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Wrong assignment after upgrade Geno 2.0 - mtDNA FGS

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  • Wrong assignment after upgrade Geno 2.0 - mtDNA FGS

    Kit #N126988 was classified as H27 by Geno 2.0.
    However after completing his mtDNA FGS test he was assigned as H2a2a1.
    His results are correctly consistent with H27, however the assignment is very wrong. His matches are also wrong - shows hundreds of matches with 0 difference at HVR1+HVR2+Coding Region, while has only 1 match at HVR1+HVR2.
    I have checked, for example he has 8 differences with a real H2a2a1, while he appears at "Matches" menu with 1 difference. Hope this is not a bug affecting all upgrades from Geno to FGS.

  • #2
    Could it be a Phylotree update issue?

    I know my FMS test here is not assigned all the way as it misses my J1c3i defining mutations, lists them as extras, and just gives me J1c3. J1c3i was added to the Phylotree for build 15, September 2012:
    http://phylotree.org/what_is_new.htm

    I sent a help ticket to FTDNA asking why it was not recognizing my J1c3i mutations and they replied that they know they are behind and are working to correct that. Frankly, I'm not holding my breath but it makes me wonder how many others are not fully assigned based on updates over the last few years?

    Of course, your situation may just be a glitch. Have you run your results through the James Lick mtdna analysis tool and what does it say? Good luck and let us know what happens.

    http://dna.jameslick.com/mthap/

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    • #3
      I think this is not the case. Both James Lick tool and Ian Logan confirmed he is H27 with unknown subbranch.
      It is most obvious this is a bug by his matches.
      He has only 1 HVR1+HVR2 match, however around 100 H2a2a1 matches with 0 differences, which is impossible, theoretically he should have at most one 0 match.
      As I mentioned above I compared with another H2a2a1, who is shown with 1 difference, while he has 8.
      H2a2a1 is usually CRS, while this person has many different mutations.

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      • #4
        Interesting. Hopefully, it will get resolved and I'll be interested in what the problem was, exactly. My FMS test doesn't have any matching irregularities that I am aware of but I am not a Geno upgrade.

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        • #5
          Geno 2.0 recently updated its haplogroup labels to correspond with the latest version of the official mtDNA tree (dated 2014), known as the PhyloTree: Build 16. On the other hand, FTDNA last updated its mtDNA haplogroup labels in 2012, and they correspond with Build 14 of the PhyloTree. So new haplogroups/subclades that were added in Builds 15 and 16 are not reflected in FTDNA's current labeling system. Therefore, not everyone has an up-to-date haplogroup label yet in the FTDNA system. It will be marvelous step forward -- benefiting members and mtDNA projects -- when the update does takes place!

          Editing to add: I cannot say for sure why the poster, above, encountered a discrepancy in label assignment (H27 vs. H2a2a1), but I have seen just one case (out of 750+ members in my project) where unusual nuances of a new subclade motif resulted the outdated labeling system assigning a label of I3a when the updated subclade should be I3d1. Perhaps an H project administrator can look into your situation and see what happened.
          Last edited by Everwaiting; 16 September 2015, 07:00 PM. Reason: Adding P.S.

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          • #6
            P.S. I'd just like to clarify that the labeling issues are temporary, while your test results are solid and permanent. Full mtDNA results enable your subclade to be determined both now and in the future as new branches are discovered.

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            • #7
              Originally posted by eastara View Post
              Kit #N126988 was classified as H27 by Geno 2.0.
              However after completing his mtDNA FGS test he was assigned as H2a2a1.
              His results are correctly consistent with H27, however the assignment is very wrong. His matches are also wrong - shows hundreds of matches with 0 difference at HVR1+HVR2+Coding Region, while has only 1 match at HVR1+HVR2.
              I have checked, for example he has 8 differences with a real H2a2a1, while he appears at "Matches" menu with 1 difference. Hope this is not a bug affecting all upgrades from Geno to FGS.
              It almost sounds as if FTDNA did not plug in your differences from the CRS,leaving you with the CRS haplogroup H2a2a1.

              Comment


              • #8
                I see the same problem for a person who tested the FMS and is in haplogroup U5. The results correctly show all of the U5 specific mutations, but inexplicably the person is assigned to H2a2a1. There appears to be a glitch in the FTDNA haplogroup assignment that affects some people.

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                • #9
                  The kit which was mentioned in the first message is actually mine. I submitted a bug report some time ago but FTDNA hasn't fixed it yet and I continue receiving tens of false matches on daily basis.

                  In the mean time I submitted my sequence to GenBank and it appeared as H27 on both GenBank and Ian Logans website.

                  I am getting tired by all of this. I have had very irritating problems with most of my FTDNA kits and as a result I moved almost all Y-DNA testing to YSEQ - they know how to take care of their customers.

                  At FTDNA, you pay crazy money, wait for months and then you get false results or results which do not display. Then you contact customer support but they ignore your problem for months and you get extremely disappointed. It's like a dejavu - it has happened once again.

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                  • #10
                    Family Tree DNA IT/Engineering is aware of a site bug that is causing many people with both National Geographic transfers and mtDNA full sequence results to be shown as H2a2a1. Our Subject Matter Expert (SME) has reviewed the problem. This is a site bug. Actual DNA test results are fine. It will be fixed ASAP. We apologize for the inconvenience.

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                    • #11
                      Another H2a2a1 result...

                      I see JeremyB acknowledged a problem with this result. I just got my mtFullSequence results back, and was quite surprised that I matched over 400 people at HVR1+HVR2+CodingRegion. Now I understand this is false (which I sort of suspected).

                      JeremyB, 6 days ago you said this would be addressed ASAP. Can you give an estimate in days (or fortnights)?

                      Thank you.

                      Gary

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                      • #12
                        I reported this bug a month ago but they haven't fixed it yet.

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                        • #13
                          The same problem

                          I have the same problem. I am Haplogroup V and have been misplaced in H2a2a1 and it is 3 weeks ago I contacted Customer support. I share trifud's frustration.
                          Last edited by jarlmos; 11 October 2015, 04:27 PM.

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                          • #14
                            Hello,

                            I followed up with the engineering team on this and it is currently one of the highest priority bugs they are working on. While I have no specific time frame for a correction they want to have it fixed very soon. I am sorry for this continued inconvenience.

                            -Darren
                            Family Tree DNA

                            Comment


                            • #15
                              This problem is still occurring. Darren or JeremyB, is there any additional information about when it might be fixed? This is a pretty serious bug, and it's been going on for over a month now.

                              Thank you.

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