6.2.4 Output Details

6.2.4 Output Details

Next we will discuss the output in detail to the standard output, in the case where details = YES, checkit = YES, and finite values for numburn and numiters. As always this output can be redirected to a file for easier viewing.

  • Input parameter file name
  • Values of all the parameters specified in this file
  • Genetic distance for all chromosomes
  • Total genomic distance
  • Details about the markers

parameter file: param1

output: (null)

### THE INPUT PARAMETERS

PARAMETER NAME: VALUE

risk: 1.5

indivname: indiv1.dat

snpname: snpcnts

genotypename: geno.dat

tlreest: YES

seed: 1011

splittau: YES

fancyxtheta: YES

checkit: YES

details: YES

numburn: 5

numiters: 5

emiter: 10

dotoysim: NO

cleaninit: YES

reestiter: 5

## ANCESTRYMAP version: 6210

###GENETIC DISTANCE FOR ALL CHROMOSOMES

##Chr_Num: chromosome num, First_SNP and Last_SNP: First and last markers, Gen_dist: Genetic distance

Chr_Num First_SNP  Last_SNP  Gen_dist

chrom:     1  first:     0  last:  478 distance:     2.834

chrom:     2  first:   479  last:  910 distance:     2.647

chrom:     3  first:   911  last:  1276 distance:     2.227

chrom:    21  first:  5493  last:  5586 distance:     0.604

chrom:    22  first:  5587  last:  5699 distance:     0.711

chrom:    23  first:  5700  last:  5902 distance:     1.180

total distance:    36.242

calling setstatus

###DETAILS ABOUT THE MARKERS

##Gen_Pos: genetic position, Phys_pos: Physical position

##PopA_vart: Parental PopA variant allele count, PopA_ref: Parental PopA reference allele count

##PopB_vart: Parental PopB variant allele count, PopB_ref:Parental PopB reference allele count

        #SNP_Id Chr_Num    Gen_Pos         Phys_PosPopA_vart  PopA_ref PopB_vart  PopB_ref Case_Cnt   Ctl_Cnt

       rs819980   1        0.031989         1510967      107       15        3       61      600    600

     rs10907185   1        0.035398         1765381       41      165      214       90      600    600

     rs10127175  23        1.202645       152805019       12       79        1       47      600    600

      rs5945413  23        1.204817       153084598       86        6        8       40        0      0

       rs884840  23        1.205566       153491735      153        4       92      162      600    600

emiter: 10

reestiter: 5

trashdir: /var/tmp

###HETXCHECK RESULTS BEGIN

##                      SNP_ID  NUM_HET NUM_HOMOZY

hetxcheck            rs6530109      0      600

hetxcheck            rs2128516      0      600

hetxcheck           rs16984097      0        0

hetxcheck            rs5948775      0      600

hetxcheck            rs7884299      0      600

hetxcheck            rs5978365      0      600

###COUNTS

Num of fake Markers: 3622  Num of real Markers: 2281 Spacing between fake markers:     0.010

Num of Markers: 5903   Num of Samples:  1201

Num of Cases:  600 Num of Controls:  600   Num of Ignored Samples: 1

### CHECKGENO RESULTS FOLLOW:

Num good genotypes: 2714260  Num bad genotypes:  0

###PHYSCHECK RESULTS FOLLOW:

##        SNP1_ID        SNP2_ID   SNP1_GEN_POS   SNP2_GEN_POS  SNP1_PHYS_POS  SNP2_PHYS_POS

###HWCHECK RESULTS FOLLOW:

##                   SNP_ID  SNP_INDEX    CHR_NUM   HW_SCORE

hwcheck             rs819980     0        1       -1.586

hwcheck           rs10907185     1        1        0.391

hwcheck             rs897634     4        1       -1.853

hwcheck            rs2817159     6        1       -0.573

hwcheck            rs1181868     9        1        0.142

hwcheck            rs8142477  5698       22       -2.308

hwcheck             rs140514  5699       22       -0.015

hwstats (chrom  1) ave:    -1.106 sigma:   -15.489

hwstats (chrom  2) ave:    -1.326 sigma:   -17.140

hwstats (chrom 21) ave:    -1.514 sigma:    -8.830

hwstats (chrom 22) ave:    -1.524 sigma:    -9.877

hwstats (autosomes) ave:    -1.209 sigma:   -56.436

###CHECKDUP RESULTS FOLLOW:

##Indiv_Id1  Indiv_Id2

##Num of genotypes matched: Num of genotypes mismatched

##If the status of the two individuals does not match Status1: Status2

match prob. mean:     0.464  s.dev:     0.058

  • Details about all the individuals
  • Details about all the markers

###DETAILS ABOUTTHE INDIVIDUALS

          Indiv_ID Gender    Status  Genotype_Cnt

          toyindiv:0 M      Control   2260

          toyindiv:1 F      Control   2260

          toyindiv:2 M         Case   2260

          toyindiv:3 F         Case   2260

          toyindiv:4 M      Control   2260

          toyindiv:5 F      Control   2260

       toyindiv:1198 M         Case   2260

       toyindiv:1199 F         Case   2260

       toyindiv:1200 F       Ignore      0

###DETAILS ABOUT THE MARKERS

##Gen_Pos: genetic position, Phys_pos: Physical position

##PopA_vart: Parental PopA variant allele count, PopA_ref: Parental PopA reference allele count

##PopB_vart: Parental PopB variant allele count, PopB_ref:Parental PopB reference allele count

        #SNP_Id Chr_Num    Gen_Pos         Phys_PosPopA_vart  PopA_ref PopB_vart  PopB_ref Case_Cnt   Ctl_Cnt

       rs819980   1        0.031989         1510967      107       15        3       61      600    600

     rs10907185   1        0.035398         1765381       41      165      214       90      600    600

       rs897634   1        0.056663         2858849       32      300      249       89      600    600

    rs10127175  23        1.202645       152805019       12       79        1       47      600    600

      rs5945413  23        1.204817       153084598       86        6        8       40        0      0

       rs884840  23        1.205566       153491735      153        4       92      162      600    600

  • Score generated per iteration by the expectation maximization algorithm. One should observe the score increasing with the number of iterations.
  • CheckindivResults
  • Results of the Markov Chain Monte Carlo iterations, which include estimation of θ and l.Note that the iteration number is negative since the iteration numbers go from 1- numburn to 0 for the burn-in iterations, and go from 1 to numiters for the follow-on iterations. Also, note that the log score is zero for the burn-in iterations since we calculate it only for the follow-on iterations. The format of the output for the estimation of θ and l is as follows:
    estglob theta   iter   a1   b1   a2   b2   c2
    estglob lambda   iter   p1    lambda1   p2   lambda2   lambdave
    The above parameters are "global parameters" (affect every individual).  See supplementary note 2 of the Patterson et. al. 2004 paper for definitions.
    lambdaave is the average λ across individuals.

The format of the output which begins with bigiter is as follows:

bigiter   iter    ylike    LOD sc.   tau(A)    tau(E)     thetaave    lambdaave    xtave(M)   xlave(M)    xtave(F)   xlave(F)
 ylike is the slowly mixing statistic of little intrinsic interest described in the above mentioned supplementary note. xtave(M) and xtave(F) are the average θ on X chromosme for males and females respectively, xlave(M) and xlave(F) are the average l on X chromosome for males and females respectively.

  • Posterior estimates of mean, variance and standard deviation for θ, θX, λ, λX, t(Afr), t(Eur). The user should look at the value of t(African) and t(European) carefully, since they are an indicator of how well the ancestral models fit the data. It is worrisome if we see these values to be less than 100.
  • Genome-wide scores for all the models

##SCORES FROM EXPECTATION_MAXIMIZATION ALGORITHM ITERATIONS

##         Iteration_Num    Score

emsimple iter:      1          0.000

emsimple iter:      2      93775.215

emsimple iter:      9     136694.295

emsimple iter:     10     136878.752

checkindiv           toyindiv:0     0.220   -18.224    -0.774 2178   2226.073    1.022

checkindiv           toyindiv:1     0.106     8.065     0.294 2178   2091.776    0.960

checkindiv           toyindiv:2     0.226   -26.914    -1.154 2178   2325.391    1.068

checkindiv        toyindiv:1198     0.126     4.697     0.176 2178   2017.775    0.926

checkindiv        toyindiv:1199     0.161    -0.893    -0.035 2178   2217.146    1.018

muval1:     0.000

neil0:     5.935    -3.444

*** warning.  No data for rs12472692

*** warning.  No data for rs6834841

*** warning.  No data for rs434958

*** warning.  No data for rs9398581

*** warning.  No data for rs218862

*** warning.  No data for rs9387942

*** warning.  No data for rs2494674

*** warning.  No data for rs17093912

*** warning.  No data for rs2709640

*** warning.  No data for rs4363494

*** warning.  No data for rs10824303

*** warning.  No data for rs557492

*** warning.  No data for rs7900818

*** warning.  No data for rs4630293

*** warning.  No data for rs1638567

*** warning.  No data for rs4789772

*** warning.  No data for rs485401

*** warning.  No data for rs1569601

*** warning.  No data for rs16984097

*** warning.  No data for rs11093779

*** warning.  No data for rs5945413

domcm1 time:    28.000

neil1:     7.337    -2.697

###RESULTS FOR EACH MARKOV CHAIN MONTE CARLO ITERATION

##estglob theta: Iteration_Num  thp1  thp2  thxp0  thxp1  thxp2

##thp1, thp2: Are parameters for the prior distribution of theta, and thxp0,thxp1,thxp2 are the same for theta on X chromosome

##estglob lambda: Iteration_Num  lp1  lp2  lxp1  lxp2  ave_lambda

##lp1, lp2: Are parameters for the prior distribution of lambda, and lxp1,lxp2 are the same for lambda on X chromosome

estglob theta     -4     2.127     8.006       1.142     9.239    37.765

estglob lambda    -4    14.495     2.841      11.099     2.140     5.102

#iter    t mean   tx mean    t corr    l mean   lx mean    l corr   tau (A)   tau (C) log score

   -4     0.208     0.187     0.870     5.102     5.186    -0.035   100.000   100.000    10.511     0.000

domcm1 time:    27.960

estglob theta     -3     2.174     8.530       1.259    10.364    39.985

estglob lambda    -3    17.656     3.412      11.216     2.162     5.175

   -3     0.207     0.186     0.878     5.175     5.188    -0.009   132.144   275.558    10.971     0.000

estglob theta     -2     2.109     8.187       1.454    10.958    39.833

estglob lambda    -2    19.848     3.799      10.950     2.150     5.225

   -2     0.205     0.183     0.871     5.225     5.092    -0.019   120.820   214.617    11.756     0.000

###POSTERIOR ESTIMATES

theta  mean      0.2030

thetax mean      0.1751

theta  var      0.0139   sdev:     0.1177

thetax var      0.0103   sdev:     0.1015

lambda  mean      5.4372

lambdax mean      4.9482

lambda  var      1.2243   sdev:     1.1065

lambdax var     26.5802   sdev:     5.1556

tau (PopA)   117.506

tau (PopB)   123.633

###GENOME_WIDE SCORE FOR ALL THE MODELS

##risk1 and risk2 are the increased risk due to having one or two population A ancestry alleles, and  crisk: risk for controls

           risk1     risk2     crisk       score

model:     1.500     2.250     1.000      12.267

  • θ/M and λ values for all individuals
  • Allele frequency estimates with standard error:
  • Lag and correlations
    For a number of sample statistics we compute a correlation coefficient at small "lags". If the statistic at iteration i is S(i) we compute  for 1 <= lag <= 10 (default) the correlation between S(i) and S(i+lag). Large values indicate that the MCMC is not mixing very well.
    We publish this for:
    • llike:  a statistic of no intrinsic interest but mixes poorly.    
    • log10fac:  Log_10 Bayes factor (genome wide)
    • factor: Bayes factor = 10^log10fac
    • log tauscal: log (t(0)) the t value for population 0.

In our experience ii), iii) are the most important statistics which mix well, iv) mixes less well and i) mixes quite poorly.

###THETA or M, LAMBDA VALUES FOR ALL INDIVIDUALS

##Indiv_Index: individual's internal index num, tmean and txmean: average theta and thetax

##tsdev and txsdev: standard deviation for theta and thetax

##lmean and lxmean: average lambda and lambdax

##lsdev and lxsdev: standard deviation for lambda and lambdax

 Num        Indiv_ID Gender    tmean     tsdev     txmean    txsdev        lmean     lsdev     lxmean    lxsdev

   0                toyindiv:0     M     0.214     0.015      0.180     0.015        5.554     0.326      5.055     1.255

   1                toyindiv:1     F     0.116     0.021      0.118     0.029        5.686     0.253      3.598     0.267

   2                toyindiv:2     M     0.218     0.019      0.218     0.063        5.585     0.317      6.229     0.737

1197             toyindiv:1197     F     0.265     0.024      0.260     0.060        3.839     0.175      5.050     0.715

1198             toyindiv:1198     M     0.175     0.007      0.134     0.041        5.635     0.128      4.926     0.845

1199             toyindiv:1199     F     0.184     0.030      0.137     0.056        6.115     0.492      4.492     0.822

###ALLELE FREQUENCY ESTIMATES WITH STANDARD ERROR

##SNP_Index: marker internal index num

##amean and bmean are the average reference allele frequency for population A and B

##asdev and bsdev are the corresponding standard deviation

SNP_Index Chr_Num          SNP_ID   amean   asdev     bmean     bsdev

    0   1             rs819980     0.945     0.004        0.024     0.005

    1   1           rs10907185     0.253     0.009        0.659     0.023

    4   1             rs897634     0.088     0.003        0.782     0.017

5900  23           rs10127175     0.106     0.004        0.038     0.008

 5902  23             rs884840     0.983     0.003        0.329     0.027

###LAG AND CORRELATIONS

               llike mean: -3628.159 s.err:  2041.739

lag:  1 corr:     0.166 sig:     0.333

            log10fac mean:    12.263 s.err:     0.057

lag:  1 corr:     0.231 sig:     0.462

              factor mean: 1849007588331.055 s.err: 245166098869.409

lag:  1 corr:     0.260 sig:     0.520

         log tauscal mean:     2.072 s.err:     0.024

lag:  1 corr:    -0.706 sig:    -1.413

  • Scores for each marker
  • Scores for each chromosome. As one can clearly see from the output shown below, the LGS_MAX and CCS_MAX scores are the highest for chromosome number 4.
  • Bestscores: The maximum genome-wide score for the locus-genome statistic, and the maximum and minimum genome-wide scores for the case-control statistic.
  • Genome-log-factor: log-likelihood of the locus genome statistic averaged over all the markers in the genome.

The genome log factor is the most important number that is produced by the program and should be the first number that the user looks at.

           

##SCORES FOR EACH MARKER (fakes used for global score)

##LGS: locus genome statistic score, CCS:case control statistic

###SNP_Index    Chr               SNP_ID    Phys_Pos    Gen_Pos       LGS        CCS         G(case) G(control)     rpower

           0      1             rs819980   1510967        0.032    -5.393      0.809         0.206      0.194      0.810

           1      1           rs10907185   1765381        0.035    -5.370      0.777         0.206      0.195      0.798

           2      1             fake-1:0   2002021        0.040    -5.287      0.830         0.206      0.194      0.784

           3      1             fake-1:1   2516231        0.050    -5.282      0.931         0.206      0.193      0.786

           4      1             rs897634   2858849        0.057    -5.411      0.985         0.206      0.192      0.814

           5      1             fake-1:2   2959423        0.060    -5.321      1.133         0.206      0.190      0.814

5899     23            rs3027907 152800292        1.203    -2.533      0.501         0.182      0.181      0.693

        5900     23           rs10127175 152805019        1.203    -2.533      0.501         0.182      0.181      0.693

        5902     23             rs884840 153491735        1.206    -2.581      0.465         0.182      0.182      0.690

###SCORES FOR EACH CHROMOSOME

##LGS_MAX: Maximum locus genome statistic score

##CCS_MAX and CCS_MIN are the maximum and minimum case control statistic scores

##LGS_LOCAL: log likelihood of the locus genome statistic score obtained by averaging over all the markers on that chromosome

   Chr_Num  LGS_MAX   CCS_MAX  CCS_MIN  LGS_LOCAL

    1  -1.78    2.06  -1.95   -3.38

    2  15.00    7.40  -0.74   13.40

    3  -4.47    1.72  -0.60   -5.78

    4  -4.29    1.85  -1.71   -5.50

    5  -4.45    1.59  -2.00   -5.80

    6  -4.17    0.74  -2.00   -5.58

    7  -1.71    2.43  -0.81   -3.39

    8  -4.99    0.38  -2.45   -5.96

    9  -3.63    1.35  -1.01   -4.99

   10  -4.27    1.40  -1.77   -5.43

   11  -3.19    2.64  -1.23   -4.41

   12  -0.09    2.19  -2.05   -1.45

   13  -2.73    2.54  -1.33   -3.88

   14  -2.84    1.51  -1.20   -4.18

   15  -3.69    0.49  -2.11   -5.11

   16  -4.04    0.73  -1.83   -5.10

   17  -1.74    1.06  -1.02   -3.15

   18  -2.30    2.44  -2.76   -3.62

   19  -3.10    2.33  -0.85   -4.52

   20  -1.90    1.13  -0.39   -3.50

   21  -2.24    3.10  -0.00   -3.84

   22  -4.10    2.60  -1.13   -5.17

   23   0.48    2.50  -1.59   -0.53

###BESTSCORES: Maximum genome-wide score for the locus-genome statistic (LGS_MAX), and the maximum and minimum genome-wide scores fo

r the case-control statistic (CCS_MAX and CCS_MIN)

bestscores:     15.000     7.402    -2.760

###GENOME LOG FACTOR: log-likelihood of the locus genome statistic averaged over all the markers in the genome

genome log-factor:    12.267

###Entering leave1 risk:     1.500

###MAPCHECK RESULTS FOLLOW:

##                        SNP_ID  SNP_INDEX      CHROM ANCESTRY_DIFF

mapcheck                  rs819980        0          1    -126.796

mapcheck                rs10907185        1          1     -21.017

mapcheck                  rs897634        4          1     -91.155

mapcheck                 rs2817159        6          1    -146.017

mapcheck                 rs1181868        9          1     -73.279

###FREQCHECK RESULTS FOLLOW:

##For information about this check, look at the documentation included

##                      SNP_ID     CHR_NUM      S(ALL) S(CONTROLS)        F(A)        F(E)        G(A)        G(E)

freqcheck             rs819980        1       1.256       0.624       0.945       0.024         0.949       0.037

freqcheck           rs10907185        1       0.371       0.343       0.253       0.659         0.261       0.663

freqcheck             rs897634        1       0.484       0.043       0.088       0.782         0.089       0.776

freqcheck            rs2817159        1       3.359       1.905       0.948       0.093         0.944       0.061

freqcheck            rs1181868        1       1.836       0.380       0.899       0.234         0.904       0.249

scores for each fake

##base: Score for the marker without using leave1out, min and max are the minimum and maximum scores obtained when using the leave1o

ut algorithm

SNP_Index               SNP_ID chrom      base       min       max

    2   1             fake-1:0    -5.188    -5.542    -3.679

    3   1             fake-1:1    -5.186    -5.540    -4.153

    5   1             fake-1:2    -5.190    -5.467    -4.608

    7   1             fake-1:3    -4.910    -5.068    -4.408

5897  23         fake-23:3620    -2.059    -2.280    -0.988

 5898  23         fake-23:3621    -2.087    -2.275    -0.850

                     chrom      base       min       max

  best score (chrom)     1    -1.610    -1.699    -1.234

  best score (chrom)     2    15.645    15.151    15.774

  best score (chrom)     3    -4.430    -4.892    -3.957

  best score (chrom)     4    -4.658    -4.773    -3.886

  best score (chrom)     5    -4.537    -4.697    -4.276

  best score (chrom)     6    -4.135    -4.393    -3.647

  best score (chrom)     7    -2.422    -2.955    -1.913

  best score (chrom)     8    -5.104    -5.455    -4.243

  best score (chrom)     9    -3.969    -4.110    -2.908

  best score (chrom)    10    -4.511    -4.557    -3.342

  best score (chrom)    11    -3.272    -3.570    -2.829

  best score (chrom)    12     0.019    -0.034     0.554

  best score (chrom)    13    -2.606    -3.109    -2.439

  best score (chrom)    14    -2.910    -2.954    -2.737

  best score (chrom)    15    -3.960    -4.269    -3.542

  best score (chrom)    16    -4.342    -4.726    -3.508

  best score (chrom)    17    -1.760    -2.059    -1.551

  best score (chrom)    18    -2.342    -3.028    -2.269

  best score (chrom)    19    -2.819    -3.219    -2.702

  best score (chrom)    20    -1.927    -2.299    -1.600

  best score (chrom)    21    -2.453    -2.832    -1.727

  best score (chrom)    22    -4.260    -4.716    -3.328

  best score (chrom)    23     0.438     0.206     0.549

global score (leave1):    12.681

trash files deleted

 exiting leave1

##end of run