Reduced my kit to the regions painted as Oriental and loaded to GEDmatch [Archive] - The Apricity Forum: A European Cultural Community

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Nurzat

11-01-2020, 06:01 PM

Hi all, has anyone else done something similar?

1. Went to GEDmatch > DNA Applications > Admixture (heritage) > Chromosome Painting > [any project you consider relevant enough, I went for Eurogenes K13]

2. Observed each chromosome for the regions painted for Oriental components (Oceanian, South Asian, Siberian, East Asian, Amerindian) and wrote down the chromosome and the region, in cM (centiMorgans), for example: chr1 165-171 cM, chr8 78-122 cM (both shorter and longer regions of such Oriental components)

3. Copied my entire raw data from the original .txt file to Excel, filtered each chromosome (1 to 22, as it's mandatory to include data for each chromosome) and position (filtered with Number filters > Between, where for 1 cM you write 1000000 for position, for example I would filter chromosome 1 for between 165000000 and 171000000 for the first chunk mentioned above); copied each such regions (hundreds to even thousands of rows, include rsid, chromosome, position and genotype, just as you see it in the file) to a blank .txt file that will become your new GEDmatch experimental kit; do it for all 22 chromosome otherwise it will go into error on upload; find at least a tiny chunk of your desired component on each chromosome; you can go for fractions of cM as well, for example I went for chr15 58.5 to 61.3 cM (filtered chr15, position between 58500000 and 61300000).

4. ensure you have at least 50,000 rows (it won't accept shorter files, I got some 62,000 rows of data)

5. upload and start investigating your selected DNA :cool:

I want to see if I get any matches for these regions and if these matches are people from the Orient. I am waiting for the kit to be processed for matches against all users, now I can only run the different calculators for it. for example:

Eurogenes K13:
North_Atlantic 19.29 Pct
Baltic 19.8 Pct
West_Med 9.17 Pct
West_Asian -
East_Med 6.48 Pct
Red_Sea 0.77 Pct
South_Asian 2.77 Pct
East_Asian 16.75 Pct
Siberian 10.02 Pct
Amerindian 10.78 Pct
Oceanian 3.07 Pct
Northeast_African -
Sub-Saharan 1.1 Pct

Eurogenes K15:
North_Sea 11.64 Pct
Atlantic 7.17 Pct
Baltic 19 Pct
Eastern_Euro 6.63 Pct
West_Med 4.9 Pct
West_Asian 0.99 Pct
East_Med 6.25 Pct
Red_Sea -
South_Asian 1.65 Pct
Southeast_Asian 16.79 Pct
Siberian 9.94 Pct
Amerindian 10.55 Pct
Oceanian 2.91 Pct
Northeast_African -
Sub-Saharan 1.59 Pct

as you can see, my Oriental chunks of DNA point mostly to Southeast Asia, East Asia, Siberia and America, the latter must be just ANE (Ancestral North Eurasian). Interestingly on 23andme, from all the Oriental components I only get under 1% Broadly Chinese & Southeast Asian, while I don't get anything else (not even MENA, which is common in southeast Europe, I get none of it - my 23andme gives 46% Greek & Balkan - Moldova region Romania, 42% Eastern European - Ivano Frankivsk region Ukraine, 1% Broadly Chinese & Southeast Asian and the rest is Broadly European).

also, although I chose the regions painted in Oriental components, there was some Baltic and Atlantic there as well, you cannot remove the components that are mixed there, the painting is mixed for the most. still I might understand more about my overall 3 to 6% Oriental genes (it differs depending on calculator).

I shared this because some of you may be interested in exploring your exotic DNA chunks in a similar way or improving it.

Nurzat

11-01-2020, 06:13 PM

MDLP K23b:
Amerindian 7.89 Pct
Ancestral_Altaic 6.23 Pct
South_Central_Asian 3.34 Pct
Arctic -
South_Indian -
Australoid 0.36 Pct
Austronesian 3.65 Pct
Caucasian 14.34 Pct
Archaic_Human -
East_African -
East_Siberian 2.53 Pct
European_Early_Farmers 10.25 Pct
Khoisan 0.26 Pct
Melano_Polynesian -
Archaic_African 0.84 Pct
Near_East 2.01 Pct
North_African 1.44 Pct
Paleo_Siberian 0.42 Pct
African_Pygmy -
South_East_Asian 3.49 Pct
Subsaharian 1.76 Pct
Tungus-Altaic 15.02 Pct
European_Hunters_Gatherers 26.17 Pct

HarappaWorld:
S-Indian 3.77 Pct
Baloch 2.48 Pct
Caucasian 9.21 Pct
NE-Euro 31.77 Pct
SE-Asian -
Siberian 4.88 Pct
NE-Asian 19.8 Pct
Papuan 1.09 Pct
American 7.29 Pct
Beringian 0.5 Pct
Mediterranean 19.2 Pct
SW-Asian -
San -
E-African -
Pygmy -
W-African -

Dodecad K12b:
Gedrosia -
Siberian 7.58 Pct
Northwest_African 2.28 Pct
Southeast_Asian 2.88 Pct
Atlantic_Med 21.02 Pct
North_European 33.2 Pct
South_Asian 3.46 Pct
East_African -
Southwest_Asian -
East_Asian 18.52 Pct
Caucasus 11.06 Pct
Sub_Saharan -

GedrosiaDNA K3:
E_Eurasian 37.88 Pct
SSA 2.28 Pct
W_Eurasian 59.84 Pct

GedrosiaDNA Ancient Eurasia K6:
Ancestral_North_Eurasian 15.68 Pct
Ancestral_South_Eurasian -
East_Asian 35.28 Pct
West_European_Hunter_Gartherer 27.6 Pct
Natufian 21.44 Pct
Sub_Saharan -

Kaspias

11-01-2020, 06:21 PM

I had done the same process without filtering other chromosomes in order to see what population my East Eurasian chromosomes will get in single population sharing. Checking relativity is another excellent idea, thank you for posting.

Kaspias

11-01-2020, 07:35 PM

@Nurzat, you had better use Dodecad K12b, that "Amerindian" is not useful for this stuff. You should focus on pure East Asian components: East_Asian, Siberian, Southeast_Asian.

Anyway, I started to do that from the beginning, this time more carefully.

This is the result of my first 3 chromosomes(I will be continuing tomorrow, wanted to give it a try now):

Component %
Gedrosia 16,30%
Siberian 19,39%
Southeast_Asian 2,27%
Atlantic_Med 2,35%
North_European 25,62%
Southwest_Asian 6,61%
East_Asian 15,29%
Caucasus 12,18%

Mixed Mode:
1 79,30% Bashkir + 20,70% Iranians @ 7,405
2 72,27% Bashkir + 27,73% Turkmens @ 7,414
3 79,30% Bashkir + 20,70% Kurd @ 7,467
4 80,08% Bashkir + 19,92% Iran_Mazandaran @ 7,477
5 70,70% Bashkir + 29,30% Turkmen_Iran @ 7,551
6 80,08% Bashkir + 19,92% Kurds @ 7,647
7 80,08% Bashkir + 19,92% Lur_Iran @ 7,670
8 79,30% Bashkir + 20,70% Iranian @ 7,710
9 58,98% Bashkir + 41,02% Turkmen_Uzbekistan @ 7,728
10 77,73% Bashkir + 22,27% Iran_Central_East @ 7,843

Least-squares method.

Using 1 populations approximation
1 100% Bashkir @ 13,445
2 100% Crimean_Tatar_Steppe @ 14,571
3 100% Uzbeks @ 14,823
4 100% Karakalpak @ 17,782
5 100% Turkmen_Uzbekistan @ 17,789
6 100% Uygur @ 22,496
7 100% Hazara @ 23,714
8 100% Kazakh @ 24,140
9 100% Tajiks @ 26,257
10 100% Turkmen_Iran @ 27,516

Using 2 populations approximation
1 50% Bashkir + 50% Turkmen_Uzbekistan @ 8,125
2 50% Bashkir + 50% Uzbeks @ 9,275
3 50% Hazara + 50% Chuvashs @ 9,894
4 50% Bashkir + 50% Turkmen_Iran @ 10,761
5 50% Bashkir + 50% Tajiks @ 11,118
6 50% Bashkir + 50% Crimean_Tatar_Steppe @ 11,420
7 50% Bashkir + 50% Turkmens @ 11,616
8 50% Crimean_Tatar_Steppe + 50% Uzbeks @ 11,639
9 50% Uygur + 50% Chuvashs @ 12,052
10 50% Bashkir + 50% Uygur @ 12,360

Using 3 populations approximation
1 33% Kyrgyz_Bishkek + 33% Turkmens + 33% Chuvashs @ 7,222
2 33% Bashkir + 33% Bashkir + 33% Turkmen_Iran @ 7,679
3 33% Kazakh + 33% Tajiks + 33% Chuvashs @ 7,689
4 33% Bashkir + 33% Bashkir + 33% Turkmens @ 7,740
5 33% Turkmen_Uzbekistan + 33% Uygur + 33% Chuvashs @ 7,760
6 33% Bashkir + 33% Bashkir + 33% Turkmen_Uzbekistan @ 7,981
7 33% Karakalpak + 33% Turkmen_Uzbekistan + 33% Chuvashs @ 8,179
8 33% Uzbeks + 33% Uzbeks + 33% Chuvashs @ 8,226
9 33% Bashkir + 33% Bashkir + 33% Tajiks @ 8,570
10 33% Chuvashs + 33% AFG_Tajik + 33% Altai @ 9,004

Using 4 populations approximation
1 25% Bashkir + 25% Bashkir + 25% Bashkir + 25% Turkmens @ 7,500
2 25% Bashkir + 25% Bashkir + 25% Bashkir + 25% Turkmen_Iran @ 7,745
3 25% Bashkir + 25% Bashkir + 25% Bashkir + 25% Iranians @ 7,786
4 25% Bashkir + 25% Bashkir + 25% Bashkir + 25% Kurd @ 7,866
5 25% Bashkir + 25% Bashkir + 25% Bashkir + 25% Iran_Mazandaran @ 7,920
6 25% Bashkir + 25% Bashkir + 25% Bashkir + 25% Iran_Central_East @ 7,964
7 25% Uzbeks + 25% Uzbeks + 25% Uzbeks + 25% Chuvashs @ 8,063
8 25% Bashkir + 25% Bashkir + 25% Bashkir + 25% Iranian @ 8,101
9 25% Bashkir + 25% Bashkir + 25% Bashkir + 25% Lur_Iran @ 8,119
10 25% Kazakh + 25% Kazakh + 25% Tajiks + 25% Chuvashs @ 8,150

Works perfectly tbh.

Nurzat

11-01-2020, 07:43 PM

...

how do you get to run single segments or chromosomes? do you do it in R with the DIY kit? if I remove Amerindian (which is probably just ANE for non-Native Americans) I go below 50,000 data rows, so GEDmatch would not load the kit. if I can do this easier it'd be great, what you have above is a Dodecad K12b ran in R?

Kaspias

11-01-2020, 07:48 PM

how do you get to run single segments or chromosomes? do you do it in R with the DIY kit? if I remove Amerindian (which is probably just ANE for non-Native Americans) I go below 50,000 data rows, so GEDmatch would not load the kit. if I can do this easier it'd be great, what you have above is a Dodecad K12b ran in R?

Try to do it in Dodecad K12b, maybe you can pass 50.000 already, chromosome sharing there is slightly different than Eurogenes K13. You may be more broad while selecting segments(like 170-172 except for 170,2-171,8. It would make a great contribution to quantity)

I use AdmixtureStudio from DNAGenics to run incompleted data's, and DNAKitStudio while extracting segments.

For example, the result above was created by these:

Chromosome,Start Point,End Point
1,18000000,19000000
1,56800000,57500000
1,81300000,8500000
1,152000000,154000000
1,175000000,178000000
1,194000000,198000000
1,244500000,245500000
2,12800000,13900000
2,15500000,17000000
2,44500000,46200000
2,47000000,50000000
2,67800000,70500000
2,99500000,101100000
2,127000000,131000000
2,138000000,139500000
2,207000000,213500000
2,241500000,243000000
3,5000000,9000000
3,18000000,21500000
3,72000000,73000000
3,140500000,151000000
3,153500000,160000000
3,171400000,174200000
3,177000000,179000000
3,185000000,186000000
3,193000000,194000000

Kaspias

11-02-2020, 02:36 PM

Process report:

I'm on the 12th chromosome, have to give a break again, it is too painful!

Component %
Gedrosia 5,77%
Siberian 16,68%
Northwest_African 2,93%
Southeast_Asian 2,57%
Atlantic_Med 7,60%
North_European 24,25%
South_Asian 2,15%
Southwest_Asian 5,99%
East_Asian 18,76%
Caucasus 13,29%

Mixed Mode:
1 88,67% Crimean_Tatar_Steppe + 11,33% Oroqen @ 5,996
2 87,11% Crimean_Tatar_Steppe + 12,89% Buryat @ 6,125
3 87,11% Crimean_Tatar_Steppe + 12,89% Tuva @ 6,143
4 75,39% Crimean_Tatar_Steppe + 24,61% Kazakh @ 6,254
5 83,98% Crimean_Tatar_Steppe + 16,02% Altai @ 6,327
6 80,08% Crimean_Tatar_Steppe + 19,92% Kyrgyz_Bishkek @ 6,334
7 79,30% Crimean_Tatar_Steppe + 20,70% Kyrgyz @ 6,343
8 85,55% Crimean_Tatar_Steppe + 14,45% Mongol @ 6,387
9 73,05% Karakalpak + 26,95% Bosnian @ 6,444
10 67,58% Crimean_Tatar_Steppe + 32,42% Karakalpak @ 6,487

Least-squares method.

Using 1 populations approximation
1 100% Crimean_Tatar_Steppe @ 9,109
2 100% Bashkir @ 13,886
3 100% Karakalpak @ 14,942
4 100% Uzbeks @ 16,732
5 100% Turkmen_Uzbekistan @ 20,399
6 100% Kazakh @ 21,134
7 100% Uygur @ 22,394
8 100% Hazara @ 25,311
9 100% Kyrgyz @ 25,614
10 100% Kyrgyz_Bishkek @ 26,659

Using 2 populations approximation
1 50% Crimean_Tatar_Steppe + 50% Karakalpak @ 7,387
2 50% Crimean_Tatar_Steppe + 50% Bashkir @ 8,473
3 50% Kyrgyz_Bishkek + 50% Pomak @ 8,650
4 50% Kyrgyz + 50% Pomak @ 8,676
5 50% Crimean_Tatar_Steppe + 50% Crimean_Tatar_Steppe @ 9,109
6 50% Pomak + 50% Altai @ 9,138
7 50% Altai + 50% Bulgarian @ 9,163
8 50% Kyrgyz + 50% Bosnian @ 9,220
9 50% Crimean_Tatar_Steppe + 50% Kazakh @ 9,226
10 50% Altai + 50% Romanians @ 9,253

Using 3 populations approximation
1 33% Assyrian + 33% Oroqen + 33% FIN30 @ 5,228
2 33% Assyrian + 33% Oroqen + 33% Finnish @ 5,393
3 33% Russian + 33% Lebanese + 33% Oroqen @ 5,596
4 33% Oroqen + 33% Druze + 33% FIN30 @ 6,186
5 33% Oroqen + 33% Georgia_Jews + 33% FIN30 @ 6,187
6 33% Oroqen + 33% Druze + 33% Finnish @ 6,416
7 33% Oroqen + 33% Georgia_Jews + 33% Finnish @ 6,465
8 33% Crimean_Tatar_Steppe + 33% Crimean_Tatar_Steppe + 33% Karakalpak @ 6,491
9 33% Crimean_Tatar_Steppe + 33% Crimean_Tatar_Steppe + 33% Kazakh @ 6,669
10 33% Morocco_Jews + 33% Mordovians + 33% Oroqen @ 6,779

Using 4 populations approximation
1 25% Crimean_Tatar_Steppe + 25% Crimean_Tatar_Steppe + 25% Crimean_Tatar_Steppe + 25% Kazakh @ 6,255
2 25% Crimean_Tatar_Steppe + 25% Crimean_Tatar_Steppe + 25% Bashkir + 25% Karakalpak @ 6,416
3 25% Crimean_Tatar_Steppe + 25% Crimean_Tatar_Steppe + 25% Crimean_Tatar_Steppe + 25% Kyrgyz @ 6,475
4 25% Crimean_Tatar_Steppe + 25% Crimean_Tatar_Steppe + 25% Crimean_Tatar_Steppe + 25% Kyrgyz_Bishkek @ 6,524
5 25% Karakalpak + 25% Karakalpak + 25% Karakalpak + 25% Bosnian @ 6,531
6 25% Crimean_Tatar_Steppe + 25% Crimean_Tatar_Steppe + 25% Crimean_Tatar_Steppe + 25% Karakalpak @ 6,643
7 25% Crimean_Tatar_Steppe + 25% Crimean_Tatar_Steppe + 25% Bashkir + 25% Kazakh @ 6,660
8 25% Karakalpak + 25% Karakalpak + 25% Karakalpak + 25% Croat @ 6,703
9 25% Karakalpak + 25% Karakalpak + 25% Karakalpak + 25% Ukranians @ 6,823
10 25% Karakalpak + 25% Karakalpak + 25% Karakalpak + 25% Hungarians @ 6,840

Segments extracted:

I have more than 170.000 inputs already.

Chromosome,Start Point,End Point
1,18000000,19000000
1,56800000,57500000
1,81300000,8500000
1,152000000,154000000
1,175000000,178000000
1,194000000,198000000
1,244500000,245500000
2,12800000,13900000
2,15500000,17000000
2,44500000,46200000
2,47000000,50000000
2,67800000,70500000
2,99500000,101100000
2,127000000,131000000
2,138000000,139500000
2,207000000,213500000
2,241500000,243000000
3,5000000,9000000
3,18000000,21500000
3,72000000,73000000
3,140500000,151000000
3,153500000,160000000
3,171400000,174200000
3,177000000,179000000
3,185000000,186000000
3,193000000,194000000
4,5500000,5800000
4,95000000,104000000
4,114000000,121500000
4,145000000,151000000
4,156000000,163000000
4,169500000,170100000
4,171100000,172500000
4,180500000,185300000
5,0000001,2500000
5,9000000,10000000
5,11600000,21000000
5,33000000,35000000
5,39000000,40100000
5,68500000,73700000
5,76000000,78000000
5,101000000,106000000
5,122500000,123500000
5,146500000,147500000
5,150000000,151000000
5,166500000,168000000
5,168700000,169200000
5,176000000,177000000
5,179000000,180000000
6,0750000,1420000
6,20000000,21600000
6,22800000,24000000
6,40800000,41500000
6,52500000,55000000
6,65500000,69000000
6,73500000,80500000
6,99500000,108000000
6,112000000,113000000
6,143000000,145000000
6,150000000,153500000
7,0500000,3800000
7,6300000,7600000
7,9500000,15000000
7,19800000,20500000
7,27500000,28000000
7,31200000,32000000
7,34600000,38200000
7,42500000,57100000
7,70500000,72000000
7,154800000,159000000
8,0000001,1300000
8,24000000,39000000
8,50000000,62500000
8,85000000,16000000
8,39000000,40900000
8,53000000,65100000
8,70800000,79000000
8,99500000,101000000
8,111000000,114000000
8,115500000,116500000
8,127500000,129000000
9,0000001,1100000
9,4000000,5000000
9,6000000,9700000
9,77000000,78250000
9,111400000,112800000
9,119750000,120500000
9,131500000,134500000
9,137000000,140000000
10,0000001,1400000
10,5000000,5850000
10,16500000,17500000
10,18800000,19000000
10,34500000,49000000
10,54000000,62000000
10,67000000,70000000
10,71500000,82500000
10,91000000,92000000
10,102500000,103200000
10,130500000,131500000
11,32800000,34800000
11,58000000,61500000
11,108000000,110500000
11,134000000,134400000
12,0000001,0000007
12,4900000,9250000
12,43300000,45000000
12,47000000,50000000
12,54500000,55150000
12,56200000,57500000
12,63500000,65500000
12,78500000,83100000
12,105650000,106500000

Nurzat

11-02-2020, 05:34 PM

thanks for the hint, downloaded Admixture Studio v2.50.

LM Genetics K47

Tibeto-Burman 1.97
South-Caucasian 6.06
Paleo-Balkan 11.69
Turkic-Altai 7.33
Central-African_HG 1.43
Mongolian 1.50
Siberian 0.28
North-Sea_Germanic 15.87
Uralic 8.12
East-Asian 21.25
Amuro-Manchurian 18.16
Scando-Germanic 2.01
Iranian 0.39
Baltic 3.92

Using 4 populations approximation
1 25% Japanese + 25% Japanese + 25% Turkmen_UZB + 25% French_Northwest @ 24.040
2 25% Japanese + 25% Japanese + 25% Turkmen_UZB + 25% Icelandic @ 24.172
3 25% Japanese + 25% Japanese + 25% Nogay + 25% French_Northwest @ 24.201
4 25% Japanese + 25% Japanese + 25% Nogay + 25% Icelandic @ 24.350

LM Genetics Global K3

Components %
Negroid 1.17
Europeid 41.11
Mongoloid 57.72

Michal Baltic Baikal Japanese K29

Components %
Mordva 1.52
Chuvash 12.76
Chechen 6.10
Adygei 11.73
Kabardin 2.02
Megrel 5.16
Ukrainian 5.91
Cherkes 1.39
Abkhaz 1.02
Uzbek 4.08
Russian_STV 1.43
Yakut 14.44
Japanese 32.44

do you know if I can run my own calculators/populations or can I edit existing calculators in Admixture Studio?

Kaspias

11-03-2020, 12:24 PM

Nurzat

04-03-2021, 06:55 PM

Try to check the Calculators folder, maybe you can. You can use Vahaduo, too.

Have your matches batched?

yes, but I get no matches, as the threshold for this on GedMATCH is too high, 7cM :(

maybe if I upload it to MyHeritage I'd get something, will try that.

this also as a bump to the thread, which I think brings an interesting method to look at someone's exotic DNA chunks, at least for fun.

with the new update on 23andme my Asian got now refined to Mongol & Manchurian

Kaspias

04-03-2021, 08:09 PM

yes, but I get no matches, as the threshold for this on GedMATCH is too high, 7cM :(

maybe if I upload it to MyHeritage I'd get something, will try that.

this also as a bump to the thread, which I think brings an interesting method to look at someone's exotic DNA chunks, at least for fun.

with the new update on 23andme my Asian got now refined to Mongol & Manchurian

It actually worked for me. I get like 150 matches. 2 Crimean Tatars, 2 Volga Tatars, 4 Balkan Turks, 1 Anatolian Turkish from Balıkesir. Many Ukrainians, Poles, and few Chinese.

If there would be an option to set the threshold limit to lower than 7 it would work perfectly.