
IMPUTE v1.0.0
=============

Copyright 2006 Jonathan Marchini
Please see the LICENCE file included with this program for conditions of use.

haplotypes file : genotypes_chr22_CEU_r22_nr.b36_fwd_phased_by_snp
    legend file : genotypes_chr22_CEU_r22_nr.b36_fwd_legend_by_snp
 genotypes file : controls2.gen
       map file : genetic_map_chr22_combined_b36.txt
    strand file : NULL
 exclusion file : NULL
 inclusion file : NULL
    output file : controls2.imp.40-41.gen
      info file : ./info
   results file : ./summary
    sample file : NULL

imputation interval : [40000000,41000000]
reading genetic map...done
reading haplotypes
 # ind = 120
 # snps read in = 925
reading genotypes
 # ind = 970
 # SNPs with genotypes read in = 114

Summary :
151 SNPs in left-hand buffer region
198 SNPs in right-hand buffer region
495 type 1 SNPs will be in output file (type 1 = SNP in haplotype file only)
81 type 2 SNPs will be in output file (type 2 = SNP in haplotype file and genotype file)
0 type 3 SNPs will be in output file (type 3 = SNP in genotype file only)
576 SNPs will be in output file in total
925 SNPs in total

-aligning allele labels of haplotypes and genotypes
-removing non-aligned genotyped SNPs
 --removing 0 genotyped SNPs out of a total of 114

setting weights...done
setting storage space...done
setting mutation matrices...done
setting switch rates...done

Estimated RAM required is 79.049Mb


      n_hap : 120
      n_gen : 970
       nind : 970
   interval : [40000000, 41000000]
     buffer : 250
         Ne : 10000
call_thresh : 0.900
      theta : 0.18655
      modelpredicpredicted 970 individuals

Breakdown of impution accuracy at SNPs with genotypes in the input file
  This assessment only uses genotypes in input file that are called above threshold of 0.90
  There are 78570 such genotypes in total
  For each of these genotypes the maximum imputed genotype calls are distributed as follows
  Interval  #Genotypes %Concordance         Interval  %Called %Concordance
  [0.0-0.1]          0          0.0         [ >= 0.0]   100.0         99.4
  [0.1-0.2]          0          0.0         [ >= 0.1]   100.0         99.4
  [0.2-0.3]          0          0.0         [ >= 0.2]   100.0         99.4
  [0.3-0.4]          0          0.0         [ >= 0.3]   100.0         99.4
  [0.4-0.5]         12         66.7         [ >= 0.4]   100.0         99.4
  [0.5-0.6]        195         41.0         [ >= 0.5]   100.0         99.4
  [0.6-0.7]        191         66.0         [ >= 0.6]    99.7         99.6
  [0.7-0.8]        336         75.6         [ >= 0.7]    99.5         99.6
  [0.8-0.9]        551         88.9         [ >= 0.8]    99.1         99.7
  [0.9-1.0]      77285         99.8         [ >= 0.9]    98.4         99.8
