Online genome analysis [Archive] - The Apricity Forum: A European Cultural Community

06-14-2011, 12:37 PM

Bastarnae, how did you come across that website?

Forget Me Not, did you try uploading your zipped file? I did and got the exact same result as Polako, although our unzipped file results differ. I'm wondering if the zipped file results are identical to everyone.

zipped:
http://img718.imageshack.us/img718/341/zipped.jpg

unzipped with v2:
http://img197.imageshack.us/img197/8030/v2pc1pc4.jpg

Here's what I got with v3 chip:
http://img90.imageshack.us/img90/7617/v3chippc1pc2.jpg

http://img16.imageshack.us/img16/6374/paintingceu.jpg

Polako

06-14-2011, 01:08 PM

^ Use unzipped. I'm next to a couple of Poles with that one, at least, so it looks legit.

http://img84.imageshack.us/img84/2643/pca1v4b.png

06-14-2011, 07:05 PM

I did that for the second and the third pics I posted.

In your blog entry you mentioned that the team members of that project advised you to use PC1 vs. PC4 for 23andme v2 - do you think that advice is also valid for the v3?

Loki

06-14-2011, 08:00 PM

How does one get the flag cluster?

poiuytrewq0987

06-14-2011, 08:05 PM

How does one get the flag cluster?

Click on PCA tab then click on the tab that says POPRES: European and go from there.

Grumpy Cat

06-14-2011, 08:07 PM

Oddly enough, I have no Neanderthal alleles.

I thought all people of Eurasian origin had them.

poiuytrewq0987

06-14-2011, 08:10 PM

I cluster with Northern Europeans it seems but they are using French samples for Northern European so...

http://img833.imageshack.us/img833/926/hdgpnormal.png

http://img202.imageshack.us/img202/8026/hdgpdetailed.png

Loki

06-14-2011, 08:12 PM

Click on PCA tab then click on the tab that says POPRES: European and go from there.

Weird ...

poiuytrewq0987

06-14-2011, 08:14 PM

Weird ...

You messed up. :P Change Y axis to PC2.

Loki

06-14-2011, 08:17 PM

Okay this looks more like it:

http://img863.imageshack.us/img863/6184/componentseur5.jpg

06-14-2011, 08:32 PM

Oddly enough, I have no Neanderthal alleles.

I thought all people of Eurasian origin had them.Speaking of Neanderthals, I found it hilarious that they felt the need to mention this:

Neandertal
Recent evidence has suggested that humans may have interbred with Neandertals after their migration out of Africa. With the sequencing of the Neandertal genome, variants have been found in Neandertals and Europeans and Asians, but not Africans.

In this exercise, you can count the number of Neandertal alleles in your personal genotype. Note that this index is not an actual measure of your physical similarity to a Neandertal.

d3cimat3d

06-14-2011, 10:28 PM

Bastarnae, how did you come across that website?

Polako posted it on another forum.

Anyways here's mine:

http://i53.tinypic.com/2cr4k1g.png

Zoomed in:

http://i53.tinypic.com/2rc5v5z.png

Frederick

06-14-2011, 10:31 PM

Interesting stuff.

I would however like it if one could either zoom into the map or if the flags would be somewhat smaller.

10 Neandertal alleles, hmm? http://www.iheartpaws.com/forums/images/smilies/oregonian_furious.gif

d3cimat3d

06-14-2011, 10:32 PM

^ You can zoom, just select the area with your mouse.

Frederick

06-14-2011, 10:33 PM

Zoomed in:
Doh! Where is the button to do this?

Frederick

06-14-2011, 10:34 PM

^ You can zoom, just select the area with your mouse.

Ah thanks! Was trying with mousewheel and looking for a button.
HAdnt tried to draw a field.

Thank you :)

Loki

06-14-2011, 10:40 PM

Mine zoomed. I seem quite surrounded by Swiss Germans, Belgians and French.

http://img835.imageshack.us/img835/7963/componentseur6.jpg

Loki

06-14-2011, 10:54 PM

Oddly enough, I have no Neanderthal alleles.

I thought all people of Eurasian origin had them.

Looks like I've got 8 ...

poiuytrewq0987

06-14-2011, 10:57 PM

6 Neanderthal alleles for me.

Grumpy Cat

06-14-2011, 10:58 PM

Mine zoomed. I seem quite surrounded by Swiss Germans, Belgians and French.

Same as me, though Swiss French, Belgians, Dutch, and French.

Frederick

06-14-2011, 11:08 PM

The 1v4 clouds are quiet stongly overlapping.

I am where the German, Austrian, Belgian and British clouds overlap.

Also, somewhere in the middle between the Swiss and Polish clouds.
Or in the middle between the Irish and Hungarian clouds.
Or between the French and Czechian clouds.

Hmm lots of words, one meaning: Somewhere in Germany. ;)

06-14-2011, 11:23 PM

Thanks for the tip, Bastarnae!

That's what mine looks like when zoomed in:
http://img5.imageshack.us/img5/4607/zoomine.jpg

Back to Neanderthals then.
I've got 5 out of 84, seems like I'm still fine :rotfl2
http://img840.imageshack.us/img840/2879/neanderthal.jpg

poiuytrewq0987

06-15-2011, 06:16 AM

Hm I think I might immigrate to Switzerland and rediscover my Swiss identity.

http://img826.imageshack.us/img826/2160/swissfmn.png

Loki

06-15-2011, 06:48 AM

Most seem to show Swiss ... weird.

Frederick

06-15-2011, 08:03 AM

the most close to actual geography is Dimension 1 versus 4

Dimension 1 seems to spread along the North-South axis while Dimension 4 seems to represent the West-East axis.

Also, switching off most of the countries and using only few is quiet interesting too. (by clicking the country code next to the flag)

This for example is a 4v1, limited to Poland, Italy, France and Scandinavia.

Olavsson

06-15-2011, 01:41 PM

Here are some of my results...

The Neanderthal-test:

http://img687.imageshack.us/img687/2774/neanderthaly.jpg

I'm apparently more Neanderthal than Thea. :D

The painting, with standard-settings:

http://img59.imageshack.us/img59/8766/hapmap2paintingstandard.jpg

Some maps:

http://img546.imageshack.us/img546/825/hgdpeurope100000resolut.jpg

http://img689.imageshack.us/img689/4963/unledyk.jpg

Pallantides

06-15-2011, 02:28 PM

http://i911.photobucket.com/albums/ac316/Pallantides/neandertal.png
http://i911.photobucket.com/albums/ac316/Pallantides/ancestrypainting.png
http://i911.photobucket.com/albums/ac316/Pallantides/popres.png
http://i911.photobucket.com/albums/ac316/Pallantides/popreszoom.png

Oreka Bailoak

06-15-2011, 02:56 PM

Neandertal 14

PCA - I scored in the middle of Germany, France, Switzerland, Belgium.

Note that this index is not an actual measure of your physical similarity to a Neandertal.
I read once that a type of occipital bun is possibly linked to neanderthal ancestry. (I have the largest occipital bun)

Frederick

06-15-2011, 06:56 PM

I once read about a British genetican claiming, red hair could be inheritated from neandertalians. ;)

But never heard about that again afer that.

Odoacer

06-16-2011, 02:08 AM

Is anyone else using IE8? This site doesn't seem to function for me.

Frederick

06-16-2011, 02:20 AM

Is anyone else using IE8? This site doesn't seem to function for me.

Compatibility

This website requires an HTML5 compatible browser, including current versions of:
Google Chrome (≥ 6.0)
Mozilla Firefox (≥ 4.0)
RockMelt
(Safari coming soon with Safari 6!)

Odoacer

06-16-2011, 02:26 AM

Thanks, Frederick. When I go to the website with IE8, the compatibility requirements aren't even available. I guess I'll have to go ahead & download a different browser then.

EDIT: Proof of crippling IE8 fail.

11225

I've downloaded Google Chrome now, which works, but so far I still prefer IE8. I know I'm weird.

Odoacer

06-16-2011, 05:13 AM

My results. I used Polako's recommended settings for Hapmap 2. "TSI" on the 3rd attachment apparently stands for "Toscani."

Pallantides

06-19-2011, 05:18 PM

Ancestry SNPs:
http://i911.photobucket.com/albums/ac316/Pallantides/AncestrySNPs.jpg

Positive Selection:
http://i911.photobucket.com/albums/ac316/Pallantides/positiveselection.jpg

This exercise looks up your genotype at one of 200 positions in the human genome thought to be under recent positive selection. When a new mutation appears that has a selective advantage, it can have a very rapid rise in the population before recombination can occur with nearby linked SNPs. The result is that there is a long region of the chromosome with one haplotype. Two methods (long range haplotype and integrated haplotype score) have been developed to search for long haplotypes, indicative of recent positive selection.

Olavsson

06-19-2011, 06:29 PM

Ancestry SNPs:

http://img821.imageshack.us/img821/9402/ancestryalleles.jpg

Positive selection:

http://img5.imageshack.us/img5/7007/positiveselection.jpg

d3cimat3d

06-19-2011, 09:58 PM

^How accurate is the feature that detects Asian alleles? I came out with 6 Asian alleles and that's a bit much for someone like me I think.

06-20-2011, 05:37 AM

^How accurate is the feature that detects Asian alleles? I came out with 6 Asian alleles and that's a bit much for someone like me I think.
Don't mind the proportions - 20 alleles are ridiculously little to derive any prediction of admixture percentage.

What you could do is copying the dbSNP numbers of the supposedly Asian alleles (1475930, ...) and search them with another feature in the same website - "Lookup". This way you would know which chromosomes these alleles are located in and could then compare it with 23andme's and McDonald's ancestry paintings.

For example, for me this program indicates two Asian alleles - 1475930 and 2824693, located respectively in 22nd and 21st chromosomes. However, on both 23andme's and McDonald's ancestry paintings all 22 autosomal chromosomes are 100% Euro - not even a slight noise. In Olavsson's signature it says that he's 100% Euro on both too but just like for me, this program says he's got an Asian allele. So it's either McDonald who is inaccurate or this program. I'd be more inclined to trust McDonnald.
http://img339.imageshack.us/img339/5444/ancestrysnps.jpg

Positive selection:
http://img710.imageshack.us/img710/8557/selectionp.jpg

Stefan

06-20-2011, 08:59 AM

PCA Plots

HGDP: World PC1 & PC2 ( Similar to what I've seen in other assessments. My African and Asian pull me downward and towards the left respectively.)
http://www.theapricity.com/forum/attachment.php?attachmentid=11435&d=1308554419

HGDP European PC1 & PC2 ( In most dimensions I'm at the fringes of Northern Europe.)
http://www.theapricity.com/forum/attachment.php?attachmentid=11438&d=1308554844

HGDP: European Detailed PC1 & PC2( In most dimensions I'm clustered with the French samples.)
http://www.theapricity.com/forum/attachment.php?attachmentid=11437&d=1308554844

Popres: European PC1 & PC4
http://www.theapricity.com/forum/attachment.php?attachmentid=11436&d=1308554419
Zoomed
http://www.theapricity.com/forum/attachment.php?attachmentid=11440&stc=1&d=1308561126
And here's my Ancestry Painting at default settings. When I change the settings around can see my "Asian", but it isn't as significant as my African admixture. The reason why I didn't take a screen of that is because for some reason it stops half way and I only get 10 or so chromosomes loaded.
http://www.theapricity.com/forum/attachment.php?attachmentid=11439&stc=1&d=1308560035

Oh and I got 11 on the Neanderthal test.

Peasant

06-27-2011, 10:00 PM

HGDP European
http://i.imgur.com/f0fmc.jpg

POPRES European (v3)

http://i.imgur.com/BMdta.jpg

Boudica

07-07-2011, 08:52 AM

It seems like I'm closest to the Swiss-German and Belgium markers, interesting.

Boudica

07-15-2011, 09:33 AM

Interesting..

Transhumanist

07-15-2011, 10:32 AM

Neandertal. Asian. Selection. POPRES:European (rotated once to right and flipped horizontally). Mid-East/Jewish (rotated once to right).

Transhumanist

07-15-2011, 01:12 PM

A couple of Chaldean Catholic Assyrians recently received their 23andMe results. I combined the Intepretome ME-Jewish PCA results for the two Chaldean-Assyrians and myself, and removed some of the Behar samples with known ADMIXTURE (most Jewish groups, Syrians, and Lebanese).

Note all the white space between Iran/Turkey and Mesopotamia (ASY), and the Levant (IQJ), presumably created by the greater than insignificant Asian ancestry of the Iranians and Turks. The gap between the Arabian populations to the south, and the northern population cluster, is presumably an effect of the elevated African admixture in Arabian populations. As I have stated in other threads regarding Iraqi Jews, and if we can assume negligible or limited post-exilic gene flow between Iraqi Jews and the Levant, they appear to plot consistent with a population with possibly moderate to significant Israelite/Judaean ancestry.

Loki

07-15-2011, 09:52 PM

http://www.theapricity.com/forum/attachment.php?attachmentid=12564&stc=1&d=1310766702

Tarja

08-12-2011, 02:38 AM

This won't work for me :( I upload my unzipped raw data, click stuff and nothing happens. Boo.

Scrapple

08-12-2011, 07:16 PM

This won't work for me :( I upload my unzipped raw data, click stuff and nothing happens. Boo.

It works best in Google chrome: http://www.google.com/chrome/

It won't work in Internet Explorer at all.

orangepulp

02-07-2012, 01:52 PM

HGDP World:
http://img844.imageshack.us/img844/909/map8a.jpg

http://img6.imageshack.us/img6/1700/map9e.jpg
Mid Eat/Jewish:
http://img823.imageshack.us/img823/1857/map4c.jpg
HGDP European:
http://img52.imageshack.us/img52/6858/map6q.jpg
POPRES European
http://img219.imageshack.us/img219/2255/map5l.jpg
HGDP Asian:
http://img848.imageshack.us/img848/7575/map7.jpg
Chromosome painting:
http://img12.imageshack.us/img12/5795/chromosomepaint.jpg

Mortimer

02-07-2012, 01:59 PM

http://esquilax.stanford.edu

Be sure to upload the .txt file and not the zipped folder itself

I always uploaded the zipped folder and got Burusho. But now i uploaded the txt and got European.

HGDPWorld

http://s14.postimage.org/b8tfqhgtt/HGDPWorld.png (http://postimage.org/)
gif image hosting (http://postimage.org/)

Mortimer

02-07-2012, 02:03 PM

Its funny how i cluster with the Serbs and Portuguese. Next to me is the Serb Flag right and left of me.

http://s11.postimage.org/61f5du0ir/Popres_European.png (http://postimage.org/)
image hosting jpeg (http://postimage.org/)

Scrapple

02-07-2012, 02:10 PM

Mortimer

02-07-2012, 02:14 PM

You have to set the X axis to PC1 and the Y axis to PC4 to get an accurate reading.

than i cluster with romanians.

http://s13.postimage.org/rfyckf90n/PC4_Popres.png (http://postimage.org/)
jpg image hosting (http://postimage.org/)

Scrapple

02-07-2012, 02:17 PM

than i cluster with romanians.

http://s13.postimage.org/rfyckf90n/PC4_Popres.png (http://postimage.org/)
jpg image hosting (http://postimage.org/)

That make more sense, you clustering with SE Europeans.

Mortimer

02-07-2012, 02:34 PM

will it be different with the v3 results?

Mortimer

02-09-2012, 03:02 PM

I tried HGDP Asian. I cluster with the Southasian Ethnicities.

http://s17.postimage.org/3umy0gkvj/HGDPASian.png (http://postimage.org/)
hosting images (http://postimage.org/)

Jerry

02-13-2012, 09:34 PM

Very interesting site indeed! My results, I'm Finnish

POPRES European

It looks like I cluster mostly with the British near Swedish without zooming, and then zoomed I'm there between Swedish, British, Irish and German and Dutch.

http://img826.imageshack.us/img826/4425/popreseuro.jpg (http://imageshack.us/photo/my-images/826/popreseuro.jpg/)

http://img11.imageshack.us/img11/5702/popreseurozoomed.jpg (http://imageshack.us/photo/my-images/11/popreseurozoomed.jpg/)

HGDP Europe

http://img51.imageshack.us/img51/9745/hgdpeurodetailed.jpg (http://imageshack.us/photo/my-images/51/hgdpeurodetailed.jpg/)

Chromosome painting

http://img20.imageshack.us/img20/4329/chrompa.jpg (http://imageshack.us/photo/my-images/20/chrompa.jpg/)

And I score 5 in Nenderthal.. Isn't this low? Strange, because I have 3.1% similarity in 23andme it should be really high

In the SNP ancestry, it gives me 17 Euros and 3 East Asian alleles. In McDonald there is no Asian, but some very small American part in one chromosome. In 23andme however I show 0.01% Asian for some reason.

Selection:
http://img828.imageshack.us/img828/3135/selecto.jpg (http://imageshack.us/photo/my-images/828/selecto.jpg/)