************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /net/nickerson/lims/bin/phase/PHASE2 -d1 foxa2.phase.inp foxa2.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST foxa2.phase.out_freqs : haplotype frequency estimates foxa2.phase.out_pairs : most likely haplotype pairs for each individual foxa2.phase.out_recom : estimates of recombination parameters foxa2.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 13 Positions of loci: 957 2748 3510 4056 4643 4770 5699 6110 6149 6160 6392 6546 6652 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file foxa2.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ACCATTAGACCGA 1.000000 2 ACCATCAAACTCC 3.000000 3 ACCACCAAACTCC 56.000000 4 ACCACCGGTCCCC 1.000000 5 ACCGTTGGACCCC 4.000000 6 ACCGTTGGTCCCC 4.000000 7 ATCGTCAGAACGA 6.000000 8 GCCATTAGACCGA 2.000000 9 GCCGTTAGACCCC 1.000000 10 GCCGTTGGACCCC 3.000000 11 GCCGTTGAACCCC 1.000000 12 GCTGTTGGTCCCC 11.000000 13 GCTGTCAAACTCC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,5) DY02: (5,8) DY03: (2,7) DY04: (7,12) DY05: (6,12) DY06: (2,3) DY07: (10,12) DY08: (3,12) DY09: (3,11) DY10: (2,12) DY11: (4,10) DY12: (7,12) DY13: (3,6) DY14: (7,8) DY15: (3,5) DY16: (10,12) DY17: (9,13) DY18: (3,6) DY19: (3,5) DY20: (3,12) DY21: (3,12) DY22: (6,7) DY23: (3,12) DY24: (7,12) E101: (3,3) E102: (3,3) E103: (3,3) E104: (3,3) E105: (3,3) E106: (3,3) E107: (3,3) E108: (3,3) E109: (3,3) E110: (3,3) E111: (3,3) E112: (3,3) E113: (3,3) E114: (3,3) E115: (3,3) E116: (3,3) E117: (3,3) E118: (3,3) E119: (3,3) E120: (3,3) E121: (3,3) E122: (3,3) E123: (3,3) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 A C C A T T A G A C C [G] A A C C G T T G G A C C C C 0 DY02 (A) C C G T T [G] G [A] C C C C (G) C C A T T A G A C C G A 0 DY03 A C C A T C A A A C T C C A T C G T C A G A A C G A 0 DY04 A T C G T C A G A A C G A G C T G T T G G T C C C C 0 DY05 A C C G T T G G T C C C C G C T G T T G G T C C C C 0 DY06 A C C A T C A A A C T C C A C C A C C A A A C T C C 0 DY07 G C C G T T G G A C C C C G C T G T T G G T C C C C 0 DY08 A C C A C C A A A C T C C G C T G T T G G T C C C C 0 DY09 A C C A C C A A A C T C C G C C G T T [G] A A C C C C 0 DY10 A C C A T C A A A C T C C G C T G T T G G T C C C C 0 DY11 A C C A C C G G T C C C C G C C G T T G G A C C C C 0 DY12 A T C G T C A G A A C G A G C T G T T G G T C C C C 0 DY13 A C C A C C A A A C T C C A C C G T T G G T C C C C 0 DY14 (A) T C G T C A G A A C G A (G) C C A T T A G A C C G A 0 DY15 A C C A C C A A A C T C C A C C G T T G G A C C C C 0 DY16 G C C G T T G G A C C C C G C T G T T G G T C C C C 0 DY17 G C C G T T A G A C C C C G C T G T C A A A C T C C 0 DY18 A C C A C C A A A C T C C A C C G T T G G T C C C C 0 DY19 A C C A C C A A A C T C C A C C G T T G G A C C C C 0 DY20 A C C A C C A A A C T C C G C T G T T G G T C C C C 0 DY21 A C C A C C A A A C T C C G C T G T T G G T C C C C 0 DY22 A C C G T T G G T C C C C A T C G T C A G A A C G A 0 DY23 A C C A C C A A A C T C C G C T G T T G G T C C C C 0 DY24 A T C G T C A G A A C G A G C T G T T G G T C C C C 0 E101 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E102 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E103 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E104 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E105 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E106 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E107 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E108 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E109 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E110 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E111 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E112 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E113 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E114 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E115 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E116 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E117 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E118 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E119 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E120 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E121 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E122 A C C A C C A A A C T C C A C C A C C A A A C T C C 0 E123 A C C A C C A A A C T C C A C C A C C A A A C T C 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 = ? ? ? ? = = C C (G) = = A = ? ? ? ? = = G A 0 DY03 = C = ? = = ? A = C ? ? ? = T = ? = = ? G = A ? ? ? 0 DY04 A T C = = C A = A A = G A G C T = = T G = T C = C C 0 DY05 A = C ? = = = = = = = = = G = T ? = = = = = = = = = 0 DY06 = = = ? T = = ? ? ? = = = = = = ? C = = ? ? ? = = = 0 DY07 = = C = = = = = A = = = = = = T = = = = = T = = = = 0 DY08 A = C ? C C ? A A = ? ? ? G = T ? T T ? G T = ? ? ? 0 DY09 A = = A C C ? = = = T = = G = = G T T ? = = = C = = 0 DY10 A = C A = C A A A = T = = G = T G = T G G T = C = = 0 DY11 A = = A C C = = T = ? = = G = = G T T = = A = ? = = 0 DY12 A T C = = C A = A A = G A G C T = = T G = T C = C C 0 DY13 = = = A C C A ? A = T = = = = = G T T G ? T = C = = 0 DY14 (A) T = G = C = = = A = = = (G) C = A = T = = = C = = = 0 DY15 = = = A C C A A = = T = = = = = G T T G G = = C = = 0 DY16 = = C = = = = = A = = = = = = T = = = = = T = = = = 0 DY17 = = C = = T = G = = C = = = = T = = C = A = = T = = 0 DY18 = = = A C C A A A = T = = = = = G T T G G T = C = = 0 DY19 = = = A C C A A = = T = = = = = G T T G G = = C = = 0 DY20 A = C A C C A A A = T = = G = T G T T G G T = C = = 0 DY21 A = C A C C A A A = T = = G = T G T T G G T = C = = 0 DY22 = C = = = T G = T C = C C = T = = = C A = A A = G A 0 DY23 A = C A C C ? A A = ? ? ? G = T G T T ? G T = ? ? ? 0 DY24 A T C = = C ? = A A ? ? ? G C T = = T ? = T C ? ? ? 0 E101 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E102 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E103 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E104 = = = ? = = = ? ? ? = = = = = = ? = = = ? ? ? = = = 0 E105 = = = = = = ? ? ? ? = = = = = = = = = ? ? ? ? = = = 0 E106 = = = = = = ? = = = ? ? ? = = = = = = ? = = = ? ? ? 0 E107 = = = = = = ? = = = ? ? ? = = = = = = ? = = = ? ? ? 0 E108 = = = ? = = = = = = = = = = = = ? = = = = = = = = = 0 E109 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E110 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E111 = = = = = = = = = = ? ? ? = = = = = = = = = = ? ? ? 0 E112 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E113 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E114 = = = ? = = = ? ? ? = = = = = = ? = = = ? ? ? = = = 0 E115 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E116 = = ? = = = = = = = = = = = = ? = = = = = = = = = = 0 E117 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E118 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E119 = = = ? = = = = = = = = = = = = ? = = = = = = = = = 0 E120 = = = = = = ? = = = ? ? ? = = = = = = ? = = = ? ? ? 0 E121 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E122 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E123 = = = = = = = = = = = = = = = = = = = = = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = ? = 1.00 = = ? = = = ? ? ? 0.53 = = 1.00 = ? ? ? ? = = 1.00 1.00 = 1.00 = ? = = ? 1.00 = 1.00 ? ? ? 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 ? = = = = = = = = = = = = ? 1.00 = = ? ? ? = = = = = 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 = = 0.99 = 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 1.00 1.00 1.00 ? 1.00 = 1.00 = = 0.78 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 = = 0.98 = 0.94 = = 1.00 = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 = = = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 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