Reference Admixture Analysis K=6-9

Continuing the admixture analysis on my reference dataset I, let's look at K=6 ancestral components.

As before, all the results are listed in a spreadsheet.

For K=6, we get the following plot:

Admixture: Reference populations K=6

C1 (red) is the South Asian ancestral component. However, the Austronesian (Papuan/Melanesian) component has now separated from it as C5 (blue). You can see small proportions of the Papuan component among South Indian and Southeast Asian (Malay and Cambodian) populations.

C3 (green) is exactly the same as C3 in K=5 run and represents East Asian populations. C6 (magenta) is exactly the same component as C5 in the K=5 run and represents African ancestry. C4 (cyan) is the same as C4 in the K=5 run and represents Southwest/West Asia.

C2 (yellow) is the European component (maximum among North Europeans) almost the same as C2 in K=5 analysis. The major difference is that C2 (in K=6) is reduced among South Asians as compared to K=5. This is due to the South Asian component being higher for them.

Fst divergences between estimated populations for K=6:

C1 C2 C3 C4 C5
C2 0.053
C3 0.084 0.114
C4 0.068 0.052 0.130
C5 0.178 0.205 0.184 0.218
C6 0.148 0.165 0.186 0.157 0.260

When we increase the ancestral components to K=7,

Admixture: Reference populations K=7

The South Asian component (C1/red) is the same. Note that there is a significant drop from about 51% to 29% from Makranis to Iranians (ignore the Paniya as there are only 4 samples with one being very different). Looking at the 19 individual Iranian samples from our reference dataset, their South Asian ancestral component values vary from 17% to 33%.

The Southwest/West Asian component (C2/yellow) is now higher among West Asians and lower among East Africans compared to K=6 run. C3/green is the European component which now almost disappears from the Southwest Asian populations.

The East Asian component (C4/bluish green) is the same as before as is the Papuan C5/light blue component.

The African ancestry breaks into West African (C6/blue) and East African (C7/magenta).

Note that the split here is different from the batch 1 run where the East Asian split into two for K=7 and the African split happened at K=8, the opposite of what happened here.

Fst divergences between estimated populations for K=7:

C1 C2 C3 C4 C5 C6
C2 0.058
C3 0.052 0.034
C4 0.082 0.122 0.113
C5 0.176 0.210 0.204 0.184
C6 0.152 0.159 0.167 0.190 0.264
C7 0.112 0.113 0.122 0.153 0.229 0.037

At K=8, the East Asian components forks into two: A Southeast Asian (C4/bright green) one that is highest among the Dai, Malay, Cambodians and Lahu; and a Northeast Asian one (C6/blue) that is maximum among the Yakut, Oroqen, Japanese, Hezhen and Daur.

Admixture: Reference populations K=8

Among most South Asian groups in our reference dataset, the Southeast Asian component is much more common than the Northeast Asian one.

Fst divergences between estimated populations for K=8:

C1 C2 C3 C4 C5 C6 C7
C2 0.058
C3 0.052 0.034
C4 0.096 0.133 0.125
C5 0.177 0.211 0.205 0.201
C6 0.093 0.131 0.122 0.046 0.195
C7 0.152 0.159 0.167 0.200 0.266 0.201
C8 0.113 0.113 0.113 0.163 0.231 0.163 0.037

Here's the plot for K=9 ancestral components:

Reference Populations Admixture K=9

The new component here is the Kalash component which is at 94% among the Kalash but is in the 30-40% range for Caucasian and Pakistani populations. It is also present among West Asians, Europeans and Central Asians to a small degree.

Looking at the Kalash samples, they seem fairly uniform and mostly with only a little of the other ancestral components except for one sample which has 70% Kalash component.

Kalash Admixture K=9

Fst divergences between estimated populations for K=9:

C1 C2 C3 C4 C5 C6 C7 C8
C2 0.056
C3 0.064 0.072
C4 0.088 0.126 0.136
C5 0.064 0.061 0.039 0.131
C6 0.167 0.208 0.214 0.202 0.211
C7 0.084 0.124 0.133 0.045 0.127 0.195
C8 0.152 0.173 0.161 0.201 0.172 0.266 0.200
C9 0.115 0.133 0.117 0.165 0.129 0.233 0.164 0.036

From the Fst values, we can see that the Kalash component is closest to the South Asian component and then to the European component.

To summarize, here are the ancestral components inferred for different values of K.

K=2 K=3 K=4 K=5 K=6 K=7 K=8 K=9
Eurasian European S Asian S Asian S Asian S Asian S Asian S Asian
African E Asian European European European SW Asian SW Asian Kalash
African E Asian E Asian E Asian European European SW Asian
African SW Asian SW Asian E Asian SE Asian SE Asian
African Papuan Papuan Papuan European
African W African NE Asian Papuan
E African W African NE Asian
E African W African
E African

Note that for a specific value of K, they are listed in approximately decreasing average percentage among the South Asian samples in our reference dataset I.


  1. im curious how much kalash i have, i read somewhere that roma are maybe related with kalash people

    • You'll find out soon enough. The K=9 admixture run is in process on my home PC right now.

      • is there a way to find out if im related to jatts or rajputs?

        • That would not be easy. My guess is your overall similarity to either group would be about the same. However, if only your South Asian and related chromosomal segments were compared there might be a chance.

          Also we will need some decent number of samples of those groups. I don't have any Rajputs right now.

        • Rajputs have been a 'caste' for less than the last 1000 years. Rajputs could be from any ruling clan or caste Brahman, Vaisya, etc. Some of my distant relatives are now Rajputs (Bisen) other distant relatives who adopted Islam became Pathans.

          • dr.manir ali found the jatt mutation among romas...connecting them to jatts. it would be really interesting if zacks project can confirm or not any relationship of me to jatts

  2. Admixture K=6-9, HRP0001 to HRP0010 | Harappa Ancestry Project - pingback on February 9, 2011 at 2:42 pm
  3. Admixture K1

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  4. Sorry about that

    Here is a graph for admixture K1 and for K9 Here

  5. I was trying to give an interactive Map, so its here Check it out, reference pop K9

  6. Reference I Admixture Analysis K=10-12 | Harappa Ancestry Project - pingback on February 17, 2011 at 7:23 am
  7. Admixture K=9, HRP0001 to HRP0040 | Harappa Ancestry Project - pingback on February 26, 2011 at 8:30 am
  8. Admixture K=9, HRP0041-HRP0050 | Harappa Ancestry Project - pingback on March 8, 2011 at 11:34 am