Harappa Nearest IBS Neighbors

Posted by on May 4, 2011

After a long tease, here is the spreadsheet containing the top 500 nearest neighbors (using IBS similarity percentages) for the Harappa participants from HRP0001 to HRP0089.

I am also providing an R data object with the same data (except it contains all the 3,975 individual from reference 3 and Harappa). To use this data,

  1. Download R
  2. Install R on your computer
  3. When you start R, type 
    load('harappa_ibs.RData')

    to load the data

  4. Type 
    closest("HRP0001")

    to find the 20 closest IBS neighbors of HRP0001. You can use any of the Harappa IDs here.

  5. You can set the number of IBS neighbors (50, for example) to show using 
    closest("HRP0010",50)

Enjoy!

Clusters,

4 Comments.

  1. Parasar May 4, 2011 at 10:33 am

    Closest to me on HRP is Razib's dad at 74.2661%, consistent with 23andme which has it as 74.26% (v2)
    "Your nearest neighbor is 0.57 standard deviations closer to you than for the average project participant"
    V3 "1" "HRP0003" "1"
    V533 "2" "gujaratis-a" "0.745222"
    V539 "3" "gujaratis-b" "0.74337"
    V2317 "4" "singapore-indians" "0.742955"
    V547 "5" "gujaratis-b" "0.742773"
    V2343 "6" "singapore-indians" "0.742772"
    V2314 "7" "singapore-indians" "0.742766"
    V3211 "8" "vaish" "0.74276"
    V22 "9" "HRP0022" "0.742661"
    V26 "10" "HRP0026" "0.742572"

  2. sv May 4, 2011 at 10:58 am

    1 HRP0016 1
    2 gujaratis-a 0.744218
    3 HRP0031 0.744097
    4 singapore-indians 0.743883
    5 gujaratis-a 0.743876
    6 satnami 0.743859
    7 naidu 0.743758
    8 singapore-indians 0.743694
    9 singapore-indians 0.743577
    10 singapore-indians 0.743362
    11 singapore-indians 0.743352
    12 meghawal 0.743328
    13 gujaratis-a 0.743164
    14 bhil 0.743109
    15 singapore-indians 0.743063
    16 gujaratis-a 0.742961
    17 singapore-indians 0.742954
    18 gujaratis-b 0.742949
    19 gujaratis-a 0.742916
    20 HRP0041 0.74291
    21 singapore-indians 0.742904
    22 HRP0017 0.742886

  3. Vasishta May 4, 2011 at 11:47 am

    Mine:

    HRP0072 - 1
    bhil 0.742161
    Hebbar Iyengar Brahmin (HRP17) 0.741885
    Tamil Iyer Brahmin (HRP41) 0.741864
    singapore-indians 0.741754
    singapore-indians 0.741708
    gujaratis-a 0.741704
    singapore-indians 0.741681
    gujaratis-a 0.741604
    gujaratis-a 0.741597
    singapore-indians 0.741566
    singapore-indians 0.741552
    singapore-indians 0.741521
    singapore-indians 0.741509
    singapore-indians 0.74148
    kurumba 0.741344
    mala 0.741333
    singapore-indians 0.7413
    singapore-indians 0.741243
    Bengali Brahmin (HRP77) 0.741208
    satnami 0.741149
    gujaratis-b 0.741148
    kamsali 0.741131
    velama 0.741107
    singapore-indians 0.741082
    lodi 0.741042
    Tamil Brahmin (HRP57) 0.74104
    gujaratis-a 0.74101
    singapore-indians 0.740957
    Hebbar Iyengar Brahmin (HRP79) 0.740952

    Zack, do you have any information regarding where the Bhils in your reference sample are from? Your admixture exercises have illustrated that the Bhil reference has a substantial amount of Kalash admixture. Perhaps from Rajasthan or Gujarat rather than Madhya Pradesh? On a previous Harappa Median IBS with Reference 3 run, I got the same Bhil reference as my top match at 74.04%.

    Interesting..

    Also, should such IBS neighbour exercises be treated as similar to 23andMe's Compare Genes tool?