************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 cdk2c.phase.inp cdk2c.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST cdk2c.phase.out_freqs : haplotype frequency estimates cdk2c.phase.out_pairs : most likely haplotype pairs for each individual cdk2c.phase.out_recom : estimates of recombination parameters cdk2c.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 5 Positions of loci: 1227 4789 5907 6423 7635 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file cdk2c.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TACTC 116.000000 2 TATTT 3.000000 3 TATCT 4.000000 4 TGCTC 45.000000 5 AATTT 3.000000 6 AATCT 9.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,4) P002: (1,6) P003: (2,4) P004: (1,6) P005: (1,4) P006: (4,6) P007: (1,1) P008: (1,1) P009: (1,4) P010: (1,1) P011: (1,1) P012: (1,4) P013: (1,4) P014: (1,1) P015: (1,1) P016: (1,1) P017: (1,1) P018: (4,4) P019: (1,4) P020: (1,4) P021: (1,4) P022: (1,1) P023: (1,1) P024: (1,1) P025: (1,1) P026: (1,4) P027: (1,1) P028: (1,1) P029: (4,4) P030: (1,1) P031: (1,1) P032: (4,4) P033: (1,1) P034: (1,1) P035: (1,4) P036: (1,1) P037: (1,1) P038: (4,4) P039: (1,4) P040: (1,6) P041: (3,3) P042: (1,1) P043: (1,4) P044: (1,4) P045: (1,1) P046: (1,1) P047: (4,6) P048: (1,1) P049: (1,4) P050: (1,4) P051: (1,1) P052: (1,1) P053: (1,4) P054: (1,1) P055: (1,1) P056: (1,5) P057: (1,4) P058: (1,1) P059: (1,4) P060: (1,1) P061: (1,5) P062: (1,1) P063: (1,1) P064: (2,5) P065: (2,4) P066: (1,4) P067: (1,1) P068: (1,4) P069: (1,4) P070: (1,1) P071: (1,1) P072: (1,4) P073: (1,1) P074: (1,4) P075: (1,1) P076: (1,1) P077: (1,4) P078: (1,4) P079: (1,6) P080: (3,4) P081: (1,6) P082: (1,4) P083: (1,4) P084: (1,1) P085: (4,4) P086: (4,4) P087: (1,6) P088: (1,6) P089: (1,3) P090: (1,4) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 T A C T C T G C T C 0 P002 T A C T C A A T C T 0 P003 T A T T T T G C T C 0 P004 T A C T C A A T C T 0 P005 T A C T C T G C T C 0 P006 T G C T C A A T C T 0 P007 T A C T C T A C T C 0 P008 T A C T C T A C T C 0 P009 T A C T C T G C T C 0 P010 T A C T C T A C T C 0 P011 T A C T C T A C T C 0 P012 T A C T C T G C T C 0 P013 T A C T C T G C T C 0 P014 T A C T C T A C T C 0 P015 T A C T C T A C T C 0 P016 T A C T C T A C T C 0 P017 T [A] C T C T A C T C 0 P018 T G C T C T G C T C 0 P019 T A C T C T G C T C 0 P020 T A C T C T G C T C 0 P021 T A C T C T G C T C 0 P022 T A C T C T A C T C 0 P023 T A C T C T A C T C 0 P024 T A C T C T A C T C 0 P025 T A C T C T A C T C 0 P026 T A C T C T G C T C 0 P027 T A C T C T A C T C 0 P028 T [A] C T C T A C T C 0 P029 T G C T C T G C T C 0 P030 T A C T C T A C T C 0 P031 T A C T C T A C T C 0 P032 T G C T C T G C T C 0 P033 T A C T C T A C T C 0 P034 T A C T C T A C T C 0 P035 T A C T C T G C T C 0 P036 T A C T C T A C T C 0 P037 T A C T C T A C T C 0 P038 T G C T C T G C T C 0 P039 T A C T C T G C T C 0 P040 T A C T C A A T C T 0 P041 T A T C T T A T C T 0 P042 T A C T C T A C T C 0 P043 T A C T C T G C T C 0 P044 T A C T C T G C T C 0 P045 T A C T C T A C T C 0 P046 T [A] C T C T A C T C 0 P047 T G C T C A A T C T 0 P048 T [A] C T C T A C T C 0 P049 T A C T C T G C T C 0 P050 T A C T C T G C T C 0 P051 T A C T C T A C T C 0 P052 T A C T C T A C T C 0 P053 T A C T C T G C T C 0 P054 T A C T C T A C T C 0 P055 T A C T C T A C T C 0 P056 T A C T C A A T T T 0 P057 T A C T C T G C T C 0 P058 T A C T C T A C T C 0 P059 T A C T C T G C T C 0 P060 T A C T C T A C T C 0 P061 T A C T C A A T T T 0 P062 T A C T C T A C T C 0 P063 T A C T C T A C T C 0 P064 T A T T T A A T T T 0 P065 T A [T] T T T G C T C 0 P066 T A C T C T G C T C 0 P067 T A C T C T A C T C 0 P068 T A C T C T G C T C 0 P069 T A C T C T G C T C 0 P070 T A C T C T A C T C 0 P071 T A C T C T A C T C 0 P072 T A C T C T G C T C 0 P073 T A C T C T A C T C 0 P074 T A C T C T G C T C 0 P075 T A C T C T A C T C 0 P076 T [A] C T C T A C T C 0 P077 T A C T C T G C T C 0 P078 T A C T C T G C T C 0 P079 T A C T C A A T C T 0 P080 T A T C T T G C T C 0 P081 T A C T C A A T C T 0 P082 T A C T C T G C T C 0 P083 T A C T C T G C T C 0 P084 T A C T C T A C T C 0 P085 T G C T C T G C T C 0 P086 T G C T C T G C T C 0 P087 T A C T C A A T C T 0 P088 T [A] C T C [A] A T C T 0 P089 T A C T C T A T C T 0 P090 T A C T C T G C T 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 = = = = G = = = 0 P002 T = C T C A = T C T 0 P003 = A T = T = G C = C 0 P004 T = C T C A = T C T 0 P005 = A = = = = G = = = 0 P006 T G C T C A A T C T 0 P007 ? = = = = ? = = = = 0 P008 = = = = = = = = = = 0 P009 = A = = = = G = = = 0 P010 = = = = = = = = = = 0 P011 = = = = = = = = = = 0 P012 = A = = = = G = = = 0 P013 = A = = = = G = = = 0 P014 = = = = = = = = = = 0 P015 = = = = = = = = = = 0 P016 = = = = = = = = = = 0 P017 = ? ? = = = ? ? = = 0 P018 = = = = = = = = = = 0 P019 = A = = = = G = = = 0 P020 = A = = = = G = = = 0 P021 = A = = = = G = = = 0 P022 = = = = = = = = = = 0 P023 = = = = = = = = = = 0 P024 = = = = = = = = = = 0 P025 = = = = = = = = = = 0 P026 = A = = = = G = = = 0 P027 = = = = = = = = = = 0 P028 = ? = = = = ? = = = 0 P029 = = = = = = = = = = 0 P030 = = = = = = = = = = 0 P031 = = = = = = = = = = 0 P032 = = = = = = = = = = 0 P033 = = = = = = = = = = 0 P034 = = = = = = = = = = 0 P035 = A = = = = G = = = 0 P036 = = = = = = = = = = 0 P037 = = = = = = = = = = 0 P038 = = = = = = = = = = 0 P039 = A = = = = G = = = 0 P040 T = ? T C A = ? C T 0 P041 = = ? = = = = ? = = 0 P042 = = = = = = = = = = 0 P043 = A = = = = G = = = 0 P044 = A = = = = G = = = 0 P045 = = = = = = = = = = 0 P046 = ? = = = = ? = = = 0 P047 T G C T C A A T C T 0 P048 = ? = = = = ? = = = 0 P049 = A = = = = G = = = 0 P050 = A = = = = G = = = 0 P051 = = = = = = = = = = 0 P052 = = = = = = = = = = 0 P053 = A = ? = = G = ? = 0 P054 = = ? = = = = ? = = 0 P055 ? = = = = ? = = = = 0 P056 T = C = C A = T = T 0 P057 = A = = = = G = = = 0 P058 = = = = = = = = = = 0 P059 = A = = = = G = = = 0 P060 = = = = = = = = = = 0 P061 T = C = C A = T = T 0 P062 = = = = = = = = = = 0 P063 ? = = = = ? = = = = 0 P064 T = = = = A = = = = 0 P065 = A ? = T = G ? = C 0 P066 = A = = = = G = = = 0 P067 = = = = = = = = = = 0 P068 = A = = = = G = = = 0 P069 = A = = = = G = = = 0 P070 = = = = = = = = = = 0 P071 = = = = = = = = = = 0 P072 = A = = = = G = = = 0 P073 = = = = = = = = = = 0 P074 = A = = = = G = = = 0 P075 = = = = = = = = = = 0 P076 = ? = = = = ? = = = 0 P077 = A = = = = G = = = 0 P078 = A = = = = G = = = 0 P079 T = C T C A = T C T 0 P080 = A T C T = G C T C 0 P081 T = C T C A = T C T 0 P082 = A = = = = G = = = 0 P083 = A = = = = G = = = 0 P084 = = = = = = = = = = 0 P085 = = = = = = = = = = 0 P086 = = = = = = = = = = 0 P087 T = C T C A = T C T 0 P088 ? ? C T C ? ? T C T 0 P089 = = ? T C = = ? C T 0 P090 = A = = = = G = = = 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 = 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 ? = = = = = = = = = = 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 = = = = = 0.91 ? = 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 = = = = 1.00 = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 ? ? 1.00 1.00 1.00 = = ? 1.00 1.00 = 1.00 = = = END PHASEPROBS