Gedmatch calculators on Vahaduo

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03-19-2021, 08:57 PM
Lucas

Quote:

Originally Posted by vbnetkhio

then it's probably hg18, which isn't offered here..

Maybe, but even one snp wasn't converted?
03-19-2021, 09:12 PM
vbnetkhio

Quote:

Originally Posted by Lucas

Maybe, but even one snp wasn't converted?

maybe that's how it is with bams.

can you check this?
http://genometoolbox.blogspot.com/20...8-or-hg19.html

edit:
or this, if there's no header:

Code:

samtools view filename.bam | head -n 5
03-19-2021, 09:47 PM
Lucas

Quote:

Originally Posted by vbnetkhio

maybe that's how it is with bams.

can you check this?
http://genometoolbox.blogspot.com/20...8-or-hg19.html

edit:
or this, if there's no header:

Code:

samtools view filename.bam | head -n 5

samtools view -H filename.bam
This command should show only header, but it shows thousands lines and I'm still waiting for end of this shit:)

This shows me this:)
https://i.imgur.com/KnpsWVW.png
03-19-2021, 09:58 PM
vbnetkhio

Quote:

Originally Posted by Lucas

samtools view -H filename.bam
This command should show only header, but it shows thousands lines and I'm still waiting for end of this shit:)

This shows me this:)
https://i.imgur.com/KnpsWVW.png

could this actually be fastq files, labelled as BAM?

fastq files have lines like this (with the "HWUSI", etc.)
https://en.wikipedia.org/wiki/FASTQ_...ce_identifiers
03-19-2021, 10:50 PM
Lucas

Quote:

Originally Posted by vbnetkhio

could this actually be fastq files, labelled as BAM?

fastq files have lines like this (with the "HWUSI", etc.)
https://en.wikipedia.org/wiki/FASTQ_...ce_identifiers

Yes.... possible:) Those who made it are not the smartest ones geneticists.
03-21-2021, 01:37 PM
vbnetkhio

Quote:

Originally Posted by Lucas

Yes.... possible:) Those who made it are not the smartest ones geneticists.

they are in hg19 according to the study. did you try running them trough fastq to bam?
03-22-2021, 12:38 AM
Dick

Quote:

Originally Posted by Lucas

Yes.... possible:) Those who made it are not the smartest ones geneticists.

Are you implying they're not Slavs
03-23-2021, 07:39 PM
Leto

@Lucas,
You've ignored me for some reason but I'm trying to unify the name on Dodecad K12b 'cause there is an unnecessary discrepancy going on there.
Please delete these:
Iran_Arab, Iraqi_Arab, Lur_Iran, Iraqi_Turkmen, Iran_Bandari, Iran_Mazandaran, Iran_Khorasan, Yagnobi
and replace them with these:

Code:

Arab_Iran,18.52,0.29,2.61,0.21,6.69,3.63,4.18,3.35,23.35,0.45,34.63,1.87 Arab_Iraq,16.56,0.45,2.95,0.27,8.15,3,3.31,3.67,25.43,0.78,33.56,1.82 Iranian_Bandari,35.42,0.33,0.37,0.70,2.01,6.42,11.00,1.81,11.25,0.00,25.24,5.46 Iranian_Khorasan,28.01,1.89,0.34,0.29,6.34,9.65,7.63,0.44,10.14,2.84,32.17,0.26 Iranian_Lur,27.78,1.32,0.8,0.37,6.35,4.08,4.03,0.5,14.64,0.61,39.33,0.2 Iranian_Mazandaran,33.07,0.48,0.25,0.26,2.86,5.68,5.27,0.32,10.96,0.26,40.38,0.19 Turkmen_Iraq,21.88,1.97,1.20,0.49,7.52,5.40,4.10,0.79,16.48,1.12,38.44,0.59 Yaghnobi_Tajikistan,30.81,3.92,0,0.44,7.54,22.11,5.62,0,4.15,2.22,23.18,0

(Yaghnobi is also recalculated, so it's a tiny bit different)

- - - - - -

Adding the Russian average is up to you.
03-23-2021, 11:43 PM
Lucas

Quote:

Originally Posted by Leto

@Lucas,
You've ignored me for some reason but I'm trying to unify the name on Dodecad K12b 'cause there is an unnecessary discrepancy going on there.
Please delete these:
Iran_Arab, Iraqi_Arab, Lur_Iran, Iraqi_Turkmen, Iran_Bandari, Iran_Mazandaran, Iran_Khorasan, Yagnobi
and replace them with these:

Code:

Arab_Iran,18.52,0.29,2.61,0.21,6.69,3.63,4.18,3.35,23.35,0.45,34.63,1.87 Arab_Iraq,16.56,0.45,2.95,0.27,8.15,3,3.31,3.67,25.43,0.78,33.56,1.82 Iranian_Bandari,35.42,0.33,0.37,0.70,2.01,6.42,11.00,1.81,11.25,0.00,25.24,5.46 Iranian_Khorasan,28.01,1.89,0.34,0.29,6.34,9.65,7.63,0.44,10.14,2.84,32.17,0.26 Iranian_Lur,27.78,1.32,0.8,0.37,6.35,4.08,4.03,0.5,14.64,0.61,39.33,0.2 Iranian_Mazandaran,33.07,0.48,0.25,0.26,2.86,5.68,5.27,0.32,10.96,0.26,40.38,0.19 Turkmen_Iraq,21.88,1.97,1.20,0.49,7.52,5.40,4.10,0.79,16.48,1.12,38.44,0.59 Yaghnobi_Tajikistan,30.81,3.92,0,0.44,7.54,22.11,5.62,0,4.15,2.22,23.18,0

(Yaghnobi is also recalculated, so it's a tiny bit different)

- - - - - -

Adding the Russian average is up to you.

No, I was just busy. Added:)
03-25-2021, 02:04 AM
Dr_Maul

Quote:

Originally Posted by Lucas

No, I was just busy. Added:)

Now there are 2 identical averages with different names in it
Lur_Iran and Iranian_Lur (for naming purposes you should remove Lur_Iran)
Edit: same for Arab_Iraq and Iraq_arab
03-25-2021, 11:20 PM
Leto

For Euro K13
Instead of Erzya_Mordovian

Code:

Mordovian,22.53,47.66,6.87,7.66,3.52,0.71,1.62,1.04,6.12,1.30,0.53,0.24,0.20

(Can be also used as a proxy for "Eastern Russian", although in terms of IBD sharing Mordovians and Russians are markedly different)

Instead of Russian_Pinega (some Pinega kits were used for this one too)

Code:

Russian_Northern_Dvina,26.52,49.43,5.57,4.65,1.14,0.51,0.99,0.44,8.60,1.19,0.47,0.17,0.34

https://en.wikipedia.org/wiki/Northern_Dvina

For Dodecad K12b
Instead of Russian_Arkhangelsk

Code:

Russian_Northern_Dvina,3.41,8.26,0.08,0.49,17.35,60.85,0.64,0,0.55,1.13,7.23,0

I wanted to do two more Finno-Ugric pops for K13 but sadly the kits I had are now deleted.
03-26-2021, 07:45 PM
smd555

Does anybody have these Lithuanian regional averages, but in K-13?:

Quote:

Lithuanian_PA,0.1337421,0.1241485,0.0796195,0.074613,0.0421616, 0.0291092,0.0087244,0.0134128,-0.0037324,-0.0263102,-0.0035118,-0. 091044,0.0186756,0.0266472,-0.0118755,0.0034972,0.0042865,0.0010292,0.0039282, 0.0012351,-0.0060519,-0.0032921,0.0093979,-0.006552,-0.0002845
Lithuanian_PZ,0.1356773,0.1255195,0.0883971,0.0871131,0.044562, 0.035447,0.0106459,0.0156685,-0.0030065,-0.0347524,-0.0067879,-0.0129784,0.0230573,0.0315155,-0.0071118,-0.0032219,-0.0034813,-0.0016344,0.000817,0.0034265,-0.0023459,-0.0059477,0.0084426,-0.0090132,0.0005148
Lithuanian_RA,0.135108,0.1240977,0.083306,0.0805239,0.0431158,0 .0294229,0.0123146,0.015207,-0.0044994,-0.0323469,-0.0030203,-0.012469,0.0240532,0.0300018,-0.0152957,0.0017237,0.0070014,-0.0013936,0.00494,0.0030138,-0.0053282,-0.0060342,0.010057,-0.0066392,-0.0003714
Lithuanian_SZ,0.1347664,0.1258242,0.0861344,0.0877268,0.0448392 ,0.0315424,0.0128081,0.0185529,-0.0019633,-0.0353537,-0.0039137,-0.0127386,0.0235031,0.0296026,-0.0123914,0.0018563,0.005111,-0.0012796,0.0020866,0.0021511,-0.0029574,-0.0067636,0.0070251,-0.0104229,0.0029337
Lithuanian_VA,0.1344249,0.1257226,0.0824762,0.0750975,0.0433311 ,0.027889,0.0099878,0.014884,-0.0020454,-0.0298685,-0.0029553,-0.0138328,0.0200394,0.0280062,-0.0110613,0.0029435,0.0061411,-0.0005702,0.0023129,0.0061155,-0.003731,-0.00481,0.0072346,-0.0078805,-0.0008622
Lithuanian_VZ,0.1372991,0.1261795,0.0850879,0.082365,0.0444314, 0.0326652,0.0104872,0.0176242,-0.0036048,-0.0315269,-0.0036131,-0.0097039,0.0199762,0.0301394,-0.0104505,-0.0045578,-0.0006029,0.0012828,0.0032525,0.0013445,-0.0043829,-0.0056728,0.00835,-0.005874,-0.001317
03-26-2021, 08:53 PM
Peterski

Quote:

Originally Posted by smd555

Does anybody have these Lithuanian regional averages, but in K-13?:

I can calculate.
03-26-2021, 09:19 PM
Leto

Quote:

Originally Posted by Peterski

I can calculate.

Hey Piotr, please calculate Komi and Udmurt for K13. I'm sure you know that old data, I had the kits but they're deleted now, I don't know who else can do it.
03-27-2021, 06:03 PM
smd555

Quote:

Originally Posted by Peterski

I can calculate.

It would be great!
03-27-2021, 07:28 PM
Leto

Some more renaming: instead of Sweden, Norway and Denmark

Code:

Danish,50.61,28.70,10.19,5.00,2.12,0.52,0.99,0.19,0.42,0.59,0.23,0.12,0.17 Norwegian_South_Central,50.83,28.97,9.61,4.78,1.91,0.62,0.94,0.11,0.63,0.68,0.56,0.13,0.23 Swedish_Götaland,50.53,29.29,9.86,4.67,1.88,0.62,0.93,0.21,0.69,0.55,0.41,0.18,0.2 Swedish_Svealand_East,46.74,34.13,8.85,3.92,1.19,0.53,0.97,0.27,1.69,0.86,0.56,0.19,0.12 Swedish_Svealand_West,49.72,30.6,9.57,4.11,1.75,0.46,1.03,0.19,1.05,0.53,0.45,0.27,0.27
03-28-2021, 01:04 PM
Kyp

For Dodecadk12b:

Code:

Iranian_Fars,27.45,0.89,1.31,0.74,5.59,6.25,6.10,1.25,14.09,1.23,34.77,0.33 Kurd_Feyli,27.47,1.12,1.26,0.33,4.98,5.36,3.77,0.34,14.60,0.30,40.12,0.14 Iranian_Kerman,29.71,0.99,0.30,0.21,6.09,8.31,7.60,0.85,12.19,0.34,32.96,0.49
03-28-2021, 01:42 PM
Lucas

Quote:

Originally Posted by Kyp

For Dodecadk12b:

Code:

Iranian_Fars,27.45,0.89,1.31,0.74,5.59,6.25,6.10,1.25,14.09,1.23,34.77,0.33 Kurd_Feyli,27.47,1.12,1.26,0.33,4.98,5.36,3.77,0.34,14.60,0.30,40.12,0.14 Iranian_Kerman,29.71,0.99,0.30,0.21,6.09,8.31,7.60,0.85,12.19,0.34,32.96,0.49

added
03-28-2021, 01:51 PM
Leto

Kurd_Adygea can be safely removed, it's not a separate population.
04-02-2021, 03:12 PM
J. Ketch

Dodecad K12b update

Code:

Belgian,7.56,0.17,0.66,0.09,37.35,40.90,0.43,0.10,2.17,0.12,10.34,0.06 English,8.91,0.26,0.35,0.02,38.59,43.44,0.20,0.08,0.86,0.04,7.16,0.03 Irish,10.60,0.28,0.05,0.04,39.14,44.43,0.21,0.03,0.08,0.02,5.06,0.01 Scottish,10.19,0.22,0.19,0.12,38.52,44.22,0.22,0.01,0.47,0.03,5.74,0.00

Belgian - 15
English_mixed - 56
Irish - 37
Scottish - 26
04-02-2021, 03:38 PM
Leto

Quote:

Originally Posted by Creoda

Dodecad K12b update

Code:

Belgian,7.56,0.17,0.66,0.09,37.35,40.90,0.43,0.10,2.17,0.12,10.34,0.06 English_mixed,8.91,0.26,0.35,0.02,38.59,43.44,0.20,0.08,0.86,0.04,7.16,0.03 Irish,10.60,0.28,0.05,0.04,39.14,44.43,0.21,0.03,0.08,0.02,5.06,0.01 Scottish,10.19,0.22,0.19,0.12,38.52,44.22,0.22,0.01,0.47,0.03,5.74,0.00

Belgian - 15
English_mixed - 56
Irish - 37
Scottish - 26

Great stuff but is the word "mixed" really necessary? Maybe just call it English?
04-02-2021, 03:54 PM
J. Ketch

Quote:

Originally Posted by Leto

Great stuff but is the word "mixed" really necessary? Maybe just call it English?

OK, I changed it.
04-03-2021, 10:16 PM
celticdragongod

Distance to: CDG
1.27432335 Irish
1.49361976 Scottish
3.35353545 English
7.89397872 Belgian

Target: CDG
Distance: 1.2421% / 1.24211513
74.4 Irish
25.6 Scottish
04-03-2021, 11:18 PM
Peterski

For K13 and K15:

Code:

Polish_HolyCross,29.30,45.17,10.56,5.45,5.36,0.76,1.36,0.15,0.37,0.81,0.40,0.28,0.03 Polish_HolyCross,22.19,16.32,28.41,19.86,6.10,3.84,1.17,0.65,0.82,0,0,0.21,0.19,0.20,0.02

Also change the name "Ukrainian_Kiev_Avg" to just "Ukrainian_Kiev".
04-04-2021, 10:22 PM
Leto

@Lucas
Can you please add "_Kurd" to Yazidi and Zaza? Not my wish, there were some serious complaints about it.
04-05-2021, 02:23 AM
Kaazi

@Lucas, A correction was due. Please update/replace this in harappaworld. n=9

Code:

Nepali_Khas_Kshatriya,32.61,26.61,4.74,7.90,1.88,3.58,18.85,0.66,0.93,0.65,0.92,0.54,0.09,0.00,0.02,0.01
04-05-2021, 01:33 PM
Kyp

For Dodecadk12b (replace with the old one pls):

Code:

Kurd_Sorani,26.73,0.81,0.71,0.51,6.50,6.64,3.39,0.24,14.97,0.66,38.80,0.03
04-05-2021, 05:20 PM
Dr_Maul

Not Gedmatch but vahaduo related, 2 of the Iraqi Individual modern samples on G25 are very clearly 50% White or European of some sort.

Target: Iraqi:5AJ1
Distance: 2.0560% / 0.02056050 | R2P
56.6 Talysh_Azerbaijan
43.4 French_Pas-de-Calais

Target: Iraqi:11AR126
Distance: 1.8420% / 0.01841985 | R2P
50.2 Afrikaner
49.8 Karaite_Egypt
04-11-2021, 04:10 PM
vbnetkhio

could you add these to g25?

Code:

Scaled HUN_Gava_BA:I20771,0.144555,0.133034,0.063356,0.047481,0.051394,0.018407,0.00282,0.004384,0.010431,0.011481,-0.000487,-0.01139,-0.001635,0.003578,-0.007736,0.017369,0.024903,-0.011149,0,0.013632,0.007736,0.003586,0.000739,-0.014339,-0.00491 HUN_Hatvan-Fuzesabony_BA:I20772,0.134311,0.132019,0.065996,0.057494,0.031083,0.026216,0.008695,0.007846,0.008181,-0.015672,-0.002598,-0.003297,0.005203,0.004266,0.007872,0.010475,-0.001434,-0.003294,-0.000377,0.008754,0.010981,0.002226,0.000739,-0.006386,-0.003832 HUN_LaTene_IA:I20774,0.137726,0.137096,0.061471,0.046835,0.042469,0.020638,0.00376,0.008307,0.00634,-0.000911,-0.01023,0.000599,-0.001933,0.011698,0.006107,-0.00358,-0.019297,0.008361,0.007668,-0.003752,0.004367,0.006306,-0.001356,-0.004699,0.003473 HUN_Vekerzug_IA:I20743,0.141141,0.140143,0.075047,0.046189,0.047086,0.014781,0.004465,0.004846,0.017794,0.007289,-0.000812,0.001948,0.00223,0.004129,-0.002443,0.012994,0.008345,-0.008995,0.000377,0.016883,0.007612,0.007666,0.003574,-0.024582,0.000599 HUN_Vekerzug_IA:I20745,0.141141,0.135065,0.075424,0.070414,0.042777,0.014502,0.002585,-0.000231,0.000818,-0.012574,0,-0.004946,0.010852,0.00867,-0.00095,0.006762,0.016168,-0.000127,0.01169,0.007128,0.001373,-0.007296,0.000123,-0.009037,-0.001676 HUN_Vekerzug_IA:I20746,0.141141,0.136081,0.054682,0.017119,0.045239,0.013108,0.000235,-0.001154,0.013294,0.010387,-0.002273,0.003447,-0.004608,-0.000413,-0.00855,0.007292,0.020861,0.004307,0.006159,0.01063,0.002745,-0.000989,0.001972,0.00241,0.000599 RUS_Fatyanovo_BA:I20784,0.141141,0.117801,0.045632,0.07429,0.002462,0.022311,0.002115,0.012461,-0.00634,-0.032074,-0.004872,0.003147,-0.003271,-0.025735,0.007057,0.015248,0.010822,-0.004181,-0.008045,0.014882,0.00287,0.002597,-0.008627,0.003615,-0.008742 UKR_Meso:I20753_dup.I5885,0.142279,0.089367,0.16367,0.180881,0.068936,0.049921,0.001645,0.014769,0.024134,-0.044101,0.004222,-0.019033,0.03107,-0.019267,0.017508,0.032219,0.009779,-0.001267,-0.005405,0.032391,0.028325,0.014344,-0.015159,-0.07001,0.005987 Raw HUN_Gava_BA:I20771,0.0127,0.0131,0.0168,0.0147,0.0167,0.0066,0.0012,0.0019,0.0051,0.0063,-0.0003,-0.0076,-0.0011,0.0026,-0.0057,0.0131,0.0191,-0.0088,0,0.0109,0.0062,0.0029,0.0006,-0.0119,-0.0041 HUN_Hatvan-Fuzesabony_BA:I20772,0.0118,0.013,0.0175,0.0178,0.0101,0.0094,0.0037,0.0034,0.004,-0.0086,-0.0016,-0.0022,0.0035,0.0031,0.0058,0.0079,-0.0011,-0.0026,-0.0003,0.007,0.0088,0.0018,0.0006,-0.0053,-0.0032 HUN_LaTene_IA:I20774,0.0121,0.0135,0.0163,0.0145,0.0138,0.0074,0.0016,0.0036,0.0031,-0.0005,-0.0063,0.0004,-0.0013,0.0085,0.0045,-0.0027,-0.0148,0.0066,0.0061,-0.003,0.0035,0.0051,-0.0011,-0.0039,0.0029 HUN_Vekerzug_IA:I20743,0.0124,0.0138,0.0199,0.0143,0.0153,0.0053,0.0019,0.0021,0.0087,0.004,-0.0005,0.0013,0.0015,0.003,-0.0018,0.0098,0.0064,-0.0071,0.0003,0.0135,0.0061,0.0062,0.0029,-0.0204,0.0005 HUN_Vekerzug_IA:I20745,0.0124,0.0133,0.02,0.0218,0.0139,0.0052,0.0011,-0.0001,0.0004,-0.0069,0,-0.0033,0.0073,0.0063,-0.0007,0.0051,0.0124,-0.0001,0.0093,0.0057,0.0011,-0.0059,0.0001,-0.0075,-0.0014 HUN_Vekerzug_IA:I20746,0.0124,0.0134,0.0145,0.0053,0.0147,0.0047,0.0001,-0.0005,0.0065,0.0057,-0.0014,0.0023,-0.0031,-0.0003,-0.0063,0.0055,0.016,0.0034,0.0049,0.0085,0.0022,-0.0008,0.0016,0.002,0.0005 RUS_Fatyanovo_BA:I20784,0.0124,0.0116,0.0121,0.023,0.0008,0.008,0.0009,0.0054,-0.0031,-0.0176,-0.003,0.0021,-0.0022,-0.0187,0.0052,0.0115,0.0083,-0.0033,-0.0064,0.0119,0.0023,0.0021,-0.007,0.003,-0.0073 UKR_Meso:I20753_dup.I5885,0.0125,0.0088,0.0434,0.056,0.0224,0.0179,0.0007,0.0064,0.0118,-0.0242,0.0026,-0.0127,0.0209,-0.014,0.0129,0.0243,0.0075,-0.001,-0.0043,0.0259,0.0227,0.0116,-0.0123,-0.0581,0.005
04-12-2021, 12:36 PM
Leto

Overlooked back in December 2020!

Quote:

Originally Posted by Leto

For K13 from an academic source

Code:

Libyan,6.27,0.45,16.18,1.23,31.33,22.97,0.17,0.57,0.54,0.38,0.36,10.54,9.00 North_Moroccan,13.61,0.33,24.13,0.00,26.53,15.06,0.11,0.30,0.43,0.27,0.41,9.87,8.94 South_Moroccan,7.36,0.01,24.75,0.00,23.90,18.04,0.00,0.14,0.32,0.07,0.35,12.66,12.39

Also Creoda's update for Dodecad

Quote:

Originally Posted by Creoda

Dodecad K12b update

Code:

Belgian,7.56,0.17,0.66,0.09,37.35,40.90,0.43,0.10,2.17,0.12,10.34,0.06 English,8.91,0.26,0.35,0.02,38.59,43.44,0.20,0.08,0.86,0.04,7.16,0.03 Irish,10.60,0.28,0.05,0.04,39.14,44.43,0.21,0.03,0.08,0.02,5.06,0.01 Scottish,10.19,0.22,0.19,0.12,38.52,44.22,0.22,0.01,0.47,0.03,5.74,0.00

Belgian - 15
English_mixed - 56
Irish - 37
Scottish - 26
04-12-2021, 01:00 PM
Eleonor

K15 updated

Distance to: Eleonor
4.97232340 French_North-East
5.23052579 German_Bavarian
5.31031073 French_Alsace
5.45021101 Dutch_South
5.77921275 Belgian
6.00448999 Afrikaner
6.17663339 Swiss_German
6.86713186 French_Brittany
7.64792782 Pennsylvania_Dutch
7.92807038 English_Southeast
8.03269569 French_Central
8.20984165 West_German
8.47274454 English_Midlands
8.56854130 English
8.61048198 English_Southwest
8.64942773 North_German
9.14555630 Welsh
9.17817520 English_North
9.48264731 Dutch
9.55251276 Austria-Burgenland

More accurate for me than other calculators :)

Target: Eleonor
Distance: 1.1389% / 1.13885436
55.6 West_Norwegian
19.6 French_Basque
10.0 Lithuanian
8.9 Sardinian
5.9 North_Ossetian

Distance to: Eleonor
3.79790235 85.80% North_German + 14.20% Sardinian
3.89382498 32.00% English_Southwest + 68.00% French_Alsace
3.92996994 69.80% French_Alsace + 30.20% Welsh
3.96487063 24.80% East_German + 75.20% French_North-East
3.98044908 61.40% French_Alsace + 38.60% French_Brittany
3.99495766 29.80% English_North + 70.20% French_Alsace
4.00597242 31.60% English + 68.40% French_Alsace
4.04285027 33.60% English_Southeast + 66.40% French_Alsace
4.04510947 31.60% English_Midlands + 68.40% French_Alsace
4.07125831 74.00% French_Alsace + 26.00% Irish_Leinster
4.07587666 92.00% French_North-East + 8.00% Lithuanian
4.08467180 75.00% French_Alsace + 25.00% Irish_Munster
4.08995627 75.40% French_Alsace + 24.60% Irish_Ulster
4.09234242 75.20% French_Alsace + 24.80% Irish
4.09442766 88.40% French_North-East + 11.60% Polish_Masuria
4.09462097 92.60% French_North-East + 7.40% Latvian
4.12601640 89.40% French_North-East + 10.60% Polish
4.13026314 9.40% Estonian + 90.60% French_North-East
4.13975531 73.80% French_Brittany + 26.20% Slovenian
4.14302072 74.80% French_Alsace + 25.20% Scottish
4.16594040 77.20% French_Alsace + 22.80% Irish_Connacht
4.18004854 48.40% Dutch_South + 51.60% French_Alsace
4.18158131 87.80% French_North-East + 12.20% Sorb_Lusatia
4.19210442 8.40% Estonian_Polish + 91.60% French_North-East
4.19969059 8.40% Belorussian + 91.60% French_North-East
04-13-2021, 06:39 PM
Jana

Could you replace old Montenegrin average with new, weighted one?

Code:

Montenegrin,24.13,26.54,18.30,9.74,17.15,2.10,0.23,0.26,0.68,0.40,0.32,0.07,0.06

Vbnethkio made it.
04-15-2021, 12:43 PM
Ajeje Brazorf

This may be of interest to some of you.

Quote:

Originally Posted by Arza

Another off-topic:

https://www.ebi.ac.uk/ena/browser/view/PRJEB39997

Ancient DNA from pre-Slavic and Slavic individuals was extracted to compare human genetic diversity before and after a possible demographic event traditionally associated with Slavic ethnogenesis.
Study Title: Genetic Diversity in Migration Period and Early Middle Ages
Center Name: University of Fribourg
Study Name: Pre-Slavic and Slavic Ancient DNA

Each sample consists of 10 or 12 paired reads (20 or 24 fastq files), but I've used only one file per sample because all of them combined weight more than a half terabyte. Outcome is quite noisy as the reads weren't processed in any way besides mapping and genotyping. Treat everything here as preliminary.

LIB11 https://www.yfull.com/tree/E-L241/
LIB2 https://www.yfull.com/tree/I-Z180/
LIB3 NA
POH11 https://www.yfull.com/tree/R-Z283/
POH13 NA
POH27 https://www.yfull.com/tree/R-P312/ eventually https://www.yfull.com/tree/R-Y3267/
POH28 https://www.yfull.com/tree/R-Z92/
POH3 NA
POH36 https://www.yfull.com/tree/I-S17250/
POH40 NA
POH41 https://www.yfull.com/tree/I-Z16971/
POH44 in progress
April 15, 2021 at 1:26 AM

Quote:

Originally Posted by ambron

Arza, I already know - LIB is Breclav-Libiva (5th century), POH is Pohansko (early Middle Ages). There is little LIB, so maybe you can analyze it.
April 15, 2021 at 2:48 AM

Quote:

Originally Posted by Davidski

@Arza

https://drive.google.com/file/d/1-j0...ew?usp=sharing

Code:

Vahaduo Admixture JS Target: Migration:POH41 Distance: 2.5056% / 0.02505599 | R3P 75.4 Latvian 15.0 Spanish_La_Rioja 9.6 Greek_Central_Anatolia Target: Migration:POH40 Distance: 2.9513% / 0.02951252 | R3P 55.4 Lithuanian_SZ 39.6 French_Pas-de-Calais 5.0 Georgian_Imer Target: Migration:POH36 Distance: 2.9708% / 0.02970802 | R3P 47.4 Sorb_Niederlausitz 39.0 Lithuanian_VA 13.6 Spanish_La_Rioja Target: Migration:POH28 Distance: 3.3861% / 0.03386055 | R3P 91.8 Lithuanian_PZ 8.2 Sardinian Target: Migration:POH27 Distance: 2.9932% / 0.02993200 | R3P 66.8 Rumelia_East 22.4 Sorb_Niederlausitz 10.8 Spanish_Soria Target: Migration:POH13 Distance: 2.6572% / 0.02657205 | R3P 90.0 Lithuanian_VZ 6.2 Lithuanian_PZ 3.8 Berber_MAR_TIZ Target: Migration:POH11 Distance: 2.8810% / 0.02880995 | R3P 52.2 Bosnian 24.4 Lithuanian_RA 23.4 Sorb_Niederlausitz Target: Migration:POH3 Distance: 3.1256% / 0.03125567 | R3P 68.4 Russian_Voronez 21.0 Sardinian 10.6 Abkhasian Target: Migration:LIB11 Distance: 2.2954% / 0.02295351 | R3P 84.8 Sorb_Niederlausitz 8.0 Berber_Tunisia_Chen 7.2 Georgian_Imer Target: Migration:LIB3 Distance: 2.8603% / 0.02860342 | R3P 38.0 Spanish_Asturias 36.6 Italian_Molise 25.4 Italian_Liguria Target: Migration:LIB2 Distance: 2.9582% / 0.02958156 | R3P 64.4 Danish 25.0 Icelandic 10.6 Lithuanian_PZ
04-15-2021, 08:32 PM
Lucas

Quote:

Originally Posted by Ajeje Brazorf

This may be of interest to some of you.

Code:

Vahaduo Admixture JS Target: Migration:POH41 Distance: 2.5056% / 0.02505599 | R3P 75.4 Latvian 15.0 Spanish_La_Rioja 9.6 Greek_Central_Anatolia Target: Migration:POH40 Distance: 2.9513% / 0.02951252 | R3P 55.4 Lithuanian_SZ 39.6 French_Pas-de-Calais 5.0 Georgian_Imer Target: Migration:POH36 Distance: 2.9708% / 0.02970802 | R3P 47.4 Sorb_Niederlausitz 39.0 Lithuanian_VA 13.6 Spanish_La_Rioja Target: Migration:POH28 Distance: 3.3861% / 0.03386055 | R3P 91.8 Lithuanian_PZ 8.2 Sardinian Target: Migration:POH27 Distance: 2.9932% / 0.02993200 | R3P 66.8 Rumelia_East 22.4 Sorb_Niederlausitz 10.8 Spanish_Soria Target: Migration:POH13 Distance: 2.6572% / 0.02657205 | R3P 90.0 Lithuanian_VZ 6.2 Lithuanian_PZ 3.8 Berber_MAR_TIZ Target: Migration:POH11 Distance: 2.8810% / 0.02880995 | R3P 52.2 Bosnian 24.4 Lithuanian_RA 23.4 Sorb_Niederlausitz Target: Migration:POH3 Distance: 3.1256% / 0.03125567 | R3P 68.4 Russian_Voronez 21.0 Sardinian 10.6 Abkhasian Target: Migration:LIB11 Distance: 2.2954% / 0.02295351 | R3P 84.8 Sorb_Niederlausitz 8.0 Berber_Tunisia_Chen 7.2 Georgian_Imer Target: Migration:LIB3 Distance: 2.8603% / 0.02860342 | R3P 38.0 Spanish_Asturias 36.6 Italian_Molise 25.4 Italian_Liguria Target: Migration:LIB2 Distance: 2.9582% / 0.02958156 | R3P 64.4 Danish 25.0 Icelandic 10.6 Lithuanian_PZ

added
Do you know link to paper?
04-15-2021, 08:33 PM
Leto

Hey Luke, don't miss the Creoda update! ;)
04-15-2021, 08:35 PM
Leto

By the way, can someone add Lezgins to G25? You may as well use the old Behar data, doesn't matter since the calculator effect doesn't apply to G25.
04-15-2021, 09:17 PM
Lucas

Quote:

Originally Posted by Leto

By the way, can someone add Lezgins to G25? You may as well use the old Behar data, doesn't matter since the calculator effect doesn't apply to G25.

They aren't there????????
04-15-2021, 09:39 PM
Leto

Quote:

Originally Posted by Lucas

They aren't there????????

Nope. Dawid has completely ignored them.
04-18-2021, 08:09 AM
Andrea

Could someone build a PCA chart for me to understand how he positioned me genetically?
This is my k13 results:
# Population Percent
1 North_Atlantic 28.08
2 East_Med 27.29
3 West_Med 23.49
4 Baltic 8.98
5 West_Asian 7.23
6 Red_Sea 3.34
7 Northeast_African 0.69
8 Oceanian 0.49
9 Amerindian 0.41

Single Population Sharing:

# Population (source) Distance
1 Tuscan 3.19
2 West_Sicilian 7.35
3 North_Italian 8.1
4 Italian_Abruzzo 9.07
5 Greek_Thessaly 11.41
6 East_Sicilian 12.32
7 Central_Greek 12.47
8 South_Italian 12.99
9 Ashkenazi 14.13
10 Spanish_Extremadura 15.38
11 Portuguese 15.51
12 Spanish_Murcia 15.97
13 Spanish_Andalucia 15.98
14 Italian_Jewish 16.35
15 Spanish_Valencia 16.49
16 Sephardic_Jewish 17.01
17 Bulgarian 17.03
18 Spanish_Galicia 17.15
19 Algerian_Jewish 17.49
20 Spanish_Castilla_Y_Leon 17.52

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 51.8% Italian_Jewish + 48.2% Spanish_Cataluna @ 2.27
2 67.7% North_Italian + 32.3% Italian_Jewish @ 2.49
3 59.3% Ashkenazi + 40.7% Spanish_Aragon @ 2.64
4 50.2% Italian_Jewish + 49.8% Spanish_Valencia @ 2.67
5 54% Ashkenazi + 46% Spanish_Valencia @ 2.79
6 67% Spanish_Valencia + 33% Lebanese_Druze @ 2.8
7 70% Ashkenazi + 30% French_Basque @ 2.82
8 92.6% Tuscan + 7.4% Italian_Jewish @ 2.92
9 53.2% Ashkenazi + 46.8% Spanish_Andalucia @ 2.95
10 67.5% Spanish_Valencia + 32.5% Lebanese_Christian @ 2.99
11 57.6% Italian_Jewish + 42.4% Southwest_French @ 3.03
12 95.7% Tuscan + 4.3% Tunisian_Jewish @ 3.04
13 95.8% Tuscan + 4.2% Libyan_Jewish @ 3.05
14 95% Tuscan + 5% Algerian_Jewish @ 3.06
15 95% Tuscan + 5% Sephardic_Jewish @ 3.07
16 98.3% Tuscan + 1.7% Yemenite_Jewish @ 3.09
17 97.9% Tuscan + 2.1% Lebanese_Druze @ 3.11
18 95.2% Tuscan + 4.8% Ashkenazi @ 3.11
19 73.8% North_Italian + 26.2% Tunisian_Jewish @ 3.13
20 70.9% West_Sicilian + 29.1% Spanish_Valencia @ 3.14
This i my k15 v2 results:
# Population Percent
1 East_Med 23.89
2 Atlantic 21.83
3 West_Med 19.12
4 North_Sea 15.49
5 West_Asian 8.48
6 Baltic 5.72
7 Red_Sea 3.1
8 Eastern_Euro 1.18
9 Northeast_African 0.73
10 Oceanian 0.34
11 Amerindian 0.11

Single Population Sharing:

# Population (source) Distance
1 Tuscan 4.22
2 West_Sicilian 7.32
3 North_Italian 8
4 Italian_Abruzzo 8.57
5 East_Sicilian 11.26
6 Greek 11.4
7 Greek_Thessaly 11.47
8 Central_Greek 11.6
9 South_Italian 12.11
10 Ashkenazi 13.65
11 Spanish_Murcia 14.18
12 Spanish_Extremadura 14.28
13 Spanish_Andalucia 14.57
14 Portuguese 14.65
15 Italian_Jewish 14.8
16 Bulgarian 15.51
17 Spanish_Valencia 15.66
18 Spanish_Castilla_Y_Leon 15.72
19 Spanish_Cataluna 15.72
20 Spanish_Galicia 15.87

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 54.2% South_Italian + 45.8% Spanish_Murcia @ 3.2
2 51.6% Italian_Jewish + 48.4% Spanish_Cataluna @ 3.3
3 81.7% North_Italian + 18.3% Lebanese_Druze @ 3.32
4 56.9% South_Italian + 43.1% Spanish_Cataluna @ 3.37
5 61.4% Spanish_Cataluna + 38.6% Cyprian @ 3.43
6 67.9% Spanish_Cataluna + 32.1% Lebanese_Druze @ 3.44
7 67.6% Spanish_Cataluna + 32.4% Lebanese_Christian @ 3.49
8 63.5% Spanish_Cantabria + 36.5% Lebanese_Druze @ 3.61
9 66.8% North_Italian + 33.2% Italian_Jewish @ 3.65
10 64% Spanish_Murcia + 36% Cyprian @ 3.66
11 70.7% West_Sicilian + 29.3% Spanish_Cataluna @ 3.67
12 67.9% Spanish_Castilla_Y_Leon + 32.1% Lebanese_Druze @ 3.75
13 57% South_Italian + 43% Spanish_Castilla_Y_Leon @ 3.75
14 52.9% West_Sicilian + 47.1% North_Italian @ 3.76
15 70.3% Spanish_Murcia + 29.7% Lebanese_Druze @ 3.76
16 56.9% South_Italian + 43.1% Spanish_Valencia @ 3.78
17 73.9% North_Italian + 26.1% Tunisian_Jewish @ 3.79
18 68% Spanish_Valencia + 32% Lebanese_Druze @ 3.8
19 68.7% West_Sicilian + 31.3% Spanish_Murcia @ 3.86
20 66.6% Spanish_Cataluna + 33.4% Samaritan @ 3.89
04-18-2021, 08:53 AM
Petalpusher

Quote:

Originally Posted by Andrea

Could someone build a PCA chart for me to understand how he positioned me genetically?
This is my k13 results:
# Population Percent
1 North_Atlantic 28.08
2 East_Med 27.29
3 West_Med 23.49
4 Baltic 8.98
5 West_Asian 7.23
6 Red_Sea 3.34
7 Northeast_African 0.69
8 Oceanian 0.49
9 Amerindian 0.41

You can use this K15 tool to make your own easily:
https://gen3553.pagesperso-orange.fr/ADN/K15.htm

Spoiler alert you are going to be somewhere around Tuscany, maybe a bit south of it. So regular central Italian.

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