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View Full Version : How to interpret admixture proportions percentage on chromosomes



Christos
16-06-13, 00:41
How do you interpret the admixture proportion percentage on each chromosome? For example is there any significance as to which chromosome has the largest percentage? (i.e. chromosome 22 has 40% West Asian but chromosome 16 has only 6%). Does this mean one would share 40% of DNA from this particular marker?

Any feedback would be appreciated

Thank you

zanipolo
16-06-13, 03:38
How do you interpret the admixture proportion percentage on each chromosome? For example is there any significance as to which chromosome has the largest percentage? (i.e. chromosome 22 has 40% West Asian but chromosome 16 has only 6%). Does this mean one would share 40% of DNA from this particular marker?

Any feedback would be appreciated

Thank you


doug mcdonald from BGA is the best to do your personnel admixture ( and its free )..mine is below , supplied by doug

top half is paternal lines
bottom half is maternal lines
http://img834.imageshack.us/img834/9633/ogk.png (http://imageshack.us/photo/my-images/834/ogk.png/)

Uploaded with ImageShack.us (http://imageshack.us)

the other programs calculate your markers with what other people have registered in databases.
That is the more people test in an area the more accurate these programs are.



Chr01 is from both your grand parents on both sides ...so you get one segment from one, then another segment from another then another.....there are only 4 segments.
each segment is further divided going back to the next generation, most segment should stop at 7cM , below this they are irrelevant.


ChrX is the ancient female line and also is the medical side of a person. The BGA via doug will have migrational zones , the south-asia represent anywhere in eastern europe and the middle-east represents south-west and west-asian regions

x- chromosome
http://freepages.genealogy.rootsweb.ancestry.com/~hulseberg/DNA/x%20inheritance%20woman%206%20gen.pdf

http://freepages.genealogy.rootsweb.ancestry.com/~hulseberg/DNA/x%20inheritance%20man%205%20gen.pdf


in regards to chr02 to chr22 I do not know anything about...i am still looking

zanipolo
16-06-13, 21:45
Chr07

father passes one of his number 7 chromosomes intact, his two number 7 chromosomes are shuffled together forming a new chromosome that gets passed down. The mother does the same. So the child receives one number 7 chromosome from each parent, but each of those chromosomes is a mixture of the parent’s two number 7 chromosomes. By this means, genetic information on all the autosomes from all the grandparents get passed down.

Christos
16-06-13, 22:54
@zanipolo I had my data analyzed by both 23andme; Dr. McDonald and GEDmatch. I have included my admixture as provided by GEDmatch. I suppose what I am asking is, do the percentages on each marked chromosome bear any specific relevance? In addition, when reading a chromosome painting, is the larger cm the most relevant; you mentioned any segment 7cm or smaller are considered irrelevant. Thanks for your feedback. MDLP World-22 Admixture Proportions Magnus Ducatus Lituaniae Project MDLP World-22 Populations

Population
Chr--> 1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22


Pygmy

-

-

-

-

-

-

-

-

-

-

-

1.1%

-

-

-

-

-

-

-

-

-

-


West-Asian

13.5%

19.2%

20.6%

5.1%

14.2%

10.0%

17.1%

16.5%

18.2%

6.4%

12.7%

15.5%

6.9%

12.1%

19.8%

17.8%

12.3%

6.3%

33.4%

9.0%

12.3%

21.9%


North-European-Mesolithic

-

5.0%

-

5.4%

3.4%

5.2%

-

-

6.2%

1.8%

3.1%

2.0%

8.7%

4.0%

-

-

6.0%

-

1.8%

11.0%

1.8%

-


Indo-Tibetan

1.0%

-

-

2.9%

0.8%

-

4.3%

-

-

-

-

-

-

-

-

-

-

1.9%

-

-

-

-


Mesoamerican

-

-

-

-

-

-

-

-

-

-

-

0.4%

-

-

-

-

0.5%

-

-

-

-

1.4%


Arctic-Amerind

-

-

-

2.6%

-

-

-

-

-

-

3.0%

-

-

0.2%

2.9%

1.2%

-

-

-

0.2%

6.5%

-


South-America_Amerind

-

0.6%

-

-

1.1%

0.6%

-

0.1%

1.2%

-

-

0.1%

-

-

0.3%

-

-

2.4%

-

-

-

-


Indian

-

-

-

-

-

-

-

-

-

2.9%

-

-

-

-

-

-

4.0%

-

-

-

-

-


North-Siberean

-

-

0.6%

-

-

-

1.9%

-

-

-

-

-

-

1.8%

-

-

-

-

-

-

-

-


Atlantic_Mediterranean_Neolithic

34.5%

21.7%

35.0%

35.8%

26.9%

25.0%

23.4%

19.4%

23.0%

24.5%

25.6%

34.3%

31.2%

23.0%

39.5%

25.3%

22.7%

34.9%

24.4%

34.9%

29.0%

9.0%


Samoedic

-

-

-

-

-

-

-

-

-

-

-

-

-

-

1.1%

-

-

-

-

-

-

-


Indo-Iranian

2.6%

0.5%

-

2.8%

-

-

-

1.4%

-

-

-

6.7%

-

1.1%

-

-

-

-

0.6%

-

-

6.5%


East-Siberean

-

-

-

-

1.3%

0.5%

-

-

-

-

-

-

-

-

-

-

-

-

2.3%

-

-

-


North-East-European

41.6%

37.7%

37.7%

38.8%

38.0%

41.2%

37.6%

62.6%

35.5%

48.2%

42.7%

38.0%

43.6%

41.4%

25.8%

46.9%

34.9%

50.5%

31.8%

38.6%

41.4%

43.7%


South-African

-

-

2.2%

-

0.7%

-

-

-

0.6%

-

0.9%

-

-

-

-

1.5%

-

-

0.9%

-

-

-


North-Amerind

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-


Sub-Saharian

-

-

-

-

-

-

-

-

1.2%

-

-

-

-

1.1%

0.8%

-

1.5%

-

-

1.2%

-

-


East-South-Asian

-

0.2%

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-


Near_East

6.7%

11.3%

3.9%

3.3%

13.0%

17.5%

15.7%

-

11.7%

16.3%

12.1%

1.9%

9.1%

10.9%

7.1%

7.2%

16.3%

1.2%

5.0%

1.4%

9.0%

12.5%


Melanesian

-

-

-

-

0.5%

-

-

-

-

-

-

-

0.6%

4.4%

0.8%

-

-

2.7%

-

-

-

-


Paleo-Siberian

-

3.8%

-

1.2%

-

-

-

-

-

-

-

-

-

-

0.6%

-

-

-

-

0.7%

-

1.3%


Austronesian

-

-

-

2.1%

-

-

-

-

2.3%

-

-

-

-

-

1.3%

-

1.9%

0.1%

-

3.1%

-

3.7%


Number of SNPs eval:

5994

5874

5094

4511

4417

4787

4306

4044

3754

4208

3678

3767

2960

2694

2505

2679

2428

2442

1899

2397

1360

1415




Finished.

Christos
16-06-13, 23:33
[email protected] I included my chromosome painting as provided my Dr. McDonald. Since my paternal haplogroup has been designated J2a1b*-M67, am I correct in reading that the Middle East segment(s) can actually be Caucasian, where J2 originated?

Nobody1
16-06-13, 23:36
You have to add all the figures of a Population together and than divide by 22 (number of chromosomes);
That will determine your average percentage (frequency) of each population admixture;

So every value has a relevance, but only the calculated average (all 22 chr.) will reveal the full significance of the values (combined);

zanipolo
16-06-13, 23:54
@zanipolo I had my data analyzed by both 23andme; Dr. McDonald and GEDmatch. I have included my admixture as provided by GEDmatch. I suppose what I am asking is, do the percentages on each marked chromosome bear any specific relevance? In addition, when reading a chromosome painting, is the larger cm the most relevant; you mentioned any segment 7cm or smaller are considered irrelevant. Thanks for your feedback. MDLP World-22 Admixture Proportions Magnus Ducatus Lituaniae Project MDLP World-22 Populations

Population
Chr--> 1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22


Pygmy

-

-

-

-

-

-

-

-

-

-

-

1.1%

-

-

-

-

-

-

-

-

-

-


West-Asian

13.5%

19.2%

20.6%

5.1%

14.2%

10.0%

17.1%

16.5%

18.2%

6.4%

12.7%

15.5%

6.9%

12.1%

19.8%

17.8%

12.3%

6.3%

33.4%

9.0%

12.3%

21.9%


North-European-Mesolithic

-

5.0%

-

5.4%

3.4%

5.2%

-

-

6.2%

1.8%

3.1%

2.0%

8.7%

4.0%

-

-

6.0%

-

1.8%

11.0%

1.8%

-


Indo-Tibetan

1.0%

-

-

2.9%

0.8%

-

4.3%

-

-

-

-

-

-

-

-

-

-

1.9%

-

-

-

-


Mesoamerican

-

-

-

-

-

-

-

-

-

-

-

0.4%

-

-

-

-

0.5%

-

-

-

-

1.4%


Arctic-Amerind

-

-

-

2.6%

-

-

-

-

-

-

3.0%

-

-

0.2%

2.9%

1.2%

-

-

-

0.2%

6.5%

-


South-America_Amerind

-

0.6%

-

-

1.1%

0.6%

-

0.1%

1.2%

-

-

0.1%

-

-

0.3%

-

-

2.4%

-

-

-

-


Indian

-

-

-

-

-

-

-

-

-

2.9%

-

-

-

-

-

-

4.0%

-

-

-

-

-


North-Siberean

-

-

0.6%

-

-

-

1.9%

-

-

-

-

-

-

1.8%

-

-

-

-

-

-

-

-


Atlantic_Mediterranean_Neolithic

34.5%

21.7%

35.0%

35.8%

26.9%

25.0%

23.4%

19.4%

23.0%

24.5%

25.6%

34.3%

31.2%

23.0%

39.5%

25.3%

22.7%

34.9%

24.4%

34.9%

29.0%

9.0%


Samoedic

-

-

-

-

-

-

-

-

-

-

-

-

-

-

1.1%

-

-

-

-

-

-

-


Indo-Iranian

2.6%

0.5%

-

2.8%

-

-

-

1.4%

-

-

-

6.7%

-

1.1%

-

-

-

-

0.6%

-

-

6.5%


East-Siberean

-

-

-

-

1.3%

0.5%

-

-

-

-

-

-

-

-

-

-

-

-

2.3%

-

-

-


North-East-European

41.6%

37.7%

37.7%

38.8%

38.0%

41.2%

37.6%

62.6%

35.5%

48.2%

42.7%

38.0%

43.6%

41.4%

25.8%

46.9%

34.9%

50.5%

31.8%

38.6%

41.4%

43.7%


South-African

-

-

2.2%

-

0.7%

-

-

-

0.6%

-

0.9%

-

-

-

-

1.5%

-

-

0.9%

-

-

-


North-Amerind

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-


Sub-Saharian

-

-

-

-

-

-

-

-

1.2%

-

-

-

-

1.1%

0.8%

-

1.5%

-

-

1.2%

-

-


East-South-Asian

-

0.2%

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-

-


Near_East

6.7%

11.3%

3.9%

3.3%

13.0%

17.5%

15.7%

-

11.7%

16.3%

12.1%

1.9%

9.1%

10.9%

7.1%

7.2%

16.3%

1.2%

5.0%

1.4%

9.0%

12.5%


Melanesian

-

-

-

-

0.5%

-

-

-

-

-

-

-

0.6%

4.4%

0.8%

-

-

2.7%

-

-

-

-


Paleo-Siberian

-

3.8%

-

1.2%

-

-

-

-

-

-

-

-

-

-

0.6%

-

-

-

-

0.7%

-

1.3%


Austronesian

-

-

-

2.1%

-

-

-

-

2.3%

-

-

-

-

-

1.3%

-

1.9%

0.1%

-

3.1%

-

3.7%


Number of SNPs eval:

5994

5874

5094

4511

4417

4787

4306

4044

3754

4208

3678

3767

2960

2694

2505

2679

2428

2442

1899

2397

1360

1415




Finished.

The Gedmatch results means that 13.5% of your Chr01 which is west-asian matches 13.5% of others in the data-base with similar genes in that chromosome.

doug gave you your personnel one...what was that?

For me ,
he stated Ancient old northern yugoslavian lands
Most likely fit is 100% Europe (various subcontinents)
The following are possible population sets and their fractions,
most likely at the top
English= 0.341 Tuscan= 0.659 or
French= 0.493 Tuscan= 0.507 or
Irish= 0.271 Tuscan= 0.729 or
Spain= 0.522 Romania= 0.478 or
Hungary= 0.239 Italian= 0.761

I think I can choose which I prefer.

I asked him what was tuscan and Italian...he said, tuscan is central italian, italian is north italian and greek was south italian

zanipolo
17-06-13, 00:03
[email protected] I included my chromosome painting as provided my Dr. McDonald. Since my paternal haplogroup has been designated J2a1b*-M67, am I correct in reading that the Middle East segment(s) can actually be Caucasian, where J2 originated?

interesting bar chart...doug said mine was boring, very old...LOL

unsure, I think south caucasus is west-asian and north-caucasus is european/caucusus.......I need to check. but middle-east is irak, syria, jordan etc

your maternal looks like middle-east and paternal is european ( caucasus)...so yes you can be from the caucasus........Doug must of given you some options

Christos
17-06-13, 00:17
@zanipolo I included data from both GEDmatch (above) and here is McDonald's admix. The Ashkenazi (Jewish) could be considered "noise" as its called. There is no family history. @nobody1 thank you for the fine explanation! This works best with a custom fit:

Italian 0.4584 Lithuania 0.3369 Jewish 0.2047 or
Italian 0.3801 Poland 0.4175 Jewish 0.2024 or
Italian 0.4521 Belorus 0.3831 Jewish 0.1648 or
French 0.3752 Poland 0.3460 Jewish 0.2787 or
French 0.4374 Lithuania 0.2693 Jewish 0.2934 or
Poland 0.4245 Spain 0.3258 Jewish 0.2497 or
Spain 0.0988 Hungary 0.7041 Jewish 0.1971 or
French 0.4332 Belorus 0.3065 Jewish 0.2603 or
Basque 0.0431 Hungary 0.7437 Jewish 0.2131 or
Italian 0.1062 Hungary 0.7073 Jewish 0.1864 or
French 0.1158 Hungary 0.6724 Jewish 0.2118 or
Tuscan 0.0903 Hungary 0.7269 Jewish 0.1828 or
Basque 0.0375 Germany 0.6580 Jewish 0.3045 or
French 0.3207 Belorus 0.3671 Sephardic 0.3122 or
English 0.0771 Hungary 0.6964 Jewish 0.2266

zanipolo
17-06-13, 00:39
@zanipolo I included data from both GEDmatch (above) and here is McDonald's admix. The Ashkenazi (Jewish) could be considered "noise" as its called. There is no family history. @nobody1 thank you for the fine explanation! This works best with a custom fit:

Italian 0.4584 Lithuania 0.3369 Jewish 0.2047 or
Italian 0.3801 Poland 0.4175 Jewish 0.2024 or
Italian 0.4521 Belorus 0.3831 Jewish 0.1648 or
French 0.3752 Poland 0.3460 Jewish 0.2787 or
French 0.4374 Lithuania 0.2693 Jewish 0.2934 or
Poland 0.4245 Spain 0.3258 Jewish 0.2497 or
Spain 0.0988 Hungary 0.7041 Jewish 0.1971 or
French 0.4332 Belorus 0.3065 Jewish 0.2603 or
Basque 0.0431 Hungary 0.7437 Jewish 0.2131 or
Italian 0.1062 Hungary 0.7073 Jewish 0.1864 or
French 0.1158 Hungary 0.6724 Jewish 0.2118 or
Tuscan 0.0903 Hungary 0.7269 Jewish 0.1828 or
Basque 0.0375 Germany 0.6580 Jewish 0.3045 or
French 0.3207 Belorus 0.3671 Sephardic 0.3122 or
English 0.0771 Hungary 0.6964 Jewish 0.2266

Your
Italian 0.3801 Poland 0.4175 Jewish 0.2024
based on your ethnicity looks good, but it still states 20% jewish

try to see the oracle_2 part....of MDLP

mine from MDLP which is part of BGA project, which is doug



#
Population
Percent


1
East_European
14.10


2
Paleo_Mediterranean
29.29


3
Iberian
11.23


4
Caucasian
13.59


5
Uralic_Permic
0.41


6
Balto_Finnic
2.28


7
Paleo_Balkanic
2.47


8
Celto_Germanic
20.66


9
Paleo_North_European
0.19


10
South_Central_Asian
3.74


11
Volga_Uralic
2.03


12
Altaic_Turkic
0.00




Pct. Calc. Option 2



0
Unable to determine
0.01%


1
NITAL
47.49% ............north italian


2
MRD
14.13%.............Mordovian


3
GER
10.69%.............german


4
CITAL
8.26%...............central italian


5
SLV
5.06%...............Slovenian


6
BASQ
3.49%...............Basque


7
CRS
3.14%...............cyprus


8
GYP
2.89%...............gypsy


9
KSV
2.81%...............Kosovo


10
FRN
2.03%...............northern france



Noise means under 4% , basically erred

Christos
17-06-13, 02:01
@zanipolo Here are my results of the MDLP World-22 Oracle x Admix Results:



#
Population
Percent


1
Pygmy
0.00


2
West-Asian
15.64


3
North-European-Mesolithic
2.99


4
Indo-Tibetan
0.00


5
Mesoamerican
0.00


6
Arctic-Amerind
0.55


7
South-America_Amerind
0.10


8
Indian
0.00


9
North-Siberean
0.00


10
Atlantic_Mediterranean_Neolithic
28.25


11
Samoedic
0.00


12
Indo-Iranian
0.00


13
East-Siberean
0.25


14
North-East-European
42.00


15
South-African
0.04


16
North-Amerind
0.00


17
Sub-Saharian
0.10


18
East-South-Asian
0.00


19
Near_East
9.85


20
Melanesian
0.13


21
Paleo-Siberian
0.10


22
Austronesian
0.00




Pct. Calc. Option 2



0
Unable to determine
0.02%


1
Bulgarian
32.10%


2
Croatian
26.89%


3
Macedonian
19.99%


4
North-East-European
5.60%


5
Tadjik
3.88%


6
Saami
3.11%


7
Jew-Iran
2.51%


8
Jordanian
2.30%


9
Jew_Romania
2.07%


10
Inkeri
1.52%

LeBrok
17-06-13, 06:15
You have to add all the figures of a Population together and than divide by 22 (number of chromosomes);
That will determine your average percentage (frequency) of each population admixture;

So every value has a relevance, but only the calculated average (all 22 chr.) will reveal the full significance of the values (combined);
But the chromosomes are of different length. Some are 50 and some 250 million base pairs. That mean some contain 5 times more genetic (inheritance) material than others.

LeBrok
17-06-13, 06:17
@zanipolo I included data from both GEDmatch (above) and here is McDonald's admix. The Ashkenazi (Jewish) could be considered "noise" as its called. There is no family history. @nobody1 thank you for the fine explanation! This works best with a custom fit:

Italian 0.4584 Lithuania 0.3369 Jewish 0.2047 or
Italian 0.3801 Poland 0.4175 Jewish 0.2024 or
Italian 0.4521 Belorus 0.3831 Jewish 0.1648 or
French 0.3752 Poland 0.3460 Jewish 0.2787 or
French 0.4374 Lithuania 0.2693 Jewish 0.2934 or
Poland 0.4245 Spain 0.3258 Jewish 0.2497 or
Spain 0.0988 Hungary 0.7041 Jewish 0.1971 or
French 0.4332 Belorus 0.3065 Jewish 0.2603 or
Basque 0.0431 Hungary 0.7437 Jewish 0.2131 or
Italian 0.1062 Hungary 0.7073 Jewish 0.1864 or
French 0.1158 Hungary 0.6724 Jewish 0.2118 or
Tuscan 0.0903 Hungary 0.7269 Jewish 0.1828 or
Basque 0.0375 Germany 0.6580 Jewish 0.3045 or
French 0.3207 Belorus 0.3671 Sephardic 0.3122 or
English 0.0771 Hungary 0.6964 Jewish 0.2266

You are nicely mixed. True citizen of the world. :)

Christos
18-06-13, 04:09
@LeBrok "Citizen of the World", what a thoughtful observation! I suppose we all are really!