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Thread: Gedmatch results of a Saami from Norway

  1. #71
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    Quote Originally Posted by Zoro View Post
    Interesting. I had no idea Salar is an ethnic group in NW China. Even a couple of my Kurdish cousins are named Salar lol.


    As for Kurds in Iraq it's certainly higher than their other neighbors in Iraq but E Asian or Siberian ancestry in Kurds is far from uniform just like Kurdish phenotypes are all over the place. I'm limited by the 1240K public samples which only include 2 Kayseri Turk samples and 2 Iranian-Fars samples and some Caucasian samples.

    So far I have mostly done one-to-one comparisons using the Kurds with E Asian because that's more interesting to me since I'm more interested in Absolute comparisons over relative comparisons but I would think around 10% post Neolithic accumulated E Asian is probably close. I'll start doing some of those calculations soon.



    EDIT: Forgot to mention there's one Central Asian pop that Kurds are very high on the IBS list with. It's Uyghurs. They are number 10 on the Uyghur IBS list. Pashtuns are also high on that list
    They are a Turkic ethnic group btw.

    What's the average East Eurasian amount that you have observed for Kurds? And do you think its from Steppe or from Turkic invaders into West Asia?

    Is it lower than Iraqi Turkmens?

    Damn that's remarkable. Maybe some type of connection with Uyghurs through shared potential Turkic affinity?

  2. #72
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    Quote Originally Posted by Zoro View Post
    Here's the IBS for Finland Saami and Chukchi

    Plink calculates IBS as (IBS2 + 0.5*IBS1) / (IBS0 + IBS1 + IBS2) meaning the more positions where the target and the population compared match both alleles at a position (IBS2) the higher the IBS score. What this means is since you get 1 allele from each parent that if BOTH your dad's allele and mom's allele match Saami or Chukchi at every position you get a higher IBS score

    The first set of results for CHUKCHI is without removing really ancient common alleles (very ancient ancestry) from the calculation

    ....
    Wouldn't it make sense to calculate the average IBS values of Saami relative to multiple Mongoloid populations, and not just Chukchi? Now on the second list for Chukchi, Saami rank higher than some Southeast Asians, which doesn't make sense as an overall measure of Mongoloidness.

    Or could you check how populations of the Volga-Ural compare to Saami, like for example Komis or Kazan Tatars or Maris?

    Couldn't we compile a 99x99 (or whatever) table of each population compared against every other population? Then couldn't we use it as a precalculated matrix of genetic distances? Or for example we could take the average values of the columns for multiple Mongoloid populations and sort the rows of the table based on it.

    Sorry for being like Joqool and asking too many questions.

    I combined the data you posted (without the common old alleles) into a table. I omitted the row for Chukchis because you didn't post the score of Chukchis with themselves.

    Code:
    Population,Chukchi,Saami
    Adygei,0.8405,0.8390
    Albanian.DG,0.8380,0.8337
    Ami.DG,0.8422,0.8381
    Armenian,0.8377,0.8349
    Balochi,0.8361,0.7755
    BantuHerero,0.7795,0.7803
    BantuKenya,0.7834,0.7757
    BantuTswana,0.7776,0.8405
    Basque,0.8383,0.8329
    BedouinB,0.8319,0.8256
    Bougainville,0.8303,0.8351
    Brahui,0.8370,0.8401
    Bulgarian,0.8393,0.8354
    Burmese,0.8435,0.8378
    Burusho,0.8397,0.8392
    Chechen,0.8395,0.8339
    China_Lahu,0.8425,0.8439
    Czech,0.8394,0.8419
    Dai,0.8428,0.8341
    Daur,0.8466,0.8380
    Druze,0.8335,0.8359
    Dusun,0.8416,0.8327
    English,0.8404,0.8417
    Esan,0.7791,0.7762
    Eskimo_Naukan.DG,0.8537,0.8383
    Eskimo_Sireniki.DG,0.8540,0.8387
    Estonian,0.8410,0.8429
    Even,0.8482,0.8400
    Finnish,0.8422,0.8442
    French,0.8388,0.8397
    Gambian,0.7817,0.7786
    Georgian,0.8364,0.8378
    Greek,0.8383,0.8386
    Han,0.8460,0.8358
    Hazara,0.8433,0.8391
    Hezhen,0.8479,0.8381
    Hungarian,0.8400,0.8409
    Icelandic,0.8403,0.8420
    Iranian-Fars,0.8386,0.8372
    Irula,0.8367,0.8340
    Itelmen,0.8527,0.8377
    Japanese,0.8461,0.8359
    Jew_Iraqi,0.8354,0.8358
    Jordanian,0.8317,0.8321
    Ju_hoan_North,0.7687,0.7657
    Kalash,0.8378,0.8369
    Kapu,0.8376,0.8349
    Karitiana,0.8441,0.8348
    Khomani_San,0.7690,0.7661
    Kinh,0.8436,0.8346
    Korean,0.8455,0.8370
    Kurds-IRAQ,0.8424,0.8417
    Kusunda,0.8388,0.8317
    Kyrgyz_Kyrgyzstan,0.8466,0.8405
    Lezgin,0.8386,0.8396
    Luhya,0.7825,0.7793
    Luo,0.7836,0.7799
    Makrani,0.8353,0.8341
    Mala,0.8380,0.8341
    Mandenka,0.7817,0.7780
    Mansi,0.8477,0.8436
    Masai,0.7974,0.7952
    Mayan,0.8464,0.8366
    Mbuti,0.7729,0.7702
    Mende,0.7801,0.7769
    Mixe,0.8458,0.8358
    Mixtec,0.8458,0.8373
    Mongola,0.8465,0.8373
    Mozabite,0.8215,0.8219
    Norwegian,0.8405,0.8421
    Orcadian,0.8397,0.8414
    Papuan,0.8270,0.8222
    Pathan,0.8399,0.8375
    Piapoco,0.8454,0.8350
    Pima,0.8462,0.8361
    Polish,0.8408,0.8417
    Punjabi,0.8377,0.8362
    Russia_Abkhasian,0.8387,0.8391
    Russia_NorthOssetian,0.8387,0.8390
    Russian,0.8425,0.8436
    Saami,0.8439,0.8527
    Saharawi,0.8235,0.8226
    Samaritan,0.8321,0.8324
    Sardinian,0.8373,0.8388
    She,0.8448,0.8353
    Sindhi,0.8383,0.8367
    Somali,0.8065,0.8049
    Spanish,0.8384,0.8398
    Surui,0.8438,0.8337
    Tajik,0.8396,0.8380
    Tuscan,0.8389,0.8390
    Ulchi,0.8473,0.8372
    Uyghur,0.8440,0.8391
    Xibo,0.8460,0.8367
    Yadava,0.8388,0.8353
    Yakut,0.8474,0.8386
    Yi,0.8445,0.8349
    Here's the data as a plot. I used hierarchical K-means clustering to divide the populations into 16 groups.



    Code:
    library(ggplot2);library(factoextra);library(colorspace)
    
    download.file("https://pastebin.com/raw/FnTJmkAj","chukchisaami")
    
    t<-read.csv("chukchisaami",header=T,row.names=1)
    k<-hkmeans(t,16)
    
    ggplot(t,aes(x=Chukchi,y=Saami,label=row.names(t)))+
    geom_text(aes(color=as.factor(k$cluster)),size=2.5,show.legend=F)+
    theme(
      plot.background=element_rect(fill="gray35"),
      panel.grid.major=element_line(color="gray35"),
      text=element_text(color="gray10"),
      axis.text=element_text(color="gray10"),
      axis.ticks.x=element_blank(),
      axis.ticks.y=element_blank(),
      panel.grid.minor=element_blank()
    )+
    coord_fixed()+
    xlab("430K SNPs - Max-Maf 0.3 - Chukchi")+
    ylab("430K SNPs - Max-Maf 0.3 - Saami-Finland")+
    scale_color_discrete_qualitative(palette="Set 3")
    ggsave("/tmp/a.png")
    I couldn't get the version of plink from here to compile with either gcc or clang, and when I tried running the Mac binary, it said `Bad CPU type in executable`: https://zzz.bwh.harvard.edu/plink/download.shtml. But now I realized that there's a version by another developer here, with a working Mac binary: http://www.cog-genomics.org/plink/2.0/. I'll figure it out eventually.
    Last edited by Komintasavalta; 02-25-2021 at 08:15 AM.

  3. #73
    Veteran Member Ajeje Brazorf's Avatar
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    Quote Originally Posted by Zoro View Post
    I checked your G25 Chukchi list. I see a couple of issues with it:

    1- It starts out good. The 1st few on the list down to Kirgiz or so look fine . They sort of mirror the 430K IBS list I posted but then things start to go horribly wrong with it. I'll just give one example. Look at Kurds-Iraq on the IBS list. You'll notice that Kurds-Iraq are like number 33 on the Chukchi and they're certainly higher than most Europeans and S Asians which makes sense. Yet on the G25 list they're way down.

    The reason for this issue with the G25 is these distances are based on G25 coordinates and of course the coordinates are totally dependent on all the other samples in the run. This of course is problematic because each sample out of the 1000s he uses either pulls or pushes on another sample in some way or form. For example, some W Asian or Europeans samples pull Kurds close to them which in effect distances them from Chukchi.

    Whereas with IBS you don't have all this pulling and pushing. Each sample is compared directly with Chukchi allele for allele and checked to see how many alleles it shares with Chukchi. So there's really nothing that can go wrong. You just add up the number of alleles Kurds or some other pop shares with Chukchi. It's that simple. The reason Kurds are so high on the Chukchi list is that there are many positions in their genome where they don't just share 1 allele with Chukchi but rather they share both alleles with Chukchi.

    2- The other weird thing I noticed with G25 is once you pass the 1st 10 or so pops on the list the distances start getting huge. This of course also distorts things. If you check the IBS list the distances don't get out of control when you start heading to the bottom of the list.
    So for example, would Chukchi really be more genetically akin to Iraqi Kurds than Tajiks? Wow. This contradicts what has been seen in the "vulgar" GEDmatch calculators and on Global25 in general. After years, most of what I consider normal is now based on what those two tools easily accessible to anyone show. As for distances soaring, this happens especially in scaled coordinates but not in unscaled ones. I'll post the unscaled distances and tell me if you find more correlation with your distances. And most importantly, in your opinion, between scaled and unscaled coordinates which one is less worse?

    Here's the IBS for Finland Saami and Chukchi

    Plink calculates IBS as (IBS2 + 0.5*IBS1) / (IBS0 + IBS1 + IBS2) meaning the more positions where the target and the population compared match both alleles at a position (IBS2) the higher the IBS score. What this means is since you get 1 allele from each parent that if BOTH your dad's allele and mom's allele match Saami or Chukchi at every position you get a higher IBS score

    The first set of results for CHUKCHI is without removing really ancient common alleles (very ancient ancestry) from the calculation

    615K SNPs - Max-Maf 0.5 - Chukchi
    POPULATION IBS
    Eskimo_Sireniki.DG 0.7921
    Eskimo_Naukan.DG 0.7914
    Itelmen 0.7911
    Mansi 0.7873
    Kyrgyz_Kyrgyzstan 0.7864
    Even 0.7860
    Yakut 0.7856
    Hezhen 0.7851
    Uyghur 0.7848
    Mongola 0.7847
    Ulchi 0.7847
    Xibo 0.7840
    Mixtec 0.7835
    Daur 0.7831
    Japanese 0.7829
    Han 0.7829
    Saami 0.7825
    Korean 0.7825
    Hazara 0.7821
    Yi 0.7818
    Burmese 0.7818
    Finnish 0.7817
    Mayan 0.7816
    Russian 0.7814
    She 0.7814
    Mixe 0.7808
    Norwegian 0.7801
    Pima 0.7801
    Kinh 0.7801
    Estonian 0.7801
    Icelandic 0.7800
    Polish 0.7799
    Kurds-IRAQ 0.7799
    Piapoco 0.7798
    Burusho 0.7794
    English 0.7794
    Hungarian 0.7793
    Pathan 0.7793
    Dai 0.7790
    China_Lahu 0.7786
    Bulgarian 0.7784
    Adygei 0.7784
    Czech 0.7784
    Orcadian 0.7783
    Tajik 0.7779
    Chechen 0.7778
    French 0.7776
    Tuscan 0.7776
    Ami.DG 0.7775
    Russia_NorthOssetian 0.7775
    Iranian-Fars 0.7775
    Dusun 0.7774
    Spanish 0.7773
    Russia_Abkhasian 0.7772
    Greek 0.7771
    Lezgin 0.7770
    Yadava 0.7770
    Sindhi 0.7767
    Basque 0.7767
    Turkish 0.7766
    Kapu 0.7765
    Mala 0.7764
    Karitiana 0.7763
    Albanian.DG 0.7761
    Punjabi 0.7761
    Armenian 0.7759
    Sardinian 0.7754
    Georgian 0.7753
    Surui 0.7753
    Brahui 0.7747
    Irula 0.7747
    Kalash 0.7744
    Balochi 0.7737
    Jew_Iraqi 0.7736
    Kusunda 0.7733
    Makrani 0.7730
    Druze 0.7717
    BedouinB 0.7702
    Jordanian 0.7691
    Samaritan 0.7670
    Saharawi 0.7634
    Bougainville 0.7626
    Mozabite 0.7623
    Papuan 0.7568
    Somali 0.7475
    Masai 0.7401
    Luo 0.7274
    BantuKenya 0.7270
    Luhya 0.7261
    Mandenka 0.7256
    Gambian 0.7254
    Mende 0.7242
    BantuHerero 0.7236
    Esan 0.7231
    BantuTswana 0.7217
    Mbuti 0.7147
    Ju_hoan_North 0.7105
    Khomani_San 0.7095


    This set for CHUKCHI is after removing common old alleles (ancestry). All alleles having a minor allele frequency > 30% have been removed. I like this better because it tends to better reflect more recent ancestry


    430K SNPs - Max-Maf 0.3 - Chukchi
    POPULATION IBS
    Eskimo_Sireniki.DG 0.8540
    Eskimo_Naukan.DG 0.8537
    Itelmen 0.8527
    Even 0.8482
    Hezhen 0.8479
    Mansi 0.8477
    Yakut 0.8474
    Ulchi 0.8473
    Daur 0.8466
    Kyrgyz_Kyrgyzstan 0.8466
    Mongola 0.8465
    Mayan 0.8464
    Pima 0.8462
    Japanese 0.8461
    Xibo 0.8460
    Han 0.8460
    Mixtec 0.8458
    Mixe 0.8458
    Korean 0.8455
    Piapoco 0.8454
    She 0.8448
    Yi 0.8445
    Karitiana 0.8441
    Uyghur 0.8440
    Saami 0.8439
    Surui 0.8438
    Kinh 0.8436
    Burmese 0.8435
    Hazara 0.8433
    Dai 0.8428
    Russian 0.8425
    China_Lahu 0.8425
    Kurds-IRAQ 0.8424
    Finnish 0.8422
    Ami.DG 0.8422
    Dusun 0.8416
    Estonian 0.8410
    Polish 0.8408
    Adygei 0.8405
    Norwegian 0.8405
    English 0.8404
    Icelandic 0.8403
    Hungarian 0.8400
    Pathan 0.8399
    Orcadian 0.8397
    Burusho 0.8397
    Tajik 0.8396
    Chechen 0.8395
    Czech 0.8394
    Bulgarian 0.8393
    Tuscan 0.8389
    French 0.8388
    Yadava 0.8388
    Kusunda 0.8388
    Russia_NorthOssetian 0.8387
    Russia_Abkhasian 0.8387
    Lezgin 0.8386
    Iranian-Fars 0.8386
    Spanish 0.8384
    Basque 0.8383
    Sindhi 0.8383
    Greek 0.8383
    Albanian.DG 0.8380
    Mala 0.8380
    Kalash 0.8378
    Armenian 0.8377
    Punjabi 0.8377
    Kapu 0.8376
    Sardinian 0.8373
    Brahui 0.8370
    Irula 0.8367
    Georgian 0.8364
    Balochi 0.8361
    Jew_Iraqi 0.8354
    Makrani 0.8353
    Druze 0.8335
    Samaritan 0.8321
    BedouinB 0.8319
    Jordanian 0.8317
    Bougainville 0.8303
    Papuan 0.8270
    Saharawi 0.8235
    Mozabite 0.8215
    Somali 0.8065
    Masai 0.7974
    Luo 0.7836
    BantuKenya 0.7834
    Luhya 0.7825
    Gambian 0.7817
    Mandenka 0.7817
    Mende 0.7801
    BantuHerero 0.7795
    Esan 0.7791
    BantuTswana 0.7776
    Mbuti 0.7729
    Khomani_San 0.7690
    Ju_hoan_North 0.7687


    This set for SAAMI is after removing common old alleles (ancestry). All alleles having a minor allele frequency > 30% have been removed. I like this better because it tends to better reflect more recent ancestry



    430K SNPs - Max-Maf 0.3 - Saami -Finland
    POPULATION IBS
    Saami 0.8527
    Finnish 0.8442
    Chukchi 0.8439
    Mansi 0.8436
    Russian 0.8436
    Estonian 0.8429
    Norwegian 0.8421
    Icelandic 0.8420
    Czech 0.8419
    Polish 0.8417
    English 0.8417
    Kurds - IRAQ 0.8417
    Orcadian 0.8414
    Hungarian 0.8409
    Adygei 0.8405
    Basque 0.8405
    Kyrgyz_Kyrgyzstan 0.8405
    Bulgarian 0.8401
    Even 0.8400
    Spanish 0.8398
    French 0.8397
    Lezgin 0.8396
    Chechen 0.8392
    Uyghur 0.8391
    Hazara 0.8391
    Russia_Abkhasian 0.8391
    Russia_NorthOssetian 0.8390
    Tuscan 0.8390
    Albanian.DG 0.8390
    Sardinian 0.8388
    Eskimo_Sireniki.DG 0.8387
    Yakut 0.8386
    Greek 0.8386
    Eskimo_Naukan.DG 0.8383
    Hezhen 0.8381
    Armenian 0.8381
    Daur 0.8380
    Tajik 0.8380
    Burusho 0.8378
    Georgian 0.8378
    Itelmen 0.8377
    Pathan 0.8375
    Mongola 0.8373
    Mixtec 0.8373
    Ulchi 0.8372
    Iranians - Fars 0.8372
    Korean 0.8370
    Kalash 0.8369
    Sindhi 0.8367
    Xibo 0.8367
    Mayan 0.8366
    Punjabi 0.8362
    Pima 0.8361
    Japanese 0.8359
    Druze 0.8359
    Mixe 0.8358
    Han 0.8358
    Jew_Iraqi 0.8358
    Burmese 0.8354
    She 0.8353
    Yadava 0.8353
    Brahui 0.8351
    Piapoco 0.8350
    Kapu 0.8349
    Yi 0.8349
    Balochi 0.8349
    Karitiana 0.8348
    Kinh 0.8346
    Mala 0.8341
    Makrani 0.8341
    Dai 0.8341
    Irula 0.8340
    China_Lahu 0.8339
    Ami.DG 0.8337
    Surui 0.8337
    BedouinB 0.8329
    Dusun 0.8327
    Samaritan 0.8324
    Jordanian 0.8321
    Kusunda 0.8317
    Bougainville 0.8256
    Saharawi 0.8226
    Papuan 0.8222
    Mozabite 0.8219
    Somali 0.8049
    Masai 0.7952
    BantuKenya 0.7803
    Luo 0.7799
    Luhya 0.7793
    Gambian 0.7786
    Mandenka 0.7780
    Mende 0.7769
    Esan 0.7762
    BantuTswana 0.7757
    BantuHerero 0.7755
    Mbuti 0.7702
    Khomani_San 0.7661
    Ju_hoan_North 0.7657
    Distance to: Chukchi
    Spoiler!


    Distance to: Saami
    Spoiler!

  4. #74
    Veteran Member Zoro's Avatar
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    Quote Originally Posted by Komintasavalta View Post
    Wouldn't it make sense to calculate the average IBS values of Saami relative to multiple Mongoloid populations, and not just Chukchi? Now on the second list for Chukchi, Saami rank higher than some Southeast Asians, which doesn't make sense as an overall measure of Mongoloidness.

    Or could you check how populations of the Volga-Ural compare to Saami, like for example Komis or Kazan Tatars or Maris?

    Couldn't we compile a 99x99 (or whatever) table of each population compared against every other population? Then couldn't we use it as a precalculated matrix of genetic distances? Or for example we could take the average values of the columns for multiple Mongoloid populations and sort the rows of the table based on it.

    Sorry for being like Joqool and asking too many questions.

    I combined the data you posted (without the common old alleles) into a table. I omitted the row for Chukchis because you didn't post the score of Chukchis with themselves.

    Code:
    Population,Chukchi,Saami
    Adygei,0.8405,0.8390
    Albanian.DG,0.8380,0.8337
    Ami.DG,0.8422,0.8381
    Armenian,0.8377,0.8349
    Balochi,0.8361,0.7755
    BantuHerero,0.7795,0.7803
    BantuKenya,0.7834,0.7757
    BantuTswana,0.7776,0.8405
    Basque,0.8383,0.8329
    BedouinB,0.8319,0.8256
    Bougainville,0.8303,0.8351
    Brahui,0.8370,0.8401
    Bulgarian,0.8393,0.8354
    Burmese,0.8435,0.8378
    Burusho,0.8397,0.8392
    Chechen,0.8395,0.8339
    China_Lahu,0.8425,0.8439
    Czech,0.8394,0.8419
    Dai,0.8428,0.8341
    Daur,0.8466,0.8380
    Druze,0.8335,0.8359
    Dusun,0.8416,0.8327
    English,0.8404,0.8417
    Esan,0.7791,0.7762
    Eskimo_Naukan.DG,0.8537,0.8383
    Eskimo_Sireniki.DG,0.8540,0.8387
    Estonian,0.8410,0.8429
    Even,0.8482,0.8400
    Finnish,0.8422,0.8442
    French,0.8388,0.8397
    Gambian,0.7817,0.7786
    Georgian,0.8364,0.8378
    Greek,0.8383,0.8386
    Han,0.8460,0.8358
    Hazara,0.8433,0.8391
    Hezhen,0.8479,0.8381
    Hungarian,0.8400,0.8409
    Icelandic,0.8403,0.8420
    Iranian-Fars,0.8386,0.8372
    Irula,0.8367,0.8340
    Itelmen,0.8527,0.8377
    Japanese,0.8461,0.8359
    Jew_Iraqi,0.8354,0.8358
    Jordanian,0.8317,0.8321
    Ju_hoan_North,0.7687,0.7657
    Kalash,0.8378,0.8369
    Kapu,0.8376,0.8349
    Karitiana,0.8441,0.8348
    Khomani_San,0.7690,0.7661
    Kinh,0.8436,0.8346
    Korean,0.8455,0.8370
    Kurds-IRAQ,0.8424,0.8417
    Kusunda,0.8388,0.8317
    Kyrgyz_Kyrgyzstan,0.8466,0.8405
    Lezgin,0.8386,0.8396
    Luhya,0.7825,0.7793
    Luo,0.7836,0.7799
    Makrani,0.8353,0.8341
    Mala,0.8380,0.8341
    Mandenka,0.7817,0.7780
    Mansi,0.8477,0.8436
    Masai,0.7974,0.7952
    Mayan,0.8464,0.8366
    Mbuti,0.7729,0.7702
    Mende,0.7801,0.7769
    Mixe,0.8458,0.8358
    Mixtec,0.8458,0.8373
    Mongola,0.8465,0.8373
    Mozabite,0.8215,0.8219
    Norwegian,0.8405,0.8421
    Orcadian,0.8397,0.8414
    Papuan,0.8270,0.8222
    Pathan,0.8399,0.8375
    Piapoco,0.8454,0.8350
    Pima,0.8462,0.8361
    Polish,0.8408,0.8417
    Punjabi,0.8377,0.8362
    Russia_Abkhasian,0.8387,0.8391
    Russia_NorthOssetian,0.8387,0.8390
    Russian,0.8425,0.8436
    Saami,0.8439,0.8527
    Saharawi,0.8235,0.8226
    Samaritan,0.8321,0.8324
    Sardinian,0.8373,0.8388
    She,0.8448,0.8353
    Sindhi,0.8383,0.8367
    Somali,0.8065,0.8049
    Spanish,0.8384,0.8398
    Surui,0.8438,0.8337
    Tajik,0.8396,0.8380
    Tuscan,0.8389,0.8390
    Ulchi,0.8473,0.8372
    Uyghur,0.8440,0.8391
    Xibo,0.8460,0.8367
    Yadava,0.8388,0.8353
    Yakut,0.8474,0.8386
    Yi,0.8445,0.8349
    Here's the data as a plot. I used hierarchical K-means clustering to divide the populations into 16 groups.



    Code:
    library(ggplot2);library(factoextra);library(colorspace)
    
    download.file("https://pastebin.com/raw/FnTJmkAj","chukchisaami")
    
    t<-read.csv("chukchisaami",header=T,row.names=1)
    k<-hkmeans(t,16)
    
    ggplot(t,aes(x=Chukchi,y=Saami,label=row.names(t)))+
    geom_text(aes(color=as.factor(k$cluster)),size=2.5,show.legend=F)+
    theme(
      plot.background=element_rect(fill="gray35"),
      panel.grid.major=element_line(color="gray35"),
      text=element_text(color="gray10"),
      axis.text=element_text(color="gray10"),
      axis.ticks.x=element_blank(),
      axis.ticks.y=element_blank(),
      panel.grid.minor=element_blank()
    )+
    coord_fixed()+
    xlab("430K SNPs - Max-Maf 0.3 - Chukchi")+
    ylab("430K SNPs - Max-Maf 0.3 - Saami-Finland")+
    scale_color_discrete_qualitative(palette="Set 3")
    ggsave("/tmp/a.png")
    I couldn't get the version of plink from here to compile with either gcc or clang, and when I tried running the Mac binary, it said `Bad CPU type in executable`: https://zzz.bwh.harvard.edu/plink/download.shtml. But now I realized that there's a version by another developer here, with a working Mac binary: http://www.cog-genomics.org/plink/2.0/. I'll figure it out eventually.

    Makes good sense. I just didn’t time. Will try to get to it.

    It’s good to have both plink 1.9 and 2.0 since 2 doesn’t have all the programs 1.9 does. Download it from https://www.cog-genomics.org/plink/
    Muzh ba staso la tyaro tsakha ra wubaasu

    [IMG][/IMG]

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    Quote Originally Posted by Ajeje Brazorf View Post
    So for example, would Chukchi really be more genetically akin to Iraqi Kurds than Tajiks? Wow. This contradicts what has been seen in the "vulgar" GEDmatch calculators and on Global25 in general. After years, most of what I consider normal is now based on what those two tools easily accessible to anyone show. As for distances soaring, this happens especially in scaled coordinates but not in unscaled ones. I'll post the unscaled distances and tell me if you find more correlation with your distances. And most importantly, in your opinion, between scaled and unscaled coordinates which one is less worse?
    ]
    To be fair we should use a couple more Siberian pops and maybe separate the Tajiks out to see if an outlier is causing issues. I did find some sequencing errors in some of the Simons samples so that should also be looked into.

    G25 is a PCA program that’s mostly suitable for PCA work and not for distances or admix proportions. Like I explained in my previous post it seems to work for distances for the 1st few on the list then goes wacko for the rest. Also for some reason distances get huge as you go down the list. Biggest problem is unknown push-pull of other 1000s of samples he used in run. With IBS you just compare 2 samples or pops allele for allele and you don’t have these unknown forces from 1000s of samples affecting coordinates of your target in 25 dimensional space

    Scaled of course for PCA work

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    Quote Originally Posted by Joqool View Post
    They are a Turkic ethnic group btw.

    What's the average East Eurasian amount that you have observed for Kurds? And do you think its from Steppe or from Turkic invaders into West Asia?

    Is it lower than Iraqi Turkmens?

    Damn that's remarkable. Maybe some type of connection with Uyghurs through shared potential Turkic affinity?
    Will get back to you later today

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    Quote Originally Posted by Zoro View Post
    Will get back to you later today
    How are the results?

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    Quote Originally Posted by Joqool View Post
    How are the results?
    Eurasian DNA has a pretty detailed study where they model whole genome Turks and Kurds as modern Iranian/Armenian/Georgian/Adygei/Abkhasian/Jordanian + E. Asian and Siberian . They said it’ll be out soon but based on https://eurasiandna.com/2659-2/ it looks like around 10% E. Asian

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    Its normal for a hybride population to have among them a part of ''european'' face.

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    Quote Originally Posted by Zoro View Post
    That’s not true otherwise chinese would look African or European . Everything in your body is dictated by genes. They shape your eyes, nose etc.

    Now what you maybe referring to is that if you have 2 brothers with 10% E. Asian. It’s possible one brother’s 10% would include genes that affect facial features whereas the other brothers 10% E Asian doesn’t include genes affecting facial features and would thus look more European than his Asian looking brother
    This.

    Genotype = phénotype.

    A sami with 75% euro and 25% ''siberian like'' could look european, his brother more 50-50, other almost fully siberian.

    Same thing with askenazi.

    Not a surprise...

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