Output Details

6.2.3 Output Details

Next we will discuss the output in detail to the standard output, in the case where details = YES, checkit = YES, numburn = 0 and numiters= 0. 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

Here is an example of the output generated:

parameter file: param0

output: (null)

### THE INPUT PARAMETERS

PARAMETER NAME: VALUE

risk: 1.5

indivname: indiv.dat

snpname: snpcnts

genotypename: geno.dat

tlreest: YES

seed: 1011

splittau: YES

fancyxtheta: YES

checkit: YES

details: YES

numburn: 0

numiters: 0

emiter: 10

dotoysim: NO

cleaninit: YES

reestiter: 5

indoutfilename: indjunk

snpoutfilename: snpjunk

## 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:     4  first:  1277  last:  1617 distance:     2.131

chrom:     5  first:  1618  last:  1961 distance:     2.012

chrom:     6  first:  1962  last:  2272 distance:     1.914

chrom:     7  first:  2273  last:  2581 distance:     1.871

chrom:     8  first:  2582  last:  2862 distance:     1.677

chrom:     9  first:  2863  last:  3133 distance:     1.777

chrom:    10  first:  3134  last:  3420 distance:     1.809

chrom:    11  first:  3421  last:  3682 distance:     1.552

chrom:    12  first:  3683  last:  3961 distance:     1.723

chrom:    13  first:  3962  last:  4169 distance:     1.258

chrom:    14  first:  4170  last:  4360 distance:     1.162

chrom:    15  first:  4361  last:  4559 distance:     1.245

chrom:    16  first:  4560  last:  4772 distance:     1.340

chrom:    17  first:  4773  last:  4971 distance:     1.272

chrom:    18  first:  4972  last:  5161 distance:     1.160

chrom:    19  first:  5162  last:  5329 distance:     1.069

chrom:    20  first:  5330  last:  5492 distance:     1.067

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

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
  • Fastdup results
  • Checkgeno results
  • Physcheck 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

hetxcheck            rs1474458      0      600

hetxcheck            rs1013549      0      600

hetxcheck            rs1007420      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:  601 Num of Controls:  600   Num of Ignored Samples: 0

dup? toyindiv:539 toyindiv:1200

 match: 2260 mismatch: 0   2260 2260

dup.  toyindiv:539 ignored

### 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       -1.595

hwcheck           rs10907185     1        1        0.376

hwcheck             rs897634     4        1       -1.861

hwcheck            rs2817159     6        1       -0.582

hwcheck            rs1181868     9        1        0.134

hwcheck            rs7548756    12        1       -0.058

hwcheck            rs8142477  5698       22       -2.327

hwcheck             rs140514  5699       22       -0.021

hwstats (chrom  1) ave:    -1.110 sigma:   -15.543

hwstats (chrom  2) ave:    -1.330 sigma:   -17.183

hwstats (autosomes) ave:    -1.210 sigma:   -56.448

###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

## no iterations:  end of run