************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 c4bpb.phase.inp c4bpb.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST c4bpb.phase.out_freqs : haplotype frequency estimates c4bpb.phase.out_pairs : most likely haplotype pairs for each individual c4bpb.phase.out_recom : estimates of recombination parameters c4bpb.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 24 Positions of loci: 602 1293 1700 2056 2386 3235 4064 5491 6127 6128 6880 7500 8622 9189 9236 9269 9330 12903 13001 13162 13212 13331 13335 13368 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file c4bpb.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AAAGGATGGGCADACTTGGCTITA 1.000000 2 AAAGTATGGGCADGCTTGGCTITA 7.000000 3 AAAGTATGGGCADGCTTGGTTITA 6.000000 4 AAAGTATGGGCADGCTCGGTGITA 22.000000 5 AAAGTATGGGCADGCCTAGCTDCG 4.000000 6 AAAGTATGGGCADATTTGGCTITA 1.000000 7 AAAGTATGGGCAIGCTTGGTTITA 2.000000 8 AAAGTATGGGCAIGCTCGGTGITA 1.000000 9 AAAGTATGGGCAIGCCTAGCTDCG 5.000000 10 AAGGTACCGGCADGCCTAGCTDCG 1.000000 11 AAGAGACCGGCADGCTTGGTTITA 1.000000 12 AAGAGACCGGCADGCCTAGCTDCG 1.000000 13 AAGAGACCGGCADATTTGACTITA 2.000000 14 AAGAGACCGGCAIGCCTAGCTDCG 1.000000 15 AGAGGATCGGCADGCTTAGCTITA 1.000000 16 AGAGGATGGGCADGCTTGGCTITA 1.000000 17 AGAGGATGGGCADGCTTGGTTITA 4.000000 18 AGAGGATGGGCADGCTTGATTITA 1.000000 19 AGAGGATGGGCADGCTCGGTGITA 4.000000 20 AGAGGATGGGCADGCCTAGCTDCG 1.000000 21 AGAGGATGGGCAIGCTTGGCTITA 6.000000 22 GAAGGGTGGGTCDATTTGACTITA 2.000000 23 GAAGGGTGTTTCDGCTTGGCTITA 1.000000 24 GAAGGGTGTTTCDGCTTGGTGITA 1.000000 25 GAAGGGTGTTTCDGCTCGGTGITA 16.000000 26 GAAGGGTGTTTCDGCCTAGCTDCG 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (2,16) DY02: (5,17) DY03: (14,17) DY04: (4,5) DY05: (2,9) DY06: (17,26) DY07: (3,9) DY08: (12,24) DY09: (10,21) DY10: (20,21) DY11: (19,21) DY12: (21,22) DY13: (9,13) DY14: (19,22) DY15: (2,7) DY16: (2,3) DY17: (2,6) DY18: (3,15) DY19: (1,21) DY20: (17,19) DY21: (4,13) DY22: (2,21) DY23: (11,19) DY24: (3,18) E101: (4,25) E102: (4,25) E103: (4,25) E104: (4,25) E105: (2,4) E106: (3,25) E107: (4,9) E108: (8,25) E109: (5,25) E110: (3,4) E111: (4,4) E112: (4,25) E113: (4,4) E114: (4,25) E115: (4,4) E116: (25,25) E117: (4,25) E118: (7,25) E119: (4,25) E120: (4,4) E121: (9,23) E122: (25,25) E123: (4,5) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 A A A G T A T G G G C A D G C T T G G C T I T A A G A G G A T [G] G G C A D G C T T [G] G C T I T A 0 DY02 A (A) A G (T) A T G G G C A D G C C T A G C T D C G A (G) A G (G) A T G G G C A D G C T T G G T T I T A 0 DY03 A [A] (G) (A) G A (C) (C) G G C A (I) G C C T A G C T D C G A [G] (A) (G) G A (T) (G) G G C A (D) G C T T G G T T I T A 0 DY04 A A A G T A T G G G C A D G C T C G G T G I T A A A A G T A T G G G C A D G C C T A G C T D C G 0 DY05 A A A G T A T G G G C A (D) G C T T G G C T I T A A A A G T A T G G G C A (I) G C C T A G C T D C G 0 DY06 (A) (G) A G G (A) T G (G) (G) (C) (A) D G C T T G G T T I T A (G) (A) A G G (G) T G (T) (T) (T) (C) D G C C T A G C T D C G 0 DY07 A A A G T A T G G G C A (D) G C T T G G T T I T A A A A G T A T G G G C A (I) G C C T A G C T D C G 0 DY08 A A G A G A C C G G C A D G C (C) T A G (C) T (D) (C) (G) G A A G G G T G T T T C D G C (T) T [G] G (T) G (I) (T) (A) 0 DY09 A (A) (G) G (T) A (C) (C) G G C A (D) G C C T A G C T D C G A (G) (A) G (G) A (T) (G) G G C A (I) G C T T G G C T I T A 0 DY10 A G A G G A T G G G C A (D) G C C T A G C T D C G A G A G G A T G G G C A (I) G C T T [G] G C T I T A 0 DY11 A G A G G A T G G G C A (D) G C T C G G T G I T A A G A G G A T G G G C A (I) G C T T G G C T I T A 0 DY12 A G A G G A T G G G C A I G C T T G G C T I T A G A A G G G T G G G T C D A T T T G A C T I T A 0 DY13 A A (A) (G) (T) A (T) (G) G G C A I G C C T A G C T D C G A A (G) (A) (G) A (C) (C) G G C A D A T T T G A C T I T A 0 DY14 A G A G G A T G G G C A D G C T C G G T G I T A G A A G G G T G G G T C D A T T T G A C T I T A 0 DY15 A A A G T A T G G G C A (D) G C T T G G C T I T A A A A G T A T G G G C A (I) G C T T G G T T I T A 0 DY16 A A A G T A T G G G C A D G C T T G G C T I T A A A A G T A T G G G C A D G C T T G G T T I T A 0 DY17 A A A G T A T G G G C A D (G) C T T G G C T I T A A A A G T A T G G G C A D (A) T T T G G C T I T A 0 DY18 A A A G T A T (G) G G C A D G C T T (G) G (T) T I T A A G A G G A T (C) G G C A D G C T T (A) G (C) T I T A 0 DY19 A (A) A G G A T G G G C A (D) (A) C T T G G C T I T A A (G) A G G A T G G G C A (I) (G) C T T G G C T I T A 0 DY20 A G A G G A T G G G C A [D] G C T T G G T T I T A A G A G G A T G G G C A D G C T C G G T G I T A 0 DY21 A A (A) (G) (T) A (T) (G) G G C A D G C T C G G T G I T A A A (G) (A) (G) A (C) (C) G G C A D A T T T G A C T I T A 0 DY22 A A A G T A T G G G C A D G C T T G G C T I T A A G A G G A T G G G C A [I] G C T T G G C T I T A 0 DY23 A A G A G A C C G G C A D G C T (T) G G T (T) I T A A G A G G A T G G G C A D G C T (C) G G T (G) I T A 0 DY24 A A A G T A T G G G C A D G C T T G (G) T T I T A A G A G G A T G G G C A D G C T T G (A) T T I T A 0 E101 A A A G T A T G G G C A D G C T C G G T G I T A G A A G G G T G T T T C D G C T C G G T G I T A 0 E102 A A A G T A T G G G C A D G C T C G G T G I T A G A A G G G T G T T T C D G C T C G G T G I T A 0 E103 A A A G T A T G G G C A D G C T C G G T G I T A G A A G G G T G T T T C D G C T C G G T G I T A 0 E104 A A A G T A T G G G C A D G C T C G G T G I T A G A A G G G T G T T T C D G C T C G G T G I T A 0 E105 A A A G T A T G G G C A D G C T T G G C T I T A A A A G T A T G G G C A D G C T C G G T G I T A 0 E106 A A A G T A T G G G C A D G C T (T) G G T (T) I T A G A A G G G T G T T T C D G C T (C) G G T (G) I T A 0 E107 A A A G T A T G G G C A (D) G C T C G G T G I T A A A A G T A T G G G C A (I) G C C T A G C T D C G 0 E108 A A A G T A T G G G C A (I) G C T C G G T G I T A G A A G G G T G T T T C (D) G C T C G G T G I T A 0 E109 (A) A A G (T) (A) T G (G) (G) (C) (A) D G C C T A G C T D C G (G) A A G (G) (G) T G (T) (T) (T) (C) D G C T C G G T G I T A 0 E110 A A A G T A T G G G C A D G C T T G G T T I T A A A A G T A T G G G C A D G C T C G G T G I T A 0 E111 A A A G T A T G G G C A D G C T C G G T G I T A A A A G T A T G G G C A D G C T C G G T G I T A 0 E112 A A A G T A T G G G C A D G C T C G G T G I T A G A A G G G T G T T T C D G C T C G G T G I T A 0 E113 A A A G T A T G G G C A D G C T C G G T G I T A A A A G T A T G G G C A D G C T C G G T G I T A 0 E114 A A A G T A T G G G C A D G C T C G G T G I T A G A A G G G T G T T T C D G C T C G G T G I T A 0 E115 A A A G T A T G G G C A D G C T C G G T G I T A A A A G T A T G G G C A D G C T C G G T G I T A 0 E116 G A A G G G T G T T T C D G C T C G G T G I T A G A A G G G T G T T T C D G C T C G G T G I T A 0 E117 A A A G T A T G G G C A D G C T C G G T G I T A G A A G G G T G T T T C D G C T C G G T G I T A 0 E118 A A A G T A T G G G C A (I) G C T (T) G G T (T) I T A G A A G G G T G T T T C (D) G C T (C) G G T (G) I T A 0 E119 A A A G T A T G G G C A D G C T C G G T G I T A G A A G G G T G T T T C D G C T C G G T G I T A 0 E120 A A A G T A T G G G C A D G C T C G G T G I T A A A A G T A T G G G C A D G C T C G G T G I T A 0 E121 A A A G T A T G G G C A (I) G C (C) T (A) G C T (D) (C) (G) G A A G G G T G T T T C (D) G C (T) T (G) G C T (I) (T) (A) 0 E122 G A A G G G T G T T T C D G C T C G G T G I T A G A A G G G T G T T T C D G C T C G G T G I T A 0 E123 A A A G T A T G G G C A D G C T C G G T G I T A A A A G T A T G G G C A D G C C T A G C T D C G 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 = = ? = = = ? = = = = = ? ? = = = = = = G = = G = = ? = = = ? = = = = = ? ? = = = = = 0 DY02 = (A) = = (T) = = ? = = = = = = = C = ? ? C = D C ? = (G) = = (G) = = ? = = = = = = = T = ? ? T = I T ? 0 DY03 = ? (G) (A) = = (C) (C) ? ? = = (I) = = C = ? = C = D C G = ? (A) (G) = = (T) (G) ? ? = = (D) = = T = ? = T = I T A 0 DY04 = = = = = = = ? = = = = = = = T C G ? T G I T A = = = = = = = ? = = = = = = = C T A ? C T D C G 0 DY05 = = = = = = = = = = = = (D) = = T = G = = = I T ? = = = = = = = = = = = = (I) = = C = A = = = D C ? 0 DY06 (A) (G) = = = (A) = ? (G) (G) (C) (A) = = = T = ? ? T = I T A (G) (A) = = = (G) = ? (T) (T) (T) (C) = = = C = ? ? C = D C G 0 DY07 = = = = = = = = = = = = (D) = = T = G = T = I T A = = = = = = = = = = = = (I) = = C = A = C = D C G 0 DY08 A ? G A = ? C ? G G ? A = = = (C) = ? ? (C) T (D) (C) (G) G ? A G = ? T ? T T ? C = = = (T) = ? ? (T) G (I) (T) (A) 0 DY09 = (A) (G) = (T) = (C) (C) = = = = (D) = = C = A = = = D C ? = (G) (A) = (G) = (T) (G) = = = = (I) = = T = G = = = I T ? 0 DY10 = = = = = ? = ? = = = = (D) = = C = ? = = = D C ? = = = = = ? = ? = = = = (I) = = T = ? = = = I T ? 0 DY11 = = = = = ? = = = = = = (D) = = = C = = T G = = = = = = = = ? = = = = = = (I) = = = T = = C T = = = 0 DY12 A G = = = A = = = = C A I G C = = = G ? ? ? ? ? G A = = = G = = = = T C D A T = = = A ? ? ? ? ? 0 DY13 = ? (A) (G) (T) = (T) (G) = = = = I G C C = A G = = D C G = ? (G) (A) (G) = (C) (C) = = = = D A T T = G A = = I T A 0 DY14 A G = = = A = = = = C A = G C = C ? ? T G = = = G A = = = G = = = = T C = A T = T ? ? C T = = = 0 DY15 = = = = ? = = = = = = = (D) = = = = = = C = = = = = = = = ? = = = = = = = (I) = = = = = = T = = = = 0 DY16 = = = = = = = = = = = = ? = = = = = = C = = = ? = = = = = = = = = = = = ? = = = = = = T = = = ? 0 DY17 = = = = = = = = = = = = = (G) C = = = = = = = = = = = = = = = = = = = = = = (A) T = = = = = = = = = 0 DY18 = A = = T = = (G) = = = = = = = = = (G) = (T) = = = = = G = = G = = (C) = = = = = = = = = (A) = (C) = = = = 0 DY19 = (A) = = = ? = = = = = = (D) (A) = = = = = = = = = = = (G) = = = ? = = = = = = (I) (G) = = = = = = = = = = 0 DY20 = = = = = ? = = = = = = ? = = = T = = = T = = = = = = = = ? = = = = = = ? = = = C = = = G = = = 0 DY21 = = (A) (G) (T) = (T) (G) = = = = = G C = C = G T G = = = = = (G) (A) (G) = (C) (C) = = = = = A T = T = A C T = = = 0 DY22 = A = = T = = = = = = = ? = = = = ? = = = = = = = G = = G = = = = = = = ? = = = = ? = = = = = = 0 DY23 = ? G A = ? C C = = = = = = = = (T) = = = (T) = = = = ? A G = ? T G = = = = = = = = (C) = = = (G) = = = 0 DY24 = A = = T = = = = = = = = = = = = = (G) = = = = = = G = = G = = = = = = = = = = = = = (A) = = = = = 0 E101 A = = = T A = = G G C A = = = = = = = = = = = = G = = = G G = = T T T C = = = = = = = = = = = = 0 E102 A = = = T A = = G G C A = = = = = ? ? = = = = = G = = = G G = = T T T C = = = = = ? ? = = = = = 0 E103 A = = = T A = = G G C A = = = = = = = = = = = = G = = = G G = = T T T C = = = = = = = = = = = = 0 E104 A = = = T A = = G G C A = = = = = = = = = = = = G = = = G G = = T T T C = = = = = = = = = = = = 0 E105 = = = = = = = = = = = = = = = = T = = C T = = = = = = = = = = = = = = = = = = = C = = T G = = = 0 E106 A = = = T A = = G G C A = = = = (T) = = = (T) = = = G = = = G G = = T T T C = = = = (C) = = = (G) = = = 0 E107 = = = = = = = = = = = = (D) = = T C G = T G I T A = = = = = = = = = = = = (I) = = C T A = C T D C G 0 E108 A = = = T A = = G G C A (I) = = = = = = = = = = = G = = = G G = = T T T C (D) = = = = = = = = = = = 0 E109 (A) = = = (T) (A) = = (G) (G) (C) (A) = = = C T A = C T D C G (G) = = = (G) (G) = = (T) (T) (T) (C) = = = T C G = T G I T A 0 E110 = = = = = = = = = = = = = = = = T = = = T = = = = = = = = = = = = = = = = = = = C = = = G = = = 0 E111 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E112 A = = = T A = = G G C A = = = = = ? = = = = = = G = = = G G = = T T T C = = = = = ? = = = = = = 0 E113 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E114 A = = = T A = = G G C A = = = = = = ? = = = = = G = = = G G = = T T T C = = = = = = ? = = = = = 0 E115 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E116 = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = 0 E117 A = = = T A = ? G G C A = = = = = = = = = = = = G = = = G G = ? T T T C = = = = = = = = = = = = 0 E118 A = = = T A = ? ? ? C A (I) = = = (T) ? = = (T) = = = G = = = G G = ? ? ? T C (D) = = = (C) ? = = (G) = = = 0 E119 A = = = T A = = ? ? C A = = = = = = = = = = = = G = = = G G = = ? ? T C = = = = = = = = = = = = 0 E120 ? = = = = = = ? ? ? = = = = = = = = = = = = = = ? = = = = = = ? ? ? = = = = = = = = = = = = = = 0 E121 A = = = T A = = G G C A (I) = = (C) = (A) = = = (D) (C) (G) G = = = G G = = T T T C (D) = = (T) = (G) = = = (I) (T) (A) 0 E122 = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = 0 E123 = = = = = = = = = = = = = = = T C G = T G I T ? = = = = = = = = = = = = = = = C T A = C T D 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 = = ? = = = ? = = = = = ? ? = = = = = = 0.72 = = 0.72 = = ? = = = = = = = 1.00 = ? ? 1.00 = 1.00 1.00 ? = ? 0.58 0.58 = = 0.58 0.58 ? ? = = 0.54 = = 1.00 = ? = 1.00 = 1.00 1.00 1.00 = = = = = = = ? = = = = = = = 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = 0.69 = = 1.00 = 1.00 = = = 1.00 1.00 ? 0.77 0.77 = = = 0.77 = ? 0.77 0.77 0.77 0.77 = = = 1.00 = ? ? 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = = 0.66 = = 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 ? 1.00 1.00 = ? 1.00 ? 1.00 1.00 ? 1.00 = = = 0.80 = ? ? 0.80 1.00 0.80 0.80 0.80 = 0.65 0.62 = 0.57 = 0.74 0.73 = = = = 0.60 = = 1.00 = 1.00 = = = 1.00 1.00 ? = = = = = ? = ? = = = = 0.59 = = 1.00 = ? = = = 1.00 1.00 ? = = = = = ? = = = = = = 0.85 = = = 1.00 = = 1.00 1.00 = = = 1.00 1.00 = = = 1.00 = = = = 1.00 1.00 0.99 1.00 1.00 = = = 1.00 ? ? ? ? ? = ? 0.86 0.86 0.86 = 0.86 0.86 = = = = 0.95 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 0.99 0.99 = = = 0.99 = = = = 0.99 0.99 = 1.00 1.00 = 1.00 ? ? 1.00 1.00 = = = = = = = ? = = = = = = = 0.56 = = = = = = 0.99 = = = = = = = = = = = = = = = = ? = = = = = = 1.00 = = = ? = = = = = = = = = = = = = 0.89 1.00 = = = = = = = = = = 0.93 = = 0.93 = = 0.72 = = = = = = = = = 0.77 = 0.69 = = = = = 0.86 = = = ? = = = = = = 0.84 0.76 = = = = = = = = = = = = = = = ? = = = = = = ? = = = 1.00 = = = 1.00 = = = = = 0.90 0.90 0.90 = 0.90 0.90 = = = = = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = = = 0.93 = = 0.93 = = = = = = = ? = = = = ? = = = = = = = ? 1.00 1.00 = ? 1.00 0.99 = = = = = = = = 0.55 = = = 0.55 = = = = 1.00 = = 1.00 = = = = = = = = = = = = = 0.65 = = = = = 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = = = ? ? = = = = = 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 = = = 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = = 0.79 = = = 0.79 = = = = = = = = = = = = = = = 0.86 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 0.85 = = = = = = = = = = = 0.63 = = = 0.63 0.63 = = 0.63 0.63 0.63 0.63 = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = 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 = = = 0.84 ? = = 0.84 = = = 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 = = 0.52 = 0.52 = = = 0.52 0.52 0.52 = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 ? END PHASEPROBS