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Thread: Gedmatch calculators on Vahaduo

  1. #201
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    Quote Originally Posted by Lemgrant View Post
    but it is better than k13 in your case. You are closer to Irish/Orcadian/Scottish cluster in EUtest than in k13. In k13 you are closer to Dutch from 2x adc results.

    also try the pca tool: https://lemgrant.github.io/eutest2dpca/

    Code:
    name,SOUTH_BALTIC,EAST_EURO,NORTH-CENTRAL_EURO,ATLANTIC,WEST_MED,EAST_MED,WEST_ASIAN,MIDDLE_EASTERN,SOUTH_ASIAN,EAST_AFRICAN,EAST_ASIAN,SIBERIAN,WEST_AFRICAN
    Thanks that's a great tool.

    The Irish Brigade's battle cry at Fontenoy, "Cuimhnigí ar Luimneach agus ar feall na Sasanaigh," translates to "Remember Limerick and the treachery of the English." After seeing the devastation caused by the Irish Brigade, the Duke of Cumberland reportedly remarked, "God curse the laws that made those men our enemies".


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    Quote Originally Posted by Grace O'Malley View Post
    Thanks that's a great tool.

    No Amerimutt here : strictly British isles. I'll take a martini shaken but not stirred :




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    Quote Originally Posted by JamesBond007 View Post
    No Amerimutt here : strictly British isles. I'll take a martini shaken but not stirred :



    That's just where you plot. You are still a product of all your ancestries. Gosh you are desperate to be British. If I plot as Dutch do I go around calling myself Dutch or Orcadian etc? I thought you said all this stuff was not to be taken seriously? Perhaps you should heed your own advice.
    The Irish Brigade's battle cry at Fontenoy, "Cuimhnigí ar Luimneach agus ar feall na Sasanaigh," translates to "Remember Limerick and the treachery of the English." After seeing the devastation caused by the Irish Brigade, the Duke of Cumberland reportedly remarked, "God curse the laws that made those men our enemies".


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    Quote Originally Posted by Grace O'Malley View Post
    Thanks that's a great tool.

    you score some Scandinavian on 23andme?

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    Quote Originally Posted by Lemgrant View Post
    you score some Scandinavian on 23andme?
    No mostly all British & Irish. I used to score a tiny amount but with trace these come and go. Modern dna companies are just comparing you against people of your own ethnicity and the British & Irish category is very much geared to Irish. On Ancestry I'm 100% Ireland & Scotland.
    The Irish Brigade's battle cry at Fontenoy, "Cuimhnigí ar Luimneach agus ar feall na Sasanaigh," translates to "Remember Limerick and the treachery of the English." After seeing the devastation caused by the Irish Brigade, the Duke of Cumberland reportedly remarked, "God curse the laws that made those men our enemies".


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    Quote Originally Posted by Grace O'Malley View Post
    No mostly all British & Irish. I used to score a tiny amount but with trace these come and go. Modern dna companies are just comparing you against people of your own ethnicity and the British & Irish category is very much geared to Irish. On Ancestry I'm 100% Ireland & Scotland.
    can you post your 23andme results at 90% confidence level?

    https://customercare.23andme.com/hc/...ry-Composition

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    Quote Originally Posted by Grace O'Malley View Post
    That's just where you plot. You are still a product of all your ancestries. Gosh you are desperate to be British. If I plot as Dutch do I go around calling myself Dutch or Orcadian etc? I thought you said all this stuff was not to be taken seriously? Perhaps you should heed your own advice.
    If you raise a pig in a horses stable does that make it a horse ?

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    Quote Originally Posted by Lemgrant View Post
    can you post your 23andme results at 90% confidence level?

    https://customercare.23andme.com/hc/...ry-Composition
    No problems.

    The Irish Brigade's battle cry at Fontenoy, "Cuimhnigí ar Luimneach agus ar feall na Sasanaigh," translates to "Remember Limerick and the treachery of the English." After seeing the devastation caused by the Irish Brigade, the Duke of Cumberland reportedly remarked, "God curse the laws that made those men our enemies".


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    Quote Originally Posted by Grace O'Malley View Post
    No problems.

    that's close to your EUtest results at 0x, 0.25x adc

    Target: Grace
    Distance: 3.1696% / 3.16960499 | ADC: 0.5x
    76.2 Orcadian
    11.8 South_&_Central_Swedish
    11.4 Scottish
    0.6 Lezgin

    Target: Grace
    Distance: 2.4577% / 2.45774713 | ADC: 0.25x
    67.6 Scottish
    30.0 South_&_Central_Swedish
    2.4 German

    Target: Grace
    Distance: 2.4318% / 2.43184921
    65.8 Scottish
    31.2 South_&_Central_Swedish
    3.0 German

    https://www.23andme.com/ancestry-composition-guide/
    This is the output of the smoother analysis of one copy of chromosome 2. Starting on the left, there is a short run of pink, then a wider run of green, then another run of pink. In this chart, pink is the color for Sub-Saharan African ancestry, and green is the color for Native American. The y-axis runs from 0 to 100 percent, and it shows the probability that the DNA in that region of the chromosome comes from each Ancestry Composition population. These pink and green regions fill the entire vertical space of the graph, which means that we are 100 percent confident that the DNA in those regions has Sub-Saharan African and Native American genetic ancestry, respectively.

    The next region to the right — between positions 50 and 100 on the x-axis — is a stretch of multi-colored blue. The thickest strip at the bottom is dark teal, which is the color for British & Irish. This segment of DNA has somewhere between a 50 percent chance and a 60 percent chance of reflecting from British & Irish ancestry. The other shades of blue show that the same DNA segment also has a chance of reflecting Italian, Iberian, or French & German ancestry. If you think back to the haplogroup example above, this result makes sense: it is normal for a DNA marker to match reference DNA from lots of places, even if it matches some places better than others. In this example, the result shows that this DNA segment matches reference DNA from all over Europe. We can very confidently conclude that this stretch of DNA reflects European ancestry, but the evidence isn't strong enough to assign it to one specific region of Europe with high confidence.

    Step 4: Re-calibration
    This plot shows a lot of information, but how do we know it's correct? We use a calibration step to correct for systematic bias.

    First, we ran some tests to establish whether we needed to correct for any bias. To do so, we simulated a large set of admixed individuals. Because we simulated them ourselves, we knew the "true" ancestry of each part of their genome. Then we ran these simulated individuals through the entire Ancestry Composition pipeline, and we compared their results with their true ancestries.

    We found that most of the reference populations were already fairly well calibrated, which means the ancestry probabilities we estimated closely matched the empirical results. But there were a few populations, in particular the Scandinavian and Balkan reference populations, that required some adjustment.

    To correct these probability estimates, we developed a re-calibration step that adjusts the ancestry proportions produced by the smoother so that each population is assigned in proportion to how often it actually occurs.

    Step 5: Aggregation & Reporting
    The last step is to summarize the results and display them in your Chromosome Painting. The way we do this is to apply a threshold to the probability plot as in this figure:


    The horizontal line in this image indicates a 70 percent confidence threshold, which we will use for this example. You can view your own Chromosome Painting at different confidence thresholds ranging from 50 percent (speculative) to 90 percent (conservative).

    We look across the entire chromosome and ask whether any ancestry has an estimated probability exceeding the specified threshold (in this case 70 percent). In this example, with the exception of the blue European stretch, the ancestry estimates exceed 70 percent over the majority of the chromosome. Each region contributes to your overall Ancestry Composition in proportion to its size: For example, the green Native American segment near the end of this plot makes up about 0.26 percent of the entire genome. Even though there is some probability that the segment comes from a different population, the Native American proportion exceeds the 70 percent threshold, and so we add 0.26 percent Native American to the overall Ancestry Composition at this threshold.

    In the case of the European segment, no single ancestry exceeds the 70 percent threshold, so we don't assign that DNA to any fine-grained ancestries. Instead, we refer to our hierarchy of ancestries. There is a Broadly Northern European ancestry that includes four fine-level ancestries: British & Irish, Scandinavian, Finnish, and French & German. If, when we add up the contributions of each of these subgroups, the total contribution toward Broadly Northern European exceeds the 70 percent threshold, then we will report the region as Broadly Northern European.

    In this example, the Broadly Northern European reference populations still don't exceed the 70 percent threshold, but the combined probabilities of all the European populations do. So this region is assigned Broadly European ancestry.

    We use broad Ancestry Composition categories to avoid making assumptions about your ancestry when your DNA matches several different country-level populations. In regions where no ancestry — including the broad ancestries — exceeds the specified threshold, we report Unassigned ancestry. You can see the entire ancestry hierarchy in your Ancestry Composition report by clicking "See all tested populations."

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    Father

    K13
    Distance to: Dad
    4.10701838 Russian_Smolensk
    4.63800604 Estonian_Polish
    5.69217884 Lithuanian
    6.02474896 Belorussian
    6.36462096 Kargopol_Russian
    6.48374120 Southwest_Russian
    6.54298097 Ukrainian_Belgorod
    6.64012048 Cossacks_Kuban
    6.91393520 Polish
    8.22541792 Estonian
    8.56315946 Ukrainian
    8.90010674 Erzya
    9.78843195 Ukrainian_Lviv
    10.67548125 South_Polish
    10.72325044 East_Finnish
    11.53281405 Finnish
    14.94786607 Southwest_Finnish
    16.19407916 Czech
    17.28545921 Croatian
    20.30789502 Moldavian
    21.74784127 Hungarian
    22.19717324 East_German
    23.02870166 North_Swedish
    23.69651873 Tatar
    23.94240798 Serbian_Bosnia

    Target: Dad
    Distance: 2.2006% / 2.20058529
    75.4 Lithuanian
    17.2 Erzya
    3.0 Sardinian
    1.6 French_Basque
    1.6 Kabardin
    1.2 Kalash

    K15
    Distance to: Dad
    4.28070088 Estonian_Polish
    5.55037837 Southwest_Russian
    6.11714803 Belorussian
    6.33441394 Ukrainian_Belgorod
    6.34936217 Russian_Smolensk
    8.37834709 Kargopol_Russian
    8.66419644 Lithuanian
    8.84724251 Polish
    9.82215862 Erzya
    10.94472476 South_Polish
    11.28490585 Ukrainian
    11.93082981 Estonian
    12.78882715 Ukrainian_Lviv
    14.89130283 East_Finnish
    16.38241130 Croatian
    18.19792296 Finnish
    18.79384474 Moldavian
    19.34038521 Southwest_Finnish
    20.74253360 Hungarian
    21.25009412 Austrian
    22.22782490 East_German
    22.86254142 Tatar
    25.65222408 Serbian
    27.76688855 North_Swedish
    28.37943446 Romanian

    Target: Dad
    Distance: 3.2957% / 3.29566496
    77.2 Estonian_Polish
    22.8 Erzya

    EUtest
    Distance to: Dad
    5.08226328 Northwest_Russian
    5.87823953 Ukrainian-Russian
    5.98392012 Belorussian
    6.04619715 West_Russian
    8.14204520 Ukrainian
    8.73492416 Lithuanian
    9.08970297 Estonian
    9.22799545 Polish
    9.60285895 East_Russian
    9.81746912 North_Russian
    11.33745121 Erzya
    13.31471742 East_Finnish
    15.35368360 South_Finnish
    15.41366926 Slovakian_1
    16.86811526 Czech
    18.04451243 Croatian
    18.40419246 Slovenian_1
    20.65300220 Komi
    20.73444477 Udmurt
    20.91812611 Hungarian
    21.05056769 Moldavian_1
    21.87743986 SerbianBosnia
    22.88133519 North_Swedish
    25.12897133 Austrian
    26.62433661 South_&_Central_Swedish

    Target: Dad
    Distance: 3.4436% / 3.44360605
    69.2 Northwest_Russian
    7.6 East_Russian
    7.2 Erzya
    6.0 Lithuanian
    6.0 Ukrainian-Russian
    3.4 Kalash
    0.6 Sardinian

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