************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 ltbxx.phase.inp ltbxx.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ltbxx.phase.out_freqs : haplotype frequency estimates ltbxx.phase.out_pairs : most likely haplotype pairs for each individual ltbxx.phase.out_recom : estimates of recombination parameters ltbxx.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 4 Positions of loci: 399 870 2380 4422 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ltbxx.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GGAC 128.000000 2 GGAA 19.000000 3 GGCC 12.000000 4 GCAC 7.000000 5 CCAC 14.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,3) P002: (1,3) P003: (1,2) P004: (1,4) P005: (1,2) P006: (1,1) P007: (1,2) P008: (1,3) P009: (1,2) P010: (1,5) P011: (1,1) P012: (1,1) P013: (1,1) P014: (1,1) P015: (1,2) P016: (1,2) P017: (1,4) P018: (1,1) P019: (1,5) P020: (1,1) P021: (1,4) P022: (1,1) P023: (3,5) P024: (1,5) P025: (1,5) P026: (1,1) P027: (2,3) P028: (1,1) P029: (1,1) P030: (1,1) P031: (1,2) P032: (1,1) P033: (1,5) P034: (1,1) P035: (1,5) P036: (1,1) P037: (1,1) P038: (1,1) P039: (1,1) P040: (1,1) P041: (3,4) P042: (1,1) P043: (1,1) P044: (1,1) P045: (1,1) P046: (1,5) P047: (1,1) P048: (1,5) P049: (1,1) P050: (1,1) P051: (2,3) P052: (1,2) P053: (1,1) P054: (1,1) P055: (1,2) P056: (1,5) P057: (1,1) P058: (1,3) P059: (1,2) P060: (1,1) P061: (1,1) P062: (1,1) P063: (1,3) P064: (1,4) P065: (1,1) P066: (4,5) P067: (1,1) P068: (1,2) P069: (1,1) P070: (2,2) P071: (1,1) P072: (1,2) P073: (1,1) P074: (1,1) P075: (1,2) P076: (1,1) P077: (1,3) P078: (5,5) P079: (1,2) P080: (1,4) P081: (1,5) P082: (1,1) P083: (1,3) P084: (1,1) P085: (1,1) P086: (1,1) P087: (1,1) P088: (1,1) P089: (2,3) P090: (1,1) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 G G A C G G C C 0 P002 G G A C G G C C 0 P003 G G A C G G A A 0 P004 G G A C G C A C 0 P005 G G A C G G A A 0 P006 G G A C G G A C 0 P007 G G A C G G A A 0 P008 G G A C G G C C 0 P009 G G A C G G A A 0 P010 G G A C C C A C 0 P011 G G A C G G A C 0 P012 G G A C G G A C 0 P013 G G A C G G A C 0 P014 G G A C G G A C 0 P015 G G A C G G A A 0 P016 G G A C G G A A 0 P017 G G A C G C A C 0 P018 G G A C G G A C 0 P019 G G A C C C A C 0 P020 G G A C G G A C 0 P021 G G A C G C A C 0 P022 G G A C G G A C 0 P023 G G C C C C A C 0 P024 G G A C C C A C 0 P025 G G A C C C A C 0 P026 G G A C G G A C 0 P027 G G (A) A G G (C) C 0 P028 G G A C G G A C 0 P029 G G A C G G A C 0 P030 G G A C G G A C 0 P031 G G A C G G A A 0 P032 G G A C G G A C 0 P033 G G A C C C A C 0 P034 G G A C G G A C 0 P035 G G A C C C A C 0 P036 G G A C G G A C 0 P037 G G A C G G A C 0 P038 G G A C G G A C 0 P039 G G A C G G A C 0 P040 G G A C G G A C 0 P041 G G C C G C A C 0 P042 G G A C G G A C 0 P043 G G A C G G A C 0 P044 G G A C G G A C 0 P045 G G A C G G A C 0 P046 G G A C C C A C 0 P047 G G A C G G A C 0 P048 G G A C C C A C 0 P049 G G A C G G A C 0 P050 G G A C G G A C 0 P051 G G (A) A G G (C) C 0 P052 G G A C G G A A 0 P053 G G A C G G A C 0 P054 G G A C G G A C 0 P055 G G A C G G A A 0 P056 G G A C [C] C A C 0 P057 G G A C G G A C 0 P058 G G A C G G C C 0 P059 G G A C G G A A 0 P060 G G A C G G A C 0 P061 G G A C G G A C 0 P062 G G A C G G A C 0 P063 G G A C G G C C 0 P064 G G A C G C A C 0 P065 G G A C G G A C 0 P066 [G] C A C [C] C A C 0 P067 G G A C G G A C 0 P068 G G A C G G A A 0 P069 G G A C G G A C 0 P070 G G A A G G A A 0 P071 G G A C G G A C 0 P072 G G A C G G A A 0 P073 G G A C G G A C 0 P074 G G A C G G A C 0 P075 G G A C G G A A 0 P076 G G A C G G A C 0 P077 G G A C G G C C 0 P078 C C A C C C A C 0 P079 G G A C G G A A 0 P080 G G A C G C A C 0 P081 G G A C C C A C 0 P082 G G A C G G A C 0 P083 G G A C G G C C 0 P084 G G A C G G A C 0 P085 G G A C G G A C 0 P086 G G A C G G A C 0 P087 G G A C G G A C 0 P088 G G A C G G A C 0 P089 G G (A) A G G (C) C 0 P090 G G A C G G 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 = = A = = = C = 0 P002 = = A = = = C = 0 P003 = = = C = = = A 0 P004 = G = = = C = = 0 P005 = = = C = = = A 0 P006 = = = = = = = = 0 P007 = = = C = = = A 0 P008 = = A = = = C = 0 P009 = = = C = = = A 0 P010 G G ? = C C ? = 0 P011 = = = = = = = = 0 P012 = = = = = = = = 0 P013 = = = = = = = = 0 P014 = = = = = = = = 0 P015 = = = C = = = A 0 P016 = = = C = = = A 0 P017 = G = = = C = = 0 P018 = = = = = = = = 0 P019 G G = = C C = = 0 P020 = = = = = = = = 0 P021 = G = = = C = = 0 P022 = = = = = = = = 0 P023 G G C = C C A = 0 P024 G G = = C C = = 0 P025 G G = = C C = = 0 P026 = = = = = = = = 0 P027 = = (A) A = = (C) C 0 P028 = = = = = = = = 0 P029 = = = = = = = = 0 P030 = = ? = = = ? = 0 P031 = = = C = = = A 0 P032 = = = = = = = = 0 P033 G G = = C C = = 0 P034 = = = = = = = = 0 P035 G G = = C C = = 0 P036 = = = = = = = = 0 P037 = ? = = = ? = = 0 P038 = = = = = = = = 0 P039 ? ? = = ? ? = = 0 P040 ? ? = = ? ? = = 0 P041 = G C = = C A = 0 P042 = = = = = = = = 0 P043 = = = = = = = = 0 P044 = = = = = = = = 0 P045 = = = = = = = = 0 P046 G G = = C C = = 0 P047 = = = = = = = = 0 P048 G G = = C C = = 0 P049 = = = = = = = = 0 P050 = = = = = = = = 0 P051 = = (A) A = = (C) C 0 P052 = = = C = = = A 0 P053 = = = = = = = = 0 P054 = = = = = = = = 0 P055 = = = C = = = A 0 P056 ? G = = ? C = = 0 P057 = = = = = = = = 0 P058 = = A = = = C = 0 P059 = = = C = = = A 0 P060 = = = = = = = = 0 P061 = = = = = = = = 0 P062 = = = = = = = = 0 P063 = = A = = = C = 0 P064 = G ? = = C ? = 0 P065 = = = = = = = = 0 P066 ? = = = ? = = = 0 P067 = = = = = = = = 0 P068 = = = C = = = A 0 P069 = = = = = = = = 0 P070 = = = = = = = = 0 P071 = = = = = = = = 0 P072 = = = C = = = A 0 P073 = = = = = = = = 0 P074 = = = = = = = = 0 P075 = = = C = = = A 0 P076 = = = = = = = = 0 P077 = = A = = = C = 0 P078 = = = = = = = = 0 P079 = = = C = = = A 0 P080 = G = = = C = = 0 P081 G G = = C C = = 0 P082 = = = = = = = = 0 P083 = = A = = = C = 0 P084 = = = = = = = = 0 P085 = = = = = = = = 0 P086 = = = = = = = = 0 P087 = = = = = = = = 0 P088 = = = = = = = = 0 P089 = = (A) A = = (C) C 0 P090 = = = = = = = = 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 0.98 = 1.00 1.00 = = 1.00 1.00 = = = = = = = = 0.87 1.00 = = = = = = = = = = ? = = = = 1.00 = = = = 1.00 1.00 = = = = = = 1.00 1.00 = = = = = = = ? = = = = = = ? ? = = ? ? = = = 0.96 1.00 = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = 1.00 1.00 = = = = = = = = = = = = 0.89 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 = = = = = = = = = = = = = = = = = = = = = = = 0.87 1.00 = = = = END PHASEPROBS