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
- Count of individuals, cases, controls and ignores used in the analysis; and also the number of real and fake markers
- Checkgeno results
- Physcheck results
- Hardy-Weinberg results
- Checkdup results
###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
- Freqcheck results
- leave1out scores for each marker
- leave1out scores for each chromosome
###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