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Kurd
05-06-2015, 08:07 PM
I was interested in assessing Interpretome's PCAs, and was also curious to see where everyone plotted around me. For those not familiar with Interpretome here are the steps you need to take:

1- Go to Interpretome.com using either Firefox or Google Chrome. Their site does not support Internet Explorer
2- Click on Ancestry, then click on PCA
3- Click on upload/add genome. They support only 23andme. Make sure you upload an unzipped version of your genome. This should take a couple of seconds.
4- Choose a resolution of 100,000 SNPs
5- For the 1st plot choose Reference Populations, PC1/ PC2. It takes a couple of seconds to plot
6- To zoom in, left click with your mouse, and drag it to cover the area you want to zoom into
7- For the 2nd plot, choose HGDP World, PC3/PC4, and repeat step 6
8- For the 3rd plot, choose Mid East/Jewish, PC1/PC2
9- For the 4th plot, choose HGDP Asian, PC1/PC2, Detailed Regional.
10- Take screen shots, and upload to photo sharing website such as imgur.com

Although the 3rd and 4th plots are most relevant to W Asians and S Asians, respectively, Europeans can also give it a try.


http://i.imgur.com/Vha2OUy.jpg
http://i.imgur.com/SsV8XJN.jpg
http://i.imgur.com/B2q90Rp.jpg
http://i.imgur.com/eSwETCU.jpg

Anabasis
05-06-2015, 09:22 PM
I wish i had 23andme results

Anabasis
05-06-2015, 09:48 PM
I tested my friends results. Which we have similar calculator results. I cant share the PCAs without his permision but what i can say is,
in 1st PCA, he is between West European and Middle Eastern,
In second on he is middle in Near Eastern,
in third PCA he is with Armenians,
and fourth one is he is close to Kalashes

BalkanKiwi
05-06-2015, 09:51 PM
Reference Populations

http://i.imgur.com/zwgYD1J.png

HGDP World

http://i.imgur.com/mWe5Iod.png

Mid East/Jewish

http://i.imgur.com/bvmlJs9.png

HGDP Asian

http://i.imgur.com/r3MJmgl.png

MonkeyDLuffy
05-06-2015, 10:20 PM
http://i.imgur.com/A0X5l6P.png

http://i.imgur.com/cj2DBeJ.png

http://i.imgur.com/FbzkOH8.png

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

Kurd
05-06-2015, 10:54 PM
http://i.imgur.com/A0X5l6P.png

http://i.imgur.com/cj2DBeJ.png

http://i.imgur.com/FbzkOH8.png

http://i.imgur.com/FbzkOH8.png

It is interesting that on the References plot you are east if me but still west of the S Asian cluster, which indicates that their S Asian references are likely from central or S India. We will have a better idea when more S Asians post
BTW, you have 2 Mid East plots and no HGDP Asian plot

MonkeyDLuffy
05-06-2015, 11:06 PM
It is interesting that on the References plot you are east if me but still west of the S Asian cluster, which indicates that their S Asian references are likely from central or S India. We will have a better idea when more S Asians post
BTW, you have 2 Mid East plots and no HGDP Asian plot

Yeah I just edited my post, you can see my asian plot now. Probably some kind of error with my image uploader before. The south asian population is probably south Indian or bengali, seeing there is a huge gap between me and them. If there were central Indians, they would have filled the gap.

Kurd
05-06-2015, 11:23 PM
Reference Populations

http://i.imgur.com/zwgYD1J.png

HGDP World

http://i.imgur.com/mWe5Iod.png

Mid East/Jewish

http://i.imgur.com/bvmlJs9.png

HGDP Asian

http://i.imgur.com/r3MJmgl.png

On the references chart you plot between Mid East and Europe which would indicate some Mid Eastern ancestry if the charts are accurate. We will have a better idea of accuracy when more Europeans Ashkenazis and W Asians post

Stephen1986
05-06-2015, 11:47 PM
Here are my plots, I've added my brother as well and edited my marker to differentiate mine from his.

http://i975.photobucket.com/albums/ae239/quotablepatella/plotone_zpsnlmufug7.png (http://s975.photobucket.com/user/quotablepatella/media/plotone_zpsnlmufug7.png.html)
http://i975.photobucket.com/albums/ae239/quotablepatella/plottwo_zpsx0ty8v90.png (http://s975.photobucket.com/user/quotablepatella/media/plottwo_zpsx0ty8v90.png.html)
http://i975.photobucket.com/albums/ae239/quotablepatella/plotthree_zpsjwdih5ng.png (http://s975.photobucket.com/user/quotablepatella/media/plotthree_zpsjwdih5ng.png.html)
http://i975.photobucket.com/albums/ae239/quotablepatella/plotfour_zpsjoxj3nnj.png (http://s975.photobucket.com/user/quotablepatella/media/plotfour_zpsjoxj3nnj.png.html)

The Barnacle
05-06-2015, 11:50 PM
Here are my plots, I've added my brother as well and edited my marker to differentiate mine from his.

http://i975.photobucket.com/albums/ae239/quotablepatella/plotone_zpsnlmufug7.png (http://s975.photobucket.com/user/quotablepatella/media/plotone_zpsnlmufug7.png.html)
http://i975.photobucket.com/albums/ae239/quotablepatella/plottwo_zpsx0ty8v90.png (http://s975.photobucket.com/user/quotablepatella/media/plottwo_zpsx0ty8v90.png.html)
http://i975.photobucket.com/albums/ae239/quotablepatella/plotthree_zpsjwdih5ng.png (http://s975.photobucket.com/user/quotablepatella/media/plotthree_zpsjwdih5ng.png.html)
http://i975.photobucket.com/albums/ae239/quotablepatella/plotfour_zpsjoxj3nnj.png (http://s975.photobucket.com/user/quotablepatella/media/plotfour_zpsjoxj3nnj.png.html)

Why are Africans clustering with Europeans and not South Asians? Huh? I'm confused
Quoted the wrong person great, it was meant Jason ( jtom?..)

newtoboard
05-06-2015, 11:55 PM
Why are Africans clustering with Europeans and not South Asians? Huh? I'm confused

Why should they cluster with South Asians? Because of skin color? Or because they have similar noses? I can't even believe someone made this type of unscientific comment. Europeans (and Middle Easterns and probably Afghans and Tajiks etc) are obviously closer to Africans than South Asians are. This isn't anything new given South Asians have a lot of ancestry from ASI and East Eurasian like groups, which are more distant to Africans than West Eurasian groups, that groups west of South Asia lack or have very little of. Not to mention many West Eurasian groups share E1b with Africans as well as have actual African ancestry.

BalkanKiwi
05-07-2015, 12:16 AM
Why are Africans clustering with Europeans and not South Asians? Huh? I'm confused
Quoted the wrong person great, it was meant Jason ( jtom?..)

A plot graph in particular?

Anabasis
05-07-2015, 12:27 AM
Why should they cluster with South Asians? Because of skin color? Or because they have similar noses? I can't even believe someone made this type of unscientific comment. Europeans (and Middle Easterns and probably Afghans and Tajiks etc) are obviously closer to Africans than South Asians are. This isn't anything new given South Asians have a lot of ancestry from ASI and East Eurasian like groups, which are more distant to Africans than West Eurasian groups, that groups west of South Asia lack or have very little of. Not to mention many West Eurasian groups share E1b with Africans as well as have actual African ancestry.

Well i think due to he is north european, YDNA similarities between south asians and the bronze age migrations from stepe to europe and asia he might expected more similarities between North West europeans and South Asians rather then North West Europeans and African. If he was southern european i would not suprise for African similarities but what he say in his profile is he is british-scothish. Actualy i m also a bit suprised. But you are right that i also heard that South and East asians have more similarities to African people rather then Europeans and Anatolians as well. (I might be wrong)

MonkeyDLuffy
05-07-2015, 12:35 AM
Why should they cluster with South Asians? Because of skin color? Or because they have similar noses? I can't even believe someone made this type of unscientific comment. Europeans (and Middle Easterns and probably Afghans and Tajiks etc) are obviously closer to Africans than South Asians are. This isn't anything new given South Asians have a lot of ancestry from ASI and East Eurasian like groups, which are more distant to Africans than West Eurasian groups, that groups west of South Asia lack or have very little of. Not to mention many West Eurasian groups share E1b with Africans as well as have actual African ancestry.

Lol i can stab someone with my nose.

Although i am surprised too. I've seen south asians who Look more african than africans. And yet there is so much difference genetically.

surbakhunWeesste
05-07-2015, 12:39 AM
A plot graph in particular?

The controversy that may follow, I think he was referring your Middle East/Jewish plot which has Central South Asian, African, European,Near East......asking for an explanation!

BalkanKiwi
05-07-2015, 12:54 AM
The controversy that may follow, I think he was referring your Middle East/Jewish plot which has Central South Asian, African, European,Near East......asking for an explanation!

I appear to plot close to Turks? Actually I seem to be in the middle of Turks and Lezgins.

surbakhunWeesste
05-07-2015, 12:58 AM
I appear to plot close to Turks? Actually I seem to be in the middle of Turks and Lezgins.

Ah, my bad I meant HGDP world.



HGDP World

http://i.imgur.com/mWe5Iod.png

jesus
05-07-2015, 01:01 AM
It doesn't seem to be accurate with 23andme V4 kits.

BalkanKiwi
05-07-2015, 01:04 AM
Ah, my bad I meant HGDP world.

Zoomed in if you're curious.

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

Kurd
05-07-2015, 01:14 AM
Why are Africans clustering with Europeans and not South Asians? Huh? I'm confused
Quoted the wrong person great, it was meant Jason ( jtom?..)

I believe you are referring to the HGDP World PC3/PC4. This plot is deceiving. I'm not sure if you recall in one of my posts when I did PCAs for one of the gedmatch calculators, I had mentioned that to get total distance from one group (or one individual) to the other you would have to add the distances from all PCAs. In this case you would have to add the distances from HGDP World PC1/PC2 .........PC7/PC8 (though the variation/information drops off with higher PCs). I recall from looking at HGDP PC1/PC2, the distance between Africans and Europeans was very large.

The reason the plot is deceiving is that we don't have the eigenvector values for any of these plots. My guess is that in PC3/PC4, the African component is poorly represented and has a low eigenvalue. In hindsight, I should have asked for PC1/PC2, instead of PC3/PC4. If you look at the other plots you will notice that Africans are off the chart, and the reason being is that those plots are properly representing the African component.

With regards to genetic distance between Africans and Asians, I would have to defer to a FST table, but I suspect E Africans would genetically be closest to S Asians.

surbakhunWeesste
05-07-2015, 01:22 AM
Zoomed in if you're curious.

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

I am fine but thanks anyway, its much clearer view.
It was The Barnacle who had confusion and needed an explanation as to why Europeans clustered with Africans and not Central South Asians HDGP sample (Balochi, Brahui, Burusho, Hazara, Kalash, Makrani, Pashtun, Sindhi, and Uyghur).

Varun R
05-07-2015, 03:28 AM
4508
4509
4510
4511

fil
05-07-2015, 03:38 AM
4512
4513
4514
4515

Varun R
05-07-2015, 03:54 AM
Re-uploaded files with x-axes shown :/

4518
4519
4520
4521

The Barnacle
05-07-2015, 09:09 AM
I believe you are referring to the HGDP World PC3/PC4. This plot is deceiving. I'm not sure if you recall in one of my posts when I did PCAs for one of the gedmatch calculators, I had mentioned that to get total distance from one group (or one individual) to the other you would have to add the distances from all PCAs. In this case you would have to add the distances from HGDP World PC1/PC2 .........PC7/PC8 (though the variation/information drops off with higher PCs). I recall from looking at HGDP PC1/PC2, the distance between Africans and Europeans was very large.

The reason the plot is deceiving is that we don't have the eigenvector values for any of these plots. My guess is that in PC3/PC4, the African component is poorly represented and has a low eigenvalue. In hindsight, I should have asked for PC1/PC2, instead of PC3/PC4. If you look at the other plots you will notice that Africans are off the chart, and the reason being is that those plots are properly representing the African component.

With regards to genetic distance between Africans and Asians, I would have to defer to a FST table, but I suspect E Africans would genetically be closest to S Asians.

Thanks for the explanation Kurd, btw what I meant was that South Asians are closer to Europeans than Africans are to Europeans are right? Don't know why that guy ^was throwing a fit.

The Barnacle
05-07-2015, 09:18 AM
Why should they cluster with South Asians? Because of skin color? Or because they have similar noses? I can't even believe someone made this type of unscientific comment. Europeans (and Middle Easterns and probably Afghans and Tajiks etc) are obviously closer to Africans than South Asians are. This isn't anything new given South Asians have a lot of ancestry from ASI and East Eurasian like groups, which are more distant to Africans than West Eurasian groups, that groups west of South Asia lack or have very little of. Not to mention many West Eurasian groups share E1b with Africans as well as have actual African ancestry.

Stop getting emotional. I made one statement due to some confusion . And yes, Africans and austrnnesians( aboriginals) are the most distant from Europeans and Central Asians in terms of genetics, nothing new there. I did not expect Africans clustering right next to Europeans while South Asians were distant from them. If you look at admixtyre calculators etc South Asians score pretty much the same conponents but in different levels to Europeans +ASI, whereas Africans do not. So yeah forgive me for making that preposterous statement( sarcasm level 100).

The Barnacle
05-07-2015, 09:20 AM
Why should they cluster with South Asians? Because of skin color? Or because they have similar noses? I can't even believe someone made this type of unscientific comment. Europeans (and Middle Easterns and probably Afghans and Tajiks etc) are obviously closer to Africans than South Asians are. This isn't anything new given South Asians have a lot of ancestry from ASI and East Eurasian like groups, which are more distant to Africans than West Eurasian groups, that groups west of South Asia lack or have very little of. Not to mention many West Eurasian groups share E1b with Africans as well as have actual African ancestry.

You misunderstood what I was saying for gods sake. I meant why are South Asians not clustering with EUROPEANS

Stephen1986
05-07-2015, 10:57 AM
What are people's opinions on mine?


Here are my plots, I've added my brother as well and edited my marker to differentiate mine from his.

http://i975.photobucket.com/albums/ae239/quotablepatella/plotone_zpsnlmufug7.png (http://s975.photobucket.com/user/quotablepatella/media/plotone_zpsnlmufug7.png.html)
http://i975.photobucket.com/albums/ae239/quotablepatella/plottwo_zpsx0ty8v90.png (http://s975.photobucket.com/user/quotablepatella/media/plottwo_zpsx0ty8v90.png.html)
http://i975.photobucket.com/albums/ae239/quotablepatella/plotthree_zpsjwdih5ng.png (http://s975.photobucket.com/user/quotablepatella/media/plotthree_zpsjwdih5ng.png.html)
http://i975.photobucket.com/albums/ae239/quotablepatella/plotfour_zpsjoxj3nnj.png (http://s975.photobucket.com/user/quotablepatella/media/plotfour_zpsjoxj3nnj.png.html)

Anabasis
05-07-2015, 11:16 AM
We dont know whats the PCAx-PCAy refers. I have no idea how to have conclusions with that PCAs

Kurd
05-07-2015, 11:58 AM
These are for Zahra's dad, Kandhari Pashtun. I have added myself as a frame of reference. I substituted PC1/PC2 for PC3/PC4 on the HGDP World, since PC3/PC4 was not useful as it showed me closer to SC Asians than him. PC3/PC4 does not appear to capture S Asian admixture as well as PC1/PC2. On the 2nd chart I zoomed out a little to show Africans, since there was a bit of discussion about them. This would be a more accurate depiction than the PC3/PC4 plot, which I do not believe captures as much of the African admixture.


http://i.imgur.com/CLpIoBP.jpg
http://i.imgur.com/9UZ2OGX.jpg
http://i.imgur.com/viYlEfL.jpg
http://i.imgur.com/yDWL1M1.jpg

The Barnacle
05-07-2015, 12:04 PM
I'm going to pass on this thread, way too confusing for me lol

Kurd
05-07-2015, 02:13 PM
We dont know whats the PCAx-PCAy refers. I have no idea how to have conclusions with that PCAs

In PCAs each admixture component is represented by an eigenvector, and these are not usually parallel to the x and y axis. You are correct we don't know which eigenvectors are represented in PC1/Pc2......, and what their eigenvalues are (representation). However, most variation (information) is captured with PC1/PC2, and less as you move up to higher PCs

vettor
05-07-2015, 05:58 PM
In PCAs each admixture component is represented by an eigenvector, and these are not usually parallel to the x and y axis. You are correct we don't know which eigenvectors are represented in PC1/Pc2......, and what their eigenvalues are (representation). However, most variation (information) is captured with PC1/PC2, and less as you move up to higher PCs

thanks

You need to help me in plotting the following on the world stage.

This is what I did , I used my son's genome...........all parameters as you required in post#1 plots european. so i ignore them. But here is the one you can use, based on 9- For the 4th plot, choose HGDP Asian, PC1/PC2, Detailed Regional.

http://i103.photobucket.com/albums/m153/vicpret/ap%20full_zpsz7zxp7ri.jpg (http://s103.photobucket.com/user/vicpret/media/ap%20full_zpsz7zxp7ri.jpg.html)

The above one is my son's FULL genome

Below is my Son's phased genome for only the Paternal line

http://i103.photobucket.com/albums/m153/vicpret/ap%20paternal_zpsjefeo9xz.jpg (http://s103.photobucket.com/user/vicpret/media/ap%20paternal_zpsjefeo9xz.jpg.html)


How much difference is there between his plot for Full and his plot for Paternal lines in terms of geography?

Hanna
05-07-2015, 06:22 PM
This is from 4 years ago. I don't know if it has been updated since but it seems to have changed?? Perhaps I should do it again??


https://scontent-sin.xx.fbcdn.net/hphotos-xtp1/v/t1.0-9/11181731_474902222685455_592924436402928496_n.jpg? oh=f238542d78432ff296bf00f3a88d76ed&oe=55C709EF
https://scontent-sin.xx.fbcdn.net/hphotos-xta1/v/t1.0-9/11109491_474902252685452_1146090049785158760_n.jpg ?oh=6a6cf260180eef00c15361395115360a&oe=55E20367
https://fbcdn-sphotos-h-a.akamaihd.net/hphotos-ak-xap1/v/t1.0-9/11207362_474902322685445_6848286670986644510_n.jpg ?oh=aea39aa51f471549b46d6e23d93ba5ae&oe=55CA1054&__gda__=1439437960_0244f0e0e1e730e535075164336c5fb e
https://fbcdn-sphotos-g-a.akamaihd.net/hphotos-ak-xpt1/v/t1.0-9/11060315_474902356018775_7873990852705231797_n.jpg ?oh=2e502fc35060d3dc2eff5c63dffe049c&oe=55BF7C99&__gda__=1439451549_4318dac6e62f0fae15ee47f4179604d 0
https://fbcdn-sphotos-e-a.akamaihd.net/hphotos-ak-xtf1/v/t1.0-9/11118461_474902392685438_1828616337028508142_n.jpg ?oh=b481f1a2052ba09e22c0dfd89deaab7d&oe=55D31DD3&__gda__=1439240584_9049574ab3053e75f9be0c3926e0517 c

Kurd
05-07-2015, 09:49 PM
Re-uploaded files with x-axes shown :/

4518
4519
4520
4521

Varun, I can't make any sense of your 1st plot. You are further away from the S Asian cluster than I am. What chip were you genotyped with?

fil
05-07-2015, 10:30 PM
Varun, I can't make any sense of your 1st plot. You are further away from the S Asian cluster than I am. What chip were you genotyped with?

Varun's is kind of similar to mine. I am really confused what South Asian population is used as the reference.

newtoboard
05-07-2015, 10:39 PM
Stop getting emotional. I made one statement due to some confusion . And yes, Africans and austrnnesians( aboriginals) are the most distant from Europeans and Central Asians in terms of genetics, nothing new there. I did not expect Africans clustering right next to Europeans while South Asians were distant from them. If you look at admixtyre calculators etc South Asians score pretty much the same conponents but in different levels to Europeans +ASI, whereas Africans do not. So yeah forgive me for making that preposterous statement( sarcasm level 100).

Africans are the most distant from East Asians and Australian aboriginals are the most distant from Africans. So the misinformed statements from you keep on coming.

And stop throwing a hissy fit because I didn't understand what you meant to write. Write what you mean rather than expecting other people to waste their valuable time trying to read your mind. I can't believe somebody is upset because they wrote what appears to be an ignorant and ill informed statement and the other person couldn't read their mind to really thing they meant something else. Hilarious.

Kurd
05-07-2015, 11:16 PM
Varun's is kind of similar to mine. I am really confused what South Asian population is used as the reference.

I meant to ask you as well. Were you genotyped with V4? If so that may be throwing your results off as there is less marker overlap with their program, but then mine are also V4, unless many of your S Asian alleles happened not to overlap, but the odds of that happening with both of you are low. BTW it may be helpful if you post another plot of the References chart since I cant see the ME cluster

MonkeyDLuffy
05-08-2015, 12:00 AM
I meant to ask you as well. Were you genotyped with V4? If so that may be throwing your results off as there is less marker overlap with their program, but then mine are also V4, unless many of your S Asian alleles happened not to overlap, but the odds of that happening with both of you are low. BTW it may be helpful if you post another plot of the References chart since I cant see the ME cluster

I got my results in January this year, so it was probably v4 too but my results seems normal

Kurd
05-08-2015, 12:12 AM
I got my results in January this year, so it was probably v4 too but my results seems normal
I agree, your results, and mine for that matter, are still likely affected because of V4, but not as much as Varun.

icebreaker
05-08-2015, 12:25 AM
1.
http://i.imgur.com/Bao1kpp.gif

2.
http://i.imgur.com/BHeRR5A.gif

3.
http://i.imgur.com/Hqqcwkb.gif

4.
http://i.imgur.com/0VS4tJS.gif

(I just used PC1/PC2)
5. HGDP EURO
http://i.imgur.com/4LctGHB.gif

6. POPRES_EURO
http://i.imgur.com/vXlszaY.gif

fil
05-08-2015, 02:12 AM
I meant to ask you as well. Were you genotyped with V4? If so that may be throwing your results off as there is less marker overlap with their program, but then mine are also V4, unless many of your S Asian alleles happened not to overlap, but the odds of that happening with both of you are low. BTW it may be helpful if you post another plot of the References chart since I cant see the ME cluster

I did mine in fall of 2014 around September or October. So I think it is V4.

I redid it. The original one made the ME cluster a weird color and I had to tilt my computer screen just to see it.

4532

Kurd
05-08-2015, 02:35 AM
That does not look right. It is strange that you and Varun are affected the most

MonkeyDLuffy
05-08-2015, 03:10 AM
Even i am not that west shifted on the plot.

Varun R
05-08-2015, 03:45 AM
I was genotyped using the V3 platform....

Kurd
05-08-2015, 03:56 AM
The following plots contain Sapporo, Rukha, myself, and my daughter. Everyone is V4, except for Rukha who may be V3, because his file contains 900,000 SNPs vs 590,000 for V4. Sapporo seems to be in the same boat as Varun and Fil on plot 1 :confused:. For some reason they are plotting furthest from the S Asian cluster.

http://i.imgur.com/B2bLcRs.jpg
http://i.imgur.com/8xY88ZX.jpg
http://i.imgur.com/yS94REt.jpg
http://i.imgur.com/aruFbw1.jpg

Sapporo
05-08-2015, 07:21 AM
@Kurd

Actually, I am on the V3 chip as well. At least I should be. I took my test back in 2013 before 23andMe converted to the V4 chip. Not sure what is with the wacky PCA results.

Hanna
05-08-2015, 05:14 PM
I did it again and this is what my updated PCA plots look like:

1- Reference Populations, PC1/ PC2:
https://scontent-sin.xx.fbcdn.net/hphotos-xft1/v/t1.0-9/10155176_475457835963227_4056983838857140873_n.jpg ?oh=825942ad32b1f6f789bf97c4a91a895d&oe=55C65FB1
2- HGDP World, PC3/PC4:
https://fbcdn-sphotos-b-a.akamaihd.net/hphotos-ak-xpf1/v/t1.0-9/1610924_475457949296549_261529276077513437_n.jpg?o h=b2bebd07174cddda41673e1c758dd66f&oe=55D61C16&__gda__=1443563258_d52a36933cc6534523c6e22bb628ddb 0
3- Mid East/Jewish, PC1/PC2:
https://scontent-sin.xx.fbcdn.net/hphotos-xaf1/v/t1.0-9/10423976_475457962629881_334610278435083565_n.jpg? oh=29d8f9a071ee05a49c54b9ef9458d47b&oe=55CE89A8
4- HGDP Asian, PC1/PC2, Detailed Regional:
https://fbcdn-sphotos-f-a.akamaihd.net/hphotos-ak-xap1/v/t1.0-9/11048753_475457985963212_7484571923046620312_n.jpg ?oh=4e18d871bfe82c97cc9089c29f4ad43c&oe=55DA3EDE&__gda__=1439341314_52f05f389d9e9ea9055bf59e481f3cf e

John Doe
05-08-2015, 05:33 PM
4533453445354536

Here are mine, thought it'll be nice to add the European version as well.

vettor
05-08-2015, 06:37 PM
thanks

You need to help me in plotting the following on the world stage.

This is what I did , I used my son's genome...........all parameters as you required in post#1 plots european. so i ignore them. But here is the one you can use, based on 9- For the 4th plot, choose HGDP Asian, PC1/PC2, Detailed Regional.

http://i103.photobucket.com/albums/m153/vicpret/ap%20full_zpsz7zxp7ri.jpg (http://s103.photobucket.com/user/vicpret/media/ap%20full_zpsz7zxp7ri.jpg.html)

The above one is my son's FULL genome

Below is my Son's phased genome for only the Paternal line

http://i103.photobucket.com/albums/m153/vicpret/ap%20paternal_zpsjefeo9xz.jpg (http://s103.photobucket.com/user/vicpret/media/ap%20paternal_zpsjefeo9xz.jpg.html)


How much difference is there between his plot for Full and his plot for Paternal lines in terms of geography?

I did mine and the only useful indicators are that I fit with Hazara and Burusho in this HGDP Asian, PC1/PC2, Detailed Regional.
All the others are European

The HGDP Asian, PC1/PC2, Detailed Regional with a PC3/PC4 instead as per post#1 instructions .............shows Kalash

PureEvil
05-09-2015, 01:06 AM
Reference Populations:
http://i1154.photobucket.com/albums/p535/PureEvil91/Interpretome/interrefpop_zpscv3r1t8d.png (http://s1154.photobucket.com/user/PureEvil91/media/Interpretome/interrefpop_zpscv3r1t8d.png.html)

HGDP Asian:
http://i1154.photobucket.com/albums/p535/PureEvil91/Interpretome/hdgpasian_zpsnlekuwi1.png (http://s1154.photobucket.com/user/PureEvil91/media/Interpretome/hdgpasian_zpsnlekuwi1.png.html)

HGDP World:
http://i1154.photobucket.com/albums/p535/PureEvil91/Interpretome/interprethdgpworld_zpsla6k1pat.png (http://s1154.photobucket.com/user/PureEvil91/media/Interpretome/interprethdgpworld_zpsla6k1pat.png.html)

Middle East/Jewish:
http://i1154.photobucket.com/albums/p535/PureEvil91/Interpretome/mideastjewish_zpsotzpudzd.png (
http://i1154.photobucket.com/albums/p535/PureEvil91/Interpretome/mideastjewish_zpsotzpudzd.png)

HGDP Europe:
http://i1154.photobucket.com/albums/p535/PureEvil91/Interpretome/hdgpeuro_zpsrfnlpbl3.png (http://s1154.photobucket.com/user/PureEvil91/media/Interpretome/hdgpeuro_zpsrfnlpbl3.png.html)

Hanna
05-09-2015, 07:38 AM
Reference Populations

http://i.imgur.com/zwgYD1J.png




Why do you plot with Middle Easterners here? I appear to be plotted closer towards the Europeans than you, this does not make sense!

https://scontent-sin.xx.fbcdn.net/hphotos-xft1/v/t1.0-9/10155176_475457835963227_4056983838857140873_n.jpg ?oh=825942ad32b1f6f789bf97c4a91a895d&oe=55C65FB1


And in the Middle Eastern plot you are not too far from me.

You:

http://i.imgur.com/bvmlJs9.png

Me:
https://scontent-sin.xx.fbcdn.net/hphotos-xaf1/v/t1.0-9/10423976_475457962629881_334610278435083565_n.jpg? oh=29d8f9a071ee05a49c54b9ef9458d47b&oe=55CE89A8

neuandertal
05-15-2015, 08:08 AM
Reference Populations:
http://i.imgur.com/OMc9io4.jpg

HGDP World:
http://i.imgur.com/1FXU9IW.jpg

Middle East/Jewish
http://i.imgur.com/IzvwB2l.jpg

HGDP Asian
http://i.imgur.com/VV80TXs.jpg

HGDP Europe
http://i.imgur.com/mhclOaX.jpg


Like Jtoml4, perhaps I pull a bit middle eastern? Not sure what to think or how I compare to other europeans. I have gotten odd results on gedmatch before (e.g. Druze commonly shows up). 23andme identifies me as 98.6% northern european and 1.4% unassigned on conservative mode, 100% euro in speculative, while FTDNA says that I have 3% Middle Eastern (Asia Minor subgroup: Turkey/Georgia/Azerbaijan/Syria). This shows up in my mother as well but not my brother (I'm female). I have a theory that it's coming from our maternal line, which seems to have origins in the Asia Minor area. Not sure how viable this theory is but I have no other way to explain it.

Varun R
05-15-2015, 08:28 AM
@ Neuandertal,

For whatever reason the reference population plot seems to be off for a lot of people. I wouldn't read too much into it.

Koshur_Sam
08-26-2015, 09:36 PM
In the Middle East and Jewish section i'm clustering directly on top of Yemenjew with Ashkenazy directly under me, does that indicate what my Middle Eastern ancestry as shown in 23andme probably means ?

firemonkey
08-26-2015, 11:40 PM
http://i4.photobucket.com/albums/y126/labile/genealogy/interpretcome%201%20and%202a.png

http://i4.photobucket.com/albums/y126/labile/genealogy/interpretcome%203%20and%204a.png

Dorkymon
08-27-2015, 09:49 AM
I can see your name on the genome file. Maybe you'd want to blur it out.

firemonkey
08-27-2015, 07:03 PM
I can't see a way on photobucket of doing that.

ViktorL1
08-28-2015, 03:12 AM
Here are my results! Middle East/Jewish took too long to load.

Reference:
5693
World:
5694
Asian"
5695

The thumbnails are tiny, but it automatically enlarges if you click :)

tippy
05-15-2016, 09:25 AM
I can't believe I've never seen this before, sorry for the threadnecro but I thought it's worth posting

Attached: hgdp world (100k snps), mideast/jewish (100k snps)