************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 aqp3x.phase.inp aqp3x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST aqp3x.phase.out_freqs : haplotype frequency estimates aqp3x.phase.out_pairs : most likely haplotype pairs for each individual aqp3x.phase.out_recom : estimates of recombination parameters aqp3x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 24 Positions of loci: 450 1443 2823 2978 3096 5541 5644 6402 7296 7416 7450 8576 9437 9786 10188 10574 10665 11107 11143 11252 11344 13121 13159 13263 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file aqp3x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GAACCGTCCTTGATCGGCGICGCC 2.000000 2 GAACCGTCCTCGATCGGCGDCGAC 3.000000 3 GGACCACCCGTGATCGGCGDCGAC 1.000000 4 GGACCACCCGTGATAGGCGICGCC 1.000000 5 GGACCACGCGTGATCGGCGITGCC 1.000000 6 GGACCGCGCGTGATCAGCGICGCC 1.000000 7 GGACCGCGCGTGACCAGCGICTCG 1.000000 8 GGACCGCGCGTTACCAGCGICTCG 1.000000 9 GGACCGCGTGTTACCAGCGICGCC 1.000000 10 GGACCGTCCGTGATCGGCGICGCC 2.000000 11 GGACCGTCCGTGATCGTCAICGCC 1.000000 12 GGACCGTCCGTGATAAGCGICGCC 6.000000 13 GGACCGTCCGTGGTCGGCGICGCC 2.000000 14 GGACCGTCCTCGGTCGGCGICTCG 1.000000 15 GGACCGTGCGTGATCGGCGITGCC 2.000000 16 GGACGACGCGTGATCGGCGICGCC 1.000000 17 GGACGACGCGTGATCGGCGICTCG 1.000000 18 GGAGGGCCCGTGATCGGCGITGCC 1.000000 19 GGAGGGCGCGTTACCAGCGICTCG 1.000000 20 GGAGGGTCCTCGATCGGCGICGAC 5.000000 21 GGAGGGTCCTCGATCGGCGDCGAC 4.000000 22 GGAGGGTCCTCGATCGGTGDCGCC 2.000000 23 GGAGGGTCCTCGATCGGTGDCGAC 7.000000 24 GGAGGGTCCTCGATCGGTGDCTCG 1.000000 25 GGGCCACCCGTGATCGGCGDCGAC 9.000000 26 GGGCCACCCGTGATCGTCGICGCC 1.000000 27 GGGCCACCCGTGATCGTCAICGCC 9.000000 28 GGGCCACCCGTGATAAGCGICGCC 8.000000 29 GGGCCGCCCGTGATCGGCGICGCC 2.000000 30 GGGCCGCCCGTGATCGGCGITGCC 4.000000 31 GGGCCGCCCGTGATCGTCADCTCG 1.000000 32 GGGCCGCCCGTGGTCGGCGICGCC 2.000000 33 GGGCCGTCCTCGATCGGCGDCGAC 1.000000 34 AAACCGCGTGTGATCGGCGICGCC 2.000000 35 AAACCGCGTGTTACCAGCGICTCG 5.000000 36 AAACCGTGTGTGATCGGCGICGCC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,13) DY02: (13,22) DY03: (26,27) DY04: (14,28) DY05: (27,28) DY06: (17,23) DY07: (27,31) DY08: (10,12) DY09: (12,27) DY10: (3,29) DY11: (1,11) DY12: (12,12) DY13: (23,27) DY14: (9,16) DY15: (19,23) DY16: (23,28) DY17: (28,28) DY18: (12,20) DY19: (28,32) DY20: (23,28) DY21: (12,32) DY22: (4,10) DY23: (27,27) DY24: (27,28) E101: (15,22) E102: (25,30) E103: (20,21) E104: (25,25) E105: (25,25) E106: (25,30) E107: (2,35) E108: (8,21) E109: (5,25) E110: (23,36) E111: (30,35) E112: (29,35) E113: (7,35) E114: (20,23) E115: (20,34) E116: (2,35) E117: (20,30) E118: (15,21) E119: (21,33) E120: (6,34) E121: (2,18) E122: (25,27) E123: (24,25) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 G A A C C G T C C T T G A T C G G C G I C G C C G G A C C [G] [T] C C G T G G T C G G C G I C G C C 0 DY02 G G A C C [G] [T] C C G T G G T C G G C G I C G C C G G A G G G T C C T C G A T C G G T G D C G C C 0 DY03 G G G C C A C C C G T G A T C G T C G I C G C C G G G C C A C C C G T G A T C G T C A I C G C C 0 DY04 G G (A) C C (G) (T) C C (T) (C) G (G) T C G G C G I C (T) C (G) G G (G) C C (A) (C) C C (G) (T) G (A) T A A G C G I C (G) C (C) 0 DY05 G G G C C A C C C G T G A T C G T C A I C G C C G G G C C A C C C G T G A T A A G C G I C G C C 0 DY06 G G A C G A C G C G T G A T C G G (C) G (I) C (T) (C) [G] G G A G G G T C C T C G A T C G G (T) G (D) C (G) (A) C 0 DY07 G G G C C (A) C C C G T G A T C G T C A (I) C G C C G G G C C (G) C C C G T G A T C G T C A (D) C T C G 0 DY08 G G A C C G T C C G T G A T C G G C G I C G C C G G A C C G T C C G T G A T A A G C G I C G C C 0 DY09 G G (A) C C [G] [T] C C G T G A T A [A] G C G I C G C C G G (G) C C A C C C G T G A T C G T C A I C G C C 0 DY10 G G A C C [A] [C] C C G T G A T C G G C G D C G A C G G G C C [G] C C C G T G A T C G G C G I C G C C 0 DY11 G (A) A C C G T C C (T) T G A T C G G C G I C G C C G (G) A C C G T C C (G) T G A T C G T C A I C G C C 0 DY12 G G A C C G T C C G T G A T A A G C G I C G C C G G A C C [G] [T] C C G T G A T A A G C G I C G C C 0 DY13 G G A G G G T C C T C G A T C G G T G D C G A C G G G C C A C C C G T G A T C G T C A I C G C C 0 DY14 G G A C (C) G C G (T) G T T A C C A G C G I C G C C G G A C (G) A C G (C) G T G A T C G G C G I C G C C 0 DY15 G G A G G G [C] G C G T T A C C A G C G I C T C G G G A G G G T C C T C G A T C G G T G D C G A C 0 DY16 G G A G G G T C C T C G A T C G G T G D C G A C G G G C C A C C C G T G A T A A G C G I C G C C 0 DY17 G G G C C A C C C G T G A T A A G C G I C G C C G G G C C A C C C G T G A T A A G C G I C G C C 0 DY18 G G A C C G T C C G T G A T A A G C G I C G C C G G A G G G T C C T C G A T C G G C G I C G [A] C 0 DY19 G G G C C A C C C G T G A T A A G C G I C G C C G G G C C G C C C G T G G T C G G C G I C G C C 0 DY20 G G A G G G T C C T C G A T C G G T G D C G A C G G G C C A C C C G T G A T A A G C G I C G C C 0 DY21 G G (A) C C G (T) C C G T G A T A A G C G I C G C C G G (G) C C G (C) C C G T G G T C G G C G I C G C C 0 DY22 G G A C C A C C C G T G A T (A) G G C G I C G C C G G A C C G T C C G T G A T (C) G G C G I C G C C 0 DY23 G G G C C A C C C G T G A T C G T C A I C G C C G G G C C A C C C G T G A T C G T C A I C G C C 0 DY24 G G G C C A C C C G T G A T C G T C A I C G C C G G G C C A C C C G T G A T A A G C G I C G C C 0 E101 G G A C C [G] [T] G C G T G A T C G G C G I T G C C G G A G G G T C C T C G A T C G G [T] G D C G C C 0 E102 G G G C C A C C C G T G A T C G G C G D C G A C G G G C C G C C C G T G A T C G G C G I T G C C 0 E103 G G A G G G T C C T C G A T C G G C G I C G A C G G A G G G T C C T C G A T C G G C G D C G A C 0 E104 G G G C C A C C C G T G A T C G G C G D C G A C G G G C C A C C C G T G A T C G G C G D C G A C 0 E105 G G G C C A C C C G T G A T C G G C G D C G A C G G G C C A C C C G T G A T C G G C G D C G A C 0 E106 G G G C C A C C C G T G A T C G G C G D C G A C G G G C C G C C C G T G A T C G G C G I T G C C 0 E107 G A A C C G T C C T C G A T C G G C G D C G A C A A A C C G C G T G T T A C C A G C G I C T C G 0 E108 G G A (C) (C) G C G C G T T A C C A G C G I C T C G G G A (G) (G) G T C C T C G A T C G G C G D C G A C 0 E109 G G (A) C C A C G C G T G A T C G G C G I T G C C G G (G) C C A C C C G T G A T C G G C G D C G A C 0 E110 G G A G G G T C C T C G A T C G G [T] G D C G [A] C A A A C C G T G T G T G A T C G G C G I C G C C 0 E111 G G G C C G C C C G T G A T C G G C G I T G C C A A A C C G C G T G T T A C C A G C G I C T C G 0 E112 G G G C C G C C C G T G A T C G G C G I C G C C A A A C C G C G T G T T A C C A G C G I C T C G 0 E113 G G A C C G C G C G T (G) A C C A G C G I C T C G A A A C C G C G T G T (T) A C C A G C G I C T C G 0 E114 G G A G G G T C C T C G A T C G G C G I C G A C G G A G G G T C C T C G A T C G G [T] G D C G A C 0 E115 G G A G G G T C C T C G A T C G G C G I C G A C A A A C C G C G T G T G A T C G G C G I C G C C 0 E116 G A A C C G T C C T C G A T C G G C G D C G A C A A A C C G C G T G T T A C C A G C G I C T C G 0 E117 G G A G G G T C C T C G A T C G G C G I C G A C G G G C C G C C C G T G A T C G G C G I [T] G C C 0 E118 G G A C C G T G C G T G A T C G G C G I T G C C G G A G G G T C C T C G A T C G G C G D C G [A] C 0 E119 G G A G G G T C C T C G A T C G G C G D C G A C G G G C C G T C C T C G A T C G G C G D C G A C 0 E120 G G A C C G C G C G T G A T C (A) G C G I C G C C A A A C C G C G T G T G A T C (G) G C G I C G C C 0 E121 G (A) A (C) (C) G T C C T C G A T C G G C G D C G A C G (G) A (G) (G) G C C C G T G A T C G G C G I T G C C 0 E122 G G G C C A C C C G T G A T C G G C G D C G A C G G G C C A C C C G T G A T C G T C A I C G C C 0 E123 G G A G G G T C C T C G A T C G G T G D C (T) (C) (G) G G G C C A C C C G T G A T C G G C G D C (G) (A) (C) 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 = A = = = ? ? = = T = = A = = = = = = ? ? = = = = G = = = ? ? = = G = = G = = = = = = ? ? = = = 0 DY02 = = = C C ? ? = = G T = G = = = = C = I = = = = = = = G G ? ? = = T C = A = = = = T = D = = = = 0 DY03 = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = A = = = = = 0 DY04 ? = (A) = = (G) (T) = = (T) (C) = (G) = C G = = = = = (T) = (G) ? = (G) = = (A) (C) = = (G) (T) = (A) = A A = = = = = (G) = (C) 0 DY05 ? = = = = = = = = = = = = = C G T = A ? ? = = = ? = = = = = = = = = = = = = A A G = G ? ? = = = 0 DY06 = = = C = A C G = G T = = = = = = (C) = (I) = (T) (C) ? = = = G = G T C = T C = = = = = = (T) = (D) = (G) (A) ? 0 DY07 = = = = = (A) = = = = = = = = = = = = = (I) = G = C = = = = = (G) = = = = = = = = = = = = = (D) = T = G 0 DY08 = = = = = = = = = = = = = = C G = = = = = ? ? ? = = = = = = = = = = = = = = A A = = = = = ? ? ? 0 DY09 = = (A) = = ? ? = = = = = = = A ? ? = G = = = = = = = (G) = = ? ? = = = = = = = C ? ? = A = = = = = 0 DY10 = = A = = ? ? = = = = = = = = = = = = D = ? ? ? = = G = = ? ? = = = = = = = = = = = = I = ? ? ? 0 DY11 = (A) = = = = = = = (T) = = = = = = ? = G ? = = = = = (G) = = = = = = = (G) = = = = = = ? = A ? = = = = 0 DY12 ? = = = = ? ? = = = = = = = = = = = = ? ? = = = ? = = = = ? ? = = = = = = = = = = = = ? ? = = = 0 DY13 = = A G G G T = = T C = = = = = G T G D = = A = = = G C C A C = = G T = = = = = T C A I = = C = 0 DY14 = = = = (C) ? ? = (T) = = T = C = A = = = = = = = = = = = = (G) ? ? = (C) = = G = T = G = = = = = = = = 0 DY15 = = = = = ? ? G = G T T = C = A = C = I = T C G = = = = = ? ? C = T C G = T = G = T = D = G A C 0 DY16 = = A G G G T = = T C = = = C G = T = D = = A = = = G C C A C = = G T = = = A A = C = I = = C = 0 DY17 = = = = = ? ? = = = = = = = = ? ? = = = = = = = = = = = = ? ? = = = = = = = = ? ? = = = = = = = 0 DY18 = = = C C = = = = G T = = = A A = = = = = = ? ? = = = G G = = = = T C = = = C G = = = = = = ? ? 0 DY19 = = = = = A = = = = = = A = A A = = = = = = = = = = = = = G = = = = = = G = C G = = = = = = = = 0 DY20 = = A G G G T = = T C = = = C G = T = D = = A = = = G C C A C = = G T = = = A A = C = I = = C = 0 DY21 = = (A) = = = (T) = = = = = A = A A = = = = = = = = = = (G) = = = (C) = = = = = G = C G = = = = = = = = 0 DY22 = = = = = A C = = = = = = = (A) = = = = = = = = = = = = = = G T = = = = = = = (C) = = = = = = = = = 0 DY23 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY24 = = = = = ? ? = = = = = = = C G T = A = = = = = = = = = = ? ? = = = = = = = A A G = G = = = = = 0 E101 = = = C C ? ? G = G T = = = = = = ? ? I T = = = = = = G G ? ? C = T C = = = = = = ? ? D C = = = 0 E102 = = = = = A = = = = = = = = = = = = = D C ? ? ? = = = = = G = = = = = = = = = = = = = I T ? ? ? 0 E103 = = = = = = = = = = = = = = = = = = = I = = = = = = = = = = = = = = = = = = = = = = = D = = = = 0 E104 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E105 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E106 = = = = = A = = = = = = = = = = = = = D C = A = = = = = = G = = = = = = = = = = = = = I T = C = 0 E107 G = = = = = T C C T C G = T = G = ? ? D = G A C A = = = = = C G T G T T = C = A = ? ? I = T C G 0 E108 = = = (C) (C) = C G = G T T = C = A = = = I = T C G = = = (G) (G) = T C = T C G = T = G = = = D = G A C 0 E109 = = (A) = = = = G = = = = = = = = = = = I T = C = = = (G) = = = = C = = = = = = = = = = = D C = A = 0 E110 G G = G G = = C C T C = = = = = = ? ? D = ? ? ? A A = C C = = G T G T = = = = = = ? ? I = ? ? ? 0 E111 G G G = = = = C C = = G = T = G = = = = T G = C A A A = = = = G T = = T = C = A = = = = C T = G 0 E112 ? G G = = = = C C = = G = T = G = = = = = G = C ? A A = = = = G T = = T = C = A = = = = = T = G 0 E113 G G = = = = = = C = = (G) = = = = = = = = = = = = A A = = = = = = T = = (T) = = = = = = = = = = = = 0 E114 = = = = = = = = = = = = = = = = = ? ? I = = = = = = = = = = = = = = = = = = = = = ? ? D = = = = 0 E115 G G = G G = T ? C T C = = = = = = = = = = = A = A A = C C = C ? T G T = = = = = = = = = = = C = 0 E116 ? = = = = = T C C T C G = T = G = = = D = G A C ? = = = = = C G T G T T = C = A = = = I = T C G 0 E117 = = A G G = T = = T C = = = = = = = = = ? = A = = = G C C = C = = G T = = = = = = = = = ? = C = 0 E118 ? = = C C = = G = G T = = = = = = = = I T ? ? ? ? = = G G = = C = T C = = = = = = = = D C ? ? ? 0 E119 = = A G G = = = = = = = = = = = = = = = = = = = = = G C C = = = = = = = = = = = = = = = = = = = 0 E120 G G = = = = = = C = = = = = = (A) = = = = = = = = A A = = = = = = T = = = = = = (G) = = = = = = = = 0 E121 = (A) = (C) (C) = T = = T C = = = = = = = = D C = A = = (G) = (G) (G) = C = = G T = = = = = = = = I T = C = 0 E122 = = = = = = = = = = = = = = = = G = G ? ? = A = = = = = = = = = = = = = = = = = T = A ? ? = C = 0 E123 ? = A G G ? ? = = T C = = = = ? ? T = = = (T) (C) (G) ? = G C C ? ? = = G T = = = = ? ? C = = = (G) (A) (C) END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = 1.00 = = = ? ? = = 0.99 = = 0.92 = = = = = = ? ? = = = = = = 1.00 1.00 ? ? = = 1.00 1.00 = 1.00 = = = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = ? = 0.68 = = 0.75 0.75 = = 0.83 0.83 = 0.82 = 0.92 0.92 = = = = = 0.61 = 0.61 ? = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 ? ? = = = = = = 0.98 = 0.96 0.98 0.98 = 0.98 0.98 = = = = = = 0.89 = 0.88 = 0.75 0.75 ? = = = = = 0.50 = = = = = = = = = = = = = 0.76 = 1.00 = 1.00 = = = = = = = = = = = = = = 1.00 1.00 = = = = = ? ? ? = = 0.87 = = ? ? = = = = = = = 1.00 ? ? = 1.00 = = = = = = = 0.93 = = ? ? = = = = = = = = = = = = 0.93 = ? ? ? = 0.77 = = = = = = = 0.77 = = = = = = ? = 0.97 ? = = = = ? = = = = ? ? = = = = = = = = = = = = ? ? = = = = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = = = = 1.00 1.00 1.00 1.00 = = 0.99 = = = = = 0.85 ? ? = 0.76 = = 0.92 = 0.92 = 0.92 = = = = = = = = = = = = = ? ? 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 = = 0.98 = = = = = = ? ? = = = = = = = = ? ? = = = = = = = = = = 1.00 1.00 = = = = 1.00 1.00 = = = 0.97 0.97 = = = = = = ? ? = = = = = 0.97 = = = = = = 0.95 = 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 = = = 0.90 = = = 0.90 = = = = = 1.00 = 1.00 1.00 = = = = = = = = = = = = = 1.00 1.00 = = = = = = = 0.57 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = = = = = = = = = = = = = 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 = = = 0.72 0.72 = 0.96 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = 1.00 = 1.00 1.00 1.00 = = 0.78 = = = = 0.94 = = = = = = = = = = = 1.00 1.00 = 1.00 = 0.99 0.99 = 0.99 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 = = 0.94 = 0.94 = 0.94 = = = = = 0.93 = 0.93 0.99 1.00 = = = = = = 1.00 = = 0.66 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? 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 = = = = = = = = = ? = 0.99 = ? = = 0.95 0.95 = = 0.98 = 1.00 1.00 = = = = = = = = 0.99 0.99 ? ? ? = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = 0.97 0.97 = = = = = = 0.99 = = = = = = 0.78 = = = = = = = = = 0.61 = 0.60 0.60 = 0.99 = = 0.99 0.99 = = = = = = = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = 1.00 = 1.00 ? ? = 1.00 = ? = 1.00 1.00 1.00 ? ? = = 1.00 1.00 = = = = ? ? 0.95 = = = 0.61 0.61 0.61 END PHASEPROBS