Eurogenes Biogeographic Ancestry Project

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Originally Posted by Fearless Leader

If you were in the Pagani_8 run you should be included in this also. One way to check for sure is to go here http://bga101.blogspot.com/2012/07/p...c-genomic.html and click on "Chromosome 1" which is a link that will take you to the actual files then go to the very bottom and click on samples.txt and see if you are included in the list.

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Thanks. So, I found myself on the list. What is the next step?

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Originally Posted by xajapa

Thanks. So, I found myself on the list. What is the next step?

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Now is the annoying part. You are either in the EU "European" or WA "West Asian group. You have to click on each file entitled 'outSupportMix.png' to find where he has you listed for the chromosome #1 painting. You have to look through each 'outSupportMix.png' image file to try to locate where your listed at which is the annoying part.

Here's my chromossome 1, thanks to plastictuga:

http://i50.tinypic.com/2rcbx5i.jpg

http://i1252.photobucket.com/albums/...hromosome1.jpg

Distinguishing between some of the color schemes, in order to ascertain the actual ethnicity, is challenging. I believe these two lines represent my parents. The top would be my mother (plenty of East English, which possibly could substitute for German as well, since there is no German category). the bottom is my father, with a large Ukrainian segment.

Can't distinguish between the colours. Would be good if a could lol.

Quote:

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Originally Posted by Graham

Can't distinguish between the colours. Would be good if a could lol.

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So isn't yours just huge chunks of 'Irish' and 'East English' segments... shouldn't be so hard:D;)

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Originally Posted by Pallantides

So isn't yours just huge chunks of 'Irish' and 'East English' segments... shouldn't be so hard:D;)

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:D
ha I'll post it. It's a mix of whatever.

http://i55.photobucket.com/albums/g1...ru293/mine.png

Quote:

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Originally Posted by Graham

:D
ha I'll post it. It's a mix of whatever.

http://i55.photobucket.com/albums/g1...ru293/mine.png

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Look at mine for reference, it has the names of some of the colors. Apparently your biggest segments are swedish and irish. Also, i seem to have a bigger east english segment than you? :confused:

The large segments are easier to distinguish. It's those small segments, which may be interesting regarding one's ancestry, that are sometimes hard to distinguish.

Quote:

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Originally Posted by Graham

:D
ha I'll post it. It's a mix of whatever.

http://i55.photobucket.com/albums/g1...ru293/mine.png

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Wow, how do I have a little bit larger Irish segment than you!?!?!? Then again this is only from chromosome #1.
http://s19.postimage.org/xdj55d0sj/Eurogenes2.jpg

Quote:

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Originally Posted by Fearless Leader

Wow, how do I have a little bit larger Irish segment than you!?!?!? Then again this is only from chromosome #1.

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Yes, but I only have a minute amount of traceable Irish ancestry in the family tree. You'd have to go way way back.

Quote:

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Originally Posted by Graham

Can't distinguish between the colours. Would be good if a could lol.

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If you have a program like paintshop or photoshop you could use the color pick tool to check any colors you can't figure out.

Mine:

http://i50.tinypic.com/5tvsw4.jpg

http://i45.tinypic.com/246w9y9.jpg

http://i49.tinypic.com/2hpoopw.jpg

http://i47.tinypic.com/1htlw1.jpg

http://i50.tinypic.com/2e4kihj.jpg


4 down 18 to go :)

A "must read" before interpreting..

Mine so far, i have not checked them versus gedmatch or anything yet...

http://img815.imageshack.us/img815/1779/123tk.png

It seems the first chr is extremely western oriented with domination of "English", the second seem more oriented around the Baltic/Russia area, and the third seem more oriented towards Caucasus..i am struggling allot with the colours, thank god i am not colour blind though! But i think i am correct so far:) looking forward to the whole thing so i can better compare myself with other Norwegians:) PS: i noted that Brits have allot of South Indian showing up, would be interesting to see if these segments have moved in from southern or eastern europe :)...

Here are my first 3 chromossomes:

http://i50.tinypic.com/2rcbx5i.jpg

http://oi46.tinypic.com/30myc9j.jpg

http://oi49.tinypic.com/2en6mwx.jpg

Chromosomes 2 and 3 for me:

Chromosome 1

http://img88.imageshack.us/img88/843...me1labeled.jpg

Chromosome 2

http://img215.imageshack.us/img215/8...me2labeled.jpg

Chromosome 3

http://img96.imageshack.us/img96/668...me3labeled.jpg

Chromosome 4

http://img560.imageshack.us/img560/4...me4labeled.jpg

Chromosome 5

http://img51.imageshack.us/img51/131...me5labeled.jpg

Chromosome 6

http://img525.imageshack.us/img525/7...me6labeled.jpg

Chromosome 7

http://img850.imageshack.us/img850/4...me7labeled.jpg

Chromosome 8

http://img209.imageshack.us/img209/4...me8labeled.jpg

Chromosome 9

http://img585.imageshack.us/img585/3...me9labeled.jpg

Chromosome 10

http://img155.imageshack.us/img155/9...e10labeled.jpg

Chromosome 11

http://img51.imageshack.us/img51/202...e11labeled.jpg

Chromosome 12

http://img803.imageshack.us/img803/2...e12labeled.jpg

Chromosome 13

http://img15.imageshack.us/img15/577...e13labeled.jpg

Chromosome 14

http://img834.imageshack.us/img834/2...e14labeled.jpg

Chromosome 15

http://img221.imageshack.us/img221/9...e15labeled.jpg

Chromosome 16

http://img341.imageshack.us/img341/2...e16labeled.jpg

Chromosome 17

http://img600.imageshack.us/img600/1...e17labeled.jpg

Chromosome 18

http://img18.imageshack.us/img18/624...e18labeled.jpg

Chromosome 19

http://img193.imageshack.us/img193/9...e19labeled.jpg

Chromosome 20

http://img6.imageshack.us/img6/4605/...e20labeled.jpg

Chromosome 21

http://img268.imageshack.us/img268/9...e21labeled.jpg

Chromosome 22

http://img545.imageshack.us/img545/1...e22labeled.jpg

Added the 4th, here's what they look like so far:

http://i50.tinypic.com/2rcbx5i.jpg

http://oi46.tinypic.com/30myc9j.jpg

http://oi49.tinypic.com/2en6mwx.jpg

http://oi49.tinypic.com/wgopkz.jpg

How do I do the chromosome test? I dont have a computer right now so if it requires software i cant do it..

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Originally Posted by Sicilianu101

How do I do the chromosome test? I dont have a computer right now so if it requires software i cant do it..

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No, just download them from here and unzip:

http://bga101.blogspot.pt/2012/07/pi...c-genomic.html

These are 5 of mine:

http://www.theapricity.com/forum/pic...pictureid=4645

All five chromosomes.

http://s19.postimage.org/qzgqg98oz/E..._111111111.jpg

Chromosome 1
http://i.imgur.com/5qwph.png

Chromosome 2
http://i.imgur.com/r5b4J.png

Chromosome 3
http://i.imgur.com/Juqcq.png

Chromosome 4
http://i.imgur.com/SFLid.png

Chromosome 5
http://i.imgur.com/U8mp8.png

Chromosome 6
http://i.imgur.com/mRTQx.png

Chromosome 7
http://i.imgur.com/HbbCt.png

Chromosome 8
http://i.imgur.com/0qz8t.png

Chromosome 9
http://i.imgur.com/tmmS0.png

http://i.imgur.com/TX4x0.png

My biggest segments so far:


Chr 1
b: East English
(2nd Swedish)
a: Lithuanian
(2nd East English)

Chr 2
b: Ukrainian
(2nd Ukrainian)
a: Bulgarian Romanian
(2nd Ukrainian)

Chr 3
b: Chechen Lezgin
(2nd Saudi Arabian)
a: Bulgarian Romanian
(2nd Vologoda Russian)

Chr 4
b: Spanish
(2nd Vologoda Russian)
a: Chechen Lezgin
(2nd Spanish)

Chr 5
b:East English
(2nd Ukrainian)
a: Spanish
(2nd East English)

Chr 6
b: East English
(2nd Chechen Lezgin)
a: Swedish
(2nd Swedish)

Chr 7
b: Irish
(2nd Vologoda Russian)
a: Tuscan
(2nd Vologoda Russian)

Chr 8
b: Chechen Lezgin
(2nd Vologoda Russian)
a: Chechen Lezgin
(2nd East English)

Chr 9
b: Tuscan
(2nd Saudi Arabian)
a:Chechen Lezgin
(2nd Vologoda Russian)


Allot of large Chechen/Lezgin segments, quite odd actually...i have not looked at other Norwegians in this respect, will do that when all the chromosomes are out..

can someone please tell me how I can do this with my results, if I'm not part of the project? I am a bit technologically retarded too.

Quote:

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Originally Posted by fergusgiselle

can someone please tell me how I can do this with my results, if I'm not part of the project? I am a bit technologically retarded too.

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You need to be a part of the project to see your results. However he has this on his blog:

Quote:

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Submissions are closed
Please note; I'm currently not accepting new members, but I’ll make an announcement here when that changes. Meantime, some of my ancestry tests are available at GEDmatch, and they're easy to use. Good luck.

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10 chromosomes are out right now.

Chromosome 10
http://i.imgur.com/qO6AU.png

Interesting, on my chromosome 9 I have a pretty large segment of the Ethiopian_Ari population component.

http://s19.postimage.org/ybmn567ur/Chr9_Eurogenes.jpg

My first 10 Chromosomes:

http://i49.tinypic.com/t9y06r.jpg
http://i46.tinypic.com/263c5kl.jpg
http://i46.tinypic.com/feq8ht.jpg
http://i49.tinypic.com/9fwffk.jpg
http://i45.tinypic.com/inhllf.jpg
http://i50.tinypic.com/nz3ia.jpg
http://i46.tinypic.com/2e3tu9h.jpg
http://i45.tinypic.com/zooz5.jpg
http://i48.tinypic.com/55pcnp.jpg
http://i48.tinypic.com/25j8840.jpg

#'s 11 & 12

http://i49.tinypic.com/357pr1t.jpg
http://i48.tinypic.com/15x8y9c.jpg

Here is the 16 chr that have been released so far:

http://img825.imageshack.us/img825/6597/123msn.png

The biggest surprise so far is the low number of East Asian segments, as well as a limited number of Swedish segments, a small Sub saharan segment, and the high number of Caucasus segments.

Quote:

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Originally Posted by evon

Here is the 16 chr that have been released so far:

http://img825.imageshack.us/img825/6597/123msn.png

The biggest surprise so far is the low number of East Asian segments, as well as a limited number of Swedish segments, a small Sub saharan segment, and the high number of Caucasus segments.

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You should check the score:

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“outSupportMix.Probs.tped” shows the posterior probabilities for each of the SNP windows, and lines up with the “outSupportMix.tped” file. So, for instance, let's say your Irish segment, marked by the number 13 in the “outSupportMix.tped” file, is given a score of 0.75. That would be a pretty decent probability of the classification being a correct one. On the other hand, I'd say that something like 0.15 would be a fairly uncertain result.

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Quote:

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Originally Posted by plastictuga

You should check the score:

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I could not figure out that part, so i will see if someone else can check it for me...

Quote:

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Originally Posted by evon

I could not figure out that part, so i will see if someone else can check it for me...

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I found it for you: 0.157 & 0.117

My chromosome:

http://img845.imageshack.us/img845/1673/7by1dshfsl.jpg

I have not compared myself too much with the others since it takes so much time, so who knows if this is typical or not for my region in general..?

Quote:

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Originally Posted by evon

IBD analysis...

Biggest matches -19> if i got it right (the lower the E value, the higher the match):

1-5:

IS1 NO1 9080 9473 1.72E-19
NO1 SV1 33468 33777 1.73E-19
NO1 RU18 36982 37317 4.74E-19
NO1 NA12751 (CEU) 37516 37875 3.14E-19
GSM536643 (Lithuanian) NO1 79939 80195 5.14E-20
NO1 NO6 25908 26472 2.44E-20
NO1 HG00115 (UK) 86587 86786 6.40E-21
NO1 SE4 76503 76987 1.12E-21
NO1 HG00102 (UK) 52111 52424 2.25E-23
NO1 NO10 65168 65467 5.82E-24
NO1 NO10 66463 66735 2.24E-24
NO1 NA12812 (CEU) 86526 86845 9.03E-25

6-11:

UK42 NO1 41673 42108 3.22E-19
NO1 SENO2 77412 78004 1.22E-19
CA4 NO1 13617 13913 3.80E-19
NO1 NO2 36459 36743 4.30E-20
NO1 HG00107 (UK) 68764 69242 3.63E-20
NO1 HGDP00899 (Russian) 79085 79256 1.46E-21
NO1 HGDP00796 (Orcadian) 9915 10227 1.71E-21
NO1 WEUFI1 58093 58368 2.59E-23
UK39 NO1 80269 80853 4.26E-25
NO1 NO2 12802 13316 7.24E-31

12-22:

HGDP00539 (French) NO1 77711 77903 2.49E-19
NO1 RU6 45751 46019 6.00E-19
NO1 SE22 52691 53079 8.55E-25
NO1 HGDP00799 (Orcadian) 68718 69063 1.24E-25

I did not expect Russians to be among my top matches (where in Russia are they from?), the rest are less of a surprise though..

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Here is the last run, i went down to E-16 this time..

1-5:

NO1 SE13 2412 2613 9.60E-16
GSM536624 NO1 9080 9268 3.19E-16 (Hungarian)
DK5 NO1 13519 13694 2.43E-16
NO1 HG00110 20939 21134 5.34E-16 ????
NO1 RU14 24929 25111 1.16E-16
NO1 NO6 26752 27071 1.41E-16
NO1 NA07347 28703 29092 1.02E-16 (CEU)
GSM536737 NO1 31487 31693 2.96E-16 (Chuvash)
NO1 NA12751 37516 37875 2.01E-16 (CEU)
BY3 NO1 42384 42550 4.32E-16
GSM536621 NO1 42373 42550 1.57E-16 (Hungarian)
NO1 HGDP00892 42371 42550 1.57E-16 (Russian)
NO1 HGDP00894 42373 42550 1.57E-16 (Russian)
DEPL1 NO1 42373 42550 1.57E-16
belorus10 NO1 42373 42554 1.88E-16
NO1 GSM558777 66471 66641 1.16E-16 (Western Greenland)
Kumyk13Y NO1 70486 70713 9.88E-16
HG00242 NO1 70486 70734 2.94E-16 ???
NO1 GSM536777 84476 84705 1.56E-16 (Uzbek)
NO1 HGDP00961 83935 84179 5.84E-16 (Yakut)
FI14 NO1 83949 84179 5.94E-16
ashkenazy2e NO1 24921 25116 2.68E-17
IS1 NO1 9080 9358 1.27E-17
HG00264 NO1 24927 25116 8.39E-17 ????
HG00126 NO1 71785 71946 6.64E-17 ???
GSM558737 NO1 83935 84191 9.94E-17 (Evenk)
NO1 NA12156 81369 81576 7.30E-17 (CEU)
GSM536643 NO1 79941 80195 3.51E-17 (Lithuanian)
HG00137 NO1 81092 81321 1.95E-18 ???
belorus5 NO1 27637 27913 9.59E-18
NO1 HG00102 52156 52424 2.71E-20 ???
NO1 SV1 33477 33777 4.97E-20
NO1 RU18 37006 37317 2.49E-21
NO1 PL3 37036 37350 8.12E-21
NO1 NO6 27182 27590 5.55E-22
NO1 NO10 66463 66735 3.13E-22
NO1 NO10 65171 65460 1.91E-23
NO1 SE4 76529 76989 1.16E-24
NO1 HG00115 86574 86845 1.19E-24 ???
NO1 NA12812 86533 86845 1.76E-25 (CEU)
NO1 NO6 26064 26742 6.84E-31

6-11:



FI7 NO1 10216 10479 2.60E-16
HG00132 NO1 20064 20253 5.55E-16 ???
GSM558726 NO1 20064 20271 4.45E-16 (Altai)
UK42 NO1 41673 42108 5.47E-16
NO1 NA12249 51780 51971 4.15E-16 (CEU)
NO1 WEUFI1 58132 58289 2.34E-16
NO1 HG00107 68766 69167 2.49E-16 ???
NO1 HGDP00795 73413 73610 1.54E-16 (Orcadian)
NO1 HG00122 73422 73610 6.82E-16 ???
NO1 HGDP00733 8623 8895 1.30E-17 (Palestinian)
NO1 HG00121 50835 51152 5.10E-17 ???
NO1 SE21 55795 56082 5.74E-17
UK36 NO1 64206 64354 9.35E-17
HGDP00527 NO1 77099 77457 5.68E-17 (French)
CA4 NO1 13614 13822 7.12E-18
NO1 NO12 13591 13869 9.01E-19
NOUK1 NO1 79116 79246 5.22E-19
UK35 NO1 54853 55188 9.98E-21
NO1 NA07055 68755 69285 7.07E-21 ???
HG00127 NO1 73358 73610 4.85E-21 ???
NO1 NA11930 78798 79069 1.52E-22 (CEU)
NO1 NO2 12800 13142 1.37E-23
NO1 HGDP00899 79066 79256 1.83E-24 (Russian)
UK39 NO1 80357 80853 7.66E-24
NO1 NO2 36718 37156 9.06E-25
NO1 HGDP00796 9681 10227 1.08E-33 (Orcadian)


12-22:


HGDP00536 NO1 27595 27838 8.22E-16 (French)
NO1 RU36 55241 55450 1.92E-16
NO1 HGDP00199 70010 70284 1.17E-16 (Sindhi)
NO1 Romanian_Jew_3 45085 45269 1.92E-17
NO1 NA12749 46723 46885 2.16E-17 (CEU)
NO1 NA12056 31681 31869 4.64E-17 (CEU)
NO1 NA12815 36328 36776 7.21E-18 (CEU)
ashkenazy9w NO1 5750 5982 4.36E-18
NO1 SE13 76310 76552 9.59E-19
NO1 HGDP00799 68754 69341 2.24E-33 (Orcadian)
NO1 SE22 52688 53091 1.76E-26

Could someone please tell me where i can look up the HG samples and NA07055?

Looking at the results i am somewhat dumbfounded, i did not expect Western Greenland, South/Central Asia and various Siberian matches, but ive gotten used to Russians and Caucasus matches, but these other matches must be really old right, so what age scale can i use for the various matches based on these results?

http://eurogenes.blogspot.com.au/201...ucture-of.html

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Europeans are mainly the descendants of Neolithic farmers from the Near East and native European Mesolithic hunter-gatherers, with the Mesolithic component peaking in Northeastern Europe. Moreover, all Europeans have prehistoric East Asian admixture, but Northern Europeans have more of it than Southern Europeans. However, Southern Europeans have recent Sub-Saharan African ancestry that Northern Europeans lack.

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