OUTPUT FILES GENERATED BY ANCESTRYMAP

 

act.out

Output for each iteration

Here t_mean is average  or M for the autosomes, tx_mean is the average t or M for the X chromosome, t_corr is

l_mean is average l for the autosomes, lx_mean is the average l for the X chromosome, l_corr is

tau(A) is the African t, and tau(C) is the European t value, log score

 

Iter_Num    t_mean   tx_mean    t_corr    l_mean   lx_mean    l_corr    tau(A)    tau(B) log score

  -99     0.201     0.181     0.878     5.941     6.238     0.025   100.000   100.000     4.057     0.000

  -98     0.201     0.181     0.881     5.930     6.298     0.030   104.451   330.940     3.927     0.000

  -97     0.201     0.179     0.875     5.935     6.142     0.000   136.273   218.875     5.307     0.000

  -96     0.201     0.177     0.860     5.941     6.102     0.058   127.126   171.340     6.187     0.000

  -95     0.200     0.175     0.843     5.850     6.117     0.015    94.072   125.312     6.175     0.000

  -94     0.198     0.176     0.833     5.872     6.220     0.053    97.022   105.920     5.588     0.000

  -93     0.198     0.176     0.837     5.848     6.031     0.032    91.925    92.764     6.530     0.000

  -92     0.198     0.179     0.834     5.873     5.840     0.029    96.560    90.360     7.145     0.000

 

  197     0.198     0.185     0.933     6.046     4.432     0.066    96.851    80.848     7.183     8.170

  198     0.199     0.191     0.928     6.027     4.468     0.034    99.158    82.527     7.686     8.169

  199     0.199     0.190     0.930     6.064     4.409     0.012   104.487    89.506     7.516     8.167

  200     0.199     0.193     0.930     6.045     4.331     0.029    91.103    81.868     7.030     8.165

 

ethnic.out

For all the markers averaged over all the iterations and samples:

SNP_Index is the marker’s internal index number

 

SNP_Index  SNP_ID  Chr_Num Avg_Ethnicity

    0             rs897634   1    0.212

    1             fake-1:0   1    0.212

    2             rs905135   1    0.212

    3             fake-1:1   1    0.212

 

 

 4748            rs2027812  23    0.180

 4749         fake-23:3578  23    0.180

 4750         fake-23:3579  23    0.179

 4751           rs12557310  23    0.179

 

freq.out

For all the markers averaged over all the iterations and the samples:

SNP_Index is the marker’s internal Index number, anaive and bnaive are the naïve African and European frequencies, amean and bmean are the calculated African and European frequencies, asdev and bsdev are the corresponding standard deviation

 

SNP_Index          SNP_ID Chr_Num    anaive     amean     asdev     bnaive     bmean     bsdev

   0        rs897634  1     0.104     0.148     0.010      0.741     0.766     0.030

   2        rs905135  1     0.333     0.240     0.012      0.934     0.917     0.025

   7      rs12071910  1     0.398     0.374     0.014      0.927     0.939     0.020

  12       rs1534997  1     0.806     0.747     0.011      0.100     0.045     0.013

  14       rs3007429  1     0.500     0.593     0.013      0.041     0.027     0.013

 

 

4744        rs760109 23     0.013     0.019     0.004      0.448     0.466     0.028

4748       rs2027812 23     0.175     0.152     0.011      0.639     0.602     0.030

4751      rs12557310 23     0.955     0.994     0.004      0.258     0.311     0.036

 

ind.out

For all the individuals

 

          Indiv_Id     Gender Status Num_valid_genotypes

          toyindiv:0 M      Control  1252

          toyindiv:1 F      Control  1252

          toyindiv:2 M         Case  1252

          toyindiv:3 F         Case  1252

          toyindiv:4 M      Control  1252

….

toyindiv:997 F      Control  1252

        toyindiv:998 M         Case  1252

        toyindiv:999 F         Case  1252

 

lambda.out

For all the individuals averaged over all the iterations

Here Indiv_Index is the individual’s internal index number, λ mean and λx  mean are the average λ for the autosomes and the X chromosome,

λ sdev and λx  sdev are the corresponding standard deviation

 

Indiv_Index  Indiv_Id      lam_mean  lam_sdev lamX_mean lamX_sdev

    0                toyindiv:0    6.172     0.901     4.045     1.519

    1                toyindiv:1    7.368     1.090     5.604     1.858

    2                toyindiv:2    6.421     1.107     4.377     1.438

 

 

snp.out

For all the markers:

###DETAILS ABOUT THE MARKERS

##Gen_Pos: genetic position, Phys_pos: Physical position

##Afr_vart: Parental African variant allele count, Afr_ref: Parental African reference allele count

##Eur_vart: Parental European variant allele count, Eur:ref:Parental European reference allele count

 

          SNP_Id Chr_Num    Gen_Pos           Phys_Pos  Afr_vart   Afr_ref  Eur_vart   Eur_ref

          rs897634   1        0.093937         2858849       22      190      243       85

          rs905135   1        0.105907         3222641       36       72      282       20

          rs12071910   1        0.148204         4620948       43       65      278       22

           rs1534997   1        0.186068         6177981       87       21       30      270

 

theta.out

For all the individuals averaged over all the iterations:

Th_mean and thX_mean are the average M for the autosomes and X chromosome, th_sdev and thX_sdev are the corresponding standard deviation

 

Indiv_Index    Indiv_Id   th_mean   th_sdev  thX_mean  thX_sdev    Status

    0                toyindiv:0     0.344     0.032     0.297     0.061 Control

    1                toyindiv:1     0.140     0.022     0.144     0.043 Control

    2                toyindiv:2     0.096     0.019     0.119     0.042    Case

    3                toyindiv:3     0.091     0.019     0.090     0.034    Case