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  • Y-DNA Haplogroup Confusion

    I recently transferred my results from the National Geographic Gen 2.0 Test. That test listed my haplogroup as P310.
    It seems strange if I did not have any SNPs downstream of P310. After the transfer it only became more strange, FTDNA has changed my haplogroup to F-M89. If I really am P310, then the FTDNA classification taken from the same test results with a new classification of 'F-M89' doesn't make any sense.
    I have a Y-DNA 37 test in progress. Will this clear up the haplogroup issue?
    It seems I am spending a lot of money and getting very few answers. Any advice or explanations would be greatly appreciated
    Thanks in advance.

  • #2
    Adding the additional markers will not change your Haplogroup.

    When you go to your "Y-DNA Haplogroup & SNP" page there should be a list of your SNP results at the bottom of the page. Is P310 included and if it is, is it + or -?

    On the same page, up at the top right of the Haplotree chart there is a search box. Enter P310 in it and click on "Search". Is P310 found? If so what color is it?

    ISOGG doesn't include P310 in their F Haplogroup list -
    http://isogg.org/tree/ISOGG_HapgrpF.html

    Comment


    • #3
      You are very likely to belong to R1b-P310 or one of its subclades (like R1b-DF27). When your 37 markers arrive, join the R1b Project.

      Comment


      • #4
        Originally posted by MLT View Post
        I recently transferred my results from the National Geographic Gen 2.0 Test. That test listed my haplogroup as P310.
        It seems strange if I did not have any SNPs downstream of P310.
        The reason that you did not have any downstream SNPs is because Geno 2.0 tests a limited number of SNPs. It does not test P312, DF27, and many other SNPs that are included in the R1b - M343&M269 Backbone SNP Pack. It also means that you are negative for Z195 since that SNP is included in the Geno 2.0 test. If you were to get SNP Packs or BigY then you would find your terminal SNP below P310.


        Originally posted by MLT View Post
        After the transfer it only became more strange, FTDNA has changed my haplogroup to F-M89. If I really am P310, then the FTDNA classification taken from the same test results with a new classification of 'F-M89' doesn't make any sense.
        The Geno 2.0 test has a lot of false positives and false negatives which causes FTDNA to get confused and provide the incorrect terminal SNP after the transfer from Geno 2.0. P310 is not one of the false positive or false negative SNPs through Geno 2.0 so you were given the correct terminal SNP at Geno 2.0 and it will show up as positive at the bottom of https://www.familytreedna.com/my/y-dna-haplotree. If you download the Genographic Y-DNA SNPs as a CSV file on your default page after logging in such as seen in the screenshot at http://i.imgur.com/gcRTGZr.jpg then you can see that P312 and DF27 are not in the list and also that you have G for the Z195 allele which means that you are negative for it. If you would have had A you would have been positive. If you upload the file to a file sharing site and send me the link to the file I can run it through a spreadsheet that compares the CSV file with a CSV file from Ybrowse and reports the longhand HG name of each SNP and your positive and negative results along with the source info and which SNPs are false positives. The FTDNA haplotree page only provides the positive results and includes false positives.

        Originally posted by MLT View Post
        I have a Y-DNA 37 test in progress. Will this clear up the haplogroup issue?
        The Y-DNA 37 test does not provide a haplogroup other than a predicted one such as M269. You already know that you are M269 since you are P310 at Geno 2.0. However, it might cause FTDNA to rerun your Geno 2.0 results but that is just a guess. You would have to ask FTDNA that question by creating a ticket. If you have a close match at 37 markers and that person has had advanced SNP testing at FTDNA then there is a possibility but not a guarantee that you belong to the same terminal SNP as that person. Sometimes, but rarely, there are STRs that will put you into a specific subclade after an analysis by a haplogroup admin, not what FTDNA itself assigns, and then you can get an SNP pack that is more appropriate than the general R1b - M343&M269 Backbone SNP Pack and could save you money.

        Originally posted by MLT View Post
        It seems I am spending a lot of money and getting very few answers. Any advice or explanations would be greatly appreciated
        Thanks in advance.
        To begin with Geno 2.0 test was not a good choice for getting the most up-to-date Y-DNA testing.
        Last edited by Armando; 17th December 2016, 05:34 PM.

        Comment


        • #5
          Update

          I ran the raw data received from Gen 2.0 via FTDNA through Whit Athey's halpogroup predictor. The results were 67.4% for R1b. (the next closest was 11%). This should confirm the Gen 2.0 findings of P310+ and M269.
          I have opened a ticket with FTDNA to try and clear up their finding of F-M89 which simply cannot be correct.

          Thanks for all of the help.

          Comment


          • #6
            Originally posted by MLT View Post
            I ran the raw data received from Gen 2.0 via FTDNA through Whit Athey's halpogroup predictor. The results were 67.4% for R1b. (the next closest was 11%). This should confirm the Gen 2.0 findings of P310+ and M269.
            I have opened a ticket with FTDNA to try and clear up their finding of F-M89 which simply cannot be correct.

            Thanks for all of the help.
            Whit Athey's halpogroup predictor is based on STR markers. You already have your STR results?

            F-M89 is definitely not correct. No question.

            Your haplotree page should also show you positive for the following SNPs from the Geno 2.0 test -

            SNP Longhand
            M343 R1b
            CTS2134 R1b1
            YSC0000224 R1b1a
            PF6498 R1b1a1a
            CTS11985 R1b1a1a
            L502 R1b1a1a
            L483 R1b1a1a2
            L762 R1b1a1a2
            CTS3475 R1b1a1a2
            s3 R1b1a1a2
            CTS4608 R1b1a1a2
            PF6265 R1b1a1a2
            YSC0000225 R1b1a1a2
            L23 R1b1a1a2a
            L51 R1b1a1a2a1
            YSC0000191 R1b1a1a2a1a
            P310 R1b1a1a2a1a
            L52 R1b1a1a2a1a
            YSC0000082 R1b1a1a2a1a
            L253 R1b1a1a2a1a2~
            L326 R1b1a1a2a1a2~
            CTS4528 R1b1a1a2a1a3a

            Comment


            • #7
              Originally posted by Armando View Post
              Whit Athey's halpogroup predictor is based on STR markers. You already have your STR results?

              F-M89 is definitely not correct. No question.
              No, I don't have STR results yet. I am quite new at this and appreciate the patience being shown. Just when I thought I had it figured out looks like maybe not. Interesting though that when I entered the positive SNP's from Gen 2.0 into the predictor it did give a full list of probability percentages rather than some kind of error message.
              I will check to see if the SNP's you mentioned show positive.

              Comment


              • #8
                Originally posted by Armando View Post
                L253 R1b1a1a2a1a2~
                L326 R1b1a1a2a1a2~
                CTS4528 R1b1a1a2a1a3a
                I accidentally included these three in my previous post. You will possibly be positive for L253 and L326 only if you belong to a P312 subclade. CTS4528 shouldn't be in your list of positive SNPs although it is possible.

                Comment


                • #9
                  Originally posted by Armando View Post

                  F-M89 is definitely not correct. No question.

                  Your haplotree page should also show you positive for the following SNPs from the Geno 2.0 test -

                  SNP Longhand
                  M343 R1b
                  CTS2134 R1b1
                  YSC0000224 R1b1a
                  PF6498 R1b1a1a
                  CTS11985 R1b1a1a
                  L502 R1b1a1a
                  L483 R1b1a1a2
                  L762 R1b1a1a2
                  CTS3475 R1b1a1a2
                  s3 R1b1a1a2
                  CTS4608 R1b1a1a2
                  PF6265 R1b1a1a2
                  YSC0000225 R1b1a1a2
                  L23 R1b1a1a2a
                  L51 R1b1a1a2a1
                  YSC0000191 R1b1a1a2a1a
                  P310 R1b1a1a2a1a
                  L52 R1b1a1a2a1a
                  YSC0000082 R1b1a1a2a1a
                  L253 R1b1a1a2a1a2~
                  L326 R1b1a1a2a1a2~
                  CTS4528 R1b1a1a2a1a3a

                  Below are the results from your list above.

                  M343 R1b (+)
                  CTS2134 R1b1 (?) Not shown in positive test results
                  YSC0000224 R1b1a (+)
                  PF6498 R1b1a1a (+)
                  CTS11985 R1b1a1a (+)
                  L502 R1b1a1a (+)
                  L483 R1b1a1a2 (+)
                  L762 R1b1a1a2 (+)
                  CTS3475 R1b1a1a2 (+)
                  s3 R1b1a1a2 (+)
                  CTS4608 R1b1a1a2 (?) Not shown in positive test results
                  PF6265 R1b1a1a2 (+)
                  YSC0000225 R1b1a1a2 (+)
                  L23 R1b1a1a2a (+)
                  L51 R1b1a1a2a1 (?) Not shown in positive test results
                  YSC0000191 R1b1a1a2a1a (+)
                  P310 R1b1a1a2a1a (+)
                  L52 R1b1a1a2a1a (+)
                  YSC0000082 R1b1a1a2a1a (+)
                  L253 R1b1a1a2a1a2~ (+)
                  L326 R1b1a1a2a1a2~ Not shown in positive test results
                  CTS4528 R1b1a1a2a1a3a Not shown in positive test result

                  Comment


                  • #10
                    Originally posted by MLT View Post
                    Below are the results from your list above.

                    M343 R1b (+)
                    YSC0000224 R1b1a (+)
                    PF6498 R1b1a1a (+)
                    CTS11985 R1b1a1a (+)
                    L502 R1b1a1a (+)
                    L483 R1b1a1a2 (+)
                    L762 R1b1a1a2 (+)
                    CTS3475 R1b1a1a2 (+)
                    s3 R1b1a1a2 (+)
                    PF6265 R1b1a1a2 (+)
                    YSC0000225 R1b1a1a2 (+)
                    L23 R1b1a1a2a (+)
                    YSC0000191 R1b1a1a2a1a (+)
                    P310 R1b1a1a2a1a (+)
                    L52 R1b1a1a2a1a (+)
                    YSC0000082 R1b1a1a2a1a (+)
                    That's enough to prove without a doubt that you belong to an R1b-P310 subclade because none of those are false positives and you are also positive for SNPs upstream from P310.

                    If you download the CSV file such as seen in the screenshot at http://i.imgur.com/gcRTGZr.jpg then open that file and look for the following SNPs and check the alleles then look up the SNPs and the allele_anc in the CSV file at http://ybrowse.org/gbrowse2/gff/ you will see that you have the ancestral allele for CTS4528, L238, DF19, L21, U152, and U106 meaning that you are negative for those SNPs. That leaves very few branches below P310 that Geno 2.0 didn't test that you could be positive for with DF27 being the largest one out of those. The others are DF99, A9063, and a couple more that can be seen at http://www.ytree.net/ which are also at http://www.ytree.net/DisplayTree.php?blockID=1560 and http://www.ytree.net/DisplayTree.php?blockID=202

                    Comment


                    • #11
                      Originally posted by Armando View Post
                      That's enough to prove without a doubt that you belong to an R1b-P310 subclade because none of those are false positives and you are also positive for SNPs upstream from P310.
                      Thanks for the confirmation. Now I have to wonder if anyone from FTDNA will ever respond to the ticket I opened.
                      Would be nice to get the F-M89 result corrected.

                      Thanks again for all of the help and leading me to a better understanding.

                      Comment


                      • #12
                        Hello MLT,

                        Can you please send me a private message with your kit number and a contact email address? I will try and get the ticket addressed.

                        -Darren
                        Family Tree DNA

                        Comment


                        • #13
                          Originally posted by Darren View Post
                          Hello MLT,

                          Can you please send me a private message with your kit number and a contact email address? I will try and get the ticket addressed.

                          -Darren
                          Family Tree DNA
                          That would be much appreciated Darren.
                          PM sent with requested info.

                          Comment


                          • #14
                            Ok, I have an update. The F-M89 determination which was obviously not correct was updated by FTDNA. A few days ago after my Y-STP tests came back and co-mingled (I guess), with My Geno 2.0 SNP's they changed me to Haplogroup M-269 which made sense.
                            I log in today and it now read Haplogroup R-FGC11678

                            Could someone help me understand what that means and why it keeps changing?

                            Comment


                            • #15
                              Originally posted by MLT View Post
                              Ok, I have an update. The F-M89 determination which was obviously not correct was updated by FTDNA. A few days ago after my Y-STP tests came back and co-mingled (I guess), with My Geno 2.0 SNP's they changed me to Haplogroup M-269 which made sense.
                              I log in today and it now read Haplogroup R-FGC11678

                              Could someone help me understand what that means and why it keeps changing?
                              FTDNA is very good at accurate testing, but they do have problems with their haplotree. My understanding is that it's not uncommon for someone who's R1b and transfers their Geno 2.0 results into an FTDNA account to end up with the obviously wrong haplogroup of F-M89. I don't know what the discrepancy is between Geno 2.0's tree and that of FTDNA that causes this.

                              Once you received your STR results, FTDNA was able to make a prediction of R-M269. Haplogroup predictions for those without SNP tests at FTDNA (yours are from Geno 2.0) are made based on ths STR results.

                              Now, it seems that after further analysis of your Geno 2.0 SNP results (maybe in light of their prediction of R-M269), they've determined that your confirmed haplogroup is R-FGC11678. So, it must be that your Geno 2.0 results have you as FGC11678+.

                              You've correctly noted in another thread that FGC11678 is a subclade of U106. More specifically, based on consulting the U106 Project tree, it's a subclade of Z156, a major branch of U106. Please join the R1b-U106 Project at https://www.familytreedna.com/groups/u106/about. We have over 800 Big Y results of project members (about 25% of the total membership) and use a comparison spreadsheet to continually find new subclades. We may be able to place you in a more downstream subclade - FGC11678 has two known subclades (FGC14326 and A5396) - which may not be tested by Geno 2.0.

                              Comment

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