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  • DODECAD/Oracle/Me/Question(s)

    I finally got around to installing the very cool DIY DODECAD tools and am now thouroughly confused. My K12B results follow

    8.17% Gedrosia
    0.21% Siberian
    1.11% Northwest_African
    0.00% Southeast_Asian
    37.24% Atlantic_Med
    45.26% North_European
    0.00% South_Asian
    0.00% East_African
    0.59% Southwest_Asian
    0.00% East_Asian
    7.41% Caucasus
    0.00% Sub_Saharan

    Paternal grandfathers family all predate the revolutionary war by at least a few decades so far as I can tell, paternal grandmothers family appear to have come to this country from the souther part of Ireland in the early to mid 19th centurym. Mom was born in London and adopted so she is a mystery though there are hints of easter eurpopean based on my results.

    When I feed the above results into the K12B Oracle I get the following results

    > DodecadOracle(c(8.17,.21,1.11,0,37.24,45.26,0,0,.5 9,0,7.41,0),mixedmode=T,k=20)
    [,1] [,2]
    [1,] "55.5% ASW25 + 44.5% Bhunjia_M" "7.4524"
    [2,] "55.4% ASW25 + 44.6% Santhal_Ch" "7.5584"
    [3,] "55.6% ASW25 + 44.4% Dhurwa_M" "7.855"
    [4,] "54.7% ASW25 + 45.3% ASUR_Ch" "8.3137"
    [5,] "54.6% ASW25 + 45.4% Mawasi_Ch" "8.5599"
    [6,] "54.9% ASW25 + 45.1% Ho_Ch" "8.8779"
    [7,] "49.1% Bantu_S.W._Ovambo + 50.9% ASUR_Ch" "9.1603"
    [8,] "49.8% Bantu_S.W._Ovambo + 50.2% Santhal_Ch" "9.166"
    [9,] "48.4% Mandenka + 51.6% ASUR_Ch" "9.2319"
    [10,] "54.9% ASW25 + 45.1% Savara_Ch" "9.2408"
    [11,] "49.9% Bantu_S.W._Ovambo + 50.1% Bhunjia_M" "9.2774"
    [12,] "50.4% Bantu_S.W._Herero + 49.6% Santhal_Ch" "9.2995"
    [13,] "49.1% Mandenka + 50.9% Santhal_Ch" "9.3106"
    [14,] "49.7% Bantu_S.W._Herero + 50.3% ASUR_Ch" "9.3603"
    [15,] "50.5% Bantu_S.W._Herero + 49.5% Bhunjia_M" "9.3924"
    [16,] "49% Bantu_S.W._Ovambo + 51% Mawasi_Ch" "9.422"
    [17,] "47.5% Yoruba + 52.5% ASUR_Ch" "9.4343"
    [18,] "47.5% YRI25 + 52.5% ASUR_Ch" "9.4343"
    [19,] "49.3% Mandenka + 50.7% Bhunjia_M" "9.4385"
    [20,] "48.3% Mandenka + 51.7% Mawasi_Ch" "9.4807"

    Two questions, one am I doing something wrong here because those populations don't look familiar for the most part and the numbers at the end seem to indicate that even my best match isn't that great if I'm reading things correctly. Second question, are these populations defined somewhere? I've spent a fair chunk of time searching with Google but can't seem to find anything that tells me what they are.

  • #2
    It turns out that my Oracle was apparently messed up. My actual closest matches are much different. These are less mysterious and actually make sense.

    It would be nice to find a place where each population were concisely explained though.

    > DodecadOracle(c(8.17,.21,1.11,*0,37.24,45.26,0,0,. 59,0,7.41,0*),mixedmode=T,k=20)
    [,1] * [,2]
    [1,] "31% Hungarians + 69% Kent_1KG" "1.2688"
    [2,] "39.1% Hungarians + 60.9% Cornwall_1KG" "1.3557"
    [3,] "69.1% English_D + 30.9% Hungarians" "1.3811"
    [4,] "69.8% CEU30 + 30.2% Hungarians" "1.3995"
    [5,] "60.9% British_D + 39.1% Hungarians" "1.4538"
    [6,] "53.1% German_D + 46.9% Kent_1KG" "1.7217"
    [7,] "89.6% Dutch_D + 10.4% Bulgarians_Y" "1.7224"
    [8,] "69.5% Norwegian_D + 30.5% N_Italian_D" "1.7299"
    [9,] "81% Dutch_D + 19% Hungarians" "1.7339"
    [10,] "62.1% German_D + 37.9% Cornwall_1KG" "1.761"
    [11,] "88.9% Dutch_D + 11.1% Romanians" "1.7801"
    [12,] "89.7% Dutch_D + 10.3% Bulgarian_D" "1.8167"
    [13,] "66.3% British_Isles_D + 33.7% Hungarians" "1.9375"
    [14,] "33.2% German_D + 66.8% Mixed_Germanic_D" "1.9438"
    [15,] "74.2% Norwegian_D + 25.8% TSI30" "1.9487"
    [16,] "53.2% German_D + 46.8% English_D" "1.9865"
    [17,] "52.3% German_D + 47.7% CEU30" "2.0087"
    [18,] "62.4% German_D + 37.6% British_D" "2.0539"
    [19,] "87.3% German_D + 12.7% Pais_Vasco_1KG" "2.0546"
    [20,] "84.4% Mixed_Germanic_D + 15.6% Hungarians" "2.0972"

    Comment


    • #3
      All populations with _D are people who volunteered their data to the Doecad project. All the _1KG are from the 1000 Genome Project http://www.genome.gov/27528684 . All the other populations are freely available from research projects like http://www.sanger.ac.uk/resources/do...n/hapmap3.html and http://www.cephb.fr/en/cephdb

      If you have a question about any group a google search will usually return results about the group. Otherwise you are welcome to ask a specific question about the samples. Some are not obvious like TSI are the Northern Italian samples. AWS are the African Americans from the South Western US.
      Last edited by thetick; 26th March 2012, 07:14 PM.

      Comment


      • #4
        Thanks thetick, interesting resources that I have missed.
        One question though, that I cannot seem to find a straight answer to is.. what is a "decorated" fasta file?

        Comment


        • #5
          Originally posted by Jomid59 View Post
          Thanks thetick, interesting resources that I have missed.
          One question though, that I cannot seem to find a straight answer to is.. what is a "decorated" fasta file?
          I know a fasta file is used to show full genome data. For example I have done my MtDNA FGS (now called FMS) and can download my results in a fasta file. It only has a one line define with my "kit#,HVR2,CR,HVR1" and then my DNA string of alleles.

          Now the term "decorated" means something ornamental so I just suspect the decorated fasta data includes meta data like ethnic group, date created/submitted, who submitted etc.

          See http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html which shows all the meta data used at GenBank.

          Comment


          • #6
            Thank you the_tick.

            When I Google search I tend to find endless links to threads on various DNA boards where people are sharing their results. It's more than a little confusing/frustrating but I understand why Google returns results in that way.

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