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Thread: MDLP K10 Ancient_Roots (beta)

  1. #1
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    MDLP K10 Ancient_Roots (beta)

    I am staring a new thread dedicated to the discussion of my new MDLP K10 beta (bundled with the Oracle of ancient samples).

    I'll explain the technical details of this calculator later, when i'll have more free time.

    //todo

    https://drive.google.com/file/d/0B6n...ew?usp=sharing

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  3. #2
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    Thanks for your efforts. I tried running it, but gotthe following error message:

    10 ancestral populations
    91042 total SNPs
    At line 113 of file DIYDodecad.f90 file: "k-10.txt"
    Traceback: not available, compile with -ftrace=frame or -ftrace=full
    Fortran runtime error: Das System kann die angegebene Datei nicht finden.

  4. #3
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    H5a1

    Normandie Orkney Netherlands Friesland East Frisia Finland
    Yeeah, I'm the first one! Thanks for all Vadim
    23.87% ENF
    15.03% MHG
    27.21% OOA-Basal
    3.27% East-Eurasian
    3.40% Amerindian
    0.55% Archaic-Man
    1.82% African
    1.08% Oceanian
    0.99% ASA
    22.78% ANE

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  6. #4
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    Normandie Orkney Netherlands Friesland East Frisia Finland
    forgot he Oracles:
    > ModOracle(c(23.87,15.03,27.21,3.27,3.4,0.55,1.82,1 .08,0.99,22.78))
    [,1] [,2]
    [1,] "Nordic-IA" "9.7913"
    [2,] "Sintashta" "13.6392"
    [3,] "Karsdorf_LN" "15.0629"
    [4,] "Esperstedt_MN" "15.4228"
    [5,] "Hungary-Vatya" "15.8777"
    [6,] "Andronovo" "17.8129"
    [7,] "HungaryGamba_IA" "18.672"
    [8,] "Baalberge_MN" "19.1173"
    [9,] "Bell_Beaker_LN" "19.4307"
    [10,] "Spain_MN" "22.7267"
    [11,] "EuropeanIronAge" "23.0734"
    [12,] "SwedenSkoglund_MN_lessThan20K" "23.3607"
    > ModOracle(c(23.87,15.03,27.21,3.27,3.4,0.55,1.82,1 .08,0.99,22.78),mixedmode=T)
    [,1] [,2]
    [1,] "21% Basal_Eurasian + 79% Nordic-IA" "3.0466"
    [2,] "67.6% Karsdorf_LN + 32.4% LBK_EN" "3.3678"
    [3,] "55.7% HungaryGamba_IA + 44.3% SwedenSkoglund_MN_lessThan20K" "3.3689"
    [4,] "56.6% Andronovo + 43.4% EuropeanIronAge" "3.4166"
    [5,] "22.1% HungaryGamba_EN + 77.9% Karsdorf_LN" "3.4342"
    [6,] "36.6% EuropeanIronAge + 63.4% Sintashta" "3.4419"
    [7,] "58.2% EuropeanIronAge + 41.8% Russia-Yamnaya" "3.5881"
    [8,] "28.4% EuropeanIronAge + 71.6% Nordic-IA" "3.7839"
    [9,] "27.3% Basal_Eurasian + 72.7% Sintashta" "3.7908"
    [10,] "54.4% Bell_Beaker_LN + 45.6% EuropeanIronAge" "3.8"
    [11,] "79.7% Karsdorf_LN + 20.3% Spain_EN" "3.8916"
    [12,] "71% Karsdorf_LN + 29% Starcevo_EN" "3.9838"
    >
    Last edited by anglesqueville; 06-25-2015 at 01:45 PM.

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  8. #5
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    Change the file name to "k10.txt"

  9. #6
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    Quote Originally Posted by Vadim Verenich View Post
    Change the file name to "k10.txt"
    The name of which file? There is already a k10.txt.

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  11. #7
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    In k10.par

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  13. #8
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    Quote Originally Posted by Vadim Verenich View Post
    In k10.par
    I see, there were hyphens that I had to delete. "k10" instead of "k-10" in the par file.

  14. #9
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    mtDNA (M)
    U4c1a

    France France Bretagne
    Mine:
    10 ancestral populations
    91042 total SNPs
    0 flipped SNPs
    26785 heterozygous SNPs
    1362 no-calls
    258 absent SNPs
    0.982206 genotype rate
    mode genomewide

    1620 SNPs missing (no-call or absent)

    Code:
    22.99%  ENF                 
     14.60%  MHG                 
     28.45%  OOA-Basal           
      2.27%  East-Eurasian       
      2.79%  Amerindian          
      0.18%  Archaic-Man         
      1.66%  African             
      1.77%  Oceanian            
      1.37%  ASA                 
     23.92%  ANE    
    
          [,1]                            [,2]     
     [1,] "Nordic-IA"                     "10.4394"
     [2,] "Sintashta"                     "14.3835"
     [3,] "Karsdorf_LN"                   "14.4766"
     [4,] "Esperstedt_MN"                 "16.7634"
     [5,] "Hungary-Vatya"                 "17.1885"
     [6,] "HungaryGamba_IA"               "18.0747"
     [7,] "Andronovo"                     "18.5651"
     [8,] "Bell_Beaker_LN"                "19.598" 
     [9,] "Baalberge_MN"                  "19.9805"
    [10,] "EuropeanIronAge"               "22.7845"
    [11,] "Spain_MN"                      "24.268" 
    [12,] "SwedenSkoglund_MN_lessThan20K" "24.3587"
    [13,] "BenzigerodeHeimburg_LN"        "24.3791"
    [14,] "Nordic-BattleAxe"              "24.5411"
    [15,] "AG2"                           "27.5765"
    [16,] "Stuttgart"                     "27.7895"
    [17,] "HungaryGamba_BA"               "29.0154"
    [18,] "Bell_Beaker_Nordic"            "30.0006"
    [19,] "Unetice_Poland"                "30.6416"
    [20,] "LBK_EN"                        "31.9071"
    
         [,1]                                                          [,2]    
     [1,] "23.1% Basal_Eurasian + 76.9% Nordic-IA"                      "2.1185"
     [2,] "15.5% Near_East + 84.5% Sintashta"                           "2.9357"
     [3,] "29.2% Basal_Eurasian + 70.8% Sintashta"                      "3.1768"
     [4,] "11.4% Near_East + 88.6% Nordic-IA"                           "3.3574"
     [5,] "53.9% Bell_Beaker_LN + 46.1% EuropeanIronAge"                "3.4497"
     [6,] "65.1% Andronovo + 34.9% Basal_Eurasian"                      "3.5646"
     [7,] "80.8% Andronovo + 19.2% Near_East"                           "3.7181"
     [8,] "58.8% EuropeanIronAge + 41.2% Russia-Yamnaya"                "3.7248"
     [9,] "51.9% EuropeanIronAge + 48.1% Nordic-BattleAxe"              "3.817" 
    [10,] "71.4% Baalberge_MN + 28.6% Corded_Ware_LN"                   "3.9439"
    [11,] "75.2% Baalberge_MN + 24.8% Yamnaya"                          "4.022" 
    [12,] "66.5% Karsdorf_LN + 33.5% Stuttgart"                         "4.3743"
    [13,] "57.7% HungaryGamba_IA + 42.3% SwedenSkoglund_MN_lessThan20K" "4.4158"
    [14,] "69.6% Karsdorf_LN + 30.4% LBK_EN"                            "4.4456"
    [15,] "29.7% EuropeanIronAge + 70.3% Nordic-IA"                     "4.4463"
    [16,] "62.6% EuropeanIronAge + 37.4% Nordic-LN"                     "4.4648"
    [17,] "72.5% Karsdorf_LN + 27.5% Starcevo_EN"                       "4.4694"
    [18,] "38% EuropeanIronAge + 62% Sintashta"                         "4.4699"
    [19,] "55.4% Andronovo + 44.6% EuropeanIronAge"                     "4.6006"
    [20,] "48.2% BenzigerodeHeimburg_LN + 51.8% EuropeanIronAge"        "4.7358"
    Y haplogroup: R1b: L21 --> DF13 --> BY145002
    The oldest L21 known are I2457 et I2565 from Stonehenge (Beaker Culture, 2400-1900 BC)

    MTDNA: U4c1
    The oldest U4c1 known are "poz224", Yamnaya culture (2882-2698 BC), and 2 Bell-Beaker in Germany (Karsdorf, 2314-2042 BC)

    Paternal MTDNA: K1b2b
    The oldest K1b2 are Eastern European Mesolithic: Kunda Donkalnis5 (Lithuania), 6000 BC and Meso-Ene Lepenski Vir Lepe28 in Serbia, 5900 BC.
    The oldest K1b2b is Alt-3, Corded-Ware Germany (2500 BC)

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  16. #10
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    Y-DNA (P)
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    Philippines
    Admixture Proportions:

    1.79% ENF
    0.47% MHG
    4.39% OOA-Basal
    68.74% East-Eurasian
    4.28% Amerindian
    0.33% Archaic-Man
    1.21% African
    14.27% Oceanian
    2.54% ASA
    1.98% ANE

    Single Population:

    [1,] "Botocudo" "33.541"
    [2,] "East-Eurasian" "35.1252"
    [3,] "Karasuk" "50.2773"
    [4,] "Ust_Ishim" "51.0688"
    [5,] "Aleutian" "60.5299"
    [6,] "AusAboriginal" "66.7964"
    [7,] "AG2" "74.1455"
    [8,] "Karsdorf_LN" "75.9847"
    [9,] "HungaryGamba_IA" "77.1653"
    [10,] "LateDorset" "78.6057"
    [11,] "Andronovo" "80.3747"
    [12,] "Nordic-IA" "80.7947"
    [13,] "Sintashta" "81.0087"
    [14,] "Esperstedt_MN" "81.4519"
    [15,] "Spain_MN" "82.1617"
    [16,] "Bell_Beaker_LN" "82.4573"
    [17,] "Baalberge_MN" "82.6107"
    [18,] "EuropeanIronAge" "83.1613"
    [19,] "Hungary-Vatya" "83.8531"
    [20,] "Greenland" "84.0403"

    Mixed Mode:

    [1,] "34.2% AusAboriginal + 65.8% East-Eurasian" "6.0118"
    [2,] "59.7% East-Eurasian + 40.3% Ust_Ishim" "8.836"
    [3,] "51.4% Botocudo + 48.6% East-Eurasian" "13.8893"
    [4,] "22.8% Papuan + 77.2% East-Eurasian" "14.046"
    [5,] "30.1% AG2 + 69.9% East-Eurasian" "16.1137"
    [6,] "39.6% Karasuk + 60.4% East-Eurasian" "16.1984"
    [7,] "29.3% Karsdorf_LN + 70.7% East-Eurasian" "17.0499"
    [8,] "34.5% Aleutian + 65.5% East-Eurasian" "17.1797"
    [9,] "72.2% East-Eurasian + 27.8% Nordic-IA" "17.6084"
    [10,] "27.6% Esperstedt_MN + 72.4% East-Eurasian" "17.9014"
    [11,] "73.2% East-Eurasian + 26.8% SwedenSkoglund_MN_lessThan20K" "18.0852"
    [12,] "72.4% East-Eurasian + 27.6% Sintashta" "18.1528"
    [13,] "27.7% Andronovo + 72.3% East-Eurasian" "18.2509"
    [14,] "27.1% Baalberge_MN + 72.9% East-Eurasian" "18.28"
    [15,] "28.6% HungaryGamba_IA + 71.4% East-Eurasian" "18.3243"
    [16,] "26.7% Hungary-Vatya + 73.3% East-Eurasian" "18.5349"
    [17,] "27.1% Bell_Beaker_LN + 72.9% East-Eurasian" "18.5841"
    [18,] "72.9% East-Eurasian + 27.1% Spain_MN" "18.7171"
    [19,] "26.8% EuropeanIronAge + 73.2% East-Eurasian" "18.7507"
    [20,] "26.5% BenzigerodeHeimburg_LN + 73.5% East-Eurasian" "18.9357"

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