************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 fgf11.phase.inp fgf11.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST fgf11.phase.out_freqs : haplotype frequency estimates fgf11.phase.out_pairs : most likely haplotype pairs for each individual fgf11.phase.out_recom : estimates of recombination parameters fgf11.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 8 Positions of loci: 781 927 1315 3145 4469 4956 5696 5777 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file fgf11.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TACCDTAC 67.000000 2 TACCICCT 6.000000 3 TACTDTCC 33.000000 4 TATCICCT 22.000000 5 TATTDTCC 1.000000 6 AACCDTAC 2.000000 7 AATCICCT 1.000000 8 AGCCDTCC 8.000000 9 AGTCICCT 37.000000 10 AGTCITCT 3.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,4) P002: (1,1) P003: (1,10) P004: (3,9) P005: (1,9) P006: (2,9) P007: (1,1) P008: (3,3) P009: (9,9) P010: (1,3) P011: (8,8) P012: (3,4) P013: (1,1) P014: (1,3) P015: (2,3) P016: (1,1) P017: (3,9) P018: (1,1) P019: (1,9) P020: (1,4) P021: (1,8) P022: (1,1) P023: (1,3) P024: (3,3) P025: (4,4) P026: (1,3) P027: (2,3) P028: (1,9) P029: (4,9) P030: (1,4) P031: (1,1) P032: (4,9) P033: (4,9) P034: (1,1) P035: (1,3) P036: (1,1) P037: (1,3) P038: (1,9) P039: (1,3) P040: (4,4) P041: (1,3) P042: (4,4) P043: (1,9) P044: (4,9) P045: (1,1) P046: (1,9) P047: (1,1) P048: (1,9) P049: (1,3) P050: (1,8) P051: (1,1) P052: (1,9) P053: (1,9) P054: (1,9) P055: (1,4) P056: (1,10) P057: (3,4) P058: (1,4) P059: (1,9) P060: (1,2) P061: (9,10) P062: (4,9) P063: (1,1) P064: (9,9) P065: (1,1) P066: (3,3) P067: (1,3) P068: (3,3) P069: (1,3) P070: (3,9) P071: (1,3) P072: (1,4) P073: (2,3) P074: (9,9) P075: (1,1) P076: (6,6) P077: (9,9) P078: (4,9) P079: (3,5) P080: (8,8) P081: (1,9) P082: (1,3) P083: (9,9) P084: (9,9) P085: (2,9) P086: (7,9) P087: (3,4) P088: (3,8) P089: (4,8) P090: (1,3) 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 C D T A C T A T C I C C T 0 P002 T A C C D T A C T A C C D T A C 0 P003 T A C C D T A C A G T C I T C T 0 P004 T A C T D T C C A G T C I C C T 0 P005 T A C C D T A C A G T C I C C T 0 P006 T A C C I C C T A G T C I C C T 0 P007 T A C C D T A C T A C C D T A C 0 P008 T A C T D T C C T A C T D T C C 0 P009 A G T C I C C T A G T C I C C T 0 P010 T A C C D T A C T A C T D T C C 0 P011 A G C C D T C C A G C C D T C C 0 P012 T A C T D T C C T A T C I C C T 0 P013 T A C C D T A C T A C C D T A C 0 P014 T A C C D T A C T A C T D T C C 0 P015 T A C C I C C T T A C T D T C C 0 P016 T A C C D T A C T A C C D T A C 0 P017 T A C T D T C C A G T C I C C T 0 P018 T A C C D T A C T A C C D T A C 0 P019 T A C C D T A C A G T C I C C T 0 P020 T A C C D T A C T A T C I C C T 0 P021 T A C C D T A C A G C C D T C C 0 P022 T A C C D T A C T A C C D T A C 0 P023 T A C C D T A C T A C T D T C C 0 P024 T A C T D T C C T A C T D T C C 0 P025 T A T C I C C T T A T C I C C T 0 P026 T A C C D T A C T A C T D T C C 0 P027 T A C C I C C T T A C T D T C C 0 P028 T A C C D T A C A G T C I C C T 0 P029 T A T C I C C T A G T C I C C T 0 P030 T A C C D T A C T A T C I C C T 0 P031 T A C C D T A C T A C C D T A C 0 P032 T A T C I C C T A G T C I C C T 0 P033 T A T C I C C T A G T C I C C T 0 P034 T A C C D T A C T A C C D T A C 0 P035 T A C C D T A C T A C T D T C C 0 P036 T A C C D T A C T A C C D T A C 0 P037 T A C C D T A C T A C T D T C C 0 P038 T A C C D T A C A G T C I C C T 0 P039 T A C C D T A C T A C T D T C C 0 P040 T A T C I C C T T A T C I C C T 0 P041 T A C C D T A C T A C T D T C C 0 P042 T A T C I C C T T A T C I C C T 0 P043 T A C C D T A C A G T C I C C T 0 P044 T A T C I C C T A G T C I C C T 0 P045 T A C C D T A C T A C C D T A C 0 P046 T A C C D T A C A G T C I C C T 0 P047 T A C C D T A C T A C C D T A C 0 P048 T A C C D T A C A G T C I C C T 0 P049 T A C C D T A C T A C T D T C C 0 P050 T A C C D T A C A G C C D T C C 0 P051 T A C C D T A C T A C C D T A C 0 P052 T A C C D T A C A G T C I C C T 0 P053 T A C C D T A C A G T C I C C T 0 P054 T A C C D T A C A G T C I C C T 0 P055 T A C C D T A C T A T C I C C T 0 P056 T A C C D T A C A G T C I T C T 0 P057 T A C T D T C C T A T C I C C T 0 P058 T A C C D T A C T A T C I C C T 0 P059 T A C C D T A C A G T C I C C T 0 P060 T A C C D T A C T A C C I C C T 0 P061 A G T C I C C T A G T C I T C T 0 P062 T A T C I C C T A G T C I C C T 0 P063 T A C C D T A C T A C C D T A C 0 P064 A G T C I C C T A G T C I C C T 0 P065 T A C C D T A C T A C C D T A C 0 P066 T A C T D T C C T A C T D T C C 0 P067 T A C C D T A C T A C T D T C C 0 P068 T A C T D T C C T A C T D T C C 0 P069 T A C C D T A C T A C T D T C C 0 P070 T A C [T] D T C C [A] [G] T C I C C T 0 P071 T A C C D T A C T A C T D T C C 0 P072 T A C C D T A C T A T C I C C T 0 P073 T A C C I C C T T A C T D T C C 0 P074 A G T C I C C T A G T C I C C T 0 P075 T A C C D T A C T A C C D T A C 0 P076 A A C C D T A C A A C C D T A C 0 P077 A G T C I C C T A G T C I C C T 0 P078 T A T C I C C T A G T C I C C T 0 P079 T A C T D T C C T A T T D T C C 0 P080 A G C C D T C C A G C C D T C C 0 P081 T A C C D T A C A G T C I C C T 0 P082 T A C C D T A C T A C T D T C C 0 P083 A G T C I C C T A G T C I C C T 0 P084 A G T C I C C T A G T C I C C T 0 P085 T A C C I C C T A G T C I C C T 0 P086 A A T C I C C T A G T C I C C T 0 P087 T A C T D T C C T A T C I C C T 0 P088 T A C T D T C C A G C C D T C C 0 P089 (T) (A) T C I C C T (A) (G) C C D T C C 0 P090 T A C C D T A C T A C T D T C 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 = = C = ? T A C = = T = ? C C T 0 P002 = = = = ? = = = = = = = ? = = = 0 P003 ? A C ? ? = A C ? G T ? ? = C T 0 P004 T A C T ? T = C A G T C ? C = T 0 P005 T A C ? ? T A C A G T ? ? C C T 0 P006 T A C ? ? = = = A G T ? ? = = = 0 P007 = = = ? ? = = = = = = ? ? = = = 0 P008 = = = = = = = = = = = = = = = = 0 P009 = = = = = = = = = = = = = = = = 0 P010 = = = C ? = A = = = = T ? = C = 0 P011 = = = = ? = = = = = = = ? = = = 0 P012 = = C T D T = C = = T C I C = T 0 P013 = = = = = = = = = = = = = = = = 0 P014 = = = C = = A = = = = T = = C = 0 P015 = = = C I C = T = = = T D T = C 0 P016 = = = = = = = = = = = = = = = = 0 P017 ? A C T D T = C ? G T C I C = T 0 P018 = = = = ? = = = = = = = ? = = = 0 P019 ? A C = ? T A C ? G T = ? C C T 0 P020 = = C ? D T A C = = T ? I C C T 0 P021 ? A = = = = A = ? G = = = = C = 0 P022 = = = ? = = = = = = = ? = = = = 0 P023 = = = C = = A = = = = T = = C = 0 P024 = = = = = = = = = = = = = = = = 0 P025 = = = = = = = = = = = = = = = = 0 P026 = = = C = = A = = = = T = = C = 0 P027 = = = C ? C = T = = = T ? T = C 0 P028 ? A C = D T A C ? G T = I C C T 0 P029 ? A = = = = = = ? G = = = = = = 0 P030 = = C = ? T A C = = T = ? C C T 0 P031 = = = = = = = = = = = = = = = = 0 P032 T A = = = = = = A G = = = = = = 0 P033 T A = = = = = = A G = = = = = = 0 P034 = = = = = = = = = = = = = = = = 0 P035 = = = C ? = A = = = = T ? = C = 0 P036 = = = = = = = = = = = = = = = = 0 P037 = = = C = = A = = = = T = = C = 0 P038 T A C = D T A C A G T = I C C T 0 P039 = = = C = = A = = = = T = = C = 0 P040 = = = = = = = = = = = = = = = = 0 P041 = = = C = = A = = = = T = = C = 0 P042 = = = = = = = = = = = = = = = = 0 P043 T A C = ? T ? C A G T = ? C ? T 0 P044 T A = ? = = = = A G = ? = = = = 0 P045 = = = = = = = = = = = = = = = = 0 P046 T A C ? D T A C A G T ? I C C T 0 P047 = = = = = = = = = = = = = = = = 0 P048 T A C = D T A C A G T = I C C T 0 P049 = = = ? = = A = = = = ? = = C = 0 P050 T A = = = = A = A G = = = = C = 0 P051 = = = = ? = = = = = = = ? = = = 0 P052 ? A C = ? T A C ? G T = ? C C T 0 P053 ? A C = D T ? C ? G T = I C ? T 0 P054 T A C = ? T A C A G T = ? C C T 0 P055 = = C = D T A C = = T = I C C T 0 P056 T A C = D = A C A G T = I = C T 0 P057 = = C T ? T = C = = T C ? C = T 0 P058 = = C = D T A C = = T = I C C T 0 P059 T A C = ? T A C A G T = ? C C T 0 P060 = = = = D T A C = = = = I C C T 0 P061 = = = = = C = = = = = = = T = = 0 P062 T A = = = = = = A G = = = = = = 0 P063 = = = = = = = = = = = = = = = = 0 P064 = = = = = = = = = = = = = = = = 0 P065 = = = = = = = = = = = = = = = = 0 P066 = = = = = = = = = = = = = = = = 0 P067 = = = C ? = ? = = = = T ? = ? = 0 P068 = = = ? = = = = = = = ? = = = = 0 P069 = = = C = = A = = = = T = = C = 0 P070 ? ? C ? ? T = C ? ? T ? ? C = T 0 P071 = = = C = = A = = = = T = = C = 0 P072 = = C = D T A C = = T = I C C T 0 P073 = = = C I C = T = = = T D T = C 0 P074 = = = = = = = = = = = = = = = = 0 P075 = = = = ? = = = = = = = ? = = = 0 P076 = = = = = = = = = = = = = = = = 0 P077 = = = = = = = = = = = = = = = = 0 P078 T A = = = = = = A G = = = = = = 0 P079 = = C = = = = = = = T = = = = = 0 P080 = = = = ? = = = = = = = ? = = = 0 P081 ? A C = D T A C ? G T = I C C T 0 P082 = = = C = = A = = = = T = = C = 0 P083 = = = = ? = = = = = = = ? = = = 0 P084 = = = = = = = = = = = = = = = = 0 P085 ? A C = = = = = ? G T = = = = = 0 P086 = A = = = = = = = G = = = = = = 0 P087 = = C T D T = C = = T C I C = T 0 P088 ? A = T = = = = ? G = C = = = = 0 P089 (T) (A) T = I C = T (A) (G) C = D T = C 0 P090 = = = C = = A = = = = T = = 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 = = = = = ? = = = = = 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 ? 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 = 0.99 0.99 1.00 = 1.00 1.00 1.00 1.00 = = = 1.00 = = 1.00 = = = = = = = = = = = = 1.00 = = 1.00 = = = = = = = = = 0.93 0.93 1.00 = ? 1.00 ? 1.00 1.00 1.00 = ? = = = = = = = = = = = = 0.99 0.99 1.00 ? 1.00 1.00 1.00 1.00 = = = = = = = = 0.99 0.99 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 = = 0.99 1.00 ? 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 0.99 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 = = = = = = = = = ? = = = ? 0.99 1.00 = 1.00 1.00 1.00 1.00 = = = 1.00 = = 1.00 = = = = = ? = = = = = = = = = = = ? 1.00 0.98 = = = = = = 1.00 = = = = = = = = 0.99 1.00 1.00 1.00 = 1.00 ? 1.00 = 1.00 = = = = 0.80 0.80 0.99 = 1.00 1.00 = 1.00 = = = 1.00 = = 1.00 = END PHASEPROBS