************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 cdc6x.phase.inp cdc6x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST cdc6x.phase.out_freqs : haplotype frequency estimates cdc6x.phase.out_pairs : most likely haplotype pairs for each individual cdc6x.phase.out_recom : estimates of recombination parameters cdc6x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 6 Positions of loci: 1368 4301 5306 5753 13084 14890 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file cdc6x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AATDIG 140.000000 2 AGTDIA 1.000000 3 GGTDIG 2.000000 4 GGTDIA 22.000000 5 GGCIDA 15.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,1) P002: (1,4) P003: (1,5) P004: (1,5) P005: (1,1) P006: (1,1) P007: (1,1) P008: (1,1) P009: (1,4) P010: (1,1) P011: (1,1) P012: (1,3) P013: (1,1) P014: (4,4) P015: (1,1) P016: (1,1) P017: (1,1) P018: (1,5) P019: (1,5) P020: (1,4) P021: (4,5) P022: (1,1) P023: (1,1) P024: (1,1) P025: (1,1) P026: (1,2) P027: (1,1) P028: (1,1) P029: (1,5) P030: (1,1) P031: (1,1) P032: (1,1) P033: (1,1) P034: (1,1) P035: (1,1) P036: (1,1) P037: (1,1) P038: (1,5) P039: (1,1) P040: (1,1) P041: (1,5) P042: (1,5) P043: (1,1) P044: (1,1) P045: (1,4) P046: (1,1) P047: (1,1) P048: (4,4) P049: (1,1) P050: (1,1) P051: (1,1) P052: (1,1) P053: (1,1) P054: (1,1) P055: (1,1) P056: (1,5) P057: (1,1) P058: (1,4) P059: (1,1) P060: (1,3) P061: (1,5) P062: (1,1) P063: (1,4) P064: (4,5) P065: (1,5) P066: (1,1) P067: (1,4) P068: (1,4) P069: (1,1) P070: (1,1) P071: (1,1) P072: (1,1) P073: (1,1) P074: (1,4) P075: (1,1) P076: (4,4) P077: (1,1) P078: (1,1) P079: (1,1) P080: (1,5) P081: (1,1) P082: (1,1) P083: (1,4) P084: (1,4) P085: (1,1) P086: (1,1) P087: (1,5) P088: (1,4) P089: (1,1) P090: (4,4) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 A A T D I G A A T D I G 0 P002 A A T D I G G G T D I [A] 0 P003 A A T D I G G G C I D A 0 P004 A A T D I G G G C I D A 0 P005 A A T D I G A A T D I G 0 P006 A A T D I G A A T D I G 0 P007 A A T D I G A A T D I G 0 P008 A A T D I G A A T D I G 0 P009 A A T D I G G G T D I [A] 0 P010 A A T D I G A A T D I G 0 P011 A A T D I G A A T D I G 0 P012 A A T D I G G G T D I G 0 P013 A A T D I G A A T D I G 0 P014 G G T D I A G G T D I A 0 P015 A A T D I G A A T D I G 0 P016 A A T D I G A A T D I G 0 P017 A A T D I G A A T D I G 0 P018 A A T D I G G G C I D A 0 P019 A A T D I G G G C I D A 0 P020 A A T D I G G G T D I A 0 P021 G G T D I A G G C I D A 0 P022 A A T D I G A A T D I G 0 P023 A A T D I G A A T D I G 0 P024 A A T D I G A A T D I G 0 P025 A A T D I G A A T D I G 0 P026 A A T D I G A G T D I A 0 P027 A A T D I G A A T D I G 0 P028 A A T D I G A A T D I G 0 P029 A A T D I G G G C I D A 0 P030 A A T D I G A A T D I G 0 P031 A A T D I G A A T D I G 0 P032 A A T D I G A A T D I G 0 P033 A A T D I G A A T D I G 0 P034 A A T D I G A A T D I G 0 P035 A A T D I G A A T D I G 0 P036 A A T D I G A A T D I G 0 P037 A A T D I G A A T D I G 0 P038 A A T D I G G G C I D A 0 P039 A A T D I G A A T D I G 0 P040 A A T D I G A A T D I G 0 P041 A A T D I G G G C I D A 0 P042 A A T D I G G G C I D A 0 P043 A A T D I G A A T D I G 0 P044 A A T D I G A A T D I G 0 P045 A A T D I G G G T D I A 0 P046 A A T D I G A A T D I G 0 P047 A A T D I G A A T D I G 0 P048 G G T D I A G G T D I A 0 P049 A A T D I G A A T D I G 0 P050 A A T D I G A A T D I G 0 P051 A A T D I G A A T D I G 0 P052 A A T D I G A A T D I G 0 P053 A A T D I G A A T D I G 0 P054 A A T D I G A A T D I G 0 P055 A A T D I G A A T D I G 0 P056 A A T D I G G G C I D A 0 P057 A A T D I G A A T D I G 0 P058 A A T D I G G G T D I A 0 P059 A A T D I G A A T D I G 0 P060 A A T D I G G G T D I G 0 P061 A A T D I G G G C I D A 0 P062 A A T D I G A A T D I G 0 P063 A A T D I G G G T D I A 0 P064 G G T D I A G G C I D A 0 P065 A A T D I G G G C I D A 0 P066 A A T D I G A A T D I G 0 P067 A A T D I G G G T D I A 0 P068 A A T D I G G G T D I A 0 P069 A A T D I G A A T D I G 0 P070 A A T D I G A A T D I G 0 P071 A A T D I G A A T D I G 0 P072 A A T D I G A A T D I G 0 P073 A A T D I G A A T D I G 0 P074 A A T D I G G G T D I A 0 P075 A A T D I G A A T D I G 0 P076 G G T D I A G G T D I A 0 P077 A A T D I G A A T D I G 0 P078 A A T D I G A A T D I G 0 P079 A A T D I G A A T D I G 0 P080 A A T D I G G G C I D A 0 P081 A A T D I G A A T D I G 0 P082 A A T D I G A A T D I G 0 P083 A A T D I G G G T D I A 0 P084 A A T D I G G G T D I A 0 P085 A A T D I G A A T D I G 0 P086 A A T D I G A A T D I G 0 P087 A A T D I G G G C I D A 0 P088 A A T D I G G G T D I A 0 P089 A A T D I G A A T D I G 0 P090 G G T D I A [G] G T D I A 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 ? A ? = = ? ? G ? = = ? 0 P003 ? A T D I G ? G C I D A 0 P004 A A T D I G G G C I D A 0 P005 = = = = = = = = = = = = 0 P006 = = = = = = = = = = = = 0 P007 ? = = = = = ? = = = = = 0 P008 ? = = = = = ? = = = = = 0 P009 ? A ? = ? ? ? G ? = ? ? 0 P010 ? = ? = = = ? = ? = = = 0 P011 = = = = = = = = = = = = 0 P012 A A = = = = G G = = = = 0 P013 = = = = = = = = = = = = 0 P014 = = = = = = = = = = = = 0 P015 = = = = = = = = = = = = 0 P016 = = = = = = = = = = = = 0 P017 ? = ? = = = ? = ? = = = 0 P018 ? A ? D I G ? G ? I D A 0 P019 A A T D I G G G C I D A 0 P020 A A = = = G G G = = = A 0 P021 = = T D I = = = C I D = 0 P022 = = = = = = = = = = = = 0 P023 = = = = = = = = = = = = 0 P024 = = = = = = = = = = = = 0 P025 = = = = = = = = = = = = 0 P026 = A = = = G = G = = = A 0 P027 = = = = = = = = = = = = 0 P028 = = = = = = = = = = = = 0 P029 A A T D I G G G C I D A 0 P030 = = = = = = = = = = = = 0 P031 = = = = = = = = = = = = 0 P032 = = = = = = = = = = = = 0 P033 = = = = = = = = = = = = 0 P034 = = = = = = = = = = = = 0 P035 = = = = = = = = = = = = 0 P036 = = = = = = = = = = = = 0 P037 = = = = = = = = = = = = 0 P038 A A T D I G G G C I D A 0 P039 = = = = = = = = = = = = 0 P040 = = = = = = = = = = = = 0 P041 A A T D I G G G C I D A 0 P042 A A T D I G G G C I D A 0 P043 = = = = = = = = = = = = 0 P044 = = = = = = = = = = = = 0 P045 A A = = = G G G = = = A 0 P046 = = = = = = = = = = = = 0 P047 = = = = = = = = = = = = 0 P048 = = = = = = = = = = = = 0 P049 ? = ? = = = ? = ? = = = 0 P050 = = = = = = = = = = = = 0 P051 = = = = = = = = = = = = 0 P052 = = = = = = = = = = = = 0 P053 = = = = = = = = = = = = 0 P054 = = = = = = = = = = = = 0 P055 = = = = = = = = = = = = 0 P056 A A T D I G G G C I D A 0 P057 = = = = = = = = = = = = 0 P058 A A = = = G G G = = = A 0 P059 = = = = = = = = = = = = 0 P060 A A = = = = G G = = = = 0 P061 A A T ? I G G G C ? D A 0 P062 = = = = = = = = = = = = 0 P063 A A = = = G G G = = = A 0 P064 = = T D I = = = C I D = 0 P065 A A T D I G G G C I D A 0 P066 = = = = = = = = = = = = 0 P067 A A = = = G G G = = = A 0 P068 A A = = = G G G = = = A 0 P069 = = = = = = = = = = = = 0 P070 = = = = = = = = = = = = 0 P071 ? = ? = = = ? = ? = = = 0 P072 = = = = = = = = = = = = 0 P073 ? = ? = = = ? = ? = = = 0 P074 ? A = = = G ? G = = = A 0 P075 = = = = = = = = = = = = 0 P076 = = = = = = = = = = = = 0 P077 = = = = = = = = = = = = 0 P078 = = = = = = = = = = = = 0 P079 = = = = = = = = = = = = 0 P080 A A T D I G G G C I D A 0 P081 = = = = = = = = = = = = 0 P082 = = = = = = = = = = = = 0 P083 A A = = = G G G = = = A 0 P084 A A = = = G G G = = = A 0 P085 = = = = = = = = = = = = 0 P086 = = = = = = = = = = = = 0 P087 A A T D I G G G C I D A 0 P088 A A = = = G G G = = = A 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 ? = = ? ? 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 = = = 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 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