
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+YRI_consensus_r22_nr.b36_fwd_phased_by_snp
    legend file : genotypes_chr22_CEU+YRI_consensus_r22_nr.b36_fwd_legend_by_snp
 genotypes file : ASW.chr22.gen.gz
       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+YRI.txt
    sample file : NULL

<<<<<<< .mine
imputation interval : [40000000,45000000]
=======
imputation interval : [40000000,50000000]
>>>>>>> .r78
reading genetic map...done
reading haplotypes
 # ind = 240
<<<<<<< .mine
 # snps read in = 4556
=======
 # snps read in = 9362
>>>>>>> .r78
reading genotypes
 # ind = 49
<<<<<<< .mine
 # SNPs with genotypes read in = 3337
=======
 # SNPs with genotypes read in = 6512
>>>>>>> .r78

Summary :
<<<<<<< .mine
60 SNPs in left-hand buffer region
93 SNPs in right-hand buffer region
=======
60 SNPs in left-hand buffer region
0 SNPs in right-hand buffer region
>>>>>>> .r78
0 type 1 SNPs will be in output file (type 1 = SNP in haplotype file only)
<<<<<<< .mine
2124 type 2 SNPs will be in output file (type 2 = SNP in haplotype file and genotype file)
=======
4447 type 2 SNPs will be in output file (type 2 = SNP in haplotype file and genotype file)
>>>>>>> .r78
0 type 3 SNPs will be in output file (type 3 = SNP in genotype file only)
<<<<<<< .mine
2124 SNPs will be in output file in total
3337 SNPs in total
=======
4447 SNPs will be in output file in total
6512 SNPs in total
>>>>>>> .r78

-aligning allele labels of haplotypes and genotypes
-removing non-aligned genotyped SNPs
<<<<<<< .mine
 --removing SNP 22 rs2032494 genotype alleles A- != haplotype alleles AC
 --removing SNP 22 rs9333347 genotype alleles C- != haplotype alleles CT
 --removing SNP 22 rs2076507 genotype alleles C- != haplotype alleles CT
 --removing SNP 22 rs139151 genotype alleles C- != haplotype alleles CT
 --removing SNP 22 rs3810624 genotype alleles G- != haplotype alleles AG
 --removing SNP 22 rs12627790 genotype alleles T- != haplotype alleles CT
 --removing SNP 22 rs4253790 genotype alleles C- != haplotype alleles CT
 --removing 7 genotyped SNPs out of a total of 2277
=======
 --removing SNP 22 rs2032494 genotype alleles A- != haplotype alleles AC
 --removing SNP 22 rs9333347 genotype alleles C- != haplotype alleles CT
 --removing SNP 22 rs2076507 genotype alleles C- != haplotype alleles CT
 --removing SNP 22 rs139151 genotype alleles C- != haplotype alleles CT
 --removing SNP 22 rs3810624 genotype alleles G- != haplotype alleles AG
 --removing SNP 22 rs12627790 genotype alleles T- != haplotype alleles CT
 --removing SNP 22 rs4253790 genotype alleles C- != haplotype alleles CT
 --removing SNP 22 rs130985 genotype alleles C- != haplotype alleles CT
 --removing SNP 22 rs9615651 genotype alleles G- != haplotype alleles AG
 --removing SNP 22 rs2064806 genotype alleles C- != haplotype alleles CT
 --removing SNP 22 rs9617402 genotype alleles G- != haplotype alleles AG
 --removing SNP 22 rs9616350 genotype alleles G- != haplotype alleles AG
 --removing 12 genotyped SNPs out of a total of 4507
>>>>>>> .r78

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

<<<<<<< .mine
Estimated RAM required is 779.608Mb
=======
Estimated RAM required is 1521.097Mb
>>>>>>> .r78


      n_hap : 240
      n_gen : 49
       nind : 49
<<<<<<< .mine
   interval : [40000000, 45000000]
=======
   interval : [40000000, 50000000]
>>>>>>> .r78
     buffer : 250
         Ne : 14000
call_thresh : 0.900
      theta : 0.16513
      model : 4

predicted 49 individuals
