************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 dombg.phase.inp dombg.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST dombg.phase.out_freqs : haplotype frequency estimates dombg.phase.out_pairs : most likely haplotype pairs for each individual dombg.phase.out_recom : estimates of recombination parameters dombg.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 17 Positions of loci: 638 3425 3572 4175 4230 4476 4645 7061 7279 7388 7476 7484 7497 12879 15732 16417 16520 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file dombg.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TACGCTATCCGTTTCCI 13.000000 2 TACGCTATCCGTTTCCD 3.000000 3 TACGCTATCCGTTTCTI 4.000000 4 TACGCTATCCGTCTCCD 1.000000 5 TGCGTTACCCGTTCCCI 4.000000 6 TGGGTCACTTATCCCCD 1.000000 7 TGGGTCGCTTATCCCCI 5.000000 8 TGGGTCGCTTATCCCCD 6.000000 9 TGGTCCGCCTATCCCCI 1.000000 10 CGCGTTACCCGTTCCCI 1.000000 11 CGGGTCGCCTATCCCCI 1.000000 12 CGGGTCGCCTATCCCCD 3.000000 13 CGGGTCGCCTATCCGCI 1.000000 14 CGGGTCGCTTATCCCCI 7.000000 15 CGGGTCGCTTATCCCCD 24.000000 16 CGGGTCGCTTATCCCTI 4.000000 17 CGGGTCGCTTATCCGCI 4.000000 18 CGGGTCGCTTACCCCCD 4.000000 19 CGGGTCGCTTACCCGCI 3.000000 20 CGGTCCGCCTATCCGCI 4.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,1) DY02: (7,15) DY03: (14,20) DY04: (15,20) DY05: (10,12) DY06: (8,9) DY07: (7,15) DY08: (3,8) DY09: (7,13) DY10: (7,12) DY11: (5,7) DY12: (1,11) DY13: (5,14) DY14: (5,20) DY15: (14,15) DY16: (1,6) DY17: (8,15) DY18: (8,8) DY19: (1,1) DY20: (12,20) DY21: (14,14) DY22: (15,15) DY23: (14,15) DY24: (8,15) E101: (1,15) E102: (15,18) E103: (16,18) E104: (1,19) E105: (15,18) E106: (1,15) E107: (1,15) E108: (15,16) E109: (15,15) E110: (15,16) E111: (15,17) E112: (1,5) E113: (1,17) E114: (3,15) E115: (15,19) E116: (2,19) E117: (4,15) E118: (1,17) E119: (3,15) E120: (2,18) E121: (2,15) E122: (14,17) E123: (3,16) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 T A C G C T A T C C G T T T C C I T A C G C T A T C C G T T T C C I 0 DY02 (T) G G G T C G C T T A T C C C C I (C) G G G T C G C T T A T C C C C D 0 DY03 C G G G T C G C T T A T C C C C I C G G T C C G C C T A T C C G C I 0 DY04 C G G G T C G C T T A T C C C C D C G G T C C G C C T A T C C G C I 0 DY05 C G C G T T A C C C G T T C C C (I) C G G G T C G C C T A T C C C C (D) 0 DY06 T G G G T C G C T T A T C C C C (D) T G G T C C G C C T A T C C C C (I) 0 DY07 (T) G G G T C G C T T A T C C C C I (C) G G G T C G C T T A T C C C C D 0 DY08 T A C G C T A T C C G T T T C T I T G G G T C G C T T A T C C C C D 0 DY09 T G G G T C G C (T) T A T C C (C) C I C G G G T C G C (C) T A T C C (G) C I 0 DY10 T G G G T C G C (T) T A T C C C C (I) C G G G T C G C (C) T A T C C C C (D) 0 DY11 T G C G T T A C C C G T T C C C I T G G G T C G C T T A T C C C C I 0 DY12 T A C G C T A T C C G T T T C C I C G G G T C G C C T A T C C [C] C I 0 DY13 (T) G C G T T A C C C G T T C C C I (C) G G G T C G C T T A T C C C C I 0 DY14 T G C G T T A C C C G T T C C C I C G G T C C G C C T A T C C G C I 0 DY15 C G G G T C G C T T A T C C C C I C G G G T C G C T T A T C C C C D 0 DY16 T A C G C T A T C C G T T T C C (I) T G G G T C A C T T A T C C C C (D) 0 DY17 T G G G T C G C T T A T C C C C D C G G G T C G C T T A T C C C C D 0 DY18 T G G G T C G C T T A T C C C C D T G G G T C G C T T A T C C C C D 0 DY19 T A C G C T A T C C G T T T C C I T A C G C T A T C C G T T T C C I 0 DY20 C G G G T C G C C T A T C C C C (D) C G G T C C G C C T A T C C [G] C (I) 0 DY21 C G G G T C G C T T A T C C C C I C G G G T C G C T T A T C C C C I 0 DY22 C G G G T C G C T T A T C C C C D C G G G T C G C T T A T C C C C D 0 DY23 [C] G G G T C G C T T A T C C C C I [C] G G G T C G C T T A T C C C C D 0 DY24 T G G G T C G C T T A T C C C C D C G G G T C G C T T A T C C C C D 0 E101 T A C G C T A T C C G T T T C C (I) C G G G T C G C T T A T C C C C (D) 0 E102 C G G G T C G C T T A T C C C C D C G G G T C G C T T A C C C C C D 0 E103 C G G G T C G C T T A (T) C C C T I C G G G T C G C T T A (C) C C C C D 0 E104 T A C G C T A T C C G T T T (C) C I C G G G T C G C T T A C C C (G) C I 0 E105 C G G G T C G C T T A T C C C C D C G G G T C G C T T A C C C C C D 0 E106 T A C G C T A T C C G T T T C C (I) C G G G T C G C T T A T C C C C (D) 0 E107 T A C G C T A T C C G T T T C C (I) C G G G T C G C T T A T C C C C (D) 0 E108 C G G G T C G C T T A T C C C C D C G G G T C G C T T A T C C C T I 0 E109 C G G G T C G C T T A T C C C C D C G G G T C G C T T A T C C C C D 0 E110 C G G G T C G C T T A T C C C C D C G G G T C G C T T A T C C C T I 0 E111 C G G G T C G C T T A T C C C C D C G G G T C G C T T A T C C G C I 0 E112 T A C G C T A T C C G T T T C C I T G C G T T A C C C G T T C C C I 0 E113 T A C G C T A T C C G T T T (C) C I C G G G T C G C T T A T C C (G) C I 0 E114 T A C G C T A T C C G T T T C (T) (I) C G G G T C G C T T A T C C C (C) (D) 0 E115 C G G G T C G C T T A (T) C C C C D C G G G T C G C T T A (C) C C G C I 0 E116 T A C G C T A T C C G T T T (C) C (D) C G G G T C G C T T A C C C (G) C (I) 0 E117 T A C G C T A T C C G T C T C C D C G G G T C G C T T A T C C C C D 0 E118 T A C G C T A T C C G T T T (C) C I C G G G T C G C T T A T C C (G) C I 0 E119 T A C G C T A T C C G T T T C (T) (I) C G G G T C G C T T A T C C C (C) (D) 0 E120 T A C G C T A T C C G T T T C C D C G G G T C G C T T A C C C C C D 0 E121 T A C G C T A T C C G T T T C C D C G G G T C G C T T A T C C C C D 0 E122 C G G G T C G C T T A T C C C C I C G G G T C G C T T A T C C G C I 0 E123 T A C G C T A T C C G T T T C T I C G G G T C G C T T A T C C C T 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY02 (T) = = = = = = = = = = = = = = = I (C) = = = = = = = = = = = = = = = D 0 DY03 = = = G T = = = T = = = = = C = = = = = T C = = = C = = = = = G = = 0 DY04 = = = G T = = = T = = = = ? C = D = = = T C = = = C = = = = ? G = I 0 DY05 = = C = = T A = = C G = T = = = (I) = = G = = C G = = T A = C = = = (D) 0 DY06 = = = G T = = = T = = = = = = = (D) = = = T C = = = C = = = = = = = (I) 0 DY07 (T) = = = = = = = = = = = = = = = I (C) = = = = = = = = = = = = = = = D 0 DY08 = A C = C ? A T C C G = T T = T I = G G = T ? G C T T A = C C = C D 0 DY09 T = = = = = = = (T) = = = = = (C) = = C = = = = = = = (C) = = = = = (G) = = 0 DY10 T = = = = = = = (T) = = = = = = = (I) C = = = = = = = (C) = = = = = = = (D) 0 DY11 = = C = = T A = C C G = T = = = = = = G = = C G = T T A = C = = = = 0 DY12 T A C = C T A T = C G = T T ? = = C G G = T C G C = T A = C C ? = = 0 DY13 (T) = C = = T A = C C G = T = = = = (C) = G = = C G = T T A = C = = = = 0 DY14 T = C G T T A = = C G = T = C = = C = G T C C G = = T A = C = G = = 0 DY15 = = = = = = = = = = = = = = = = I = = = = = = = = = = = = = = = = D 0 DY16 = A C = C T = T C C G = T T = = (I) = G G = T C = C T T A = C C = = (D) 0 DY17 T ? = = = = = = = = = = = = = = = C ? = = = = = = = = = = = = = = = 0 DY18 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY19 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY20 = = = G T = = = = = = = = = ? = (D) = = = T C = = = = = = = = = ? = (I) 0 DY21 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY22 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY23 ? = = = = = = = = = = = = = = = I ? = = = = = = = = = = = = = = = D 0 DY24 T = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = 0 E101 T A C = C T A T C C G = T T = = (I) C G G = T C G C T T A = C C = = (D) 0 E102 = = = = = = = = = = = T = ? = = = = = = = = = = = = = = C = ? = = = 0 E103 = = = = = = = = = = = (T) = = = T I = = = = = = = = = = = (C) = = = C D 0 E104 ? A C = C T A T C C G T T T (C) = = ? G G = T C G C T T A C C C (G) = = 0 E105 = = = = = = = = = = = T = = = = = = = = = = = = = = = = C = = = = = 0 E106 T A C = C T A T C C G = T T = = (I) C G G = T C G C T T A = C C = = (D) 0 E107 T A C = C T A T C C G = T T = = (I) C G G = T C G C T T A = C C = = (D) 0 E108 = = = = = = = = = = = = = = = C D = = = = = = = = = = = = = = = T I 0 E109 = = ? = = = = = = = = = = ? = = = = = ? = = = = = = = = = = ? = = = 0 E110 = = = = = = = = = = = = = = = C D = = = = = = = = = = = = = = = T I 0 E111 = = = = = = = = = = = = = = C = D = = = = = = = = = = = = = = G = I 0 E112 = A = = C = = T = = = = = ? ? = = = G = = T = = C = = = = = ? ? = = 0 E113 T A C = C T A T C C G = T T (C) = = C G G = T C G C T T A = C C (G) = = 0 E114 T A C = C T A T C C G = T T = (T) (I) C G G = T C G C T T A = C C = (C) (D) 0 E115 = = = = = = = = = = = (T) = = C = D = = = = = = = = = = = (C) = = G = I 0 E116 T A C = C T A T C C G T T T (C) = (D) C G G = T C G C T T A C C C (G) = (I) 0 E117 T A C = C T A ? ? C G = = T = = = C G G = T C G ? ? T A = = C = = = 0 E118 T A C = C T A T C C G = T T (C) = = C G G = T C G C T T A = C C (G) = = 0 E119 T A C = C T A T C C G = T T = (T) (I) C G G = T C G C T T A = C C = (C) (D) 0 E120 T A C = C T A T C C G T T T ? = = C G G = T C G C T T A C C C ? = = 0 E121 T A C = C T A T C C G = T T = = = C G G = T C G C T T A = C C = = = 0 E122 = ? ? = = = = = = = = = = ? C = = = ? ? = = = = = = = = = = ? G = = 0 E123 T A C = ? ? ? T C C G = T T = = = C G G = ? ? ? C T T A = C C = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = = = = = = = = = = = = = = = 0.52 = = = = = = = = = = = = = = = 1.00 = = = 1.00 1.00 = = = 1.00 = = = = = 0.94 = = = = = 1.00 1.00 = = = 1.00 = = = = ? 0.95 = 0.95 = = 1.00 = = 1.00 1.00 = = 1.00 1.00 = 1.00 = = = 0.87 = = = 1.00 1.00 = = = 1.00 = = = = = = = 0.56 0.50 = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 = 1.00 ? 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 0.91 0.92 0.93 = = = = = = = 0.82 = = = = = 0.73 = = 0.96 = = = = = = = 0.85 = = = = = = = 0.60 = = 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 ? = = 0.88 = 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 = 0.99 = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 0.79 1.00 ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.96 0.96 = = = = = = = = = ? = 0.87 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = 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 = = 0.81 = = = = = = = = = = = 1.00 = ? = = = = = = = = = = = = = = 0.86 = = = 1.00 0.99 ? 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.98 1.00 1.00 0.86 = = = = = = = = = = = = = 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 = = 0.81 0.99 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 0.81 = = = = = = = = = = = = = = = 0.98 1.00 = = ? = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = 0.98 1.00 = = = = = = = = = = = = = = 0.99 = 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 0.75 = = 0.99 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 0.72 0.74 = = = = = = = = = = = 0.57 = = 1.00 = 0.98 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 0.60 = 0.55 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 0.75 = = 0.99 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 0.73 0.75 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 ? = = 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 = = = END PHASEPROBS