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  • mtFull, not so Full

    I'm somewhat dismayed at my mtFull results.

    I had previously done the mtPlus and was determined to be in the H haplogroup. So I decided to do mtFull to drill down into the sub-groups because there has been so much research work done on tracing sub-groups since that first one way back in 2007.

    Now I receive a result of...........H (again). Okay so maybe I am a basal H, right? Well, not quite.

    I went to the jameslick.com mtDNA interpreter and find out that I am also possibly H24, H82, H39, H83, H(16291T), H(16291A), H20, H20a, or H22. The mtFull test simply doesn't test the markers above 16000 (which are the ones that would define one of these alternative haplogroups)! That's just great. Thanks FTDNA.

    I did this test thinking I was going to get to the bottom of the known haplogroup science. Now it appears FTDNA is not up to date on all the markers.

    So my questions are: 1) should I accept this as a "full" mtDNA test? 2) Should FTDNA do enough testing to rule out all of these alternatives? 3) am I misinterpreting the situation?

    Thanks for your guidance.

  • #2
    mtdna full sequence tests the full mtdna genome.

    My Understanding

    Based on your known mutations, currently they can not give you anything other then H as none of your mutations match up with current known subclades of H.
    As time goes by and mtDNA tree revised new subclade branches will be defined and when that happens your haplogroup will be assigned it correct subclade placement.

    As it stands at the moment, based on current mtdna tree, your subclade branch can not be defined passed the Basal H.

    James Lick tool is only giving you best fits, but none of them seem to match up perfectly to currently known subclade branches. The ones you list above most likely list SNP mismatches in each (listed in red)

    New branches are defined as more and more people test and share the same mutations

    You should join the following projects and talk with the admins, they can probably answer your questions

    H and HV mtDNA Hg Project
    https://www.familytreedna.com/my/gro...urURSi0Q%3d%3d

    H Subclade Discovery Project
    https://www.familytreedna.com/my/gro...urURSi0Q%3d%3d
    Last edited by prairielad; 13th March 2019, 11:28 PM.

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    • #3
      @Adam, although an error by FTDNA cannot be excluded, I am afraid that you are misinterpreting your results. Region 16001-16569 is always included starting with the now discontinued basic mtDNA test. When you had taken mtDNAPlus, regions 1-574 and 16001-16569 were tested.

      Did you download the FASTA file of your mtDNAPlus? I hope yes.

      (You can add .txt extension to the FASTA file for easy viewing.)

      Please download the FASTA file of your mtDNA Full test results and compare to the old one. Are the last characters the same? Does your new FASTA file have 209 lines and 11 characters in the last line?


      Mr. W.

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      • #4
        Thanks for the feedback prairielad and dna. I did not d/l my mtDNAPlus FASTA, but I am able to look at the fullMTDNA CR Reference Sequence results in my mtDNA pages. What I see there is a list from 575 to 16000 showing a letter result at each number (i.e., 16000>>G). The jameslick results are telling me that my hg could be, for example, H82, but since jameslick doesn't see the result for position 16220 (as T) then it cannot confirm H82. This is the same situation with the other groups mentioned: jameslick doesn't see 16291, 16129, 16212, 16218, 16299, 16293, 16218, 16328, 16145, 16227 in the data. So either the data are there but jameslick isn't finding, or the data are not there. Since I do not see these numbers in the mtDNA list of CR Ref results, I presume the data are not there, but I would be happy to be shown otherwise. Here is what the jameslick program reports about the FASTA file: "FASTA format was uploaded. Based on the markers found, assuming the following regions were completely sequenced: HVR2 (1~574) CR (575~16000). Found 16000 markers at 16000 positions covering 96.6% of mtDNA." When I look at my FASTA file I see an unbroken base string (i.e. ATGTTACTCCA...) Is there a way to convert the FASTA into a properly numbered series of bases?

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        • #5
          Epilogue: I was able to get to the root of this issue: the 16001 to 16569 results do not appear in the CR Ref Results after 16000 (where I was looking), but are in the HVR1 results. The confusion was aggravated by the jameslick utility which doesn't apparently read the FASTA results from 16001 to 16569 and interprets this region as being 'untested' even though the results are there in the FASTA file. Thanks again for the feedback and helping me work through these glitches.
          Last edited by Adam; 17th March 2019, 11:36 AM.

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          • #6
            Originally posted by Adam View Post
            ..........

            When I look at my FASTA file I see an unbroken base string (i.e. ATGTTACTCCA...) Is there a way to convert the FASTA into a properly numbered series of bases?
            On your rCRS results page, under each category, click on Show All positions.
            Last edited by prairielad; 17th March 2019, 05:25 PM.

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