************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 zn202.phase.inp zn202.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST zn202.phase.out_freqs : haplotype frequency estimates zn202.phase.out_pairs : most likely haplotype pairs for each individual zn202.phase.out_recom : estimates of recombination parameters zn202.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 22 Positions of loci: 543 603 831 1244 1289 1472 1555 1572 2423 3013 3219 3591 4444 4547 4797 4868 5684 6785 7433 9229 10270 10485 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file zn202.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCGGTGATCCDCGACTCGATAT 32.000000 2 GCGGTGATCCDCGACTCGGCAC 2.000000 3 GCGGTGATCCDCGACTCGGTAT 2.000000 4 GCGGTGATCCDCGACTCTGCAT 2.000000 5 GCGGTGATCCDCGACTCTGCGT 13.000000 6 GCGGTGATCCDCGACTCTGTAT 1.000000 7 GCGGTGATCCDCAACTCTGCAT 3.000000 8 GCGGTGATCCDCAATGTTGCAT 1.000000 9 GCGGTGATCCDTGACTCGATAT 6.000000 10 GCACTAATCCDCAACTCTGCAT 2.000000 11 GCACTATTCCICAACTCTGCAT 1.000000 12 GCACTATTTCICAACTCTGCAT 1.000000 13 GCACTATTTCICAACTCTGCAC 10.000000 14 ATACAAACCTICAATGTTGCAT 6.000000 15 ATACAAACCTICAATGTTGCAC 3.000000 16 ATACAAACCTICAGTGTTGCAT 1.000000 17 ATACAAACCTICAGTGTTGCAC 8.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,4) DY02: (12,14) DY03: (1,6) DY04: (1,9) DY05: (1,9) DY06: (2,13) DY07: (1,9) DY08: (8,14) DY09: (1,10) DY10: (1,2) DY11: (1,9) DY12: (1,13) DY13: (1,9) DY14: (1,7) DY15: (9,13) DY16: (10,13) DY17: (1,1) DY18: (7,15) DY19: (1,13) DY20: (1,15) DY21: (1,13) DY22: (7,15) DY23: (1,14) DY24: (4,14) E101: (5,5) E102: (17,17) E103: (13,17) E104: (1,5) E105: (1,14) E106: (17,17) E107: (5,5) E108: (1,1) E109: (3,5) E110: (1,5) E111: (1,13) E112: (1,5) E113: (1,16) E114: (5,13) E115: (1,1) E116: (5,17) E117: (1,5) E118: (1,3) E119: (1,14) E120: (1,17) E121: (5,17) E122: (11,13) E123: (1,5) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D C G A C T C T G C A T 0 DY02 G C A C T A T T T C I C A A C T C T G C A T A T A C A A A C C T I C A A T G T T G C A T 0 DY03 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D C G A C T C T G T A T 0 DY04 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D T G A C T C G A T A T 0 DY05 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D T G A C T C G A T A T 0 DY06 G C G G T G A T C C D C G A C T C G G C A [C] G C A C T A T T T C I C A A C T C T G C A [C] 0 DY07 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D T G A C T C G A T A T 0 DY08 G C G G T G A T C C D C A A T G T T G C A [T] A T A C A A A C C T I C A A T G T T G C A [T] 0 DY09 G C G G T G A T C C D C G A C T C G A T A T G C A C T A A T C C D C A A C T C T G C A T 0 DY10 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D C G A C T C G G C A C 0 DY11 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D T G A C T C G A T A T 0 DY12 G C G G T G A T C C D C G A C T C G A T A T G C A C T A T T T C I C A A C T C T G C A C 0 DY13 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D T G A C T C G A T A T 0 DY14 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D C A A C T C T G C A T 0 DY15 G C G G T G A T C C D T G A C T C G A T A T G C A C T A T T T C I C A A C T C T G C A C 0 DY16 G C A C T A A T C C D C A A C T C T G C A T G C A C T A T T T C I C A A C T C T G C A C 0 DY17 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D C G A C T C G A T A T 0 DY18 G C G G T G A T C C D C A A C T C T G C A (T) A T A C A A A C C T I C A A T G T T G C A (C) 0 DY19 G C G G T G A T C C D C G A C T C G A T A T G C A C T A T T T C I C A A C T C T G C A C 0 DY20 G C G G T G A T C C D C G A C T C G A T A (T) A T A C A A A C C T I C A A T G T T G C A (C) 0 DY21 G C G G T G A T C C D C G A C T C G A T A T G C A C T A T T T C I C A A C T C T G C A C 0 DY22 G C G G T G A T C C D C A A C T C T G C A (T) A T A C A A A C C T I C A A T G T T G C A (C) 0 DY23 G C G G T G A T C C D C G A C T C G A T A T A T A C A A A C C T I C A A T G T T G C A T 0 DY24 G C G G T G A T C C D C [G] A C T C T G C A T A T A C A A A C C T I C A A T G T T G C A T 0 E101 G C G G T G A T C C D C G A C T C T G C G T G C G G T G A T C C D C G A C T C T G C G T 0 E102 A T A C A A A C C T I C A G T G T T G C A C A T A C A A A C C T I C A G T G T T G C A C 0 E103 G C A C T A T T T C I C A A C T C T G C A C A T A C A A A C C T I C A G T G T T G C A C 0 E104 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D C G A C T C T G C G T 0 E105 G C G G T G A T C C D C G A C T C G A T A T A T A C A A A C C T I C A A T G T T G C A T 0 E106 A T A C A A A C C T I C A G T G T T G C A C A T A C A A A C C T I C A G T G T T G C A C 0 E107 G C G G T G A T C C D C G A C T C T G C G T G C G G T G A T C C D C G A C T C T G C G T 0 E108 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D C G A C T C G A T A T 0 E109 G C G G T G A T C C D C G A C T C G G T A T G C G G T G A T C C D C G A C T C T G C G T 0 E110 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D C G A C T C T G C G T 0 E111 G C G G T G A T C C D C G A C T C G A T A T G C A C T A T T T C I C A A C T C T G C A C 0 E112 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D C G A C T C T G C G T 0 E113 G C G G T G A T C C D C G A C T C G A T A T A T A C A A A C C T I C A G T G T T G C A T 0 E114 G C G G T G A T C C D C G A C T C T G C G T G C A C T A T T T C I C A A C T C T G C A C 0 E115 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D C G A C T C G A T A T 0 E116 G C G G T G A T C C D C G A C T C T G C G T A T A C A A A C C T I C A G T G T T G C A C 0 E117 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D C G A C T C T G C G T 0 E118 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D C G A C T C G G T A T 0 E119 G C G G T G A T C C D C G A C T C G A T A T A T A C A A A C C T I C A A T G T T G C A T 0 E120 G C G G T G A T C C D C G A C T C G A T A T A T A C A A A C C T I C A G T G T T G C A C 0 E121 G C G G T G A T C C D C G A C T C T G C G T A T A C A A A C C T I C A [G] T G T T G C A C 0 E122 G C A C T A T T (C) C I C A A C T C T G C A T G C A C T A T T (T) C I C A A C T C T G C A C 0 E123 G C G G T G A T C C D C G A C T C G A T A T G C G G T G A T C C D C G A C T C T G C G T 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 = = = = = = = = = = = ? = = = = = G A T = = = = = = = = = = = = = ? = = = = = T G C = = 0 DY02 G C = = T = T T T C = = = = C T C = = = = = A T = = A = A C C T = = = = T G T = = = = = 0 DY03 = = = = = = = = = = = = = = = = = G A = = = = = = = = = = = = = = = = = = = = T G = = = 0 DY04 = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 DY05 = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 DY06 = = G G = G A = C = D = G = = = = G = = ? ? = = A C = A T = T = I = A = = = = T = = ? ? 0 DY07 = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 DY08 G C G G T G = T = C D = = = = = = = = = = ? A T A C A A = C = T I = = = = = = = = = = ? 0 DY09 = = G G = G = = = = = = G = = = = G A T = = = = A C = A = = = = = = A = = = = T G C = = 0 DY10 = = = = = = = = = = = = = = = = = = A T = T = = = = = = = = = = = = = = = = = = G C = C 0 DY11 = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 DY12 = = G G = G A = C = D = G = = = = G A T = T = = A C = A T = T = I = A = = = = T G C = C 0 DY13 = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 DY14 ? ? = = = = = = = = = = G = = = = G A T = = ? ? = = = = = = = = = = A = = = = T G C = = 0 DY15 = = G G = G A = C = D T G = = = = G A T = T = = A C = A T = T = I C A = = = = T G C = C 0 DY16 = = = = = = A = C = D = = = = = = = = = = T = = = = = = T = T = I = = = = = = = = = = C 0 DY17 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY18 G C G G T G = T = C D = = = C T C = = = = (T) A T A C A A = C = T I = = = T G T = = = = (C) 0 DY19 = = G G = G A = C = D = G = = = = G A ? = T = = A C = A T = T = I = A = = = = T G ? = C 0 DY20 G C G G T G = T = C D = G = C T C G A T = (T) A T A C A A = C = T I = A = T G T T G C = (C) 0 DY21 = = G G = G A = C = D = G = = = = G A T = T = = A C = A T = T = I = A = = = = T G C = C 0 DY22 G C G G T G = T = C D = = = C T C = = = = (T) A T A C A A = C = T I = = = T G T = = = = (C) 0 DY23 G C G G T G = T = C D = G = C T C G ? T = = A T A C A A = C = T I = A = T G T T ? C = = 0 DY24 G C G G T G = T = C D = ? = C T ? = = ? = = A T A C A A = C = T I = ? = T G ? = = ? = = 0 E101 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E102 = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = 0 E103 G C = = T = T T T C = = = A C T C = = = = = A T = = A = A C C T = = = G T G T = = = = = 0 E104 = = = = = = = = = = = = = = = = = G A T A = = = = = = = = = = = = = = = = = = T G C G = 0 E105 G C G G T G = T = C D = G = C T C G ? T = = A T A C A A = C = T I = A = T G T T ? C = = 0 E106 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E107 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E108 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E109 = = = = = = = = = = = = = = = = = G = T A = = = = = = = = = = = = = = = = = = T = C G = 0 E110 = = = = = = = = ? = = = = = = = = G A T A = = = = = = = = = ? = = = = = = = = T G C G = 0 E111 = = G G = G A = C = D = G = = = = G A T = T = = A C = A T = T = I = A = = = = T G C = C 0 E112 = = = = = = = = = = = = = = = = = G A T A = = = = = = = = = = = = = = = = = = T G C G = 0 E113 G C G ? ? ? ? ? = C D = G A C T C G A T = = A T A ? ? ? ? ? = T I = A G T G T T G C = = 0 E114 = = G G = G A = C = D = G = = = = = = = G T = = A C = A T = T = I = A = = = = = = = A C 0 E115 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E116 G C G G T G = T = C D = G A C T C = = = G T A T A C A A = C = T I = A G T G T = = = A C 0 E117 = = = = = = = = ? = = ? = = = = = G ? T A = = = = = = = = = ? = = ? = = = = = T ? C G = 0 E118 = = = = = = = = ? = = = = = = = = = A = = = = = = = = = = = ? = = = = = = = = = G = = = 0 E119 G C G G T G = T = C D = G = C T C G A T = = A T A C A A = C = T I = A = T G T T G C = = 0 E120 G C G G T G = T = C D = G A C T C G A T = T A T A C A A = C = T I = A G T G T T G C = C 0 E121 G C G G T G = T = C D = ? ? C T C = = = G T A T A C A A = C = T I = ? ? T G T = = = A C 0 E122 = = = = = = = = (C) = = = = = = = = = = = = T = = = = = = = = (T) = = = = = = = = = = = = C 0 E123 = = = = = = = = = = = = = = = = = G A T A = = = = = = = = = = = = = = = = = = T G C G = 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 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = 0.91 1.00 = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = 0.97 = = ? ? = = = = = = = = = = = 1.00 = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = = = = = = = = = ? = = 1.00 1.00 = 1.00 = = = = = = 1.00 = = = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 0.98 = = = = = = = = = = = 1.00 = = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = 1.00 = = = = = = = = = = ? ? = = = = = = = = = = 1.00 = = = = 1.00 1.00 1.00 = = = = 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 0.99 1.00 = = = = 1.00 1.00 1.00 = 1.00 = = = = = = 1.00 = 1.00 = 1.00 = = = = = = = = = = 0.99 = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 = = = = 0.61 = = 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 ? = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 0.89 = = 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 = = = = 0.62 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 ? 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = ? = 1.00 1.00 ? = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 ? 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = 1.00 1.00 = = = = = = = = = ? = = = = = = = = 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 ? ? ? ? ? = 1.00 1.00 = 1.00 0.93 1.00 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = = = = = = = = ? = = ? = = = = = 1.00 ? 1.00 1.00 = = = = = = = = = ? = = = = = = = = = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = ? ? 1.00 1.00 1.00 = = = 1.00 1.00 = = = = = = = = 0.51 = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = END PHASEPROBS