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Thread: mthap: an mtdna haplogroup analysis tool

  1. #1
    Registered Users
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    Taipei, Taiwan, R.O.C.
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    USA
    Y-DNA (P)
    I1-AS4
    mtDNA (M)
    U5a2a1b

    Taiwan United States of America

    mthap: an mtdna haplogroup analysis tool

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

    We've got updates!

    Data Version 15.0 (2012-09-30) - Data updated to PhyloTree Build 15.
    Here's the details from PhyloTree:

    New in Build 15 (30 Sep 2012)

    Defining mutations updated: A2ad, A2c, A2s, A2t, A2y, A4e, A5b, A5b1, A6, B2i, B4c1, B4c1a, B4d3, B4h, B4i, B5b, B5b1, B5b3, C4a1a, C4a1b, C5b1a1, C5d2, D4b2b, D4b2b2a, D4g2b1, D6, F1a4, F1a4a, F1g, F3b, F3b1, F4a2, G2a, G2a, G2a1d, G2a1e, G3a2, HV4a1a, J1b4, J1c, J1c10, J1c11, J1c2c, J2a1a1c, L0d1b, L0d1b1, L0d2b, L0k, L0k1, L0k2, L1b1a8, L1b1a9, L1c2a1a, L1c2b, L2a1d, L3d2, L3d5, L5a2, M11a, M11a'b, M20, M21c, M28, M28b, M30c1a, M30c1a1, M7b8, M7c, M8a2a, N9a6a, R21, R9b1a, R9b1a2, T1a3, T2, T2a1b2, T2b21, T2b23, T2b23a, T2d, T2f1, T2f1a, T2g1, U2a, U2e3, U5b2c1, U6a1b2, U6a2a, U6a3b, U6a7b, U8a1a3, X2e2, X3a.

    Newly added: A2ad1, A2ad2, A2af, A2af1, A2af1a, A2af1a1, A2af1a2, A2af1b, A2af1b1, A2af1b1a, A2af1b1b, A2af1b2, A2af2, A4e2, A4e3, A4g, A5b1a, A5b1b, A8a, A8a1, B2i1, B4b1a2e, B4b1a3a, B4c1a1, B4c1a1b, B4c1a1c, B4c1a2, B4c1a2a, B4c2b, B4d1a, B4d3a, B4d3a1, B4g1, B4g1a, B4g1b, B4i1, B4j, B5b1a2a, B5b3a, C4a1a1, C4a1b1, C4a1e, C4a4b, D4a1g, D4b2b2a1, D4h3a6, D4j1a2, D4n2, D4o2a, D4t, D5a3a1, D5a3a1a, D5b1c, D6a1a, D6a2, F1a4a1, F1g1, F2b1, F2c1, F2c2, F2e, G2a2, G2a3, G2a4, G2a'c, G2b2c, G2c, G3a2a, H100, H11a2a3, H16d, H1bz, H1j9, H3b5, H5a1q, H5b4, H5e1a1, H5u, H6c1, HV4a1a1, HV4a1a2, HV4a1a3, HV4a1a4, HV4a2b, I5a2, I5a3, I6b, J1b1a1d, J1b1a2, J1b1a2a, J1b1a2b, J1b1b1a, J1b1b1b, J1b1b2, J1b2a, J1b3b, J1b4a, J1b4a1, J1b4a2, J1b5, J1b5a, J1b5b, J1b6, J1b6a, J1b7, J1b8, J1c10a, J1c11a, J1c15, J1c15a, J1c15a1, J1c15b, J1c16, J1c17, J1c1d, J1c1e, J1c1f, J1c1g, J1c2b3, J1c2b4, J1c2c1a, J1c2e1, J1c2e2, J1c2h, J1c2i, J1c2j, J1c2k, J1c2l, J1c2m, J1c2m1, J1c2n, J1c2o, J1c2p, J1c2q, J1c2r, J1c2s, J1c3c2, J1c3h, J1c3i, J1c3j, J1c3k, J1c5e, J1c5f, J1c8a1a, J1c8a2, J1c8b, J1d1a1, J1d1a1a, J1d1b, J1d1b1, J1d2a, J1d3, J1d3a, J1d3b, J1d4, J1d5, J1d6, J1d6a, J2a1a1a3, J2a1a1d, J2a1a1e, J2a1a2a, J2a2a1, J2a2a2, J2a2b1, J2a2b2, J2a2c, J2a2c1, J2a2d, J2b1a2a, J2b1a5, J2b1a6, J2b1c, J2b1c1, J2b1d, J2b1e, J2b1e1, J2b1f, J2b1g, J2b1h, J2b2, K1a11a1, K1a1b1b1, K1a1b1f, K1a1b1g, K1a27, K1a4a1g, L0a2a1b, L0d1b2, L0k1a, L1b1a10, L1b1a10a, L1b1a10b, L1b1a12, L1b1a12a, L1b1a12b, L1b1a13, L1b1a14, L1b1a16, L1b1a17, L1b2a, L1c2a3, L1c2b1b1, L1c5, L2a1c6, L2a1d1, L2a1d2, L2a1g, L2a1l3, L2a1o, L2b1a4, L2b2a, L2b3b, L2c2a1, L3b1a7, L3d1b1a, L3d1b3a, L3d2a, L3d3a1, L3d3a1a, L3d3a1b, L3d3b, L3e1a3a, L3e1d1a, L3e1e1, L3e2b1a2, L3e3b3, L3e4a, L3e4a1, L3e5a, L3f1b1a, L3f1b1a1, L3h1a2a1, M10a1a2, M10a1a2a, M11d, M35b3, M74b2, M8a2a1, M9a4b, N21a, N22a, N9a6b, Q2a1, Q2a2, R11b1, R11b1a, R11b1b, R2a, R2b, R2c, R9b1a2a, S1a, T1a10, T1a11, T1a12, T1a13, T1a1b1, T1a1d, T1a1e, T1a1f, T1a1g, T1a1h, T1a1l, T1a2b, T1a3a, T1a7, T1a8, T1a8a, T1a8b, T1a9, T1b1, T1b2, T1b3, T1b4, T2a1a8, T2a1b1a1b, T2a1b2a, T2a1b2b, T2a2, T2b21a, T2b21b, T2b26, T2b27, T2b28, T2b29, T2b30, T2b31, T2b3a1, T2b4a1, T2b4c, T2b4d, T2b4e, T2b4g, T2b4h, T2b7a3, T2c1a2, T2c1c, T2c1c1, T2c1c2, T2c1d1, T2c1d1a, T2c1d2, T2c1d2a, T2c1f, T2d1, T2d1a, T2d1b, T2d2, T2e2a, T2e6, T2f1a1, T2i, T2i1, T2j1, T2k, T2l, U1a1b, U2a1, U2e3a, U4a2g, U4a2h, U4c2a, U5a1a1e, U5a2a1e, U5b1b1a2, U5b1d1b, U5b1d1c, U5b1d2, U5b1i, U5b2c2a, U5b2c2b, U5b3g, U6a1b2, U6a2a1, U6a3b1, U6a7c, U6b2, U6c1, U6d1b, W1h, X2e2a1, X2e2b, X2l, X2m'n, X2n, X2o, Y1b1, Y1b1a.

    Multiple rearrangements/additions within: B5b2a'b, N1, T2c.

    Relabeled: B4b'd'e->B4b'd'e'j, B4c1a1->B4c1a1a1, B4c1a1a->B4c1a1a1a, B4c1a2->B4c1a1a2, B5b1a->B5b1a1, B5b1a'b->B5b1a, B5b1b->B5b1a2, J1b1a1a<->J1b1a1b, L1b1a8->L1b1a15.

    Removed: G2a1e1, K1a22.

    Acknowledgments: William R. Hurst, Ted Kandell, Nancy Grossman, Miroslava Derenko, Antonio Salas, the EMPOP team.

  2. The Following 10 Users Say Thank You to jlick For This Useful Post:

     apophis99942 (10-11-2012),  Biloo (10-01-2012),  David (10-02-2012),  DMXX (10-02-2012),  kafky (05-19-2015),  Little bit (10-01-2012),  Scarlet Ibis (10-01-2012),  [email protected] (08-24-2016),  thetick (11-13-2012),  zaender (10-01-2012)

  3. #2
    Registered Users
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    60
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    Location
    Montréal, Qc
    Y-DNA (P)
    R1b-L2>FGC14643
    mtDNA (M)
    U5b1b1-T16192C!

    Algeria Ottoman Empire Turkey Canada Canada Quebec
    My father's maternal haplogroup is no longer J1b*, he is now J1b8. His Genbank num is JQ064573

  4. The Following User Says Thank You to Biloo For This Useful Post:

     DMXX (10-02-2012)

  5. #3
    Registered Users
    Posts
    234
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    Ethnicity
    CEU
    mtDNA (M)
    J1c3i

    United States of America
    Wow, I fully expected to have no change but I do!!!! I went from J1c3(AY495214) to J1c3i, and it looks like my 185G is back to being a mismatch. From Frankfurt, Germany. Cross-referencing with my J1c3 thread:
    http://www.anthrogenica.com/showthread.php?281-J1c3

    Mother-in-law and husband remain T2b7a1's, 23andme says they are T2b and T2b4 respectively. From Poland

    My grandfather remains a K1a4a1d, 23andme says K1a4a1. From London, England.
    My Gedmatch kits: M102536 (v3 upgrade); M054852 (v2); A449981 (Ancestry v1)
    Known: 87.5% UK/Ireland American Colonial; 12.5% PA Dutch Mennonites from Germany & Switzerland
    J1c3i mitochondrial ancestress was Swiss Mennonite from Conestoga, Lancaster PA

  6. The Following User Says Thank You to Little bit For This Useful Post:

     DMXX (10-02-2012)

  7. #4
    Administrator
    Posts
    4,721
    Sex
    Y-DNA (P)
    R2a*-M124 (L295-)
    mtDNA (M)
    D4j5*

    I'm quite decisively D4j5 now.

    Code:
    Imperfect Match. Your results contained differences with this haplogroup:
    Matches(28): 263G 489C 750G 1438G 2706G 3010A 4769G 4883T 5178A 7028T 8414T 8701G 9540C 10400T 10873C 11696A 11719A 12705T 13368A 14128G 14668T 14766T 14783C 15043A 15301A 15326G 16223T 16362C
    Extras(0): (16519C)
    No-Calls(1): 10398G
    Untested(4): 73 7445 8860 13086

  8. #5
    Registered Users
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    837
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    Korean & Anglo-American
    Y-DNA (P)
    R1b-U-152
    mtDNA (M)
    B4a
    mtDNA (P)
    H7

    United States of America Sweden South Korea United Kingdom
    Still B4a here.

  9. #6
    Registered Users
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    Imperfect match. Still L3f1b3 although I seem to be carrying four additional mtDNA mutations outside of the benchmark for the group.

  10. #7
    Registered Users
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    Taipei, Taiwan, R.O.C.
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    European
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    USA
    Y-DNA (P)
    I1-AS4
    mtDNA (M)
    U5a2a1b

    Taiwan United States of America
    As you may have heard, 23andMe is rolling out an API for third party applications to be able to directly access genotype data. This will make applications like mthap much easier to use as it will no longer be necessary to manually download and upload your raw data. Instead users will just need to log in to their 23andMe account and grant access to the application. I've applied for API access for mthap and was just given initial approval. During the testing phase I am allowed to test with up to five clients, so I'm now looking for four people who would like to help test the program when it is ready. In particular, I'm looking for those with a 23andMe account who have used mthap before, and preferably have multiple profiles in their account with a variety of haplogroups. If you are interested, please send me email at [email protected] to let me know. It will probably be a while before the application is ready to test as I still need to learn how the authentication and api access works.
    Analyze your mtDNA test results here: Hidden Content

  11. The Following 3 Users Say Thank You to jlick For This Useful Post:

     Scarlet Ibis (10-18-2012),  Spark (10-10-2012),  zaender (10-10-2012)

  12. #8
    Registered Users
    Posts
    167
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    Omitted

    L1c2b1->L1c2b1a

  13. #9
    Registered Users
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    Taipei, Taiwan, R.O.C.
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    European
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    USA
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    I1-AS4
    mtDNA (M)
    U5a2a1b

    Taiwan United States of America
    Anyone here ordered the new Genographic 2.0 test? I'd love to add support to mthap for this, so would appreciate it if an early participant would be willing to contribute a raw data sample to me. I've ordered the test, but they seem to have prioritized shipping to US customers first, so I anticipate that my results will come in at best several weeks after first results start coming in.
    Analyze your mtDNA test results here: Hidden Content

  14. #10
    Senior Member
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    106
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    Cascadia
    Y-DNA (P)
    R-L627 L626+ L625+
    mtDNA (M)
    J1b1a1a (FMS)

    Ireland Scotland England Germany Wales
    Jim, I'll send you a copy of my raw data when available. I had one of the complimentary tests, so my results will be in the initial release of results.

    Regards,
    david
    ( GenBank HQ286325)

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