Tuesday, September 19, 2017

A Gedmatch Admixture Guide: Parts 3 and 4

Continuing on from Parts 1 and 2 where I covered the different projects and calculators available for Admixture Proportions and what Oracle is and how to read it, I've had some requests to cover the other viewing options available like Admixture Proportions by Chromosome and Chromosome Painting. So that's what I'll be covering in Parts 3 and 4. For Part 5 on Spreadsheets, click here.

Part 3 - Admixture Proportions by Chromosome

How to find it: From your Gedmatch home page, under "Analyze your data" and then "DNA raw data", choose the option for Admixture (Heritage)" like you did in Part 1, but this time you're going to select " Admixture Proportions by Chromosome" from the bullet list. Be sure to select a project and then calculator and put in your kit number like normal. I would go with whatever calculator you found reflected your known ancestry best. If you haven't read Part 1 yet, you should do so first.

Admixture Proportions by Chromosome shows you your admixture proportions as broken down by individual chromosome; or, in other words, what percentages of each chromosome are most commonly found in which populations/ethnicity. This gives you a much more detailed view of where your DNA is most commonly found.

Admixture proportions (or ethnicity percentages) broken
down by chromosome
So with Eurogenes K13, it shows my chromosome 1 is 28.1% North Atlantic, 15.7% Baltic, 27.7% West Mediterranean, 16.9% West Asian, 10.9% East Mediterranean, and 1.1% Amerindian. This option can often show results in populations that don't show up in a normal Admixture Proportions calculator. However, always keep in mind small percentages may just be from "noise" - like a false positive. I have no Native American ancestry so the 1.1% Amerindian probably doesn't mean anything. You'll also note how I get some North Atlantic results, in varying amounts, on every single one of my chromosomes.

My Eurogenes K13 results
In my normal K13 results, I got 39.03% in North Atlantic, so this is just breaking that average of 39.03% down by chromosome. If you add up all the percentages for one population and divide it by 22 (number of chromosomes) you'll get your overall average for that population. You may note it's a little off from what the admixture calculator originally gave you - for example my average for North Atlantic when each chromosome is added up and divided by 22 is 38.89%, not the original 39.03%. I am not sure why that is, but it's such a small difference I'm not going to worry about it too much. If someone has more information on this discrepancy, please comment below!

At the bottom it says "Number of SNPs eval" - this is just how many of your SNPs were used for the evaluation.

It doesn't show which particular segments each percentage is found on though, but that brings us to the next options.

Part 4 - Chromosome Painting and Reduced Size

How to find it: Same as above, but select "Chromosome Painting" or "Chromosome Painting - Reduced Size" from the bullet list instead.


Chromosome Painting is a visual representation of your admixture proportions not only by chromosome but by segments of each chromosome. The different colors show which segments of each chromosome were most similar with which populations. When there are overlapping colors on the same segment, it means that segment is found in more than one population. The higher the spike, the stronger the match to that population. So segments where there are solid blocks of one color are more solidly found in only that population. Above is just a small portion of one of my chromosomes (7, I believe), as an example of the various populations that will show up for any given segment.

You'll note there are numbers along the bottom of each chromosome - this is marking the amount of base pairs in millions. One centiMorgan is one million base pairs. So if you have a segment painted with a certain color stretching from "10M" to "20M", for example, that's 10 million base pairs, or 10 cMs. Don't get too excited if you see colors for some unexpected populations - small segments could just be noise.

Chromosome painting reduced size
The reduced size option just condenses it so it's easier to view on a single screen. After viewing the full size, you'll quickly see just how cumbersome it is to get an overview, so the reduced size is ideal for that. The full size is better for examining particular portions. They don't label each chromosome but they are listed chromosome 1 to 22, from left to right. They are also rotated so the start of the chromosomes are at the bottom.

You may notice in either the full or reduced size that similar populations (though it's more noticeable in full), or neighboring regions, often spike and dip almost in unison with each other. This is because neighboring regions tend to share a lot of DNA and be genetically similar so when you see this, what you're seeing is that these portions of your DNA may be somewhat indistinguishable among two or more groups. This is important in understanding that not all DNA can be narrowed down to the more specific areas or countries that so many people wish it could, not with any reliability. It also illustrates why you might get results in a region that you have no known ancestry in when it neighbors a region you do have ancestry in.

23andMe's chromosome painting
If you tested with 23andMe, you may be somewhat familiar with chromosome painting already. 23andMe's option for it is a little more straight forward. It doesn't have all the spikes and dips, just solid blocks showing which segments were put into which groups (shown left). However, it does show the two sides of each chromosome whereas Gedmatch doesn't seem to do this. Although in some ways, Gedmatch's painting is more detailed, it is essentially the same concept, just a slightly different approach.

As another example, below is also a graphic from 23andMe - it's not a part of your results from this company, it's just showing, in part, how they determine ethnicity. Their example uses the more detailed type of chromosome painting found at Gedmatch, and it is labelled to show the probability of each ancestry on one side with increasing percentages of likelihood. It can be found in their guide article on ancestry composition. Gedmatch's chromosome painting can be read the same way (ie, the higher the peak, the higher the probability of that segment being from that population).


Disclaimer: Please note I am not a professional in the genetics industry, and it is difficult to find information particularly on some of the more advanced admixture tools on gedmatch. This is how I have come to understand the results and tools through my own experiences and research, but please, if someone more knowledgeable can correct me if I've misunderstood something, or can fill in some gaps, let me know by commenting below.

19 comments:

  1. Thanks for a good and understandable article.

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  2. This has helped me so much thank you.

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  3. Wow! Mind blown. Thank you for the tips on how to interpret my results. Suspicions confirmed... I'm from everywhere.

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  4. Thanks, I already got most of it already but you nailed a few things I had not figured out yet :) Am 100% French, but DNA gives surprising results.

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  5. thanks for you experience cheers John

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  6. Hello , i wanted to ask a question . Is the chromosome n°1 the one of the father and n°2 the one of the mother , or each chromosome is a mix of the genes of both parents. Thanks in advance

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    1. Each chromosome has two sides, one side you get from your dad, and one side you get from your mom.

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  7. This is not true. There has been many instances where I should have received 2% to 15% by adding percentages and dividing by 22 but when It shows the actual percentage on admixture proportion with oracle it simply has the - symbol for none.

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    1. You'll note that I did comment on discrepancies - there might be additional algorithms we don't know about.

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  8. In the admixture by chromosome, why are some of the percentages in the chromosome shaded with either deep or light Purple colors. How does that relate to those without shades, especially for the lightly shaded figues

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    1. The shading just reflects the percentage amount. Note the higher the percentage, the darker the shading - the lower the percentage, the lighter the shading. At some point, they get so light it's hard to tell if there's any color at all. Certainly, the boxes with no percentage are not colored. The ones under about 1% seem white too. But it doesn't really matter, it's just a visual representation of the numbers, you can ignore the colors if you want.

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    2. Thanks for the feedback, it is quite helpful.

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  9. I have a question and I apologize if it is explained. What does the population spreadsheet mean on the results pages?

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    1. I detailed what spreadsheets are in another post: http://genealogical-musings.blogspot.com/2018/03/a-gedmatch-admixture-guide-part-5.html - they are basically showing the admixture results of specific populations as though they were Gedmatch kits, which gives you an idea of what the admixture of an average person of that population would be.

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  10. Are you sure that i have to add up all the percentages and then divide them by 22? i ask because i did this way and the final result doesn't show up as 100%

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    1. You're not supposed to get 100%, you're supposed to get your overall average for that population.

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  11. I know we have Native American in my fathers family dating back to the 1700’s. I have less than 1% showing, should I count that as “noise,” or know it’s reliable?

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  12. Hi, I have a problem about the admixture proportions by chromosome. I make an example: my percentage of East African ( in MDLP K23b) is 8.8% but this population is present ONLY in chromosome 11. Should I divide 8.8 by 22 or am I simply 8.8% East African?

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