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Kurd
03-12-2015, 05:32 AM
This is part 1 of 2 of the MDLP k23b analysis project. The majority of the analysis will be done under part 2 which I will start within 2 days. The goals of part 2 of the project will be as follows:

1- To perform analysis via a PCA plot of the community member data. Component 1 of the PCA (x-axis) will consist of the sum of all the S. Asian, SE Asian, and NE Asian MDLP components minus all the West Asian components. Component 2 of the PCA (y-axis) will consist of the sum of all the MDLP European components minus all the African components. This choice of the components will nicely break up populations into clusters somewhat consistent with geographical positioning;

2- Create sorted admixture cluster graphs for the community membership;

3- Create sorted admixture overlap charts for a couple of the major ethnic groups.

I encourage members from all ethnicities to post their data under PART 2 which I will start within the next 2 days.

Part 1 is meant more of a fun thread than an analysis thread. My inspiration for part 1 was that I was a little surprised when I took a close look at my admixture breakdown by chromosome to see the large amount of variation between chromosomes. I thought that some members, like myself may find it interesting to compare their admixture variation with other members of the community, to see how they fare. I am not really sure whether their will be an observable variation pattern based on factors such as mixed ethnicities, etc.

I did a print screen for my reduced chromosome painting. For admixture by chromosome, I copied and pasted the info from Gedmatch into a spreadsheet, but I suppose you can do a print screen for that also.

The following definitions will apply throughout the project:

1- S. Asia = SC Asia + S. India
2- NE & SE Asia = The sum of Amerindian, Ancestral Altaic, Arctic, Tungus Altaic, Paleo Siberian, SE Asian, Australoid, Austronesian, Melano Polynesian
3- W. Asia = Near East + Caucasian


The following is a cluster graph of my admixtures by chromosome:

http://i1377.photobucket.com/albums/ah42/dil88888/MDLP%20k23b%20Chromosomal%20graph_zpsryvy4wfn.jpg (http://s1377.photobucket.com/user/dil88888/media/MDLP%20k23b%20Chromosomal%20graph_zpsryvy4wfn.jpg. html)

Here is my Reduced Chromosomal Painting:

http://i1377.photobucket.com/albums/ah42/dil88888/MDLP%20K23%20CHROMO_zpsjhrdnrk0.jpg (http://s1377.photobucket.com/user/dil88888/media/MDLP%20K23%20CHROMO_zpsjhrdnrk0.jpg.html)

Kurd
03-12-2015, 05:37 AM
This is a sorted table of admixture values by chromosome, showing quite a bit of variability from one chromosome to the next. I was curious to see how this compares to other members. I have grouped the components to enhance visualization:

http://i1377.photobucket.com/albums/ah42/dil88888/MDLP%20K23%20ADMIX%20BY%20CHROMO%20TABLE%201_zps4m amordp.jpg (http://s1377.photobucket.com/user/dil88888/media/MDLP%20K23%20ADMIX%20BY%20CHROMO%20TABLE%201_zps4m amordp.jpg.html)

Anabasis
03-12-2015, 06:55 AM
My results

Amerindian -
Ancestral_Altaic -
South_Central_Asian 17.90%
Arctic -
South_Indian 0.71%
Australoid -
Austronesian -
Caucasian 55.82%
Archaic_Human 0.23%
East_African -
East_Siberian -
European_Early_Farmers 7.44%
Khoisan -
Melano_Polynesian 1.06%
Archaic_African -
Near_East 12.12%
North_African 3.61%
Paleo_Siberian -
African_Pygmy 0.16%
South_East_Asian -
Subsaharian -
Tungus-Altaic -
European_Hunters_Gatherers 0.95%

4011
4018
4019

Afshar
03-12-2015, 07:13 AM
Interesting
40144013

Rukha
03-12-2015, 07:26 AM
mine:

40164017

Gray Fox
03-12-2015, 10:28 AM
Here's my chromosome percentage chart..


4020


And here's the reduced painting..


4021

Kurd
03-12-2015, 11:04 AM
This is a sorted table of admixture values by chromosome, showing quite a bit of variability from one chromosome to the next. I was curious to see how this compares to other members. I have grouped the components to enhance visualization:

http://i1377.photobucket.com/albums/ah42/dil88888/MDLP%20K23%20ADMIX%20BY%20CHROMO%20TABLE%201_zps4m amordp.jpg (http://s1377.photobucket.com/user/dil88888/media/MDLP%20K23%20ADMIX%20BY%20CHROMO%20TABLE%201_zps4m amordp.jpg.html)

Oops, just noticed that I am missing chromosomes 12 through 22. Here they are:

http://i1377.photobucket.com/albums/ah42/dil88888/MDLP%20K23%20ADMIX%20BY%20CHROMO%20TABLE%202_zpsd6 erufps.jpg (http://s1377.photobucket.com/user/dil88888/media/MDLP%20K23%20ADMIX%20BY%20CHROMO%20TABLE%202_zpsd6 erufps.jpg.html)

EDIT: The 2 highest values of a component have been highlighted with larger font on the chromosomes.

Anabasis
03-12-2015, 12:05 PM
I just wanted to make your job easier

4022

Anabasis
03-12-2015, 12:08 PM
Oops, just noticed that I am missing chromosomes 12 through 22. Here they are:

http://i1377.photobucket.com/albums/ah42/dil88888/MDLP%20K23%20ADMIX%20BY%20CHROMO%20TABLE%202_zpsd6 erufps.jpg (http://s1377.photobucket.com/user/dil88888/media/MDLP%20K23%20ADMIX%20BY%20CHROMO%20TABLE%202_zpsd6 erufps.jpg.html)

EDIT: The 2 highest values of a component have been highlighted with larger font on the chromosomes.

Actually adding such companents are not so true. Especially Ancestral Altaic companent which is also known as ANE. But lets see what will be the picture.

Kurd
03-12-2015, 12:38 PM
Actually adding such companents are not so true. Especially Ancestral Altaic companent which is also known as ANE. But lets see what will be the picture.

I needed to reduce the components to a manageable k=5 for certain plots. That happened to be the category with the best fit.

Stephen1986
03-12-2015, 01:19 PM
Here's my results -

European - 66%
West Asian - 20.52%
NE & SE Asian - 6.33%
South Asian - 6.12%
African - 0.97%

4025

4023

4024

Kurd
03-12-2015, 04:54 PM
mine:

40164017

Our paintings look somewhat similar from a distance. You show more variance in your SC Asian chromosomal admix, and less so with your S. Indian admix. Mine is the opposite. I have a S. Indian dead zone on ch18, but I guess that is compensated for by an above average SC Asian component.:)

Kaido
03-12-2015, 05:30 PM
http://www4.gedmatch.com/gifs/F401544_9C617E.gif


http://i.imgur.com/hdEt56S.png?1

Dr_McNinja
03-12-2015, 06:09 PM
chromosome breakdown:

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

MfA
03-12-2015, 06:24 PM
.....

NK19191
03-12-2015, 06:50 PM
http://i1309.photobucket.com/albums/s632/nk191919/Image1_zpsyfg7z3za.png

randwulf
03-12-2015, 11:22 PM
My chromosome results:

4034

PureEvil
03-13-2015, 04:57 AM
My Chromosome view:
http://i1154.photobucket.com/albums/p535/PureEvil91/New/mdlp2322_zps4mmfuotd.png (http://s1154.photobucket.com/user/PureEvil91/media/New/mdlp2322_zps4mmfuotd.png.html)