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Thread: Vahaduo Online tool for G25

  1. #121
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    Quote Originally Posted by evon View Post
    Pop avg:
     

    Target: Grandmother_scaled
    Distance: 0.9933% / 0.00993252
    35.6 Norwegian
    27.2 Icelandic
    12.4 Irish
    12.0 Shetlandic
    8.2 Lithuanian_VZ
    2.4 Italian_Northeast_o
    1.0 Sorb_Niederlausitz
    0.4 Berber_MAR_TIZ
    0.2 Dusun
    0.2 Ju_hoan_North
    0.2 Lithuanian_SZ
    0.2 Murut


    With the pop avg it is also way off, as we dont have any Icelandic (back in the 13-1400's only), Shetlandic, Irish, Lithuanian, Italian etc ancestry. In fact the only correct one, of these, is the Norwegian, although it should be much higher than 35.6. The rest is just statistical garbage, one might be tempted to say it is worse than Oracle..
    So I got myself and my wife G25. and looking at the PCA it works fairly well (she plots with Turks and in between two ancient Armenians, and I plot with Swedes, Dutch and in between two ancient samples, one from Sweden and the other from the Pontic steppe) , as does likely most runs with the ancient samples, but I again notice that modern samples work poorly, not just for me and my grandmother, but also for my wife, have a look here at the modern samples contrasted with the PCA:

    First, my own "pop avg":
     
    Distance: 1.2839% / 0.01283897
    Aggregated
    75.8 Icelandic
    11.4 Estonian
    10.8 Basque_Spanish
    1.2 Norwegian
    0.2 Koinanbe
    0.2 Papuan
    0.2 Spanish_La_Rioja
    0.2 Swedish


    As I expected, based on my Grandmothers run with the same samples, it is not a good estimator for modern ancestry and it looks allot like the old Oracle runs (especially the Basque was a reoccurring feature of Oracle).. Just to clarify, the only Icelandic ancestry I have is back in the 13-1400's.

    My wife's is equally off:
     
    Distance: 1.0978% / 0.01097778
    Aggregated
    20.4 Iraqi_Jew
    19.6 Armenian_Hemsheni
    15.4 Armenian
    10.6 Greek_Phokaia
    6.8 Turkish_Aydin
    6.6 Greek_Central_Anatolia
    4.2 Lithuanian_RA
    3.2 Spanish_La_Rioja
    3.0 Nivh
    2.2 French_Corsica_o
    2.0 Yakut
    1.4 Mongolian
    1.4 Nanai
    1.0 Sardinian
    0.4 Buryat
    0.4 Lithuanian_VA
    0.4 Papuan
    0.4 Yukpa
    0.2 Biaka
    0.2 Greek_Kos
    0.2 Mixe


    She is Turkish as far back as the records show and although she likely has some distant Armenian ancestry etc, she has no known Jewish ancestry. The sample that comes closest to her actual ancestry is the Aydin average, as one of her grandmothers was from Aydin province if I remember correctly, but the rest are all from around Konya..

    I will have a look at the individual samples later as I suspect they are even more off, as was the case with my Grandmother... Anyways, be careful kids, this works best for ancient pops and PCA's, not so good with modern samples...

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  3. #122
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    Quote Originally Posted by evon View Post
    So I got myself and my wife G25. and looking at the PCA it works fairly well (she plots with Turks and in between two ancient Armenians, and I plot with Swedes, Dutch and in between two ancient samples, one from Sweden and the other from the Pontic steppe) , as does likely most runs with the ancient samples, but I again notice that modern samples work poorly, not just for me and my grandmother, but also for my wife, have a look here at the modern samples contrasted with the PCA:

    First, my own "pop avg":
     
    Distance: 1.2839% / 0.01283897
    Aggregated
    75.8 Icelandic
    11.4 Estonian
    10.8 Basque_Spanish
    1.2 Norwegian
    0.2 Koinanbe
    0.2 Papuan
    0.2 Spanish_La_Rioja
    0.2 Swedish


    As I expected, based on my Grandmothers run with the same samples, it is not a good estimator for modern ancestry and it looks allot like the old Oracle runs (especially the Basque was a reoccurring feature of Oracle).. Just to clarify, the only Icelandic ancestry I have is back in the 13-1400's.

    My wife's is equally off:
     
    Distance: 1.0978% / 0.01097778
    Aggregated
    20.4 Iraqi_Jew
    19.6 Armenian_Hemsheni
    15.4 Armenian
    10.6 Greek_Phokaia
    6.8 Turkish_Aydin
    6.6 Greek_Central_Anatolia
    4.2 Lithuanian_RA
    3.2 Spanish_La_Rioja
    3.0 Nivh
    2.2 French_Corsica_o
    2.0 Yakut
    1.4 Mongolian
    1.4 Nanai
    1.0 Sardinian
    0.4 Buryat
    0.4 Lithuanian_VA
    0.4 Papuan
    0.4 Yukpa
    0.2 Biaka
    0.2 Greek_Kos
    0.2 Mixe


    She is Turkish as far back as the records show and although she likely has some distant Armenian ancestry etc, she has no known Jewish ancestry. The sample that comes closest to her actual ancestry is the Aydin average, as one of her grandmothers was from Aydin province if I remember correctly, but the rest are all from around Konya..

    I will have a look at the individual samples later as I suspect they are even more off, as was the case with my Grandmother... Anyways, be careful kids, this works best for ancient pops and PCA's, not so good with modern samples...
    I think its always fair to interpret these sorts of things with a "ballpark" mentality and not to take them too seriously, but people pick favorites and I can understand how someone can get carried away into taking a model or interpretation too seriously. I really think autosomal results and tools are best seen as a collection which can be used to identify common themes.
    Paper trail ancestry to the best of my knowledge:
    English (possibly containing some Welsh ancestry) 31.25%, Scottish 17.96%, Scotch-Irish 12.5%, Eastern German 12.5%, Eastern European (Likely Polish possibly including Romanian) 12.5%, French 8.2%, Native American (Saulteaux and Assiniboine) 1.95%, and Colonial American, 3.125%, which cannot be determined with complete certainty. With certainty, there is Dutch (at least 1.36%) and some English.

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  5. #123
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    Quote Originally Posted by evon View Post
    So I got myself and my wife G25. and looking at the PCA it works fairly well (she plots with Turks and in between two ancient Armenians, and I plot with Swedes, Dutch and in between two ancient samples, one from Sweden and the other from the Pontic steppe) , as does likely most runs with the ancient samples, but I again notice that modern samples work poorly, not just for me and my grandmother, but also for my wife, have a look here at the modern samples contrasted with the PCA:

    First, my own "pop avg":
     
    Distance: 1.2839% / 0.01283897
    Aggregated
    75.8 Icelandic
    11.4 Estonian
    10.8 Basque_Spanish
    1.2 Norwegian
    0.2 Koinanbe
    0.2 Papuan
    0.2 Spanish_La_Rioja
    0.2 Swedish


    As I expected, based on my Grandmothers run with the same samples, it is not a good estimator for modern ancestry and it looks allot like the old Oracle runs (especially the Basque was a reoccurring feature of Oracle).. Just to clarify, the only Icelandic ancestry I have is back in the 13-1400's.

    My wife's is equally off:
     
    Distance: 1.0978% / 0.01097778
    Aggregated
    20.4 Iraqi_Jew
    19.6 Armenian_Hemsheni
    15.4 Armenian
    10.6 Greek_Phokaia
    6.8 Turkish_Aydin
    6.6 Greek_Central_Anatolia
    4.2 Lithuanian_RA
    3.2 Spanish_La_Rioja
    3.0 Nivh
    2.2 French_Corsica_o
    2.0 Yakut
    1.4 Mongolian
    1.4 Nanai
    1.0 Sardinian
    0.4 Buryat
    0.4 Lithuanian_VA
    0.4 Papuan
    0.4 Yukpa
    0.2 Biaka
    0.2 Greek_Kos
    0.2 Mixe


    She is Turkish as far back as the records show and although she likely has some distant Armenian ancestry etc, she has no known Jewish ancestry. The sample that comes closest to her actual ancestry is the Aydin average, as one of her grandmothers was from Aydin province if I remember correctly, but the rest are all from around Konya..

    I will have a look at the individual samples later as I suspect they are even more off, as was the case with my Grandmother... Anyways, be careful kids, this works best for ancient pops and PCA's, not so good with modern samples...
    Running nMonte with more than 5 populations and with pen=0 will never get you close to actual ancestry.
    You should run nMonte on full spreadsheets with pen=0.001.

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  7. #124
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    Quote Originally Posted by sktibo View Post
    I think its always fair to interpret these sorts of things with a "ballpark" mentality and not to take them too seriously, but people pick favorites and I can understand how someone can get carried away into taking a model or interpretation too seriously. I really think autosomal results and tools are best seen as a collection which can be used to identify common themes.
    I agree, the way I see it now is that the various populations represent "pull" in a certain direction, but that they often "pick" wrong models for explaining that pull (which is why I compared it to Oracle which does the same thing).
    As an example, I have a well known Southern European pull, which comes up as Basque here, at Oracle too it is usually shown as Basque. At FTDNA it is interpreted as around 10% Iberian, while Myheritage lists it as about 7% Italian and 23andme as 0,3% Broadly southern European. Now I know the pull is there (and it seems real), but I want to verify with some certainty what the source of the pull actually is. The most likely explanation, that comes to mind, is that it comes from my Romani ancestry (so technically my Grandmother should have the same pull, although she also has a pull towards west and south Asia, which complicates things much more), since it is closest in time (compared to my other non-Norwegian ancestry, mostly from the 17-1600's.), and so it should be SE European and not Iberian, although I have, as of this moment, no idea on how I can verify that using G25 modeling.

    Any ideas?

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  9. #125
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    Quote Originally Posted by ph2ter View Post
    Running nMonte with more than 5 populations and with pen=0 will never get you close to actual ancestry.
    You should run nMonte on full spreadsheets with pen=0.001.
    The problem is that I have so limited time, due to the fact that I have a family to take care of, and nMonte is still relatively new to me, so I would have to "relearn" it.. But I will head your advice and try it when I have some time... It's all in R right?

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  11. #126
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    Quote Originally Posted by evon View Post
    The problem is that I have so limited time, due to the fact that I have a family to take care of, and nMonte is still relatively new to me, so I would have to "relearn" it.. But I will head your advice and try it when I have some time... It's all in R right?
    Everything is good with R.

    1. Install R.
    2. Run it
    3. Change current directory with: File/Change dir to location where all your files will be placed
    4. Download nMonte3.R file and put it into your directory
    5. Type: source('nMonte3.R')
    6. Put your G25 files into your directory
    7. type: getMonte('yourG25file.txt', 'yourSpreadsheet.txt', pen=0.001)
    8. Wait the result

    You only need to take care not to mix unscaled with scaled coordinates and to remove all 'space' characters from the spreadsheets.

    Is that so complicated?

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  13. #127
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    Quote Originally Posted by ph2ter View Post
    Everything is good with R.

    1. Install R.
    2. Run it
    3. Change current directory with: File/Change dir to location where all your files will be placed
    4. Download nMonte3.R file and put it into your directory
    5. Type: source('nMonte3.R')
    6. Put your G25 files into your directory
    7. type: getMonte('yourG25file.txt', 'yourSpreadsheet.txt', pen=0.001)
    8. Wait the result

    You only need to take care not to mix unscaled with scaled coordinates and to remove all 'space' characters from the spreadsheets.

    Is that so complicated?
    You are right, it is not so complicated, I thought nMonte was more complicated. I will try it when I have time.. Thanks.

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  15. #128
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    Quote Originally Posted by ph2ter View Post
    Everything is good with R.

    1. Install R.
    2. Run it
    3. Change current directory with: File/Change dir to location where all your files will be placed
    4. Download nMonte3.R file and put it into your directory
    5. Type: source('nMonte3.R')
    6. Put your G25 files into your directory
    7. type: getMonte('yourG25file.txt', 'yourSpreadsheet.txt', pen=0.001)
    8. Wait the result

    You only need to take care not to mix unscaled with scaled coordinates and to remove all 'space' characters from the spreadsheets.

    Is that so complicated?
    You are right, it is not so complicated, I thought nMonte was more complicated. I will try it when I have time.. Thanks.

  16. #129
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    So I have a few minutes before my baby shift starts again.

    I ran us using R with pen 0.001:

    Mine:
     
    [1] "1. CLOSEST SINGLE ITEM DISTANCE%"
    Icelandic Swedish Norwegian Orcadian Scottish Dutch Irish English
    1.611095 1.954234 2.072128 2.310496 2.342305 2.350039 2.445355 2.465628

    Icelandic,70.6
    Swedish,15.8
    Welsh,2.4
    English_Cornwall,2
    French_Brittany,1.8
    Norwegian,1.8
    Estonian,0.8
    Irish,0.8
    Latvian,0.8
    Lithuanian_PZ,0.6
    Dutch,0.4
    Orcadian,0.4
    Basque_French,0.2
    Basque_Spanish,0.2
    Belgian,0.2
    English,0.2
    French,0.2
    Italian_Trentino-Alto-Adige_o,0.2
    Lithuanian_SZ,0.2
    Lithuanian_VA,0.2
    Scottish,0.2


    I guess it is better than using Vahaduo, but it is still way off. I can see how it calculated me though, as since they lack a western Norwegian pop avg, it chose Icelandic and Swedish, which becomes a stand-in for western Norwegian. The British traces could represent a English ancestor of mine from Telford, though he dates back to 1600 I have several lines going back to him, so I guess it is theoretical that I inherited some DNA from him, which matches LivingDNA and 23andme somewhat, they too give me Shropshire/Staffordshire/Wales at low levels.. The Southern European is again all over the place, but much diminished, So I will try to remove the Icelandic and see what it gives me, since I know with 99% certainty that I have no Icelandic DNA after about 1400.

    Try two, without Icelandic sample:
     

    Swedish,54
    Norwegian,17.6
    Irish,9
    English_Cornwall,5.8
    Welsh,5.2
    English,4
    French_Brittany,2.4
    Estonian,0.8
    Scottish,0.6
    Basque_Spanish,0.2
    Orcadian,0.2
    Spanish_Castello,0.2


    I see they split the Icelandic into Norwegian and Irish, which is basically what Icelandic DNA is in a way, although heavily dominated by drifted Norwegian DNA. Since I know I have no Irish DNA I will remove Irish too and try again.


    Try three, without Icelandic and Irish samples:
     

    Swedish,54.4
    Norwegian,22
    French_Brittany,5.2
    English_Cornwall,4.8
    English,4.4
    Welsh,4.2
    Orcadian,3.8
    Scottish,0.4
    Spanish_Pais_Vasco,0.4
    Basque_Spanish,0.2
    Estonian,0.2


    Now it is starting to look like something real, although the Swedish % is of course way too high. Likewise is the British % too high, so I will remove Orcadian and Estonian, since I know I have no ancestry from either one of them.

    Try four:
     

    Swedish,53.6
    Norwegian,22
    English,7.6
    English_Cornwall,6.4
    Welsh,5.6
    French_Brittany,3
    Basque_French,0.4
    Latvian,0.4
    Scottish,0.4
    Basque_Spanish,0.2
    Lithuanian_PZ,0.2
    Spanish_Pais_Vasco,0.2


    I see it just keeps giving me Baltic in place of Estonian, I think it represents Finnish ancestry, although I have one ancestor East Prussia (Königsberg 1700's), which I guess could explain it.. It is a shame that G25 does not have any Danish samples yet, as it is much needed for my results to make sense... I am no closer to finding the actual southern European pull, as I am fairly certain that it is not Basque.

    Next I ran my Grandmother with the same edited pop sheet, and the afterwards the original.

    Edited Granny:
     

    Norwegian,52.8
    Swedish,15.2
    Shetlandic,13.4
    Dutch,6.2
    Scottish,3.8
    English,1.2
    Lithuanian_PZ,1.2
    Lithuanian_SZ,0.8
    Welsh,0.8
    Cossack_Kuban,0.6
    English_Cornwall,0.6
    Lithuanian_PA,0.6
    Latvian,0.4
    Lithuanian_RA,0.4
    Russian_Kursk,0.4
    Belarusian,0.2
    Czech,0.2
    Lithuanian_VA,0.2
    Lithuanian_VZ,0.2
    Russian_Smolensk,0.2
    Russian_Tver,0.2
    Slovakian,0.2
    Ukrainian,0.2


    This again needs allot of interpretation to work, as I see a clear south east pull, as I expected, but at the same time I see a westward pull that should be towards Denmark and Germany and not the UK.

    Now, Granny with the Original:
     
    [1] "1. CLOSEST SINGLE ITEM DISTANCE%"
    Norwegian Icelandic Swedish Dutch Shetlandic Scottish Orcadian
    1.451742 1.566638 1.651092 1.851419 1.945581 2.044468 2.092100
    Irish
    2.181008

    Norwegian,44.8
    Icelandic,23.6
    Shetlandic,8.4
    Swedish,6.8
    Irish,3.8
    Dutch,3.6
    Lithuanian_PZ,1
    Latvian,0.6
    Lithuanian_VA,0.6
    Scottish,0.6
    Slovakian,0.6
    Czech,0.4
    English_Cornwall,0.4
    Estonian,0.4
    Lithuanian_SZ,0.4
    Orcadian,0.4
    Russian_Tver,0.4
    Sorb_Niederlausitz,0.4
    Belarusian,0.2
    Cossack_Kuban,0.2
    Hungarian,0.2
    Italian_Northeast_o,0.2
    Jatt_Pathak,0.2
    Lithuanian_PA,0.2
    Lithuanian_RA,0.2
    Lithuanian_VZ,0.2
    Polish,0.2
    Russian_Kostroma,0.2
    Russian_Kursk,0.2
    Russian_Orel,0.2
    Russian_Smolensk,0.2
    Ukrainian,0.2



    I guess her south eastern pull makes her a better fit with eastern Norwegian samples than with Icelandic ones. But again these small island populations mess up the ouput and so it is not very accurate, but with a huge pinch of salt it can be make to make sense. Surprisingly her south Asian pull is actually more visible with Iceland, Orcadian etc in the pop sheet.

    Now I will run my wife using the original file:
     

    [1] "1. CLOSEST SINGLE ITEM DISTANCE%"
    Turkish_Central Turkish_Kayseri Turkish_Adana Turkish_Aydin
    2.156415 2.401573 2.413256 3.290768
    Turkish_Istanbul Turkish_Northwest Turkish_Southwest Turkish_North
    3.476113 3.557683 3.853165 4.050800

    Turkish_Kayseri,45.4
    Turkish_Aydin,11.4
    Turkish_Adana,7.4
    Turkish_Central,4.2
    Turkish_Northwest,3.2
    Turkish_Southwest,3.2
    Turkish_Trabzon,1.6
    Armenian_Hemsheni,1.2
    Greek_Trabzon,1.2
    Turkish_Balikesir,1.2
    Turkish_North,1.2
    Cypriot,1
    Druze,1
    Greek_Central_Anatolia,1
    Greek_Kos,1
    Italian_Basilica,0.8
    Italian_Calabria,0.8
    Italian_Molise,0.8
    Lebanese_Christian,0.8
    Greek_Crete,0.6
    Iraqi_Jew,0.6
    Romaniote_Jew,0.6
    Samaritan,0.6
    Greek_Phokaia,0.4
    Italian_Jew,0.4
    Italian_Liguria,0.4
    Lebanese_Druze,0.4
    Naxi,0.4
    Sephardic_Jew,0.4
    Syrian_Jew,0.4
    Tunisian_Jew,0.4
    Yemenite_Mahra,0.4
    Ashkenazi_Jew,0.2
    Aymara,0.2
    Eskimo,0.2
    Eskimo_Chaplin,0.2
    French_Corsica,0.2
    French_Corsica_o,0.2
    Greek_Smyrna,0.2
    Italian_Abruzzo,0.2
    Italian_Apulia,0.2
    Italian_Campania,0.2
    Italian_Marche,0.2
    Italian_South,0.2
    Italian_Umbria,0.2
    Kalmyk,0.2
    Khakass,0.2
    Koryak,0.2
    Maltese,0.2
    Mixtec,0.2
    Mongolian,0.2
    Nganassan,0.2
    Sicilian_West,0.2
    Spanish_La_Rioja,0.2
    Xibo,0.2
    Yakut,0.2
    Yemenite_Al_Bayda,0.2
    Yemenite_Al_Jawf,0.2
    Yemenite_Dhamar,0.2
    Yemenite_Ma'rib,0.2


    I have a feeling that there are too many Turkish samples contra surrounding populations, but it is much better than mine, or my grandmother for that matter, in that it matches her with Kayseri samples, as well as SW Anatolian samples, which matches her known ancestry somewhat. Her three regions at 23andme are Konya, Kırşehir and Gaizantep, with Konya being the only one she has confirmed ancestry from. The rest seems like allot of statistical noise and mislabeling, her distant central Asian ancestry is clearly labeled as various north and east Asian pops Native Americans pops too), such as Mongolian etc. Her Yemeni/east African % might represent the Ottoman slave trade, and the Jewish % could represent distant Jewish ancestry I guess, although I have a feeling that they all represent Mediterranean ancestry from various parts of the Med sea (she has a fair number of Sephardic DNA matches on various pile-up regions, which I guess is part of this. all in all it is much better than Vahaduo, but still very noisy and I would not take it without a grain of salt.. Impressed that hers is better than mine though, as usually northern European samples are better than west Asian ones... But I think the Turkish samples can be trimmed into four, instead of all these regional samples...
    Last edited by evon; 11-10-2019 at 03:37 PM.

  17. The Following 2 Users Say Thank You to evon For This Useful Post:

     JMcB (11-10-2019),  ph2ter (11-10-2019)

  18. #130
    Registered Users
    Posts
    3,211
    Sex
    Location
    Groningen
    Ethnicity
    Northwest European
    Nationality
    NL
    Y-DNA (P)
    E-V22

    Netherlands
    Same here Evon! From the three of us only my father comes close to the Dutch but with heavily Nordic touch. My mother looks overall excessive Scandic.

    I only took the NNW European averages.

    With 1000 cycles, 500 batches and pen=0,001

    With Iceland and Orkney:

    "sample": "Custom:AGUser_finn",
    "fit": 1.1664,
    "Icelandic": 22,
    "German": 19,
    "Norwegian": 16,
    "Swedish": 15,
    "Scottish": 14.8,
    "Dutch": 10,
    "Irish": 2.8,
    "Belgian": 0.2,
    "Orcadian": 0.2,
    "English": 0,

    "sample": "Custom:AGUser_finn_dad",
    "fit": 0.6547,
    "Dutch": 28,
    "Swedish": 21.8,
    "German": 14.8,
    "Scottish": 10.4,
    "English": 9.6,
    "Icelandic": 5.6,
    "Irish": 4.2,
    "Norwegian": 3.8,
    "Orcadian": 1.4,
    "Belgian": 0.4,

    "sample": "Custom:AGUser_finn_mom",
    "fit": 1.1764,
    "Icelandic": 40.6,
    "German": 18.8,
    "Norwegian": 17.8,
    "Scottish": 6.8,
    "Irish": 5.8,
    "Dutch": 3.2,
    "Swedish": 3.2,
    "Belgian": 1.4,
    "English": 1.2,
    "Orcadian": 1.2,

    Without iceland and Orkney
    "sample": "Custom:AGUser_finn",
    "fit": 1.2023,
    "Norwegian": 25.8,
    "German": 23.8,
    "Swedish": 22.6,
    "Scottish": 11.4,
    "Dutch": 10.4,
    "Irish": 5.4,
    "English": 0.6,
    "Belgian": 0,

    "sample": "Custom:AGUser_finn_dad",
    "fit": 0.6397,
    "Dutch": 26.8,
    "Swedish": 24.8,
    "German": 14,
    "Scottish": 13.4,
    "English": 10.6,
    "Irish": 6,
    "Norwegian": 4.4,
    "Belgian": 0,

    "sample": "Custom:AGUser_finn_mom",
    "fit": 1.277,
    "Norwegian": 26.6,
    "German": 25.6,
    "Swedish": 22.6,
    "Irish": 10.4,
    "Scottish": 8.2,
    "Dutch": 4.6,
    "Belgian": 1.2,
    "English": 0.8,

    The reason? I guess this.

    Haak 2015


    Regional differences in NW Europe in the amount HG, EEF, Steppe nears us to an average in another part of NW Europe.
    Speculative: this is due to especially my mothers Funnelbeaker area ancestry (excessive HG and also some more EEF) she comes near Iceland and when Iceland is left out then Norway comes most close. ^^^

    May be this explains in your case also something....?
    Last edited by Finn; 11-10-2019 at 08:23 PM.

  19. The Following User Says Thank You to Finn For This Useful Post:

     evon (11-11-2019)

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