************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 fen1x.phase.inp fen1x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST fen1x.phase.out_freqs : haplotype frequency estimates fen1x.phase.out_pairs : most likely haplotype pairs for each individual fen1x.phase.out_recom : estimates of recombination parameters fen1x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 3 Positions of loci: 995 1175 5213 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file fen1x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCG 93.000000 2 GTG 13.000000 3 ACT 74.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,1) P002: (3,3) P003: (1,2) P004: (1,1) P005: (1,3) P006: (1,1) P007: (1,3) P008: (1,3) P009: (1,1) P010: (2,3) P011: (1,1) P012: (2,3) P013: (1,3) P014: (3,3) P015: (1,1) P016: (1,3) P017: (1,1) P018: (3,3) P019: (1,1) P020: (1,3) P021: (1,1) P022: (3,3) P023: (3,3) P024: (3,3) P025: (1,1) P026: (1,3) P027: (1,3) P028: (1,3) P029: (1,1) P030: (1,3) P031: (3,3) P032: (1,1) P033: (2,3) P034: (1,3) P035: (1,3) P036: (1,3) P037: (3,3) P038: (1,1) P039: (2,3) P040: (3,3) P041: (1,3) P042: (1,1) P043: (3,3) P044: (1,3) P045: (3,3) P046: (1,1) P047: (1,3) P048: (1,3) P049: (1,3) P050: (1,1) P051: (3,3) P052: (2,3) P053: (1,3) P054: (2,2) P055: (2,3) P056: (1,1) P057: (1,1) P058: (2,3) P059: (1,1) P060: (1,3) P061: (1,1) P062: (1,3) P063: (3,3) P064: (1,1) P065: (1,1) P066: (3,3) P067: (3,3) P068: (3,3) P069: (3,3) P070: (3,3) P071: (1,3) P072: (1,1) P073: (1,1) P074: (1,1) P075: (1,3) P076: (1,3) P077: (1,3) P078: (2,3) P079: (1,3) P080: (1,1) P081: (1,3) P082: (1,1) P083: (1,1) P084: (1,2) P085: (1,1) P086: (2,3) P087: (1,1) P088: (1,1) P089: (1,1) P090: (3,3) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 G C G G C G 0 P002 A C T [A] C T 0 P003 G C G G T G 0 P004 G C G G C G 0 P005 G C G [A] C T 0 P006 G C G G C G 0 P007 G C G [A] C T 0 P008 G C G [A] C T 0 P009 G C G G C G 0 P010 G T (G) [A] C (T) 0 P011 G C G G C G 0 P012 G (T) G A (C) T 0 P013 G C G A C T 0 P014 A C T A C T 0 P015 G C G G C G 0 P016 G C G A C T 0 P017 G C G G C G 0 P018 A C T A C T 0 P019 G C G G C G 0 P020 G C G A C T 0 P021 G C G G C G 0 P022 A C T A C T 0 P023 A C T A C T 0 P024 A C T A C T 0 P025 G C G G C G 0 P026 G C G A C T 0 P027 G C G A C T 0 P028 G C G A C T 0 P029 G C G G C G 0 P030 G C G A C T 0 P031 A C T A C T 0 P032 G C G G C G 0 P033 G T (G) [A] C (T) 0 P034 G C G A C T 0 P035 G C G A C T 0 P036 G C G A C T 0 P037 A C T A C [T] 0 P038 G C G G C G 0 P039 G (T) G A (C) T 0 P040 A C T A C T 0 P041 G C G [A] C T 0 P042 G C G G C G 0 P043 A C T [A] C T 0 P044 G C G A C T 0 P045 A C T A C T 0 P046 G C G G C G 0 P047 G C G [A] C T 0 P048 G C G A C T 0 P049 G C G A C T 0 P050 G C G G C G 0 P051 A C T A C T 0 P052 G (T) G A (C) T 0 P053 G C G A C T 0 P054 G T G G T G 0 P055 G (T) G A (C) T 0 P056 G C G G C G 0 P057 G C G G C G 0 P058 G (T) G A (C) T 0 P059 G C G G C G 0 P060 G C G A C T 0 P061 G C G G C G 0 P062 G C G A C T 0 P063 A C T A C T 0 P064 G C G G C G 0 P065 G C G G C G 0 P066 A C T A C T 0 P067 A C T A C T 0 P068 A C T A C T 0 P069 A C T A C T 0 P070 A C T A C T 0 P071 G C G A C T 0 P072 G C G G C G 0 P073 G C G G C G 0 P074 G C G G C G 0 P075 G C G A C [T] 0 P076 G C G A C T 0 P077 G C G A C T 0 P078 G (T) G A (C) T 0 P079 G C G A C T 0 P080 G C G G C G 0 P081 G C G A C T 0 P082 G C G G C G 0 P083 G C G G C G 0 P084 G C G G T G 0 P085 G C G G C G 0 P086 G (T) G A (C) T 0 P087 G C G G C G 0 P088 G C G G C G 0 P089 G C G G C G 0 P090 A C T A C T 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 ? = = ? = = 0 P003 = C = = T = 0 P004 = = = = = = 0 P005 ? = G ? = T 0 P006 = = ? = = ? 0 P007 ? = G ? = T 0 P008 ? = G ? = T 0 P009 = = = = = = 0 P010 ? T (G) ? C (T) 0 P011 = = = = = = 0 P012 G (T) G A (C) T 0 P013 G = G A = T 0 P014 = = = = = = 0 P015 = = = = = = 0 P016 G = G A = T 0 P017 = = = = = = 0 P018 = = = = = = 0 P019 = = = = = = 0 P020 G = G A = T 0 P021 ? = = ? = = 0 P022 = = = = = = 0 P023 = = = = = = 0 P024 = = = = = = 0 P025 = = = = = = 0 P026 G = G A = T 0 P027 G = G A = T 0 P028 G = G A = T 0 P029 = = = = = = 0 P030 G = G A = T 0 P031 = = = = = = 0 P032 = = = = = = 0 P033 ? T (G) ? C (T) 0 P034 G = G A = T 0 P035 G = G A = T 0 P036 G = G A = T 0 P037 = = ? = = ? 0 P038 = = = = = = 0 P039 G (T) G A (C) T 0 P040 = = = = = = 0 P041 ? = G ? = T 0 P042 ? = = ? = = 0 P043 ? = = ? = = 0 P044 G = G A = T 0 P045 = = = = = = 0 P046 = = = = = = 0 P047 ? = G ? = T 0 P048 G = G A = T 0 P049 G = G A = T 0 P050 = = = = = = 0 P051 = = = = = = 0 P052 G (T) G A (C) T 0 P053 G = G A = T 0 P054 = = = = = = 0 P055 G (T) G A (C) T 0 P056 = = = = = = 0 P057 = = = = = = 0 P058 G (T) G A (C) T 0 P059 = = = = = = 0 P060 G = G A = T 0 P061 = = = = = = 0 P062 G = G A = T 0 P063 = = = = = = 0 P064 = = = = = = 0 P065 = = = = = = 0 P066 = = = = = = 0 P067 = = = = = = 0 P068 = = = = = = 0 P069 = = = = = = 0 P070 = = = = = = 0 P071 G = G A = T 0 P072 = = = = = = 0 P073 = = = = = = 0 P074 = = = = = = 0 P075 G = ? A = ? 0 P076 G = G A = T 0 P077 G = G A = T 0 P078 G (T) G A (C) T 0 P079 G = G A = T 0 P080 = = = = = = 0 P081 G = G A = T 0 P082 = = = = = = 0 P083 = = = = = = 0 P084 = C = = T = 0 P085 = = = = = = 0 P086 G (T) G A (C) T 0 P087 = = = = = = 0 P088 ? ? = ? ? = 0 P089 = = = = = = 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 = = = = ? = 0.97 = = ? ? = 0.97 ? = 0.97 = = = ? 0.90 0.86 = = = 0.99 0.87 0.97 0.96 = 1.00 = = = = = = 0.96 = 1.00 = = = = = = = = = 0.96 = 1.00 ? = = = = = = = = = = = = = = 0.96 = 1.00 0.96 = 1.00 0.96 = 1.00 = = = 0.96 = 1.00 = = = = = = ? 0.91 0.85 0.96 = 1.00 0.96 = 1.00 0.96 = 1.00 = = ? = = = 0.99 0.87 0.97 = = = ? = 0.97 ? = = ? = = 0.96 = 1.00 = = = = = = ? = 0.97 0.96 = 1.00 0.96 = 1.00 = = = = = = 0.99 0.87 0.97 0.96 = 1.00 = = = 0.99 0.87 0.97 = = = = = = 0.99 0.87 0.97 = = = 0.96 = 1.00 = = = 0.96 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = 0.96 = 1.00 = = = = = = = = = 0.97 = ? 0.96 = 1.00 0.96 = 1.00 0.98 0.86 0.97 0.96 = 1.00 = = = 0.96 = 1.00 = = = = = = = 1.00 = = = = 0.98 0.86 0.97 = = = ? ? = = = = = = = END PHASEPROBS