
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_consensus_r22_nr.b36_fwd_phased_by_snp
    legend file : genotypes_chr22_CEU+YRI_r22_nr.b36_fwd_legend_by_snp
 genotypes file : ASW.chr22.gen
       map file : genetic_map_chr22_combined_b36.txt
    strand file : NULL
 exclusion file : NULL
 inclusion file : NULL
    output file : ./out
      info file : ./info
   results file : CEU.txt
    sample file : NULL

imputation interval : [40000000,41000000]
reading genetic map...done
reading haplotypes
 # ind = 120
 # snps read in = 742
reading genotypes
 # ind = 49
 # SNPs with genotypes read in = 627

Summary :
60 SNPs in left-hand buffer region
91 SNPs in right-hand buffer region
0 type 1 SNPs will be in output file (type 1 = SNP in haplotype file only)
214 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)
214 SNPs will be in output file in total
627 SNPs in total

-aligning allele labels of haplotypes and genotypes
-removing non-aligned genotyped SNPs
 --removing SNP 22 rs2032494 genotype alleles A- != haplotype alleles AC
 --removing 1 genotyped SNPs out of a total of 365

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

Estimated RAM required is 38.648Mb


      n_hap : 120
      n_gen : 49
       nind : 49
   interval : [40000000, 41000000]
     buffer : 250
         Ne : 11418
call_thresh : 0.900
      theta : 0.18655
      model : 4

predicted 49 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 10425 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         83.0
  [0.1-0.2]          0          0.0         [ >= 0.1]   100.0         83.0
  [0.2-0.3]          0          0.0         [ >= 0.2]   100.0         83.0
  [0.3-0.4]          1          0.0         [ >= 0.3]   100.0         83.0
  [0.4-0.5]         54         11.1         [ >= 0.4]   100.0         83.0
  [0.5-0.6]        248         52.8         [ >= 0.5]    99.5         83.4
  [0.6-0.7]        291         48.1         [ >= 0.6]    97.1         84.1
  [0.7-0.8]        303         53.1         [ >= 0.7]    94.3         85.2
  [0.8-0.9]        511         53.8         [ >= 0.8]    91.4         86.2
  [0.9-1.0]       9017         88.0         [ >= 0.9]    86.5         88.0
