MDLP K10 Ancient_Roots (beta)

[Vadim Verenich]

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

[Sangarius]

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.

[anglesqueville]

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

[anglesqueville]

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"
>

[Vadim Verenich]

Change the file name to "k10.txt"

[Sangarius]

Change the file name to "k10.txt"

The name of which file? There is already a k10.txt.

[Vadim Verenich]

In k10.par

[Sangarius]

In k10.par

I see, there were hyphens that I had to delete. "k10" instead of "k-10" in the par file.

[Tolan]

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)

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"

[shazou]

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"