************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 hshin.phase.inp hshin.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST hshin.phase.out_freqs : haplotype frequency estimates hshin.phase.out_pairs : most likely haplotype pairs for each individual hshin.phase.out_recom : estimates of recombination parameters hshin.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 23 Positions of loci: 579 9581 10783 12625 12881 14985 15956 16472 19354 20409 22747 22905 23202 23918 23958 24559 35499 35507 39548 40747 42269 43049 43379 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file hshin.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 DAGTTCGICDGTGCAGACICGII 6.000000 2 DAGTTCGICDGTGCAGACICCII 2.000000 3 DAGTTCGICDGTGCAGACICCID 1.000000 4 DAGTTCGICDGTACAGACICGID 6.000000 5 DAGTTCGICDGTACAGACICCII 1.000000 6 DAGTTCGICDGTACAGACDCGID 3.000000 7 DAGTTCGICIGTACAGACDCGID 1.000000 8 DAGTTCGITIGCGCAGTCICCII 4.000000 9 DAGGTCGICDGTACAGACDCGID 1.000000 10 DAAGTCGDTIGTGCTGTCITCDI 12.000000 11 DAAGTCGDTIGTGCTATCITCDI 5.000000 12 DTGTTGGICDGTATAGACICGID 7.000000 13 IAGTTCGITIGTGCAGTTICCII 2.000000 14 IAGTTCAITIGTGCAGTTICCII 30.000000 15 IAGTCCAITICTGCAGTTICCII 11.000000 16 ITGTTGGICDGTATAGACICGID 2.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,12) DY02: (1,12) DY03: (14,14) DY04: (6,12) DY05: (1,4) DY06: (7,16) DY07: (3,4) DY08: (14,16) DY09: (1,13) DY10: (8,14) DY11: (1,15) DY12: (8,15) DY13: (12,14) DY14: (1,4) DY15: (12,12) DY16: (14,14) DY17: (6,14) DY18: (14,14) DY19: (6,13) DY20: (14,15) DY21: (12,14) DY22: (2,8) DY23: (2,15) DY24: (4,8) E101: (10,11) E102: (10,14) E103: (14,15) E104: (10,14) E105: (10,14) E106: (10,14) E107: (14,14) E108: (10,11) E109: (14,15) E110: (10,14) E111: (10,10) E112: (11,14) E113: (11,14) E114: (14,14) E115: (10,14) E116: (11,14) E117: (5,15) E118: (9,15) E119: (4,15) E120: (10,15) E121: (4,14) E122: (10,14) E123: (14,15) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 D A G T T C G I C D G T G C A G A C I C G I I D T G T T G G I C D G T A T A G A C I C G I D 0 DY02 D A G T T C G I C D G T G C A G A C I C G I I D T G T T G G I C D G T A T A G A C I C G I D 0 DY03 I A G T T C A I T I G T G C A G T T I C C I I I A G T T C A I T I G T G C A G T T I C C I I 0 DY04 D A G T T C G I C D G T A C A G A C D C G I D D T G T T G G I C D G T A T A G A C I C G I D 0 DY05 D A G T T C G I C D G T G C A G A C I C G I I D A G T T C G I C D G T A C A G A C I C G I D 0 DY06 (D) A G T T C G I C (I) G T A C A G A C D C G I D (I) T G T T G G I C (D) G T A T A G A C I C G I D 0 DY07 D A G T T C G I C D G T G C A G A C I C C I D D A G T T C G I C D G T A C A G A C I C G I D 0 DY08 I A G T T C A I T I G T G C A G T T I C C I I I T G T T G G I C D G T A T A G A C I C G I D 0 DY09 D A G T T C G I C D G T G C A G A C I C G I I I A G T T C G I T I G T G C A G T T I C C I I 0 DY10 D A G T T C G I T I G C G C A G T C I C C I I I A G T T C A I T I G T G C A G T T I C C I I 0 DY11 D A G T T C G I C D G T G C A G A C I C G I I I A G T C C A I T I C T G C A G T T I C C I I 0 DY12 D A G T T C G I T I G C G C A G T C I C C I I I A G T C C A I T I C T G C A G T T I C C I I 0 DY13 D T G T T G G I C D G T A T A G A C I C G I D I A G T T C A I T I G T G C A G T T I C C I I 0 DY14 D A G T T C G I C D G T G C A G A C I C G I I D A G T T C G I C D G T A C A G A C I C G I D 0 DY15 D T G T T G G I C D G T A T A G A C I C G I D D T G T T G G I C D G T A T A G A C I C G I D 0 DY16 I A G T T C A I T I G T G C A G T T I C C I I I A G T T C A I T I G T G C A G T T I C C I I 0 DY17 D A G T T C G I C D G T A C A G A C D C G I D I A G T T C A I T I G T G C A G T T I C C I I 0 DY18 I A G T T C A I T I G T G C A G T T I C C I I I A G T T C A I T I G T G C A G T T I C C I I 0 DY19 D A G T T C G I C D G T A C A G A C D C G I D I A G T T C G I T I G T G C A G T T I C C I I 0 DY20 I A G T T C A I T I G T G C A G T T I C C I I I A G T C C A I T I C T G C A G T T I C C I I 0 DY21 D T G T T G G I C D G T A T A G A C I C G I D I A G T T C A I T I G T G C A G T T I C C I I 0 DY22 D A G T T C G I C D G T G C A G A C I C C I I D A G T T C G I T I G C G C A G T C I C C I I 0 DY23 D A G T T C G I C D G T G C A G A C I C C I I I A G T C C A I T I C T G C A G T T I C C I I 0 DY24 D A G T T C G I C D G T A C A G A C I C G I D D A G T T C G I T I G C G C A G T C I C C I I 0 E101 D A A G T C G D T I G T G C T G T C I T C D I D A A G T C G D T I G T G C T A T C I T C D I 0 E102 D A A G T C G D T I G T G C T G T C I T C D I I A G T T C A I T I G T G C A G T T I C C I I 0 E103 I A G T T C A I T I G T G C A G T T I C C I I I A G T C C A I T I C T G C A G T T I C C I I 0 E104 D A A G T C G D T I G T G C T G T C I T C D I I A G T T C A I T I G T G C A G T T I C C I I 0 E105 D A A G T C G D T I G T G C T G T C I T C D I I A G T T C A I T I G T G C A G T T I C C I I 0 E106 D A A G T C G D T I G T G C T G T C I T C D I I A G T T C A I T I G T G C A G T T I C C I I 0 E107 I A G T T C A I T I G T G C A G T T I C C I I I A G T T C A I T I G T G C A G T T I C C I I 0 E108 D A A G T C G D T I G T G C T G T C I T C D I D A A G T C G D T I G T G C T A T C I T C D I 0 E109 I A G T T C A I T I G T G C A G T T I C C I I I A G T C C A I T I C T G C A G T T I C C I I 0 E110 D A A G T C G D T I G T G C T [G] T C I T C D I I A G T T C A I T I G T G C A G T T I C C I I 0 E111 D A A G T C G D T I G T G C T G T C I T C D I D A A G T C G D T I G T G C T G T C I T C D I 0 E112 D A A G T C G D T I G T G C T A T C I T C D I I A G T T C A I T I G T G C A G T T I C C I I 0 E113 D A A G T C G D T I G T G C T A T C I T C D I I A G T T C A I T I G T G C A G T T I C C I I 0 E114 I A G T T C A I T I G T G C A G T T I C C I I I A G T T C A I T I G T G C A G T T I C C I I 0 E115 D A A G T C G D T I G T G C T G T C I T C D I I A G T T C A I T I G T G C A G T T I C C I I 0 E116 D A A G T C G D T I G T G C T A T C I T C D I I A G T T C A I T I G T G C A G T T I C C I I 0 E117 D A G T T C G I C D G T A C A G A C I C C I I I A G T C C A I T I C T G C A G T T I C C I I 0 E118 D A G (G) T C G I C D G T A C A G A C D C G I D I A G (T) C C A I T I C T G C A G T T I C C I I 0 E119 D A G T T C G I C D G T A C A G A C I C G I D I A G T C C A I T I C T G C A G T T I C C I I 0 E120 D A A G T C G D T I G T G C T [G] T C I T C D I I A G T C C A I T I C T G C A G T T I C C I I 0 E121 D A G T T C G I C D G T A C A G A C I C G I D I A G T T C A I T I G T G C A G T T I C C I I 0 E122 D A A G T C G D T I G T G C T [G] T C I T C D I I A G T T C A I T I G T G C A G T T I C C I I 0 E123 I A G T T C A I T I G T G C A G T T I C C I I I A G T C C A I T I C T G C A G T T I C C I I 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 = = = C = ? = = ? ? ? C = = = = = = = = I = T = = = G = ? = = ? ? ? T = = = = = = = = D 0 DY02 = A = ? = ? = ? ? = = ? ? C = = = = = = = = I = T = ? = ? = ? ? = = ? ? T = = = = = = = = D 0 DY03 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = 0 DY04 = A = = = C = = = = = = = C = = = = D = = = = = T = = = G = = = = = = = T = = = = I = = = = 0 DY05 = = = = = = = = = = = ? ? = = = = = = = = = I = = = = = = = = = = = ? ? = = = = = = = = = D 0 DY06 (D) A = = = C = = = (I) = ? ? C = = = = D = = = = (I) T = = = G = = = (D) = ? ? T = = = = I = = = = 0 DY07 = = = = = ? = = = = = ? G = = = = = = = C = = = = = = = ? = = = = = ? A = = = = = = = G = = 0 DY08 = ? ? = = C A = ? I ? ? G C = = T T = = C = I = ? ? = = G G = ? D ? ? A T = = A C = = G = D 0 DY09 D = = = = = = = C D = ? ? = = = A C = = G ? = I = = = = = = = T I = ? ? = = = T T = = C ? = 0 DY10 D = = = = = G = = = = C = = = = = C = = = = = I = = = = = A = = = = T = = = = = T = = = = = 0 DY11 D ? = = T = ? = C D G = = = = = A C = = G = = I ? = = C = ? = T I C = = = = = T T = = C = = 0 DY12 D = = = T = G = = = G C = = = = = C = = = = = I = = = C = A = = = C T = = = = = T = = = = = 0 DY13 D T = = = G G = C D = = A T = = A C = = G = D I A = = = C A = T I = = G C = = T T = = C = I 0 DY14 = = = = = = = = = = = = G = = = = = = = = = I = = = = = = = = = = = = A = = = = = = = = = D 0 DY15 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY16 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY17 D = = = = = G = C D = = A = = = A C D = G = D I = = = = = A = T I = = G = = = T T I = C = I 0 DY18 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY19 D = = = = = = = C D = = A = = = A C D = G = D I = = = = = = = T I = = G = = = T T I = C = I 0 DY20 = = = = T = = = = = G = = = = = = = = = = = = = = = = C = = = = = C = = = = = = = = = = = = 0 DY21 D T ? = = G G = C D = = A T = = A C = = G = D I A ? = = C A = T I = = G C = = T T = = C = I 0 DY22 = = = = = = = = C D = T = = = = A = = = = = = = = = = = = = = T I = C = = = = T = = = = = = 0 DY23 D = = = T = G = C D G = = = = = A C = = = = = I = = = C = A = T I C = = = = = T T = = = = = 0 DY24 = = = = = = = = C D = T A = = = A = = = G = D = = = = = = = = T I = C G = = = T = = = C = I 0 E101 = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = 0 E102 D = A G = = G D = = = = = = T = = C = T = D = I = G T = = A I = = = = = = A = = T = C = I = 0 E103 = = = = T = = = = = G = = = = = = = = = = = = = = = = C = = = = = C = = = = = = = = = = = = 0 E104 D = A G = = G D = = = = = = T = = C = T = D = I = G T = = A I = = = = = = A = = T = C = I = 0 E105 D = A G = = G D = = = = = = T = = C = T = D = I = G T = = A I = = = = = = A = = T = C = I = 0 E106 D = A G = = G D = = = = = = T = = C = T = D = I = G T = = A I = = = = = = A = = T = C = I = 0 E107 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E108 = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = 0 E109 = = = = T = = = = = G = = ? ? ? = = = = = = = = = = = C = = = = = C = = ? ? ? = = = = = = = 0 E110 D = A G = ? G D = = = = = = T ? = C = T = D = I = G T = ? A I = = = = = = A ? = T = C = I = 0 E111 = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = 0 E112 D = A G = = G D = = = = = = T A = C = T = D = I = G T = = A I = = = = = = A G = T = C = I = 0 E113 D = A G = = G D = = = = = = T A = C = T = D = I = G T = = A I = = = = = = A G = T = C = I = 0 E114 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E115 D = A G = = G D = = = = = = T = = C = T = D = I = G T = = A I = = = = = = A = = T = C = I = 0 E116 D ? A G = = G D = = = = = = T A = C = T = D = I ? G T = = A I = = = = = = A G = T = C = I = 0 E117 D = = = T = G = C D G = A = = ? A C = = = = = I = = = C = A = T I C = G = = ? T T = = = = = 0 E118 D = = (G) T = G = C D G = A = = = A C D ? G ? ? I = = (T) C = A = T I C = G = = = T T I ? C ? ? 0 E119 D = = = T = G = C D ? ? A = = = A C = = G = D I = = = C = A = T I ? ? G = = = T T = = C = I 0 E120 D = A G T = G D = = G = = = T ? = C = T = D = I = G T C = A I = = C = = = A ? = T = C = I = 0 E121 D = = = = = G = C D = ? ? = = = A C = = G = D I = = = = = A = T I = ? ? = = = T T = = C = I 0 E122 D ? A G = = G D = = = = = = ? ? = C = T = ? = I ? G T = = A I = = = = = = ? ? = T = C = ? = 0 E123 = = = = T = = = = = G = = ? ? = = = = = = = = = = = = C = = = = = C = = ? ? = = = = = = = = 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 0.88 0.99 = = = 1.00 = = = 0.50 = ? ? 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 = = = = = 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 = 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 = = = = = = 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 = = 0.50 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 1.00 ? 1.00 1.00 = = 1.00 1.00 = = = = = = ? ? = 1.00 = 1.00 = ? = = = = = 1.00 = = = = = 1.00 = = ? ? = = = = = = = = END PHASEPROBS