Eurogenes Biogeographic Ancestry Project

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09-15-2011, 11:01 AM
Quasimodem

Northeast Euro: 33.61%
Sub-Saharan: 0.00%
North African: 0.00%
South Asian: 0.36%
West Euro: 53.08%
Southeast Asian: 0.00%
South Siberian: 0.00%
North Asian: 0.00%
East Siberian: 0.00%
East Asian: 0.00%
East Mediterranean: 5.46%
Middle Eastern: 0.09%
West Asian: 4.36%
Volga-Ural: 3.04%

By the way, could some of you do a K=12 (without Volga-Ural and Northeast Euro)? I'm curious to see how those results compare with this. Here are mine:

http://img269.imageshack.us/img269/7775/novu2.jpg

Chromosomes:

http://img405.imageshack.us/img405/5884/bychrvisual.jpg
09-15-2011, 11:07 AM
Polako

^ Yes, I recommend that everyone experiment with taking away certain clusters, especially for segment and chromosome analyses.
09-15-2011, 11:11 AM
Kadu

Quote:

Originally Posted by Quasimodem

By the way, could some of you do a K=12 (without Volga-Ural and Northeast Euro)?

What do I have to delete?
09-15-2011, 11:19 AM
Quasimodem

Quote:

Originally Posted by Kadu

What do I have to delete?

You have to delete the very first and very last columns in the .F file (as those are the ones that correspond to NE Euro and Volga-Ural). You also have to delete those two component names in the test.txt file and change the .par file to the right settings. Of course the same rules apply to any other component you want to remove.
09-15-2011, 11:21 AM
Kadu

Quote:

Originally Posted by Quasimodem

You have to delete the very first and very last columns in the .F file (as those are the ones that correspond to NE Euro and Volga-Ural).

Looks daunting, it's all scattered, I opened with it wordpad.
09-15-2011, 11:25 AM
Quasimodem

Quote:

Originally Posted by Kadu

Looks daunting, it's all scattered, I opened with it wordpad.

It's easiest to do with Open Office.
09-15-2011, 01:58 PM
Pallantides

54.94% West_Euro
33.24% Northeast_Euro
5.84% Volga-Ural
5.09% West_Asian
0.51% North_Asian
0.27% East_Siberian
0.09% East_Asian
0.02% South_Asian
0.00% Sub-Saharan
0.00% Berber
0.00% Southeast_Asian
0.00% South_Siberian
0.00% East_Mediterranean
0.00% Middle_Eastern
09-15-2011, 02:28 PM
Imperivm

Sorry chaps, I'm using a mac as my main computer and it's not letting me run the Dodecad DIY without giving me errors (I think it's because of the type of mac OS I'm running). If you don't need the raw data file for this (I assume you don't); could somebody run the tests for me, please? I'm UK35.
09-15-2011, 02:56 PM
Pallantides

Quote:

Originally Posted by Pallantides

54.94% West_Euro
33.24% Northeast_Euro
5.84% Volga-Ural
5.09% West_Asian
0.51% North_Asian
0.27% East_Siberian
0.09% East_Asian
0.02% South_Asian
0.00% Sub-Saharan
0.00% Berber
0.00% Southeast_Asian
0.00% South_Siberian
0.00% East_Mediterranean
0.00% Middle_Eastern

Without Volga Ural

56.65% West_Euro
35.59% Northeast_Euro
5.58% West_Asian
0.92% North_Asian
0.74% East_Siberian
0.47% East_Asian
0.02% South_Siberian
0.02% South_Asian
0.00% Sub-Saharan
0.00% Berber
0.00% Southeast_Asian
0.00% East_Mediterranean
0.00% Middle_Eastern

Without Volga-Ural and NE-Euro

77.05% West_Euro
15.29% West_Asian
1.95% North_Asian
1.94% South_Asian
1.88% East_Siberian
1.14% South_Siberian
0.72% East_Asian
0.01% Southeast_Asian
0.01% East_Mediterranean
0.01% Middle_Eastern
0.00% Sub-Saharan
0.00% Berber
09-15-2011, 03:09 PM
Scrapple

Quote:

Originally Posted by Quasimodem

You have to delete the very first and very last columns in the .F file (as those are the ones that correspond to NE Euro and Volga-Ural). You also have to delete those two component names in the test.txt file and change the .par file to the right settings. Of course the same rules apply to any other component you want to remove.

To expand on this edit the test.txt and delete the populations your removed and in the test.par file reduce the number in the second line to the new number of populations you are running.

Me:
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

40.36% Northeast_Euro
0.00% Sub-Saharan
0.00% Berber
0.09% South_Asian
42.95% West_Euro
0.25% Southeast_Asian
0.00% South_Siberian
0.03% North_Asian
0.04% East_Siberian
0.00% East_Asian
7.15% East_Mediterranean
1.82% Middle_Eastern
4.35% West_Asian
2.96% Volga-Ural
09-15-2011, 03:44 PM
Humanophage

Removed NE-E and Volga to break down my East European score:
West_Euro + 45.6
West_Asian + 18.8
South_Asian + 5.8
East_Med + 3.2
East_Siberian + 3.0
Mid_East + 2.8
South_Siberian + 2.2
North_Asian + 1.6

Code:

no NE-E, no Volga no NE-E full 0.00% Sub-Saharan 5.30% Sub-Saharan 0.00% Sub-Saharan 0.00% North_African 0.06% North_African 0.00% North_African 5.98% South_Asian 3.15% South_Asian 0.04% South_Asian 57.43% West_Euro 45.27% West_Euro 11.85% West_Euro 0.00% Southeast_Asian 1.43% Southeast_Asian 0.00% Southeast_Asian 2.22% South_Siberian 0.05% South_Siberian 0.00% South_Siberian 1.59% North_Asian 0.01% North_Asian 0.00% North_Asian 3.02% East_Siberian 1.21% East_Siberian 0.00% East_Siberian 0.00% East_Asian 0.12% East_Asian 0.00% East_Asian 5.63% East_Mediter 3.53% East_Mediter 2.45% East_Mediter 4.63% Middle_Eastern 3.65% Middle_Eastern 1.82% Middle_Eastern 19.49% West_Asian 14.42% West_Asian 0.72% West_Asian 21.81% Volga-Ural 82.35% Northeast_Euro 0.77% Volga-Ural

Quote:

Originally Posted by Imperivm

Sorry chaps, I'm using a mac as my main computer and it's not letting me run the Dodecad DIY without giving me errors (I think it's because of the type of mac OS I'm running). If you don't need the raw data file for this (I assume you don't); could somebody run the tests for me, please? I'm UK35.

One needs the raw data file for this. The whole thing is fairly fundamental.
09-15-2011, 05:18 PM
Rochefaton

Me:
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

30.86% Northeast_Euro
0.00% Sub-Saharan
0.23% N. African
0.95% South_Asian
57.53% West_Euro
0.00% Southeast_Asian
0.05% South_Siberian
0.00% North_Asian
0.00% East_Siberian
0.00% East_Asian
2.32% East_Mediterranean
0.67% Middle_Eastern
5.43% West_Asian
1.96% Volga-Ural

My Wife:
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

28.96% Northeast_Euro
0.80% Sub-Saharan
0.00% N. African
0.01% South_Asian
57.25% West_Euro
0.02% Southeast_Asian
0.00% South_Siberian
0.05% North_Asian
0.99% East_Siberian
0.00% East_Asian
4.65% East_Mediterranean
1.85%% Middle_Eastern
4.44% West_Asian
0.99% Volga-Ural
09-15-2011, 05:27 PM
poiuytrewq0987

Whenever I try to open the Dodecad exe, a command window opens but it immediately closes after opening. What am I doing wrong? :rolleyes:
09-15-2011, 07:28 PM
Frederick

Quote:

Originally Posted by Dušan

Whenever I try to open the Dodecad exe, a command window opens but it immediately closes after opening. What am I doing wrong? :rolleyes:

You need to have "R" installed.
And then you open the "R" exe.

Seems like you never did this before, so you need to "standarize" your genomefile first.

Here are some selected lines from the "Read Me":

Quote:

2. Download and install R (http://www.r-project.org/) if you haven't done so
already.

Quote:

3. Download and unzip your genotype data file from 23andMe or FamilyTreeDNA
into the working directory (The directory with the DiY stuff and files in). This should be a file ending in .txt for 23andMe
and .csv for
FamilyTreeDNA.

From now on, I will suppose that your genotype file is named 'johndoe.txt' or
'johndoe.csv'

4. Launch R.

Quote:

Once R is running, it will give you a command prompt where you can enter
commands. First, you must change the directory to your working directory.

You can do this from the File -> Change dir menu in Windows

Quote:

Then, enter:

source('standardize.r')

This loads a small program that will convert your data from the
company-specific format to a common format in the next step.

5. At the R prompt, enter:

a. If you have 23andMe data (either v2 or v3 chip):

standardize('johndoe.txt', company='23andMe')

Then your genomefile is "stardarized", wich you will need for all other experiments you ever do with DIY.

And then you type system('DIYDodecadWin test.par') to run it with this latest Eurogenes run. (make sure you downloaded this https://docs.google.com/viewer?a=v&p...iYTJh&hl=en_US and extract it into the "Working directory)

This line instead: system('DIYDodecadWin dv3.par') would run your Dodecad results btw.
09-15-2011, 08:56 PM
Barreldriver

Bah, I have not winrar to unpack the .rar's for the initial DIY programs or the patience to mess around with 'em. :(
09-15-2011, 09:53 PM
Scrapple

Quote:

Originally Posted by Barreldriver

Bah, I have not winrar to unpack the .rar's for the initial DIY programs or the patience to mess around with 'em. :(

http://www.7-zip.org/ will work on .rar files.
09-15-2011, 10:35 PM
Damião de Góis

65.04% West_Euro
13.71% Northeast_Euro
11.51% East_Mediterranean
5.36% Middle_Eastern
2.03% Berber
1.84% Sub-Saharan
0.28% Southeast_Asian
0.23% West_Asian

0.00% South_Asian
0.00% South_Siberian
0.00% North_Asian
0.00% East_Siberian
0.00% East_Asian
0.00% Volga-Ural
09-15-2011, 11:09 PM
Barreldriver

Quote:

Originally Posted by Commerce & Industry

http://www.7-zip.org/ will work on .rar files.

Completely forgot about this used to have much of these sorts of things on my laptop but I had a number of foul ups resulting in a restore to factory default. :P

Will post my results once I get all this stuff reinstalled and organized.
09-15-2011, 11:21 PM
Aviane

Quote:

Originally Posted by Frederick

That map has a huge overlap of Germany, Lower Countries, Kent and an undefined part of France.

I guess Johnston can keep his dream of West-Germanic unity. ;)

http://www.theapricity.com/forum/att...1&d=1315320704

I agree with this the countries mentioned cluster altogether.

Quote:

Originally Posted by Barreldriver

Completely forgot about this used to have much of these sorts of things on my laptop but I had a number of foul ups resulting in a restore to factory default. :P

Will post my results once I get all this stuff reinstalled and organized.

It's good to hear from you as being another member.
09-15-2011, 11:49 PM
Barreldriver

I must be retarded as I cannot get R to work and thus cannot run the DIY or the Eurogenes add ons. :P Still stuck at the standardize.r phase. :(

EDIT:

nvm, found I had the wrong directory selected. bwahaha
09-16-2011, 12:16 AM
Barreldriver

Alright, I got DIY Dodecad to work but how do I get the Eurogenes part to work? Trying to substitute test.par for the DIYDodecadwin dv3.par but it is not working. :(

Edit:

I'm an idiot, reread the blog and found out how to do it, my results:

28.59% Northeast_Euro
0.00% Sub-Saharan
0.08% Berber
0.36% South_Asian
55.67% West_Euro
0.01% Southeast_Asian
0.00% South_Siberian
0.00% North_Asian
0.02% East_Siberian
0.02% East_Asian
5.44% East_Mediterranean
1.70% Middle_Eastern
6.04% West_Asian
2.06% Volga-Ural
09-16-2011, 12:27 AM
Frederick

:thumb001: Fought and won, Barreldriver!
09-16-2011, 12:33 AM
Frederick

Quote:

Originally Posted by Quasimodem

[/B]By the way, could some of you do a K=12 (without Volga-Ural and Northeast Euro)? I'm curious to see how those results compare with this. Here are mine:

http://img269.imageshack.us/img269/7775/novu2.jpg

Mine look like this, if I remove the Russian and Chuvash cluster:

----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

0.01% Sub-Saharan
0.00% North_African
2.08% South_Asian
70.53% West_Euro
0.03% Southeast_Asian
1.58% South_Siberian
1.02% North_Asian
1.53% East_Siberian
0.00% East_Asian
3.88% East_Mediterranean
5.15% Middle_Eastern
14.18% West_Asian

CPU time = 416.88 sec

that was the original:

Quote:

My results in that K14, test tool:

35.26% Northeast_Euro
0.04% Sub-Saharan
0.00% North_African
0.01% South_Asian
49.38% West_Euro
0.00% Southeast_Asian
0.00% South_Siberian
0.00% North_Asian
0.01% East_Siberian
0.00% East_Asian
2.32% East_Mediterranean
3.69% Middle_Eastern
5.14% West_Asian
4.15% Volga-Ural
09-16-2011, 12:40 AM
Barreldriver

Quote:

Originally Posted by Frederick

:thumb001: Fought and won, Barreldriver!

:D Good thing I lost my hammer for a while I was getting pissed.

I like how the clusters are made up on this compared to Dodecad alone, the NW and Paeo African I scored with Dodecad with this I believe to show up as Berber, coincidentally I have a Mid East score over 1% so the Berber and that I'd think to go hand in hand since it peaks in Saudi's.
09-16-2011, 12:42 AM
Frederick

Berber....
Has Polako updated the file?
Mine says "NOrth African" instead of "Berber".
Need to check.
09-16-2011, 12:45 AM
Barreldriver

Quote:

Originally Posted by Frederick

Berber....
Has Polako updated the file?
Mine says "NOrth African" instead of "Berber".
Need to check.

Mine says Berber so he might have updated.
09-16-2011, 12:57 AM
Frederick

Quote:

Originally Posted by Barreldriver

Mine says Berber so he might have updated.

Yes he did. I just checked.
But I get absolute identical values (except tht "North African" is now named "Berber"). At least at the normal run. (havnt checked if its still the case if that Eastern European (Russian) and Volga-Ural (Chuvash) cluster are removed.
09-16-2011, 01:09 AM
Scrapple

Quote:

Originally Posted by Quasimodem

[/B]By the way, could some of you do a K=12 (without Volga-Ural and Northeast Euro)? I'm curious to see how those results compare with this. Here are mine:

http://img269.imageshack.us/img269/7775/novu2.jpg

0.00% Sub-Saharan
0.00% Berber
2.87% South_Asian
66.87% West_Euro
0.02% Southeast_Asian
0.77% South_Siberian
1.56% North_Asian
1.74% East_Siberian
0.00% East_Asian
8.39% East_Mediterranean
3.55% Middle_Eastern
14.23% West_Asian
09-16-2011, 05:19 AM
Rochefaton

I got bored, so I ran the raw data of my sister and brother-in-law:

Sister:
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

29.70% Northeast_Euro
0.00% Sub-Saharan
0.12% N. African
0.90% South_Asian
58.86% West_Euro
0.00% Southeast_Asian
0.00% South_Siberian
0.00% North_Asian
0.00% East_Siberian
0.00% East_Asian
2.12% East_Mediterranean
0.57% Middle_Eastern
6.13% West_Asian
1.60% Volga-Ural

Brother-in-law:
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

30.32% Northeast_Euro
0.19% Sub-Saharan
0.00% N. African
1.31% South_Asian
54.84% West_Euro
0.00% Southeast_Asian
0.01% South_Siberian
0.00% North_Asian
0.16% East_Siberian
0.02% East_Asian
4.79% East_Mediterranean
1.18% Middle_Eastern
5.19% West_Asian
1.97% Volga-Ural
09-16-2011, 10:27 AM
Pallantides

NO1 - West Norwegian
NO2 - Me
NO3 - East Norwegian

West_Euro

NO1 - 56.33%
NO2 - 54.94%
NO3 - 57.08%

Northeast_Euro

NO1 - 34.36%
NO2 - 33.24%
NO3 - 31.36%

West_Asian

NO1 - 4.37%
NO2 - 5.09%
NO3 - 4.78%

Volga-Ural

NO1 - 3.23%
NO2 - 5.84%
NO3 - 4.97%

East_Siberian

NO1 - 0.00%
NO2 - 0.27%
NO3 - 0.94%

Middle_Eastern

NO1 - 0.25%
NO2 - 0.00%
NO3 - 0.64%

East_Mediterranean

NO1 - 0.59%
NO2 - 0.00%
NO3 - 0.01%

Southeast_Asian

NO1 - 0.57%
NO2 - 0.00%
NO3 - 0.00%

North_Asian

NO1 - 0.00%
NO2 - 0.51%
NO3 - 0.01%

South_Asian

NO1 - 0.19%
NO2 - 0.02%
NO3 - 0.01%

South Siberian

NO1 - 0.00%
NO2 - 0.00%
NO3 - 0.20%

East_Asian

NO1 - 0.00%
NO2 - 0.09%
NO3 - 0.00%

Sub-Saharan

NO1 - 0.09%
NO2 - 0.00%
NO3 - 0.00%
09-27-2011, 10:44 PM
Damião de Góis

IBS 200K, my top 30:

North_Italian 0.738927
Tuscan 0.738918
FR 0.738794
US57 0.738792
DE13 0.738619
US131 0.738412
North_Italian 0.738392
US8 0.738301
Kent 0.738097
PL11 0.738096
US78 0.738017
North_Italian 0.738
US140 0.737993
US231 0.73795
Cornwall 0.737928
NO6 0.737914
Kent 0.737897
FR7 0.737892
Cornwall 0.737876
Tuscan 0.737864
NL3 0.737846
ES16 0.73784
US63 0.737804
US246 0.737797
US188 0.737779
DK3 0.737774
DEUK1 0.737771
ES 0.737738
HU 0.737732
IE20 0.737727
09-28-2011, 12:54 AM
Lisa

Whom to believe? Polako or Dienikis... :rolleyes:
09-28-2011, 12:58 AM
Kadu

Quote:

Originally Posted by Nero

Whom to believe? Polako or Dienikis... :rolleyes:

Different perspectives but convergent results.
09-28-2011, 12:01 PM
Loki

New results out from Polako:

Genetic similarity matrix including 1800+ project members and reference samples

I've done Boudica's Top 30 matches (US245):

US245 1
Kent 0.740478
Kent 0.740287
CA3 0.740153
US18 0.740038
FR 0.739905
NO7 0.739756
Kent 0.73975
US32 0.73967
US255 0.739637
IE8 0.739592
US164 0.739538
US92 0.739534
UK9 0.7395
FCA2 0.739481
US140 0.739347
IE16 0.739325
US88 0.739321
US110 0.739302
US165 0.739276
FR 0.739266
CA13 0.739263
Kent 0.739259
NO2 0.739237
FR 0.739194
Cornwall 0.739175
Kent 0.739108
DE9 0.739067
US105 0.739051
HU 0.739045
09-28-2011, 12:09 PM
Loki

My top 30:

SAEU1 1
US74 0.739493
US185 0.739389
US67 0.739264
Cornwall 0.738907
HU 0.738895
Kent 0.73871
DE8 0.738688
FR2 0.738661
UK28 0.738625
SE1 0.738604
US167 0.738414
US70 0.738395
IE6 0.738352
US37 0.738315
US132 0.738293
IE20 0.738268
IE15 0.73822
Kent 0.738218
US56 0.738218
RH1 0.738214
US39 0.738196
UK4 0.738194
DE9 0.73817
US104 0.738148
US41 0.738135
Kate_Morley 0.738127
ES 0.738116
Kent 0.738114
UK38 0.738103
Kent 0.738032
09-28-2011, 12:20 PM
Loki

Peasant Top 30:

UK41 1
CA5 0.741032
Kate_Morley 0.740906
Luke_Jostins 0.740853
Kent 0.740812
IE3 0.740768
IE14 0.740716
US88 0.740621
UK4 0.740609
IE20 0.740604
US26 0.740539
PL16 0.740524
UK30 0.740465
US193 0.740457
FR 0.740453
US63 0.740361
Cornwall 0.740347
AT2 0.740205
PLSK1 0.740173
US48 0.740172
Kent 0.740153
US105 0.740151
US115 0.740146
US255 0.740142
UK19 0.740111
Cornwall 0.740054
IE15 0.739975
DE14 0.739966
US37 0.739948
Kent 0.739918
US165 0.739864

I won't be able to take more requests now unfortunately, going to bed.
09-28-2011, 12:29 PM
Peasant

Quote:

Originally Posted by Loki

Peasant Top 30:

UK41 1
CA5 0.741032
Kate_Morley 0.740906
Luke_Jostins 0.740853
Kent 0.740812
IE3 0.740768
IE14 0.740716
US88 0.740621
UK4 0.740609
IE20 0.740604
US26 0.740539
PL16 0.740524
UK30 0.740465
US193 0.740457
FR 0.740453
US63 0.740361
Cornwall 0.740347
AT2 0.740205
PLSK1 0.740173
US48 0.740172
Kent 0.740153
US105 0.740151
US115 0.740146
US255 0.740142
UK19 0.740111
Cornwall 0.740054
IE15 0.739975
DE14 0.739966
US37 0.739948
Kent 0.739918
US165 0.739864

I won't be able to take more requests now unfortunately, going to bed.

:eek: Mordid will have a field day with this.
09-28-2011, 04:52 PM
Frederick

My Top 30 without Colonials:

Kent 0.741383
PL1 0.740344 (Polako)
IE8 0.740306
Kent 0.740262
LT 0.740246
IE16 0.740206
DK3 0.740114
DE14 0.739911
Kent 0.73985
DE9 0.739808
NO6 0.739763
UK22 0.739756
IE20 0.739741
DE5 0.739678
Kent 0.739663
UK32 0.739611
Cornwall 0.739601
UK29 0.739579
FR2 0.739522
Cornwall 0.739478
RU43 0.739475
PLSK1 0.739439
Kent 0.739403
UARUPL1 0.739396
RU11 0.73938
PL4 0.73938
SE1 0.739356
FR 0.739344
DE1 0.739313
NO7 0.739297

5x Kent
4x Germany
3x Ireland
3x UK
2.8x Poland
2.3x Russia
2x Norway
2x Cornwall
2x France
1x Lithuania
1x Denmark
1x Sweden
0.5x Slovakia
0.3x Ukraine
09-28-2011, 05:19 PM
Graham

Quote:

Top 30 without US etc..
UK19
UK3 0.742007
UK8 0.741462
Kent 0.741101
UK37 0.741058
IE3 0.740962
UK1 0.740875
Cornwall 0.740834
SW_Scot 0.740626
PL5 0.740582
UK25 0.740568
Cornwall 0.740567
IE18 0.740516
FR 0.740496
DE1 0.740449
IE20 0.740442
DE12 0.740392
SE7 0.7403
Cornwall 0.740288
SE4 0.740276
UK28 0.740267
NO10 0.740251
Cornwall 0.740224
Cornwall 0.740208
FR 0.740205
DESK1 0.740164
Cornwall 0.740153
Kent 0.740153
UK41 0.740111
Kent 0.740052
UK38 0.740014
09-28-2011, 05:27 PM
Frederick

On request....

Sahsons top 30, without colonials:

DEIE2 0.740699
Kent 0.740496
IE4 0.740494
Cornwall 0.740004
SE15 0.739861
DE17 0.739787
FR8 0.739768
IE16 0.739625
SE16 0.739499
NL6 0.739436
UK37 0.739379
PLSK1 0.739314
HU 0.739254
PL1 0.739246 (Polako)
SE14 0.73923
Mordvin 0.739197
IE21 0.73919
NL3 0.739029
PL15 0.739024
Cornwall 0.739004
SW_Scot 0.738981
UK6 0.738951
SENO1 0.738948
Cornwall 0.738929
Cornwall 0.738887
Kent 0.738867
IE9 0.738841
Kent 0.73879
RUUA1 0.73878
Kent 0.738743

4.5x Ireland
4x Cornwall
4x Kent
3.5x Sweden
2x UK
2.5x Poland
2x Netherlands
1.5x Germany
1x Scottland
1x France
1x Hungary
0.5x Norway
0.5x Slovakia
0.5x Russia
0.5x Ukraine

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