Admixture K=2-5, HRP0001 to HRP0010

Finally, it's time to analyze the genomes of project participants. Admixture analysis is going to be done in batches of ten so that the ancestral components are stable from one run to another.

My choice of calling them "ancestral components" is deliberate. Please do not think of them as pure ancestral populations.

First, the ethnic background of the participants in this batch. I'll give the ethnicity only if I have explicit permission from the participant to make such information public. By default, I assume it to be private. Here's the summary:

Ethnicity Count
Punjab 5
Bengal 1
Bihar 1
Tamil 1
Andhra Pradesh 1
Iran 1

Since this is the first batch, I am running admixture for all values of K to get a better handle on how things shake out. With later batches, I will run only a few specific values of K since admixture takes a long time to run.

The ancestral component percentages for project participants can be found in this spreadsheet.

It might be good to refer to the admixture runs for the reference (spreadsheet) to get a better idea of what the different ancestral components represent.

Let's start with K=2 ancestral components.

Batch 1 Admixture K=2

Cyan/African (C2) component varies from 29-51% among participants which is about what you would expect from the results for South Asian reference populations.

With K=3 where the ancestral components roughly represent European (C1/red), East Asian (C2/green) and African (C3/blue), we see the following:

Batch 1 Admixture K=3

I am HRP0001 and my number for K=3 are 77% European, 18% Asian and 5% African. This contrasts with my 23andme ancestry painting of 91.22% European, 8.69% Asian and 0.09% African. However, HRP0002 has closer numbers:

HRP0002 European Asian African
HAP 55% 43% 1%
23andme 57% 43% 0%

We (HAP) are using a much more diverse reference population while 23andme ancestry painting is based on the basic three populations of HapMap. Also, since I am a quarter Egyptian, the likelihood of some African ancestry is high in my case.

Note that the Asian (C2) percentages vary from 18% to 44% for the South Asians in this batch, but it's low (18-22%) in Punjabis and higher in southern and eastern South Asians. It's almost negligible in our Iranian Assyrian sample.

With K=4, we finally get our South Asian ancestral component (C1/red).

Batch 1 Admixture K=4

I (HRP0001) am the only one with any noticeable African component (C4/violet) while HRP0002 has some East Asian ancestry (C3/cyan). The two South Indians have lower European component (C2/green) along with HRP0002 who is from East Bengal.

Finally, let's take a look at K=5 ancestral components.

Batch 1 Admixture K=5

The South Asian (C1/red), East Asian (C3/green) and African (C5/magenta) components are about the same as in K=4. The new component here is C4/blue, which is the Southwest/West Asian component. This is basically a split from the K=4 European (C2/yellow) component. Our Assyrian sample has the highest Southwest/West Asian component while I also have it higher than the South Asians due to my quarter Egyptian ancestry.

Let's continue higher values of K next time.


  1. i'm hrp0002. i am also dod075, if you want to compare with dodecad. i am also in8 in eurogenes bga.

  2. I'm 006 (Sandhu Jatt) , wife is 005 (Shergill Jatt), 008 is a Jhaj Jatt.

  3. Im a Roma and im 0015, i will be on the next batch

  4. I am HRP0016 and I will be in the next batch. I am a Tamil Iyer.

  5. I'm HRP0003
    0003, 0004, 0005, 0006, & 0008 look very close in their admixture proportions.

  6. 0003, 0004, 0005, 0006, & 0008 northern south asians,
    0007 & 0009 southern south asians
    0002 eastern south asian
    0010 iranian
    0001 northern south asian with Egyptian admixture

      • as u know, i've enumerated my 8 great-grandparents, so i'll do so on this thread


        -pat grandfather, bengali muslim, khan
        -pat grandmother, bengali muslim
        -mat grandfather, bengali muslim, originally bengali brahmin (tagore/thakur)
        -mat grandmother, bengali muslim, khan

        -pat grandfather, bengali muslim, sarkar
        -pat grandmother, bengali muslim
        -pat grandfather, bengali muslim + middle eastern (mideast -> delhi -> bengal)
        -pat grandmother, bengali muslim

        all of my great-grandparents were born to the southeast of what is today dhaka. 7 of 8 in comilla region, 1 in noakhali (further toward chittagong).

        that's all.

  7. p.s., my mother is HRP023 and my father HRP022 (for future reference).

  8. Admixture K=6-9, HRP0001 to HRP0010 | Harappa Ancestry Project - pingback on February 8, 2011 at 8:50 am

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