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Thread: Y500 results from FTDNA are getting ready to be released

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    Y500 results from FTDNA are getting ready to be released

    If you are a haplogroup admin, you will now see dozens of pending Y500 results and in our case, we now have two testers with received results for Y500. I believe that Y500 will only be released in VCF files since the number of YSTRs would increase YSTR content by 4.5X. The results were not found in the YSTR report or in the YSTR Results screen as well. None of the Big Y Results pages have any data as well. In order to get the VCF files, you need to request these files for each Big Y tester (or find them in the Data Warehouse - if uploaded yet). If anyone has looked a Y500 results, please post.

    However, Y500 will be a long term investment and will not yield too much branching information since the data is very limited compared to 67 and 111 marker testers. For R-L226, we have 675 testers now at 67 markers or more. Only 275 are 111 markers and around 105 have completed the Big Y testing. When adding 111 markers to the 67 only R-L226 marker chart, it did add around 10 to 15 % more YSTR branching and over time, this will help more as the number 111 marker testers increase. Y500 should add another five to ten percent YSTR branches - even with 105 Big Y testers. Also, since we do not know the mutation rates of these markers, it will interesting to see how Y500 adds to charting testers (hopefully no more CDY type markers get added).

    I did complete a preliminary analysis of twenty NGS testers that submitted their data to YFULL with their Y500 - it will be interesting to see how many common markers are found between these two organizations. From my YFULL review, it is pretty easy to tell very slow marker from faster mutating markers. Using my L226 chart and 100 Big Y Y500 testers, I should be able to extract very approximate mutation rates. Unfortunately, only around 200 YSTRS have published mutation rates (Burgarella, Ballantine and Heinilla have 95 % of the 200 YSTRs) - but their mutation rates vary widely.
    Last edited by RobertCasey; 04-15-2018 at 12:07 AM.

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    Quote Originally Posted by RobertCasey View Post
    If you are a haplogroup admin, you will now see dozens of pending Y500 results and in our case, we now have two testers with received results for Y500. I believe that Y500 will only be released in VCF files since the number of YSTRs would increase YSTR content by 4.5X. The results were not found in the YSTR report or in the YSTR Results screen as well. None of the Big Y Results pages have any data as well. In order to get the VCF files, you need to request these files for each Big Y tester (or find them in the Data Warehouse - if uploaded yet). If anyone has looked a Y500 results, please post.

    However, Y500 will be a long term investment and will not yield too much branching information since the data is very limited compared to 67 and 111 marker testers. For R-L226, we have 675 testers now at 67 markers or more. Only 275 are 111 markers and around 105 have completed the Big Y testing. When adding 111 markers to the 67 only R-L226 marker chart, it did add around 10 to 15 % more YSTR branching and over time, this will help more as the number 111 marker testers increase. Y500 should add another five to ten percent YSTR branches - even with 105 Big Y testers. Also, since we do not know the mutation rates of these markers, it will interesting to see how Y500 adds to charting testers (hopefully no more CDY type markers get added).

    I did complete a preliminary analysis of twenty NGS testers that submitted their data to YFULL with their Y500 - it will be interesting to see how many common markers are found between these two organizations. From my YFULL review, it is pretty easy to tell very slow marker from faster mutating markers. Using my L226 chart and 100 Big Y Y500 testers, I should be able to extract very approximate mutation rates. Unfortunately, only around 200 YSTRS have published mutation rates (Burgarella, Ballantine and Heinilla have 95 % of the 200 YSTRs) - but their mutation rates vary widely.
    http://thednageek.com/whats-coming-d...mily-tree-dna/

    European = 99.2%............Central Asian = 0.8% .............Yfull - 1460BC
    Father's Mtdna .......T2b17
    Grandfather mtdna .......T1a1e
    Sons Mtdna .....K1a4
    Grandfather-Maternal ......I1d-P109...CTS6009
    Wife's Ydna .....R1a-Z282

    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS54+, CTS8862+, Z19945+, Y70078+ )

    The main negatives = ( M193-, P322-, P327-, Pages11- , L25- , CTS1848- )

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    Quote Originally Posted by RobertCasey View Post
    If you are a haplogroup admin
    But not surname projects or other Y-DNA projects?

    Quote Originally Posted by RobertCasey View Post
    we now have two testers with received results for Y500

    Quote Originally Posted by RobertCasey View Post
    I did complete a preliminary analysis of twenty NGS testers that submitted their data to YFULL with their Y500
    This has me confused. You have two or twenty?

    Do you have a sense of where the results will be on the end-user side? Any chance you can screenshot what it looks like?

    This is exciting news!

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    Any project is treated the same (surname, haplogroup, geographic, etc.). I was just trying to give examples of haplogroup admins
    which use Admin Tools much more in general due to its much larger scope.

    We have two testers that show received Y500 results from Big Y results. We have twenty L226 testers that already have around 500
    YSTRs from YFULL analysis. Two different sources for YSTR500 information.

    I do not normally look at VCF files as another admin analyzes NGS files for our project. If this is the only source, he may want
    me to extract the Y500 from the VCF files since I do a lot of YSTR analysis. To date, I have not seen any Y500 information in
    Admin Tools - but Big Y information is slowly loaded incrementally over time and Y500 may show up somewhere in the future.

    This may be an issue as access to Data Warehouse is very limited to a few select people. If Y500 is only found in the VCF
    files, much broader access will be needed or Big Tree could start posting Y500 data as well. For those already using YFULL
    for Y500 data, they will now have two sources. I am sure that FTDNA and YFULL will be 80 to 90 % the same - but you know
    that there will some major differences to work out.

    We also have to work out the mutation rates and may have to filter out some of the faster mutating markers like CDY and 710. The more markers that we have require one of two actions: 1) the 4.5X increase will require at least 4.5X more YDNA testers, so it will be a long time before our sample sizes can extract much information; 2) another alternative is to filter five or ten percent of the faster mutating markers to get around the insufficient sample size.
    Last edited by RobertCasey; 04-15-2018 at 06:15 PM.

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    I appear to have "Awaiting Results" for Y500. Is this an automatic upgrade associated with having ordered Big Y (and at the time of my order promotional Y111 combined)?

    Anyway it should be interesting to see how this pans out.
    Y-DNA: I-A14097 [Big Y: Complete] downstream of A13241 (Scotland)
    mtDNA: pending (Westeremden, Netherlands)
    Other lines:
    R-M222 x2 (Ireland), R-L21 x2 (Ireland & Scotland), I-M223 (Ireland), R-S1141 (Scotland), R-U198 & R-U106 (Netherlands), mtHg J1c3 (Ireland)
    Known ancestry
    Paternal: Britain & Ireland, France and Germany
    Maternal: Netherlands

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    I see. Everyone who has ordered Big Y has Y500 showing a pending lab procedure. None are completed yet. Interested to see what this looks like.

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    Robert, do you have the list of which STRs make up the 500 from your two testers who have completed the procedure? Are they all now included in their STR reports? I have 16 Big Ys in my surname project but none of them have completed it yet. I assume it's the original 111 plus 389 of the better-quality calls from the Big Ys but I haven't seen which ones those are yet.

    Quote Originally Posted by RobertCasey View Post
    I did complete a preliminary analysis of twenty NGS testers that submitted their data to YFULL with their Y500 - it will be interesting to see how many common markers are found between these two organizations. From my YFULL review, it is pretty easy to tell very slow marker from faster mutating markers. Using my L226 chart and 100 Big Y Y500 testers, I should be able to extract very approximate mutation rates. Unfortunately, only around 200 YSTRS have published mutation rates (Burgarella, Ballantine and Heinilla have 95 % of the 200 YSTRs) - but their mutation rates vary widely.
    Agree and we probably should solicit volunteer data from YFull groups to calculate mutation rates for the ones that aren't in published studies. The rates themselves SHOULD be consistent across haplogroups, but having a variety of sources especially over longer time periods will help reliability.

    I can use SAPP to generate the effective mutation rates for any group so that might be the easiest way to automate the calculation. As you said the easier question is to sort the mutations by faster and slower markers, although getting reasonably accurate rates would be important for finer branching choices and certainly for TMRCA estimation.

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    The L226 project now has two entries in our "Received Results" for two Y500 results. But Dennis Wright and myself do not see any evidence of these results being posted to date. I have looked at all the screens/reports under my Admin Tools and did not find anything to date. I sent an email to one of these testers to send me a link to the VCF files and I am awaiting a response.

    I already created a list of the Y500 from YFULL for 20 L226 testers (and this could be pulled for a larger scope). Even with only 20 testers, empirically it is pretty easy to separate slow, medium and faster mutating markers. Slow - no mutations or just one/two; Medium - many with the same value but several with other values; Fast - Many values across just 20 samples.

    I also agree that we can come up with approximate mutation rates via charting. But we need to wait until we get most of the results back for the 100 Big Y testers under L226. Even under L226, many of the faster mutating markers have 30 or 40 parallel mutations. So without charting, mutation rates would be missing 70 to 90 % of the mutations. I was thinking of expanding the scope to a higher level than L226 but charting can not be done on older YSNPs primarily due to hidden mutations (dependent events). The YFULL sample size of 20 is just too small though. I am now up to 86 % coverage of charting due to some targeted YSNP testing over the last few months. We should also do 67 and 111 markers as well to see how well charting matches published academic mutation rates - which vary wildly.

    We now have over 660 testers at 67 marker, 275 at 111 markers and 105 NGS testers. We also now have 77 branches and over 100 L226 SNP pack results. I now have three parts of my chart: 1) those that can be charted with 60 % or higher accuracy; 2) those that are not charted due to no YSNP testing but clearly share a signature (not sure if we should use these); 3) a couple of pages of those that have not YSNP tested and do not match signatures of other testers (doubtful we should use these outliers - now only 42 in this category).
    Last edited by RobertCasey; 04-16-2018 at 03:47 PM.

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    This is new to me. I wonder if the mention of Y500 and perhaps 500 STR's is FTDNA catching up with YFull's STR analysis?

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    Quote Originally Posted by gstockman View Post
    This is new to me. I wonder if the mention of Y500 and perhaps 500 STR's is FTDNA catching up with YFull's STR analysis?
    No. The data is was always there. The issues include establishing which ones should be reported and how the results can be used. FTDNA now has a sufficiently large group of BigY results which will allow for them to provide a set of CONSISTENT calls for the STRs they are reporting. It is safe to assume that YFull and FTDNA will differ on which STRs are reported and how some of the values are reported.

    From FTDNA's perspective getting this data out there in a consistent and stable way provides a way of rebranding and refocusing the BigY test so that more individuals will jump in and order multiple kits for genealogical time frame purposes. The haplogroup projects and tree structure definition and age estimation efforts will get a boost due to the increase in orders for the genealogical time frame use.

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