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.
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.
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
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