************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 bglap.phase.inp bglap.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST bglap.phase.out_freqs : haplotype frequency estimates bglap.phase.out_pairs : most likely haplotype pairs for each individual bglap.phase.out_recom : estimates of recombination parameters bglap.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 8 Positions of loci: 313 327 3923 5355 6019 7660 9351 9499 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file bglap.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TATACGGC 9.000000 2 TATATGGT 1.000000 3 TATGCGGC 20.000000 4 TGTACGGC 10.000000 5 TGTACGGT 4.000000 6 TGTACAGC 3.000000 7 TGTATGGC 5.000000 8 TGTATGGT 5.000000 9 TGTGCGGC 1.000000 10 TGCGCGGC 1.000000 11 CACACGGC 10.000000 12 CACACGCC 6.000000 13 CGTACGGC 2.000000 14 CGTACAGC 16.000000 15 CGTGCGGC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,3) DY02: (1,4) DY03: (3,7) DY04: (1,6) DY05: (3,8) DY06: (3,7) DY07: (1,4) DY08: (11,14) DY09: (3,6) DY10: (4,4) DY11: (1,3) DY12: (1,3) DY13: (1,6) DY14: (10,14) DY15: (14,14) DY16: (11,14) DY17: (3,8) DY18: (1,11) DY19: (11,11) DY20: (4,8) DY21: (3,8) DY22: (4,14) DY23: (4,4) DY24: (3,11) E101: (3,13) E102: (11,14) E103: (7,8) E104: (14,15) E105: (3,14) E106: (3,12) E107: (14,14) E108: (11,14) E109: (3,3) E110: (3,11) E111: (3,5) E112: (3,7) E113: (3,14) E114: (5,14) E115: (12,13) E116: (4,7) E117: (5,9) E118: (4,11) E119: (12,12) E120: (12,14) E121: (1,5) E122: (3,12) E123: (2,14) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 T A T A C [G] G C T A T G C G G C 0 DY02 T A T A C [G] G C T G T A C [G] G C 0 DY03 T (A) T G C G G C T (G) T A T G G C 0 DY04 T (A) T A C G G C T (G) T A C A G C 0 DY05 T (A) T G C G G (C) T (G) T A T G G (T) 0 DY06 T (A) T G C G G C T (G) T A T G G C 0 DY07 T A T A C G G C T G T A C G G C 0 DY08 C A C A C (G) G C C G T A C (A) G C 0 DY09 T (A) T G C (G) G C T (G) T A C (A) G C 0 DY10 T G T A C G G C T G T A C G G C 0 DY11 T A T A C G G C T A T G C G G C 0 DY12 T A T A C G G C T A T G C G G C 0 DY13 T (A) T A C G G C T (G) T A C A G C 0 DY14 (T) G (C) (G) C G G C (C) G (T) (A) C A G C 0 DY15 C G T A C A G C C G T A C A G C 0 DY16 C A C A C (G) G C C G T A C (A) G C 0 DY17 T (A) T (G) C G G (C) T (G) T (A) T G G (T) 0 DY18 T A T A C G G C C A C A C G G C 0 DY19 C A C A C G G C C A C A C G G C 0 DY20 T G T A (C) G G C T G T A (T) G G T 0 DY21 T (A) T (G) C G G (C) T (G) T (A) T G G (T) 0 DY22 (T) G T A C G G C (C) G T A C A G C 0 DY23 T G T A C G G C T G T A C G G C 0 DY24 T A T (G) C G G C C A C (A) C G G C 0 E101 (T) (A) T (G) C G G C (C) (G) T (A) C G G C 0 E102 C A C A C (G) G C C G T A C (A) G C 0 E103 T [G] T A T G G C T [G] T A T G G T 0 E104 C G T (A) C A G C C G T (G) C G G C 0 E105 (T) (A) T G C G G C (C) (G) T A C A G C 0 E106 (T) A (T) (G) C G (G) C (C) A (C) (A) C G (C) C 0 E107 C G T A C A G C C G T A C A G C 0 E108 C A C A C (G) G C C G T A C (A) G C 0 E109 T A T G C G G C T A T G C G G C 0 E110 T A T (G) C G G C C A C (A) C G G C 0 E111 T (A) T (G) C G G (C) T (G) T (A) C G G (T) 0 E112 T (A) T G C G G C T (G) T A T G G C 0 E113 (T) (A) T G C G G C (C) (G) T A C A G C 0 E114 (T) G T A C (G) G (T) (C) G T A C (A) G (C) 0 E115 C A C A C G (C) C C G T A C [G] (G) C 0 E116 T G T A C [G] G C T G T A T G G C 0 E117 T G T (A) C G G T T G T (G) C G G C 0 E118 T (G) T A C G G C C (A) C A C G G C 0 E119 C A C A C G C C C A C A C G C C 0 E120 C (A) (C) A C (G) (C) C C (G) (T) A C (A) (G) C 0 E121 T (A) T A C G G C T (G) T A C G G T 0 E122 (T) A (T) (G) C G (G) C (C) A (C) (A) C G (C) C 0 E123 (T) (A) T A T G G (T) (C) (G) T A C A G (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 = ? = = = = = G = ? = = 0 DY02 = A = = = ? = = = G = = = ? = = 0 DY03 = (A) = G C = = = = (G) = A T = = = 0 DY04 = (A) = = = G = = = (G) = = = A = = 0 DY05 = (A) = G C = = (C) = (G) = A T = = (T) 0 DY06 = (A) = G C = = = = (G) = A T = = = 0 DY07 = A = = = = = = = G = = = = = = 0 DY08 = A C = = (G) = = = G T = = (A) = = 0 DY09 = (A) = G = (G) = = = (G) = A = (A) = = 0 DY10 = = = = = = = = = = = = = = = = 0 DY11 = = = A = = = = = = = G = = = = 0 DY12 = = = A = = = = = = = G = = = = 0 DY13 = (A) = = = G = = = (G) = = = A = = 0 DY14 (T) = (C) (G) = G = = (C) = (T) (A) = A = = 0 DY15 = = = = = = = = = = = = = = = = 0 DY16 = A C ? ? (G) ? ? = G T ? ? (A) ? ? 0 DY17 = (A) = (G) C ? = (C) = (G) = (A) T ? = (T) 0 DY18 T = T = = = = = C = C = = = = = 0 DY19 = = = = = = = = = = = = = = = = 0 DY20 = = = = (C) = = C = = = = (T) = = T 0 DY21 = (A) = (G) C = = (C) = (G) = (A) T = = (T) 0 DY22 (T) = = = = G = = (C) = = = = A = = 0 DY23 = = = = = = = = = = = = = = = = 0 DY24 T = T (G) = = = = C = C (A) = = = = 0 E101 (T) (A) = (G) ? ? ? ? (C) (G) = (A) ? ? ? ? 0 E102 = A C = = (G) = = = G T = = (A) = = 0 E103 ? ? = = = = = C ? ? = = = = = T 0 E104 = = = (A) = A ? ? = = = (G) = G ? ? 0 E105 (T) (A) ? G = G = = (C) (G) ? A = A = = 0 E106 (T) = (T) (G) = = (G) = (C) = (C) (A) = = (C) = 0 E107 = = = = = = = = = = = = = = = = 0 E108 = A C = ? (G) ? ? = G T = ? (A) ? ? 0 E109 = = = = = ? = = = = = = = ? = = 0 E110 T = T (G) = = ? ? C = C (A) = = ? ? 0 E111 = (A) = (G) = = = (C) = (G) = (A) = = = (T) 0 E112 = (A) = G C = = = = (G) = A T = = = 0 E113 (T) (A) = G = G = = (C) (G) = A = A = = 0 E114 (T) = = = ? (G) = (T) (C) = = = ? (A) = (C) 0 E115 = A C = = ? (C) = = G T = = ? (G) = 0 E116 = = = = C ? ? ? = = = = T ? ? ? 0 E117 = = = (A) ? ? = T = = = (G) ? ? = C 0 E118 T (G) T = = ? ? ? C (A) C = = ? ? ? 0 E119 = = = = = = = = = = = = = = = = 0 E120 = (A) (C) = = (G) (C) = = (G) (T) = = (A) (G) = 0 E121 = (A) = = = = = C = (G) = = = = = T 0 E122 (T) = (T) (G) = = (G) = (C) = (C) (A) = = (C) = 0 E123 (T) (A) = = T G = (T) (C) (G) = = C 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 = ? = = = 1.00 = = = ? = = = 0.68 = 0.92 0.91 = = = = 0.50 = = = 1.00 = = = 0.59 = 0.90 0.94 = = 0.75 = 0.68 = 0.92 0.91 = = = = 1.00 = = = = = = = 0.97 0.97 = = 0.69 = = = 0.66 = 0.92 = 0.90 = = = = = = = = = = = = = 1.00 = = = = = = = 1.00 = = = = = 0.50 = = = 1.00 = = 0.54 = 0.61 0.89 = 0.93 = = = = = = = = = = = 0.98 0.98 ? ? 0.68 ? ? = 0.58 = 0.89 0.94 ? = 0.78 0.95 = 1.00 = = = = = = = = = = = = = = = = = 0.69 = = 1.00 = 0.59 = 0.90 0.94 = = 0.76 0.61 = = = = 1.00 = = = = = = = = = = 0.97 = 0.98 0.68 = = = = 0.88 0.89 = 0.68 ? ? ? ? = 0.97 0.97 = = 0.69 = = ? ? = = = = = 1.00 = = = 0.87 = 1.00 ? ? 0.61 0.65 ? 0.91 = 0.93 = = 0.81 = 0.83 0.87 = = 0.79 = = = = = = = = = = 0.97 0.97 = ? 0.71 ? ? = = = = = ? = = 0.98 = 0.99 0.67 = = ? ? = 0.79 = 0.79 = = = 0.73 = 0.68 = 0.93 0.91 = = = 0.65 0.69 = 0.92 = 0.92 = = 0.74 = = = ? 0.85 = 0.76 = 0.97 0.98 = = ? 0.62 = = = = = 1.00 ? ? ? = = = 0.56 ? ? = 1.00 0.93 0.89 0.97 = = ? ? ? = = = = = = = = = 0.79 0.82 = = 0.89 0.81 = = 0.51 = = = = = 1.00 0.81 = 0.83 0.88 = = 0.79 = 0.68 0.65 = = 0.92 0.92 = 0.81 END PHASEPROBS