************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 plg1b.phase.inp plg1b.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST plg1b.phase.out_freqs : haplotype frequency estimates plg1b.phase.out_pairs : most likely haplotype pairs for each individual plg1b.phase.out_recom : estimates of recombination parameters plg1b.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 10 Positions of loci: 3027 3630 3702 4386 5013 5556 5580 5675 6082 7533 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file plg1b.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GTGCTTAAAC 89.000000 2 GTGCTGAAAC 1.000000 3 GTACTTAAAC 1.000000 4 GTACTGAAAC 26.000000 5 GCGCATAAAC 2.000000 6 GCGTATGGAT 16.000000 7 TTGCTTAAAC 19.000000 8 TTGCTTAATC 26.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,1) P002: (1,8) P003: (1,4) P004: (1,1) P005: (1,4) P006: (1,8) P007: (1,1) P008: (8,8) P009: (4,8) P010: (1,7) P011: (1,8) P012: (1,1) P013: (1,6) P014: (1,8) P015: (4,8) P016: (1,8) P017: (2,4) P018: (4,4) P019: (6,6) P020: (7,7) P021: (1,4) P022: (6,6) P023: (1,1) P024: (8,8) P025: (6,8) P026: (4,7) P027: (1,1) P028: (1,6) P029: (1,1) P030: (1,3) P031: (1,1) P032: (4,7) P033: (1,4) P034: (1,1) P035: (8,8) P036: (6,8) P037: (1,6) P038: (4,7) P039: (1,4) P040: (1,4) P041: (1,4) P042: (4,7) P043: (1,7) P044: (1,7) P045: (1,8) P046: (1,4) P047: (1,8) P048: (1,1) P049: (1,8) P050: (4,7) P051: (1,1) P052: (1,6) P053: (1,1) P054: (6,6) P055: (1,7) P056: (1,7) P057: (1,4) P058: (1,1) P059: (1,1) P060: (1,1) P061: (1,7) P062: (1,1) P063: (1,6) P064: (1,1) P065: (1,7) P066: (6,8) P067: (1,1) P068: (1,4) P069: (1,6) P070: (1,8) P071: (1,8) P072: (1,8) P073: (1,8) P074: (1,1) P075: (4,8) P076: (7,7) P077: (1,1) P078: (1,4) P079: (1,8) P080: (1,4) P081: (1,7) P082: (1,1) P083: (4,7) P084: (1,4) P085: (1,1) P086: (1,8) P087: (1,1) P088: (4,5) P089: (1,5) P090: (6,7) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 G T G C T T A A A C G T G C T T A A A C 0 P002 G T G C T T A A A C T T G C T T A A T C 0 P003 G T G C T T A A A C G T A C T G A A A C 0 P004 G T G C T T A A A C G T G C T T A A A C 0 P005 G T G C T T A A A C G T A C T G A A A C 0 P006 G T G C T T A A A C T T G C T T A A T C 0 P007 G T G C T T A A A C G T G C T T A A A C 0 P008 T T G C T T A A T C T T G C T T A A T C 0 P009 G T A C T G A A A C T T G C T T A A T C 0 P010 G T G C T T A A A C T T G C T T A A A C 0 P011 G T G C T T A A A C T T G C T T A A T C 0 P012 G T G C T T A A A C G T G C T T A A A C 0 P013 G T G C T T A A A C G C G T A T G G A T 0 P014 G T G C T T A A A C T T G C T T A A T C 0 P015 G T A C T G A A A C T T G C T T A A T C 0 P016 G T G C T T A A A C T T G C T T A A T C 0 P017 G T G C T G A A A C G T A C T G A A A C 0 P018 G T A C T G A A A C G T A C T G A A A C 0 P019 G C G T A T G G A T G C G T A T G G A T 0 P020 T T G C T T A A A C T T G C T T A A A C 0 P021 G T G C T T A A A C G T A C T G A A A C 0 P022 G C G T A T G G A T G C G T A T G G A T 0 P023 G T G C T T A A A C G T G C T T A A A C 0 P024 T T G C T T A A T C T T G C T T A A T C 0 P025 G C G T A T G G A T T T G C T T A A T C 0 P026 G T A C T G A A A C T T G C T T A A A C 0 P027 G T G C T T A A A C G T G C T T A A A C 0 P028 G T G C T T A A A C G C G T A T G G A T 0 P029 G T G C T T A A A C G T G C T T A A A C 0 P030 G T G C T T A A A C G T A C T T A A A C 0 P031 G T G C T T A A A C G T G C T T A A A C 0 P032 G T A C T G A A A C T T G C T T A A A C 0 P033 G T G C T T A A A C G T A C T G A A A C 0 P034 G T G C T T A A A C G T G C T T A A A C 0 P035 T T G C T T A A T C T T G C T T A A T C 0 P036 G C G T A T G G A T T T G C T T A A T C 0 P037 G T G C T T A A A C G C G T A T G G A T 0 P038 G T A C T G A A A C T T G C T T A A A C 0 P039 G T G C T T A A A C G T A C T G A A A C 0 P040 G T G C T T A A A C G T A C T G A A A C 0 P041 G T G C T T A A A C G T A C T G A A A C 0 P042 G T A C T G A A A C T T G C T T A A A C 0 P043 G T G C T T A A A C T T G C T T A A A C 0 P044 G T G C T T A A A C T T G C T T A A A C 0 P045 G T G C T T A A A C T T G C T T A A T C 0 P046 G T G C T T A A A C G T A C T G A A A C 0 P047 G T G C T T A A A C T T G C T T A A T C 0 P048 G T G C T T A A A C G T G C T T A A A C 0 P049 G T G C T T A A A C T T G C T T A A T C 0 P050 G T A C T G A A A C T T G C T T A A A C 0 P051 G T G C T T A A A C G T G C T T A A A C 0 P052 G T G C T T A A A C G C G T A T G G A T 0 P053 G T G C T T A A A C G T G C T T A A A C 0 P054 G C G T A T G G A T G C G T A T G G A T 0 P055 G T G C T T A A A C T T G C T T A A A C 0 P056 G T G C T T A A A C T T G C T T A A A C 0 P057 G T G C T T A A A C G T A C T G A A A C 0 P058 G T G C T T A A A C G T G C T T A A A C 0 P059 G T G C T T A A A C G T G C T T A A A C 0 P060 G T G C T T A A A C G T G C T T A A A C 0 P061 G T G C T T A A A C T T G C T T A A A C 0 P062 G T G C T T A A A C G T G C T T A A A C 0 P063 G T G C T T A A A C G C G T A T G G A T 0 P064 G T G C T T A A A C G T G C T T A A A C 0 P065 G T G C T T A A A C T T G C T T A A A C 0 P066 G C G T A T G G A T T T G C T T A A T C 0 P067 G T G C T T A A A C G T G C T T A A A C 0 P068 G T G C T T A A A C G T A C T G A A A C 0 P069 G T G C T T A A A C G C G T A T G G A T 0 P070 G T G C T T A A A C T T G C T T A A T C 0 P071 G T G C T T A A A C T T G C T T A A T C 0 P072 G T G C T T A A A C T T G C T T A A T C 0 P073 G T G C T T A A A C T T G C T T A A T C 0 P074 G T G C T T A A A C G T G C T T A A A C 0 P075 G T A C T G A A A C T T G C T T A A T C 0 P076 T T G C T T A A A C T T G C T T A A A C 0 P077 G T G C T T A A A C G T G C T T A A A C 0 P078 G T G C T T A A A C G T A C T G A A A C 0 P079 G T G C T T A A A C T T G C T T A A T C 0 P080 G T G C T T A A A C G T A C T G A A A C 0 P081 G T G C T T A A A C T T G C T T A A A C 0 P082 G T G C T T A A A C G T G C T T A A A C 0 P083 G T A C T G A A A C T T G C T T A A A C 0 P084 G T G C T T A A A C G T A C T G A A A C 0 P085 G T G C T T A A A C G T G C T T A A A C 0 P086 G T G C T T A A A C T T G C T T A A T C 0 P087 G T G C T T A A A C G T G C T T A A A C 0 P088 G T A C T G A A A C G C G C A T A A A C 0 P089 G T G C T T A A A C G C G C A T A A A C 0 P090 G C G T A T G G A T T T G C T T A A A 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 P001 = = = = = = = = = = = = = = = = = = = = 0 P002 G = = = = = = = A ? T = = = = = = = T ? 0 P003 = = G ? = ? = = = ? = = A ? = ? = = = ? 0 P004 = = = = = = = = = ? = = = = = = = = = ? 0 P005 = = G ? = T = = = = = = A ? = G = = = = 0 P006 G = = = = = = = A ? T = = = = = = = T ? 0 P007 = = = = = = = = = = = = = = = = = = = = 0 P008 = = = = = = = = = ? = = = = = = = = = ? 0 P009 G = A = = G = = A = T = G = = T = = T = 0 P010 G ? ? ? = = = = = ? T ? ? ? = = = = = ? 0 P011 G = = = = = = = A = T = = = = = = = T = 0 P012 = = = = = = = = = ? = = = = = = = = = ? 0 P013 = T = C T = A A = C = C = T A = G G = T 0 P014 G = = = = = = = A = T = = = = = = = T = 0 P015 G = A = = G = = A ? T = G = = T = = T ? 0 P016 G = = ? = = = = A = T = = ? = = = = T = 0 P017 = = G = = = = = = ? = = A = = = = = = ? 0 P018 = = = = = = = = = = = = = = = = = = = = 0 P019 = = = = = = = = = = = = = = = = = = = = 0 P020 = = = = = = = = = = = = = = = = = = = = 0 P021 = = G = = T = = = = = = A = = G = = = = 0 P022 = = = = = = = = = = = = = = = = = = = = 0 P023 = = = = = = = = = = = = = = = = = = = = 0 P024 = = = = = = = = = = = = = = = = = = = = 0 P025 G C = ? A = G G A T T T = ? T = A A T C 0 P026 G = A = = G = = = = T = G = = T = = = = 0 P027 = = = = = = = = = ? = = = = = = = = = ? 0 P028 = T = C T = A A = ? = C = T A = G G = ? 0 P029 = = = ? ? ? ? = = = = = = ? ? ? ? = = = 0 P030 = = G = = = = = = = = = A = = = = = = = 0 P031 = = = = = = = = = ? = = = = = = = = = ? 0 P032 G = A ? = G = = = = T = G ? = T = = = = 0 P033 = = G = = T = = = = = = A = = G = = = = 0 P034 = = = = = ? ? = = ? = = = = = ? ? = = ? 0 P035 = = = = = = = = = = = = = = = = = = = = 0 P036 G C = ? ? = G G A ? T T = ? ? = A A T ? 0 P037 = T = C T = A A = C = C = T A = G G = T 0 P038 G = A = = G = = = ? T = G = = T = = = ? 0 P039 = = G = = T = = = = = = A = = G = = = = 0 P040 = = G = = T = = = = = = A = = G = = = = 0 P041 = = G = = T = = = ? = = A = = G = = = ? 0 P042 G = A ? = ? = = = = T = G ? = ? = = = = 0 P043 G = = = = = = = = = T = = = = = = = = = 0 P044 G = = = ? = = = = ? T = = = ? = = = = ? 0 P045 G = = = = = = = A = T = = = = = = = T = 0 P046 = = G = = T = = = ? = = A = = G = = = ? 0 P047 G = = = = = = = A = T = = = = = = = T = 0 P048 = = = = = = = = = = = = = = = = = = = = 0 P049 G = = ? = = = = A = T = = ? = = = = T = 0 P050 G = A = = G = = = ? T = G = = T = = = ? 0 P051 = = = = = = = = = = = = = = = = = = = = 0 P052 = ? ? C T = A A = C = ? ? T A = G G = T 0 P053 = = = = = = = = = ? = = = = = = = = = ? 0 P054 = = = = = = = = = = = = = = = = = = = = 0 P055 G = = = = = = = = ? T = = = = = = = = ? 0 P056 G = = = = = = = = ? T = = = = = = = = ? 0 P057 = = G = = T = = = = = = A = = G = = = = 0 P058 = = = = = = = = = ? = = = = = = = = = ? 0 P059 = = = = = = = = = = = = = = = = = = = = 0 P060 = = = = = = = = = ? = = = = = = = = = ? 0 P061 G = = = = = = = = ? T = = = = = = = = ? 0 P062 = = = = = = = = = = = = = = = = = = = = 0 P063 = T = ? T = A A = ? = C = ? A = G G = ? 0 P064 = = = = = = = = = ? = = = = = = = = = ? 0 P065 G = = = = = = = = ? T = = = = = = = = ? 0 P066 G C = ? A = G G A T T T = ? T = A A T C 0 P067 = = = = = = = = = = = = = = = = = = = = 0 P068 = = G = = T = = = ? = = A = = G = = = ? 0 P069 = T = C T = A A = C = C = T A = G G = T 0 P070 G = = = = = = = A ? T = = = = = = = T ? 0 P071 G = = = = = = = A = T = = = = = = = T = 0 P072 G = = = = = = = A ? T = = = = = = = T ? 0 P073 G = = ? = = = = A ? T = = ? = = = = T ? 0 P074 = = = = = = = = = ? = = = = = = = = = ? 0 P075 G = A = = G = = A = T = G = = T = = T = 0 P076 = = = = ? = = = = = = = = = ? = = = = = 0 P077 = = = = = = = = = = = = = = = = = = = = 0 P078 = = G = = T = = = ? = = A = = G = = = ? 0 P079 G = = ? = = = = A ? T = = ? = = = = T ? 0 P080 = = G = = T = = = ? = = A = = G = = = ? 0 P081 G = = ? = = = = = = T = = ? = = = = = = 0 P082 = = = ? = = = = = = = = = ? = = = = = = 0 P083 G = A = ? G = = = = T = G = ? T = = = = 0 P084 = = G = ? T = = = = = = A = ? G = = = = 0 P085 = = = = = = = = = ? = = = = = = = = = ? 0 P086 G = = = = = = = A ? T = = = = = = = T ? 0 P087 = = = = = = = = = ? = = = = = = = = = ? 0 P088 = T A = T G = = = ? = C G = A T = = = ? 0 P089 = T = = T = = = = = = C = = A = = = = = 0 P090 G C = ? A = G G = T T T = ? T = A 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 ? = = 1.00 ? = ? = = = ? = = = = = = = = = ? = = 1.00 ? = 1.00 = = = = 1.00 = = = = = = = 1.00 ? = = = = = = = = = = = = = = = = = = = ? 1.00 = 1.00 = = 1.00 = = 1.00 = 1.00 ? ? ? = = = = = ? 1.00 = = = = = = = 1.00 = = = = = = = = = = ? = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = = = = = = 1.00 = 1.00 = 1.00 = = 1.00 = = 1.00 ? 1.00 = = ? = = = = 1.00 = = = 1.00 = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = ? 1.00 = 1.00 1.00 1.00 1.00 0.97 = 1.00 = = 1.00 = = = = = = = = = = = = = ? = 1.00 = 1.00 1.00 = 1.00 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 0.97 = 1.00 = = 1.00 = = = ? = = 1.00 = = 1.00 = = = = = = 1.00 = = 1.00 = = = = = = 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 = 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 = = ? = = = = = = = = = ? = = = = = = 0.98 = 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 1.00 = ? 1.00 = 1.00 1.00 = 1.00 END PHASEPROBS