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Thread: New Calculators (k71 & k54) for Europeans essentially

  1. #1
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    New Calculators (k71 & k54) for Europeans essentially

    Based on the Recent Ancestors2 calculator, I created, in all, 54 European components.
    I made two versions: a k71 world, with this 54 European components, plus the 17 non-European components of Recent Ancestors2.
    And another by taking only the 54 European components.
    Why this last calculator, the k54-Europe?
    In front of such a number of components, the results become hyper-sensitive!
    For some, it seems to work well, if you are very close to one of the components, for other, results gives something broke.
    And for these, they may have non-European components, such as Caucasian or Indian.
    They are relics of ancient times and unrelated to recent ancestors. It is for this reason that it is wiser to do this test for 100% Europeans.
    In addition, it creates a coherent central point.
    Both calculators are in the same folder:
    https://drive.google.com/open?id=1cb...cuY-0en1CTFgny


    In relation to these two calculators, I realized two small programs to visualize the results. Because a k71 is a bit messy!
    These two programs will work with your result files: the genomewide file for the k71, and bychr file for K54.
    If you want to be on these pages, you must to make a "genomewide" for k71 (compatible for everyone, but more informative for Europeans)
    and a "bychr" for k54 (compatible only for 100% European). And copy them here.

    Exemple:
    http://gen3553.pagesperso-orange.fr/ADN/pre/k71.htm
    with central point in green

    http://gen3553.pagesperso-orange.fr/ADN/pre/bychr.htm
    The results by chromosome are too exploded because of too little snps tested. So on this page, only the center point for each of your chromosomes is reported.
    The size of the red circle is based on the number of snps tested.

    I put on these pages the results of some of which I have the file, but also some ancients genomes in comparisons.
    Obviously, this is just for fun, because it is difficult to establish a position of an ancient genome on a map of modern populations!

    PS: you can run both calculators at the same time by opening two windows of R, each with a different command: k71a.par which creates genomewide.txt and k54a.par which create bychr.txt
    Last edited by Tolan; 04-22-2019 at 04:13 PM.
    27 avril 2019!
    Hidden Content

    Y haplogroup: R1b: L21+ DF13+ (L1335- DF21- DF49- FGC11134- L513- Z251- Z253- CTS1751- CTS3386- DF41- FGC5496- L371- MC14- S1026- S1051- S16264- Z16500- Z16502- Z255-)
    For my autosomal analyses, see Hidden Content

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  3. #2
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    Looks interesting @Tolan

    Can someone run for me?

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    So i have the bychr file and the genotype file. what do i do with them?
    distance%=4.6465"
    Barcin_N,47.2
    Yamnaya_Samara,41.4
    WHG,10.6
    Ethiopia_4500BP,0.8


    E-V13 => E-PH1246 => E-BY14160
    Antonio Reale born circa 1710, Ciminà Italy

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  7. #4
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    Quote Originally Posted by digital_noise View Post
    So i have the bychr file and the genotype file. what do i do with them?
    You open them and copy them in your message.
    27 avril 2019!
    Hidden Content

    Y haplogroup: R1b: L21+ DF13+ (L1335- DF21- DF49- FGC11134- L513- Z251- Z253- CTS1751- CTS3386- DF41- FGC5496- L371- MC14- S1026- S1051- S16264- Z16500- Z16502- Z255-)
    For my autosomal analyses, see Hidden Content

  8. #5
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    The genotype file is too big

    Here's the bychr:

    Chromosome #SNPS 1-Sweden 2-Denmark 3-North_Poland 4-Poland_Sudovia 5-Belgium 6-Piedmont_Italia 7-Venezio_Italia 8-Tuscany_Italia 9-Lazio_Italia 10-Apulia_Italia 11-Corsica_France 12-Sicily_Italia 13-Sardinia_Italia 14-Canary 15-Bulgaria 16-Montenegro 17-Albania 18-Thrace_Greece 19-Peloponnes_Greece 20-Crete_Greece 21-Tyrol_Austria 22-Slovakia 23-Hungary 24-Finland_SW 25-Saami 26-Karelia 27-Norway_north 28-Estonian 29-Belarusia_East 30-Germany_East 31-Ukraine_West 32-Russia_Kursk 33-Russia_Rostov 34-Moldavian 35-Ireland 36-SW-England 37-Croatia 38-Serbia 39-Romania 40-North-Germany 41-South-Germany 42-West-Brittany 43-Rhone-Alpes 44-Armorica 45-Cotentin 46-SW_France 47-Basque 48-Baleares 49-Spain 50-Portugal 51-NE-England 52-Netherlands 53-Norway 54-Orcadia
    1117369 0.42 0.45 2.79 0.08 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.29 0.00 0.00 0.00 0.00 0.00 0.00 0.00 50.08 0.00 0.00 0.00 7.62 0.00 0.56 31.34 6.20 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.00 0.13 0.00
    2 3923 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.00 2.70 0.00 5.76 0.93 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 5.19 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2.86 30.28 0.06 0.00 0.00 0.00 0.00 0.17 0.00 0.18 0.01 0.00 0.00 40.89 10.92 0.01 0.01 0.00 0.00 0.00 0.00 0.01
    3 3580 12.63 0.30 0.01 15.54 11.64 0.00 0.01 0.00 0.00 0.00 0.00 0.00 24.11 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.00 0.00 12.48 0.00 0.01 0.03 0.09 0.14 0.01 0.03 1.49 0.00 0.12 3.86 0.00 0.00 0.00 0.43 0.01 0.02 0.01 0.04 0.10 0.48 0.00 0.00 0.00 0.00 0.08 12.70 0.38 3.24
    4 3204 0.10 0.19 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 6.08 0.00 19.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 68.98 5.63 0.01
    5 3066 0.00 0.16 3.73 29.03 0.11 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.01 0.01 0.05 1.01 0.48 64.40 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.25 0.08 0.00 0.30 0.00 0.00 0.00 0.00 0.24 0.01 0.02 0.09 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
    6 3712 0.00 0.02 0.53 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 16.32 0.00 0.00 0.00 0.00 7.98 0.00 1.11 0.00 0.00 0.00 0.00 23.76 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00 48.95 0.03 0.00 0.00 0.00 0.00 0.00 0.04 0.02 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.42 0.00 0.04 0.74
    7 2940 0.00 0.11 0.00 0.00 0.45 0.01 1.69 0.00 0.00 0.00 0.00 0.00 25.46 0.00 0.00 0.68 1.37 0.00 0.00 0.00 10.37 0.00 0.00 55.57 0.00 0.00 0.02 0.01 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.21 0.01 0.00 0.00 0.19 0.00 2.71 0.00 1.10 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00
    8 2831 0.00 0.00 0.00 0.00 0.70 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 6.51 0.00 13.05 0.00 0.00 20.38 56.30 2.95 0.00 0.00
    9 2464 0.00 0.00 0.00 32.57 0.00 0.00 0.00 0.00 0.02 0.03 0.00 24.51 17.72 6.93 0.00 0.00 0.00 0.02 0.02 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.23 17.55 0.00 0.24 0.08 0.00 0.00 0.00 0.00
    10 2655 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 1.14 93.10 0.01 5.74 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
    11 2617 0.00 0.00 0.00 29.90 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.62 0.00 0.00 57.77 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.07 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.88 7.56 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2.16 0.00 0.00 0.00 0.00 0.00 0.00 0.00
    12 2582 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.09 0.01 0.00 37.18 0.00 19.11 0.00 0.00 0.00 0.00 1.55 0.00 0.00 0.00 0.12 0.00 0.44 5.11 11.45 24.85 0.00 0.00 0.00 0.00 0.00 0.08 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00
    13 1948 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2.07 0.00 0.00 0.00 94.45 1.63 0.01 0.00 0.00 0.00 0.00 0.00 1.83 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
    14 1775 0.00 0.00 0.00 0.00 0.00 0.00 0.00 19.21 3.99 0.03 0.02 0.00 23.66 0.00 0.00 0.00 0.02 0.48 0.00 0.00 0.38 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.09 0.00 0.00 0.00 0.00 0.01 0.00 0.33 50.21 1.27 0.00 0.00 0.01 0.00 0.00 0.23 0.06 0.00 0.01
    15 1650 0.00 0.00 0.07 15.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 10.03 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.11 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.01 0.00 0.00 0.00 0.01 0.06 0.00 0.00 68.93 0.03 0.00 0.00 0.00 0.00 5.52 0.00 0.02
    16 1765 0.00 0.00 0.00 9.82 0.00 0.00 0.00 0.02 0.00 0.00 81.63 0.00 0.00 0.00 0.00 0.00 3.80 0.03 0.28 0.16 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 4.26 0.00 0.00 0.00 0.00 0.00 0.00 0.00
    17 1594 0.00 0.00 0.08 19.40 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 7.09 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.55 49.89 0.00 0.00 0.00 0.00 0.00 0.16 0.00 6.65 0.02 0.00 15.14 0.00 0.00 0.00 0.00 0.00 0.00 0.02
    18 1532 0.00 0.00 0.00 0.00 1.18 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 4.35 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.14 91.64 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 2.58 0.00 0.00 0.00 0.01 0.00 0.00 0.09
    19 1323 48.44 0.00 0.00 0.00 5.10 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.17 27.77 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.39 2.46 0.00 0.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.03 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 10.68 0.03 3.84 0.00 0.02
    20 1442 0.01 0.00 0.45 0.15 0.02 0.00 0.02 0.00 0.00 0.00 0.00 0.00 34.45 0.00 0.00 0.00 0.01 0.00 0.00 0.00 14.07 0.08 0.00 47.07 0.00 0.04 0.00 0.79 0.02 0.03 0.00 0.00 0.00 0.00 0.00 0.00 1.93 0.02 0.00 0.00 0.00 0.00 0.79 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
    21 870 0.00 0.00 6.51 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.93 0.00 0.00 0.00 0.00 0.00 0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.31 0.00 0.00 92.24
    22 846 0.00 0.00 0.00 29.46 0.00 0.14 1.74 0.00 0.00 0.00 0.00 0.00 19.89 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.16 0.00 0.00 0.00 0.00 0.00 0.00 9.21 0.00 1.11 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 4.89 33.40 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
    distance%=4.6465"
    Barcin_N,47.2
    Yamnaya_Samara,41.4
    WHG,10.6
    Ethiopia_4500BP,0.8


    E-V13 => E-PH1246 => E-BY14160
    Antonio Reale born circa 1710, Ciminà Italy

  9. #6
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    Chromosome #SNPs 1-Sweden 2-Denmark 3-North_Poland 4-Poland_Sudovia 5-Belgium 6-Piedmont_Italia 7-Venezio_Italia 8-Tuscany_Italia 9-Lazio_Italia 10-Apulia_Italia 11-Corsica_France 12-Sicily_Italia 13-Sardinia_Italia 14-Canary 15-Bulgaria 16-Montenegro 17-Albania 18-Thrace_Greece 19-Peloponnes_Greece 20-Crete_Greece 21-Tyrol_Austria 22-Slovakia 23-Hungary 24-Finland_SW 25-Saami 26-Karelia 27-Norway_north 28-Estonian 29-Belarusia_East 30-Germany_East 31-Ukraine_West 32-Russia_Kursk 33-Russia_Rostov 34-Moldavian 35-Ireland 36-SW-England 37-Croatia 38-Serbia 39-Romania 40-North-Germany 41-South-Germany 42-West-Brittany 43-Rhone-Alpes 44-Armorica 45-Cotentin 46-SW_France 47-Basque 48-Baleares 49-Spain 50-Portugal 51-NE-England 52-Netherlands 53-Norway 54-Orcadia 55-Amerindian 56-Arabia 57-South-East_Asia 58-Caucasus 59-China 60-East_Africa 61-Japon 62-India 63-Sub-Sahara 64-Turkey 65-Levant 66-North_Africa 67-Oceania 68-Pakistan 69-Siberia 70-Central_Asia 71-Iran&Assyria
    All 165688 2.33 2.30 3.44 3.42 2.72 1.62 2.01 1.58 1.17 0.89 0.96 0.56 0.11 0.37 1.72 2.00 1.51 1.73 1.12 0.58 2.20 2.69 1.75 0.50 0.00 0.26 1.12 1.43 2.87 2.70 2.00 2.20 1.09 0.91 2.40 2.85 2.40 2.10 1.67 1.67 2.31 2.80 2.14 2.78 2.51 2.00 2.87 2.51 1.49 0.54 2.72 2.59 1.96 2.94 0.00 0.00 0.00 0.47 0.00 0.00 0.00 0.00 0.00 0.23 0.07 0.00 0.00 0.00 0.00 0.00 0.14

    Thank you Tolan, here is genomewide K71a

  10. #7
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    Ah, I see. I never got those k71a results, just a huge Genotype file
    distance%=4.6465"
    Barcin_N,47.2
    Yamnaya_Samara,41.4
    WHG,10.6
    Ethiopia_4500BP,0.8


    E-V13 => E-PH1246 => E-BY14160
    Antonio Reale born circa 1710, Ciminà Italy

  11. #8
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    Quote Originally Posted by cercle View Post
    Chromosome #SNPs 1-Sweden 2-Denmark 3-North_Poland 4-Poland_Sudovia 5-Belgium 6-Piedmont_Italia 7-Venezio_Italia 8-Tuscany_Italia 9-Lazio_Italia 10-Apulia_Italia 11-Corsica_France 12-Sicily_Italia 13-Sardinia_Italia 14-Canary 15-Bulgaria 16-Montenegro 17-Albania 18-Thrace_Greece 19-Peloponnes_Greece 20-Crete_Greece 21-Tyrol_Austria 22-Slovakia 23-Hungary 24-Finland_SW 25-Saami 26-Karelia 27-Norway_north 28-Estonian 29-Belarusia_East 30-Germany_East 31-Ukraine_West 32-Russia_Kursk 33-Russia_Rostov 34-Moldavian 35-Ireland 36-SW-England 37-Croatia 38-Serbia 39-Romania 40-North-Germany 41-South-Germany 42-West-Brittany 43-Rhone-Alpes 44-Armorica 45-Cotentin 46-SW_France 47-Basque 48-Baleares 49-Spain 50-Portugal 51-NE-England 52-Netherlands 53-Norway 54-Orcadia 55-Amerindian 56-Arabia 57-South-East_Asia 58-Caucasus 59-China 60-East_Africa 61-Japon 62-India 63-Sub-Sahara 64-Turkey 65-Levant 66-North_Africa 67-Oceania 68-Pakistan 69-Siberia 70-Central_Asia 71-Iran&Assyria
    All 165688 2.33 2.30 3.44 3.42 2.72 1.62 2.01 1.58 1.17 0.89 0.96 0.56 0.11 0.37 1.72 2.00 1.51 1.73 1.12 0.58 2.20 2.69 1.75 0.50 0.00 0.26 1.12 1.43 2.87 2.70 2.00 2.20 1.09 0.91 2.40 2.85 2.40 2.10 1.67 1.67 2.31 2.80 2.14 2.78 2.51 2.00 2.87 2.51 1.49 0.54 2.72 2.59 1.96 2.94 0.00 0.00 0.00 0.47 0.00 0.00 0.00 0.00 0.00 0.23 0.07 0.00 0.00 0.00 0.00 0.00 0.14

    Thank you Tolan, here is genomewide K71a
    I think there is a problem with your file!
    It is as you would have the results without the calculation having started!
    No doubt you have too low coverage, in this case open the file k71a.par, and change 1d-6 to 1d-7.
    I still put you in the results, but in my opinion, it will change.


    digital_noise is on the page bychr
    27 avril 2019!
    Hidden Content

    Y haplogroup: R1b: L21+ DF13+ (L1335- DF21- DF49- FGC11134- L513- Z251- Z253- CTS1751- CTS3386- DF41- FGC5496- L371- MC14- S1026- S1051- S16264- Z16500- Z16502- Z255-)
    For my autosomal analyses, see Hidden Content

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    H1a1

    Sweden Italy Italy 1861-1946 Sami Vatican
    Is it possible to add it to the webtool?
    Hidden Content

    Eurogenes K13 Mixed Mode Population Sharing:
    1. 63.1% Swedish+36.9% Spanish_Andalucia @ 2.93

  14. #10
    Registered Users
    Posts
    940
    Sex
    Location
    Brittany
    Nationality
    French
    Y-DNA
    R-U106>DF98>BY650
    mtDNA
    K1a

    France Bretagne Trégor France Bretagne Kroaz Du
    Trelvern3.pngTrelvern2.pngTrelvern1.png

    Thanks to Tolan

    Central point:the Normano-Breton Gulf, on the south side of the English Channel


    one dot really far from the others (number: 2) in Russia (Caucasus mountains)
    zero with a small red dot: value less than 1


    1-West Brittany 45%
    2-SW England 39
    3-Basque 6
    4-Armorica 5
    5-Caucasus 2
    6-Rhône-Alpes 1
    and 2% (tiny values) :NE England +Ireland +Scotland+SW France+Belgium

    very focused compared to many others
    Last edited by Trelvern; 04-23-2019 at 06:27 AM.

  15. The Following 3 Users Say Thank You to Trelvern For This Useful Post:

     cercle (04-22-2019),  Jessie (04-27-2019),  JMcB (04-22-2019)

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