, which is classified as ambiguous at YFull.

    I'd heard that FTDNA were going to assign SNPs discovered in Big Y700 with the FT-prefix (replacing the BY-prefix for Big Y500) - looking up FT35578 at YBrowse, that appears to be the case - reference FTDNA (2019), I-Z2535>I-YSC0000261 https://ybrowse.org/gb2/gbrowse_deta...hrY%3Adatabase. On looking at the FTDNA public Y-DNA haplotree, FTDNA have listed FT35578 as one of the phyloequivalent variants on the I-YSC0000261 branch.

    Anyone else on the I-YSC0000261 or I-L338 branch seeing this SNP in their NGS results? Presumably this isn't a position that is consistently read in Big Y500 (or it would have been on the tree previously), but may show up more in Big Y700, YElite or WGS kits. I'm just curious as to if this is a reliable SNP in other kits on the I-YSC0000261 branch.

    Position for FT35578 is at ChrY position (Hg38):6221755 if anyone wants to check.

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  13. #177
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    Looking at the I1-Z140 group view at YFull, looks like position 6221755 not read in most kits in the group with grey "N". All of the I-Z140 kits on YSC0000261- branches are "A" if there's any reading. Under I-YSC0000261 branch, 48 kits with grey "N", two kits with derived allele T, one "W", two "X" and one "B". Some of these seem to be ambiguous calls - W represents nucleotides A and T, B represents C/G/T (but not A). Seems a bit like an unreliable one to me but only small sample size where this is being read. Perhaps FTDNA's larger database means that they have more kits than give a more conclusive call. I think we'll see a fair bit of this type of thing - newly discovered SNPs with FT prefix not really being SNPs that "novel" and rather fitting in upstream on branches of the tree.

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  15. #178
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    JonikW - there's 3 of these new SNPs with an FT prefix that FTDNA has added to their haplotree a couple of branches above you at I-Y98720:

    FT35577 10093549 G A CEN aka Y168219 registered at YBrowse by YFull
    FT3681 3746430 C T Yp11.2
    FT5175 12013675 T G Yq11.21

    Not sure if any of these are in your Big Y500 results - most likely came out of the recent Big Y700 testers on your branch. Also not sure if all of these are reliable for phylogeny - FT35577 is in the centromere.

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  17. #179
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    Quote Originally Posted by deadly77 View Post
    JonikW - there's 3 of these new SNPs with an FT prefix that FTDNA has added to their haplotree a couple of branches above you at I-Y98720:

    FT35577 10093549 G A CEN aka Y168219 registered at YBrowse by YFull
    FT3681 3746430 C T Yp11.2
    FT5175 12013675 T G Yq11.21

    Not sure if any of these are in your Big Y500 results - most likely came out of the recent Big Y700 testers on your branch. Also not sure if all of these are reliable for phylogeny - FT35577 is in the centromere.
    Thanks again deadly77. One of the people in my group is now looking into this. How do I see the haplotree by the way?
    Living DNA's former Cautious mode:
    Wales-related ancestry: 86.8%
    Cornwall: 8%
    North England-related ancestry: 5.2%
    Y line: Peak District, England. Big Y match: Scania, Sweden; TMRCA 1,280 ybp (YFull);
    mtDNA: traces to Glamorgan, Wales
    Mother's Y: traces to Llanvair Discoed, Wales

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  19. #180
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    Quote Originally Posted by JonikW View Post
    Thanks again deadly77. One of the people in my group is now looking into this. How do I see the haplotree by the way?
    Go to your FTDNA homepage - scroll down to the bottom of the page where is has the category "Partner Applications and Other Tools", click on the button that says "Public Haplotrees" - there's a couple of search bars - in the one that says "Go to Branch Name" type in the branch that you're going to eg. I-Z140, I-L338, I-Y98720. You can expand downstream branches from the branch that you're at by clicking on the "+" button to the left of the branch name. To see phyloequivalent SNPs on a branch, scroll back up to the top left and change "view by countries" to "view by variants". You can also use the public haplotree without logging in: https://www.familytreedna.com/public/y-dna-haplotree/A

    An alternative view is also from your homepage if you look in the Y-DNA section there's a button called "Haplotree and SNPs" - this one will zoom in on your terminal and has the advantage that it's colour coded to shows SNPs in your own results that you're positive (green) and negative (red) for. You can view phyloequivalent SNPs by clicking on the "More..." next to a branch. Advantages and disadvantages to both views - the Haplotree and SNPs view shows your own results on the haplotree, the public haplotree you can see the countries that other people who have tested to that branch level are from so try both.

    For looking up these in your own Big Y results, there's probably a facility to search the BAM viewer by SNP name or position. I have no idea how the Big Y tools are for this, but you can do this at YFull using their tools. The easiest way is to select "Check SNPs" option on the left hand menu of your homepage - just type in the SNP that you're interested in into the box (eg. FT35577) hit "Go" and it will bring up the result. You can click on the magnifying glass to the left of the SNP name and that will bring up more information (position, region, reads, etc.). If it's a SNP that's not listed at YBrowse or at YFull, you can instead go down to "browse raw data" on the left hand menu and type in the position and hit "Go".

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