************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 e2f1x.phase.inp e2f1x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST e2f1x.phase.out_freqs : haplotype frequency estimates e2f1x.phase.out_pairs : most likely haplotype pairs for each individual e2f1x.phase.out_recom : estimates of recombination parameters e2f1x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 11 Positions of loci: 1722 3901 4247 4513 5996 10263 10355 10589 11569 12478 13140 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file e2f1x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CCTACCACGCC 13.000000 2 CCTACCACGCT 1.000000 3 CCTACTATGCC 61.000000 4 CCTACTATTCC 14.000000 5 CCTACTTTGCC 31.000000 6 CCTATTATGCC 1.000000 7 CCTTCTTTGCC 1.000000 8 CCGACCACGCC 3.000000 9 CCGTTCACGCC 8.000000 10 CTTACCACGCT 9.000000 11 TCTACCACGCT 1.000000 12 TCTACTTTGCC 1.000000 13 TTTACCACGCT 13.000000 14 TTTACCACGGT 23.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (3,14) P002: (14,14) P003: (5,13) P004: (1,1) P005: (4,13) P006: (3,14) P007: (3,5) P008: (9,9) P009: (3,5) P010: (3,13) P011: (8,10) P012: (13,14) P013: (9,14) P014: (5,5) P015: (3,5) P016: (5,5) P017: (3,11) P018: (3,13) P019: (3,5) P020: (3,4) P021: (1,3) P022: (3,4) P023: (9,10) P024: (14,14) P025: (5,10) P026: (3,14) P027: (3,5) P028: (4,13) P029: (3,10) P030: (3,3) P031: (3,3) P032: (3,3) P033: (4,13) P034: (1,4) P035: (5,14) P036: (3,12) P037: (3,7) P038: (1,3) P039: (3,4) P040: (3,10) P041: (3,3) P042: (1,1) P043: (5,13) P044: (5,5) P045: (3,14) P046: (5,5) P047: (2,14) P048: (3,5) P049: (3,14) P050: (1,3) P051: (9,13) P052: (6,14) P053: (3,3) P054: (5,9) P055: (3,4) P056: (3,3) P057: (3,10) P058: (3,4) P059: (1,8) P060: (3,14) P061: (1,13) P062: (5,5) P063: (3,9) P064: (1,13) P065: (1,3) P066: (4,14) P067: (4,14) P068: (5,10) P069: (9,10) P070: (4,5) P071: (5,14) P072: (5,14) P073: (3,10) P074: (5,14) P075: (3,5) P076: (5,14) P077: (3,3) P078: (3,3) P079: (3,3) P080: (3,3) P081: (3,13) P082: (3,14) P083: (3,3) P084: (3,4) P085: (3,5) P086: (3,3) P087: (8,13) P088: (4,5) P089: (1,3) P090: (5,14) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 C C T A C T A T G C C T T T A C C A C G G T 0 P002 T T T A C C A C G G T T T T A C C A C G G T 0 P003 C C T A C T T T G C C T T T A C C A C G C T 0 P004 C C T A C C A C G C C C C T A C C A C G C C 0 P005 C C T A C T A T T C C T T T A C C A C G C T 0 P006 C C T A C T A T G C C T T T A C C A C G G T 0 P007 C C T A C T A T G C C C C T A C T T T G C C 0 P008 C C G T T C A C G C C C C G T T C A C G C C 0 P009 C C T A C T A T G C C C C T A C T [T] T G C C 0 P010 C C T A C T [A] T G C C T T T A C C A C G C T 0 P011 C C G A C C A C G C C C T T A C C A C G C T 0 P012 T T T A C C A C G C T T T T A C C A C G G T 0 P013 C C G T T C A C G C C T T T A C C A C G G T 0 P014 C C T A C T T T G C C C C T A C T T T G C C 0 P015 C C T A C T A T G C C C C T A C T T T G C C 0 P016 C C T A C T T T G C C C C T A C T T T G C C 0 P017 (C) C T A C T [A] T G C C (T) C T A C C A C G C T 0 P018 C C T A C T A T G C C T T T A C C A C G C T 0 P019 C C T A C T A T G C C C C T A C T T T G C C 0 P020 C C T A C T A T G C C C C T A C T A T T C C 0 P021 C C T A C C A C G C C C C T A C T A T G C C 0 P022 C C T A C T A T G C C C C T A C T A T T C C 0 P023 C C G T T C A C G C C C T T A C C A C G C T 0 P024 T T T A C C A C G G T T T T A C C A C G G T 0 P025 C C T A C T T T G C C C T T A C C A C G C T 0 P026 C C T A C T A T G C C T T T A C C A C G G T 0 P027 C C T A C T A T G C C C C T A C T T T G C C 0 P028 C C T A C T A T T C C T T T A C C A C G C T 0 P029 C C T A C T A T G C C C T T A C C A C G C T 0 P030 C C T A C T A T G C C C C T A C T A T G C C 0 P031 C C T A C T A T G C C C C T A C T A T G C C 0 P032 C C T A C T A T G C C C C T A C T A T G C C 0 P033 C C T A C T A T T C C T T T A C C A C G C T 0 P034 C C T A C C A C G C C C C T A C T A T T C C 0 P035 C C T A C T T T G C C T T T A C C A C G G T 0 P036 (C) C T A C T A T G C C (T) C T A C T T T G C C 0 P037 C C T (A) C T A T G C C C C T (T) C T T T G C C 0 P038 C C T A C C A C G C C C C T A C T A T G C C 0 P039 C C T A C T A T G C C C C T A C T A T T C C 0 P040 C C T A C T A T G C C C T T A C C A C G C T 0 P041 C C T A C T A T G C C C C T A C T A T G C C 0 P042 C C [T] A C C A C G C C C C T A C C A C G C C 0 P043 C C T A C T T T G C C T T T A C C A C G C T 0 P044 C C T A C T T T G C C C C T A C T T T G C C 0 P045 C C T A C T A T G C C T T T A C C A C G G T 0 P046 C C T A C T T T G C C C C T A C T T T G C C 0 P047 C C T A C C A C G (C) T T T T A C C A C G (G) T 0 P048 C C T A C T A T G C C C C T A C T T T G C C 0 P049 C C T A C T A T G C C T T T A C C A C G G T 0 P050 C C T A C C A C G C C C C T A C T A T G C C 0 P051 C C G T T C A C G C C T T T A C C A C G C T 0 P052 C C T A (T) T A T G C C T T T A (C) C A C G G T 0 P053 C C T A C T A T G C C C C T A C T A T G C C 0 P054 C C T A C T T T G C C C C G T T C A C G C C 0 P055 C C T A C T A T G C C C C T A C T A T T C C 0 P056 C C T A C T A T G C C C C T A C T A T G C C 0 P057 C C T A C T A T G C C C T T A C C A C G C T 0 P058 C C T A C T A T G C C C C T A C T A T T C C 0 P059 C C T A C C A C G C C C C G A C C A C G C C 0 P060 C C T A C T A T G C C T T T A C C A C G G T 0 P061 C C T A C C A C G C C T T T A C C A C G C T 0 P062 C C T A C T T T G C C C C T A C T T T G C C 0 P063 C C T A C T A T G C C C C G T T C A C G C C 0 P064 C C T A C C A C G C C T T T A C C A C G C T 0 P065 C C T A C C A C G C C C C T A C T A T G C C 0 P066 C C T A C T A T T C C T T T A C C A C G G T 0 P067 C C T A C T A T T C C T T T A C C A C G G T 0 P068 C C T A C T T T G C C C T T A C C A C G C T 0 P069 C C G T T C A C G C C C T T A C C A C G C T 0 P070 C C T A C T A T T C C C C T A C T T T G C C 0 P071 C C T A C T T T G C C T T T A C C A C G G T 0 P072 C C T A C T T T G C C T T T A C C A C G G T 0 P073 C C T A C T A T G C C C T T A C C A C G C T 0 P074 C C T A C T T T G C C T T T A C C A C G G T 0 P075 C C T A C T A T G C C C C T A C T T T G C C 0 P076 C C T A C T T T G C C T T T A C C A C G G T 0 P077 C C T A C T A T G C C C C T A C T A T G C C 0 P078 C C T A C T A T G C C C C T A C T A T G C C 0 P079 C C T A C T A T G C C C C T A C T A T G C C 0 P080 C C T A C T A T G C C C C T A C T A T G C C 0 P081 C C T A C T A T G C C T T T A C C A C G C T 0 P082 C C T A C T A T G C C T T T A C C A C G G T 0 P083 C C T A C T A T G C C C C T A C T A T G C C 0 P084 C C T A C [T] [A] [T] G C C C C T A C T A T T C C 0 P085 C C T A C T A T G C C C C T A C T T T G C C 0 P086 C C T A C T A T G C C C C T A C T A T G C C 0 P087 C C G A C C A C G C C T T T A C C A C G C T 0 P088 C C T A C T A T T C C C C T A C T T T G C C 0 P089 C C T A C C A C G C C C C T A C T A T G C C 0 P090 C C T A C T T T G C C T T T A C C A C G [G] 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 C C = = = ? = T = C C T T = = = ? = C = G T 0 P002 = = = = = ? = = = = = = = = = = ? = = = = = 0 P003 C C = = = T T T = = C T T = = = C A C = = T 0 P004 = = = = = = = = = = = = = = = = = = = = = = 0 P005 C C = = = ? ? ? T = C T T = = = ? ? ? G = T 0 P006 C C = = = T = T = C C T T = = = C = C = G T 0 P007 = = = = = = A = = = = = = = = = = T = = = = 0 P008 = = = = = = = = = = = = = = = = = = = = = = 0 P009 = = = = = ? ? = = = = = = = = = ? ? = = = = 0 P010 C C = = = T ? ? = = C T T = = = C ? ? = = T 0 P011 = C G = = = = = = = C = T T = = = = = = = T 0 P012 = = = = = = = = = C = = = = = = = = = = G = 0 P013 C C G T T = = = = C C T T T A C = = = = G T 0 P014 = = = = = = = = = = = = = = = = = = = = = = 0 P015 = = = = = = A = = = = = = = = = = T = = = = 0 P016 = = = = = = = = = = = = = = = = = = = = = = 0 P017 (C) = = = = ? ? ? ? = C (T) = = = = ? ? ? ? = T 0 P018 C C = = = T = T = = C T T = = = C = C = = T 0 P019 = = = = = = A = ? = = = = = = = = T = ? = = 0 P020 = = = = = = = = G = = = = = = = = = = T = = 0 P021 = = = = = C = C = = = = = = = = T = T = = = 0 P022 = = = = = = = = G = = = = = = = = = = T = = 0 P023 = C G T T = = = = = C = T T A C = = = = = T 0 P024 = = = = = = = = = = = = = = = = = = = = = = 0 P025 = C = = = T T T = = C = T = = = C A C = = T 0 P026 C C = = = T = T = C C T T = = = C = C = G T 0 P027 = = = = = = A = = = = = = = = = = T = = = = 0 P028 C C = = = T = T T = C T T = = = C = C G = T 0 P029 = C = = = T = T = = C = T = = = C = C = = T 0 P030 = = = = = = = = = = = = = = = = = = = = = = 0 P031 = = = = = = = = = = = = = = = = = = = = = = 0 P032 = = = = = = = = = = = = = = = = = = = = = = 0 P033 C C = = = T = T T = C T T = = = C = C G = T 0 P034 = = ? = = C = C G = = = = ? = = T = T T = = 0 P035 C C = = = T T T = C C T T = = = C A C = G T 0 P036 (C) = = = = = A = = = = (T) = = = = = T = = = = 0 P037 = = = (A) = = A = = = = = = = (T) = = T = = = = 0 P038 = = ? = = C = C = = = = = ? = = T = T = = = 0 P039 = = = = = = = = G = = = = = = = = = = T = = 0 P040 = C = = = T = T = = C = T = = = C = C = = T 0 P041 = = = = = = = = = = = = = = = = = = = = = = 0 P042 = = ? = = = = = = = = = = ? = = = = = = = = 0 P043 C C = = = T T T = = C T T = = = C A C = = T 0 P044 = = = = = = = = = = = = = = = = = = = = = = 0 P045 C C = = = T = T = C C T T = = = C = C = G T 0 P046 = ? ? = = = = = = = = = ? ? = = = = = = = = 0 P047 C C = = = = = = = (C) = T T = = = = = = = (G) = 0 P048 = = = = = = A = = = = = = = = = = T = = = = 0 P049 C C = = = T = T = C C T T = = = C = C = G T 0 P050 = = ? = = C = C = = = = = ? = = T = T = = = 0 P051 C C G T T = = = = = C T T T A C = = = = = T 0 P052 C C = = (T) T = T = C C T T = = (C) C = C = G T 0 P053 = = = = = = = = = = = = = = = = = = = = = = 0 P054 = = ? A C T T T = = = = = ? T T C A C = = = 0 P055 = = = = = = = = G = = = = = = = = = = T = = 0 P056 = = = = = = = = = = = = = = = = = = = = = = 0 P057 = C = = = T = T = = C = T = = = C = C = = T 0 P058 = = ? = = = = = G = = = = ? = = = = = T = = 0 P059 = = T = ? = = = = = = = = G = ? = = = = = = 0 P060 C C = = = T = T = C C T T = = = C = C = G T 0 P061 C C = = ? = = = = = C T T = = ? = = = = = T 0 P062 = = ? = = = = = = = = = = ? = = = = = = = = 0 P063 = = T A C T = T = = = = = G T T C = C = = = 0 P064 C C = = ? = = = = = C T T = = ? = = = = = T 0 P065 = = = = ? C = C = = = = = = = ? T = T = = = 0 P066 C C = = = T = T T C C T T = = = C = C G G T 0 P067 C C = = = T = T T C C T T = = = C = C G G T 0 P068 = C = = = T T T = = C = T = = = C A C = = T 0 P069 = C G T T = = = = = C = T T A C = = = = = T 0 P070 = = = = = = A = T = = = = = = = = T = G = = 0 P071 C C = = = T T T = C C T T = = = C A C = G T 0 P072 C C = = = T T T = C C T T = = = C A C = G T 0 P073 = C = = = T = T = = C = T = = = C = C = = T 0 P074 C C = = = T T T = C C T T = = = C A C = G T 0 P075 = = = = = = A = = = = = = = = = = T = = = = 0 P076 C C = = = T T T = C C T T = = = C A C = G T 0 P077 = = = = = = = = = = = = = = = = = = = = = = 0 P078 = = ? ? ? = = = = ? ? = = ? ? ? = = = = ? ? 0 P079 = = = = = = = = = = = = = = = = = = = = = = 0 P080 = = = = = = = = = = = = = = = = = = = = = = 0 P081 C C = = = T = T = = C T T = = = C = C = = T 0 P082 C C = = = T = T = C C T T = = = C = C = G T 0 P083 = = = = = = = = = = = = = = = = = = = = = = 0 P084 = = = = = ? ? ? G = = = = = = = ? ? ? T = = 0 P085 = = = = = = A = = = = = = = = = = T = = = = 0 P086 = = ? ? ? = = = = ? ? = = ? ? ? = = = = ? ? 0 P087 C C G = ? = = = = = C T T T = ? = = = = = T 0 P088 = = = = = = A = T = = = = = = = = T = G = = 0 P089 = = = = = C = C = = = = = = = = T = T = = = 0 P090 C C ? ? = T T T = ? C T T ? ? = C A C = ? T 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 = = = ? ? ? 0.98 = 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 = = = = = = = = = = = = = = = 0.67 = = = = ? ? ? ? = 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 0.98 = 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 0.99 = = 1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 0.52 = = = = = 1.00 = = = = = = = 0.51 = = 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 = = 1.00 = = = = = = = = = = = 1.00 1.00 = = = 1.00 = 1.00 = 1.00 1.00 = ? ? = = = = = = = = 0.98 0.96 = = = = = = = 0.73 = = = = = = = 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 = = 0.50 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 = = = = = = 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 = = = = = = = = = = = = = ? ? ? = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = 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 = = = = = = 0.99 = 1.00 = = = = = = = 1.00 = 1.00 = = = 0.99 1.00 ? ? = 1.00 1.00 1.00 = ? 1.00 END PHASEPROBS