************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 icam4.phase.inp icam4.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST icam4.phase.out_freqs : haplotype frequency estimates icam4.phase.out_pairs : most likely haplotype pairs for each individual icam4.phase.out_recom : estimates of recombination parameters icam4.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 5 Positions of loci: 174 2146 2675 2881 3075 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file icam4.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CTCCA 12.000000 2 CTCGA 3.000000 3 CTCGG 26.000000 4 CGCCA 33.000000 5 CGCGA 1.000000 6 CGCGG 1.000000 7 TTCCA 1.000000 8 TTTCA 17.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,3) DY02: (4,4) DY03: (1,3) DY04: (3,4) DY05: (3,4) DY06: (1,1) DY07: (1,4) DY08: (3,4) DY09: (3,4) DY10: (2,3) DY11: (4,4) DY12: (3,3) DY13: (1,3) DY14: (4,5) DY15: (4,4) DY16: (2,3) DY17: (4,4) DY18: (3,4) DY19: (2,4) DY20: (1,3) DY21: (1,3) DY22: (4,4) DY23: (6,8) DY24: (3,4) E101: (1,4) E102: (4,8) E103: (4,4) E104: (4,4) E105: (4,4) E106: (8,8) E107: (4,8) E108: (3,8) E109: (3,8) E110: (3,4) E111: (4,8) E112: (3,3) E113: (4,8) E114: (4,8) E115: (3,4) E116: (3,8) E117: (1,3) E118: (3,7) E119: (1,8) E120: (1,8) E121: (3,8) E122: (8,8) E123: (3,8) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 C T C C A C T C G G 0 DY02 C G C C A C G C C A 0 DY03 C T C C A C T C G G 0 DY04 C T C G G C G C C A 0 DY05 C T C G G C G C C A 0 DY06 C T C C A C T C C A 0 DY07 C T C C A C G C C A 0 DY08 C T C G G C G C C A 0 DY09 C T C G G C G C C A 0 DY10 C T C G A C T C G G 0 DY11 C G C C A C G C C A 0 DY12 C T C G G C T C G G 0 DY13 C T C C A C T C G G 0 DY14 C G C C A C G C G A 0 DY15 C G C C A C G C C A 0 DY16 C T C G A C T C G G 0 DY17 C G C C A C G C C A 0 DY18 C T C G G C G C C A 0 DY19 C (T) C G A C (G) C C A 0 DY20 C T C C A C T C G G 0 DY21 C T C C A C T C G G 0 DY22 C G C C A C G C C A 0 DY23 C (G) C (G) (G) T (T) T (C) (A) 0 DY24 C T C G G C G C C A 0 E101 C T C C A C G C C A 0 E102 C G C C A T T T C A 0 E103 C G C C A C G C C A 0 E104 C G C C A C G C C A 0 E105 C G C C A C G C C A 0 E106 T T T C A T T T C A 0 E107 C G C C A T T T C A 0 E108 C T C G G T T T C A 0 E109 C T C G G T T T C A 0 E110 C T C G G C G C C A 0 E111 C G C C A T T T C A 0 E112 C T C G G C T C G G 0 E113 C G C C A T T T C A 0 E114 C G C C A T T T C A 0 E115 C T C G G C G C C A 0 E116 C T C G G T T T C A 0 E117 C T C C A C T C G G 0 E118 (C) T C G G (T) T C C A 0 E119 C T C C A T T T C A 0 E120 C T C C A T T T C A 0 E121 C T C G G T T T C A 0 E122 T T T C A T T T C A 0 E123 C T C G G T T T C A END BESTPAIRS1 Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = BEGIN BESTPAIRS2 0 DY01 = = = C A = = = G G 0 DY02 = = = = = = = = = = 0 DY03 = = = C A = = = G G 0 DY04 = T = G G = G = C A 0 DY05 = T = G G = G = C A 0 DY06 = = = = = = = = = = 0 DY07 = T = = = = G = = = 0 DY08 = T = G G = G = C A 0 DY09 = T = G G = G = C A 0 DY10 = = = = A = = = = G 0 DY11 = = = = = = = = = = 0 DY12 = = = = = = = = = = 0 DY13 = = = C A = = = G G 0 DY14 = = = C = = = = G = 0 DY15 = = = = = = = = = = 0 DY16 = = = = A = = = = G 0 DY17 = = = = = = = = = = 0 DY18 = T = G G = G = C A 0 DY19 = (T) = G = = (G) = C = 0 DY20 = = = C A = = = G G 0 DY21 = = = C A = = = G G 0 DY22 = = = = = = = = = = 0 DY23 C (G) C (G) (G) T (T) T (C) (A) 0 DY24 = T = G G = G = C A 0 E101 = T = = = = G = = = 0 E102 C G C = = T T T = = 0 E103 = = = = = = = = = = 0 E104 = = = = = = = = = = 0 E105 = = = = = = = = = = 0 E106 = = = = = = = = = = 0 E107 C G C = = T T T = = 0 E108 C = C G G T = T C A 0 E109 C = C G G T = T C A 0 E110 = T = G G = G = C A 0 E111 C G C = = T T T = = 0 E112 = = = = = = = = = = 0 E113 C G C = = T T T = = 0 E114 C G C = = T T T = = 0 E115 = T = G G = G = C A 0 E116 C = C G G T = T C A 0 E117 = = = C A = = = G G 0 E118 (C) = = G G (T) = = C A 0 E119 C = C = = T = T = = 0 E120 C = C = = T = T = = 0 E121 C = C G G T = T C A 0 E122 = = = = = = = = = = 0 E123 C = C G G T = T C A END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = 1.00 1.00 = = = = = = = = 1.00 1.00 = 0.98 = 1.00 1.00 = 0.98 = 1.00 1.00 = = = = = = 1.00 = = = = 0.98 = 1.00 1.00 = 0.98 = 1.00 1.00 = = = = 1.00 = = = = = = = = = = = = = 1.00 1.00 = = = 1.00 = = = = = = = = = = 1.00 = = = = = = 0.98 = 1.00 1.00 = 0.83 = 1.00 = = = = 1.00 1.00 = = = 1.00 1.00 = = = = = 0.99 0.71 1.00 0.89 0.88 = 0.98 = 1.00 1.00 = 1.00 = = = 1.00 0.99 1.00 = = = = = = = = = = = = = = = = = = = = = = 1.00 0.99 1.00 = = 0.99 = 0.99 1.00 1.00 0.99 = 0.99 1.00 1.00 = 0.99 = 1.00 1.00 1.00 0.99 1.00 = = = = = = = 1.00 0.99 1.00 = = 1.00 0.99 1.00 = = = 0.98 = 1.00 1.00 0.99 = 0.99 1.00 1.00 = = = 1.00 1.00 0.68 = = 1.00 1.00 1.00 = 1.00 = = 1.00 = 1.00 = = 0.99 = 0.99 1.00 1.00 = = = = = 0.99 = 0.99 1.00 1.00 END PHASEPROBS