************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 dmc1x.phase.inp dmc1x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST dmc1x.phase.out_freqs : haplotype frequency estimates dmc1x.phase.out_pairs : most likely haplotype pairs for each individual dmc1x.phase.out_recom : estimates of recombination parameters dmc1x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 14 Positions of loci: 1649 3213 9175 10660 16313 19084 20322 23512 32230 33993 34050 42439 49635 49951 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file dmc1x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CGTTACATCTGGCC 55.000000 2 CGTCACGTCTGGCC 2.000000 3 CGTCACGCCTGGCC 6.000000 4 CGTCATGCCTGGCC 4.000000 5 CGTCATGCCTGTCC 1.000000 6 CGTCTCGTCTGGCC 2.000000 7 CGCCACGCCTAGCG 5.000000 8 CGCCTCGCCTAGCG 11.000000 9 TGTCATGCGTGTCC 2.000000 10 TGTCTCGTCTGGCC 1.000000 11 TGTCTTGCGTGTCC 5.000000 12 TTTCATGCGTGTCC 60.000000 13 TTTCATGCGTGTAC 14.000000 14 TTTCATGCGGGTCC 11.000000 15 TTTCTTGCGTGTCC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,1) P002: (1,8) P003: (11,12) P004: (2,6) P005: (1,12) P006: (1,13) P007: (9,12) P008: (1,12) P009: (12,12) P010: (1,12) P011: (6,12) P012: (1,12) P013: (1,12) P014: (1,1) P015: (3,3) P016: (1,1) P017: (8,13) P018: (1,9) P019: (1,12) P020: (12,12) P021: (1,11) P022: (14,14) P023: (1,12) P024: (12,14) P025: (12,13) P026: (8,12) P027: (4,13) P028: (1,13) P029: (7,8) P030: (12,12) P031: (12,14) P032: (1,5) P033: (1,12) P034: (14,14) P035: (1,12) P036: (1,12) P037: (13,13) P038: (10,11) P039: (12,12) P040: (12,13) P041: (1,8) P042: (7,8) P043: (1,12) P044: (1,13) P045: (1,1) P046: (12,15) P047: (1,12) P048: (1,12) P049: (1,1) P050: (1,8) P051: (1,14) P052: (12,12) P053: (13,13) P054: (3,14) P055: (1,12) P056: (3,4) P057: (1,11) P058: (1,12) P059: (1,12) P060: (1,8) P061: (8,12) P062: (1,12) P063: (4,12) P064: (11,12) P065: (7,8) P066: (1,14) P067: (12,14) P068: (1,1) P069: (1,12) P070: (1,12) P071: (1,12) P072: (1,12) P073: (12,13) P074: (1,12) P075: (1,1) P076: (12,12) P077: (4,12) P078: (1,12) P079: (12,12) P080: (3,14) P081: (1,12) P082: (1,12) P083: (7,12) P084: (1,1) P085: (12,13) P086: (12,13) P087: (2,7) P088: (8,12) P089: (3,12) P090: (1,12) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 C G T T A C A T C T G G C C C G T T A C A T C T G G C C 0 P002 C G T T A C A T C T G G C C C G C C T C G C C T A G C G 0 P003 T G T C T T G C G T G T C C T T T C A T G C G T G T C C 0 P004 C G T C A C G T C T G G C C C G T C T C G T C T G G C C 0 P005 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P006 C G T T A C A T C T G G C C T T T C A T G C G T G T A C 0 P007 T G T C A T G C G T G T C C T T T C A T G C G T G T C C 0 P008 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P009 T T T C A T G C G T G T C C T T T C A T G C G T G T C C 0 P010 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P011 C G T C T C G T C T G G C C T T T C A T G C G T G T C C 0 P012 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P013 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P014 C G T T A C A T C T G G C C C G T T A C A T C T G G C C 0 P015 C G T C A C G C C T G G C C C G T C A C G C C T G G C C 0 P016 C G T T A C A T C T G G C C C G T T A C A T C T G G C C 0 P017 C G C C [T] C G C C T A G C G T T T C A T G C G T G T A C 0 P018 C G T T A C A T C T G G C C T G T C A T G C G T G T C C 0 P019 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P020 T T T C A T G C G T G T C C T T T C A T G C G T G T C C 0 P021 C G T T A C A T C T G G C C T G T C T T G C G T G T C C 0 P022 T T T C A T G C G G G T C C T T T C A T G C G G G T C C 0 P023 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P024 T T T C A T G C G T G T C C T T T C A T G C G G G T C C 0 P025 T T T C A T G C G T G T C C T T T C A T G C G T G T A C 0 P026 C G C C T C G C C T A G C G T T T C A T G C G T G T C C 0 P027 C G T C A T G C C T G G C C T T T C A T G C G T G T A C 0 P028 C G T T A C A T C T G G C C T T T C A T G C G T G T A C 0 P029 C G C C A C G C C T A G C G C G C C T C G C C T A G C G 0 P030 T T T C A T G C G T G T C C T T T C A T G C G T G T C C 0 P031 T T T C A T G C G T G T C C T T T C A T G C G G G T C C 0 P032 C G T T A C A T C T G G C C C G T C A T G C [C] T G T C C 0 P033 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P034 T T T C A T G C G G G T C C T T T C A T G C G G G T C C 0 P035 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P036 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P037 T T T C A T G C G T G T A C T T T C A T G C G T G T A C 0 P038 T G T C T C G T C T G G C C T G T C T T G C G T G T C C 0 P039 T T T C A T G C G T G T C C T T T C A T G C G T G T C C 0 P040 T T T C A T G C G T G T C C T T T C A T G C G T G T A C 0 P041 C G T T A C A T C T G G C C C G C C [T] C G C C T A G C G 0 P042 C G C C A C G C C T A G C G C G C C T C G C C T A G C G 0 P043 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P044 C G T T A C A T C T G G C C T T T C A T G C G T G T A C 0 P045 C G T T A C A T C T G G C C C G T T A C A T C T G G C C 0 P046 T T T C A T G C G T G T C C T T T C T T G C G T G T C C 0 P047 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P048 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P049 C G T T A C A T C T G G C C C G T T A C A T C T G G C C 0 P050 C G T T A C A T C T G G C C C G C C T C G C C T A G C G 0 P051 C G T T A C A T C T G G C C T T T C A T G C G G G T C C 0 P052 T T T C A T G C G T G T C C T T T C A T G C G T G T C C 0 P053 T T T C A T G C G T G T A C T T T C A T G C G T G T A C 0 P054 C G T C A C G C C T G G C C T T T C A T G C G G G T C C 0 P055 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P056 C G T C A C G C C T G G C C C G T C A T G C C T G G C C 0 P057 C G T T A C A T C T G G C C T G T C [T] T G C G T G T C C 0 P058 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P059 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P060 C G T T A C A T C T G G C C C G C C T C G C C T A G C G 0 P061 C G C C T C G C C T A G C G T T T C A T G C G T G T C C 0 P062 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P063 C G T C A T G C C T G G C C T T T C A T G C G T G T C C 0 P064 T G T C T T G C G T G T C C T T T C A T G C G T G T C C 0 P065 C G C C [A] C G C C T A G C G C G C C [T] C G C C T A G C G 0 P066 C G T T A C A T C T G G C C T T T C A T G C G G G T C C 0 P067 T T T C A T G C G T G T C C T T T C A T G C G G G T C C 0 P068 C G T T A C A T C T G G C C C G T T A C A T C T G G C C 0 P069 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P070 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P071 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P072 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P073 T T T C A T G C G T G T C C T T T C A T G C G T G T A C 0 P074 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P075 C G T T A C A T C T G G C C C G T T A C A T C T G G C C 0 P076 T T T C A T G C G T G T C C T T T C A T G C G T G T C C 0 P077 C G T C A T G C C T G G C C T T T C A T G C G T G T C C 0 P078 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P079 T T T C A T G C G T G T C C T T T C A T G C G T G T C C 0 P080 C G T C A C G C C T G G C C T T T C A T G C G G G T C C 0 P081 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P082 C G T T A C A T C T G G C C T T T C A T G C G T G T C C 0 P083 C G C C A C G C C T A G C G T T T C A T G C G T G T C C 0 P084 C G T T A C A T C T G G C C C G T T A C A T C T G G C C 0 P085 T T T C A T G C G T G T C C T T T C A T G C G T G T A C 0 P086 T T T C A T G C G T G T C C T T T C A T G C G T G T A C 0 P087 C G T C A C G T C T G G C C C G C C A C G C C T A G C G 0 P088 C G C C T C G C C T A G C G T T T C A T G C G T G T C C 0 P089 C G T C A [C] G C C T G G C C T T T C A T G C G T G T C C 0 P090 C G T T A C A T C T G G C C T T T C A T G C G T G 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 ? = = = ? ? ? = = ? ? = = = ? = = = ? ? ? = = ? ? = = = 0 P002 = = T T A = ? T ? = G = = C = = C C T = ? C ? = A = = G 0 P003 = G = = T ? = = = = = = = = = T = = A ? = = = = = = = = 0 P004 = = = = A = = = = = = = = = = = = = T = = = = = = = = = 0 P005 C G = T = C A T C = = G = = T T = C = T G C G = = T = = 0 P006 C G = T = C A T C = = G C ? T T = C = T G C G = = T A ? 0 P007 = G = = = = = = = ? ? = = = = T = = = = = = = ? ? = = = 0 P008 ? G = T = C A T ? = = ? = = ? T = C = T G C ? = = ? = = 0 P009 = = = = ? ? = = = ? ? = ? ? = = = = ? ? = = = ? ? = ? ? 0 P010 C G = T = C A T ? = = G = = T T = C = T G C ? = = T = = 0 P011 C G = = T ? = T C = = G = = T T = = A ? = C G = = T = = 0 P012 C G = T = C A T C = = G = = T T = C = T G C G = = T = = 0 P013 C G = T = C A T ? = = G = = T T = C = T G C ? = = T = = 0 P014 ? ? = = = = = = = = = = = = ? ? = = = = = = = = = = = = 0 P015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P016 ? = = = = = = = ? = = = = = ? = = = = = = = ? = = = = = 0 P017 C G C = ? ? ? = C = A G C G T T T = ? ? ? = G = G T A C 0 P018 C = = T = C A T ? = = G = = T = = C = T G C ? = = T = = 0 P019 C G = T = C A T ? = = G = = T T = C = T G C ? = = T = = 0 P020 ? = = = = = = = = = = = = = ? = = = = = = = = = = = = = 0 P021 C = = T A C ? T ? = = G = = T = = C T T ? C ? = = T = = 0 P022 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P023 C G = T = C A T C = = G = = T T = C = T G C G = = T = = 0 P024 = = = = = = = = ? T = = = = = = = = = = = = ? G = = = = 0 P025 = = = = ? ? = = = = = = C = = = = = ? ? = = = = = = A = 0 P026 C G C = T C ? = ? = A G ? ? T T T = A T ? = ? = G T ? ? 0 P027 C G = = = = = = C = = G C = T T = = = = = = G = = T A = 0 P028 C G = T = C ? T C = = G C = T T = C = T ? C G = = T A = 0 P029 ? = = ? A = = = ? = = = = = ? = = ? T = = = ? = = = = = 0 P030 = = = = = = = ? = = = = = = = = = = = = = ? = = = = = = 0 P031 = = = = = = = = = T = = = = = = = = = = = = = G = = = = 0 P032 = = = ? = C A T ? = = G ? ? = = = ? = T G C ? = = T ? ? 0 P033 C G = T ? ? A T C = = G ? ? T T = C ? ? G C G = = T ? ? 0 P034 = = = = = = = = ? = = ? = = = = = = = = = = ? = = ? = = 0 P035 C G = T = C A T C = = G = = T T = C = T G C G = = T = = 0 P036 C G = T = C ? T C = = G = = T T = C = T ? C G = = T = = 0 P037 = = = = = = = = ? = = = = = = = = = = = = = ? = = = = = 0 P038 = = = = = C = T C = = G = = = = = = = T = C G = = T = = 0 P039 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P040 = = = ? = = = = ? = = = C = = = = ? = = = = ? = = = A = 0 P041 ? = T T ? ? ? T = = G = ? ? ? = C C ? ? ? C = = A = ? ? 0 P042 = = = = A = = = ? = = = ? ? = = = = T = = = ? = = = ? ? 0 P043 C ? = T = C A T C = = G = = T ? = C = T G C G = = T = = 0 P044 C G = T = C ? T C = = G C = T T = C = T ? C G = = T A = 0 P045 = = = = = = = = ? = = = = = = = = = = = = = ? = = = = = 0 P046 = = = = A = = = = = = = = = = = = = T = = = = = = = = = 0 P047 C G = T = C A T C = = G = = T T = C = T G C G = = T = = 0 P048 ? G = T = C A T ? = = G ? ? ? T = C = T G C ? = = T ? ? 0 P049 = = = = ? ? ? = = = = = = ? = = = = ? ? ? = = = = = = ? 0 P050 = = T T A = ? T ? = G = = C = = C C T = ? C ? = A = = G 0 P051 C G = T = C A T C T = G = = T T = C = T G C G G = T = = 0 P052 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P053 = = = = = = ? = = = = = = = = = = = = = ? = = = = = = = 0 P054 C G = = = C = = C T = G = = T T = = = T = = G G = T = = 0 P055 C G = T = C A T C = = G = = T T = C = T G C G = = T = = 0 P056 ? = = = = C = = ? = = = = = ? = = = = T = = ? = = = = = 0 P057 C = = T ? ? A T C = = G = ? T = = C ? ? G C G = = T = ? 0 P058 C G = T = C A T ? = = G = = T T = C = T G C ? = = T = = 0 P059 C G = T = C A T C = = G = = T T = C = T G C G = = T = = 0 P060 ? = T T A = ? ? = = G = = C ? = C C T = ? ? = = A = = G 0 P061 C ? ? = T C ? = ? = A G = ? T ? ? = A T ? = ? = G T = ? 0 P062 C ? = T = C A T C = = G = = T ? = C = T G C G = = T = = 0 P063 C G = = = = = = C = = G = = T T = = = = = = G = = T = = 0 P064 = G = = T = = = ? = ? = = = = T = = A = = = ? = ? = = = 0 P065 ? = = = ? ? = = = = = = = = ? = = = ? ? = = = = = = = = 0 P066 C G = T = C ? T ? T = G = = T T = C = T ? C ? G = T = = 0 P067 = = = = = ? = = = T = = = = = = = = = ? = = = G = = = = 0 P068 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P069 C G = T = C A T ? = = G = = T T = C = T G C ? = = T = = 0 P070 C G = T = C A T ? = = G = = T T = C = T G C ? = = T = = 0 P071 C G = T = C A T C = = G = = T T = C = T G C G = = T = = 0 P072 ? G = T = C A T ? = ? G = = ? T = C = T G C ? = ? T = = 0 P073 = = = = ? ? = = = = = = C = = = = = ? ? = = = = = = A = 0 P074 ? G = T = ? A T ? = = G ? ? ? T = C = ? G C ? = = T ? ? 0 P075 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P076 = = = = = = ? = = = = = = ? = = = = = = ? = = = = = = ? 0 P077 C G = = = = = = ? = ? G = = T T = = = = = = ? = ? T = = 0 P078 C G = T = C A T C = = G = = T T = C = T G C G = = T = = 0 P079 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P080 ? G = = = C = = ? T = G ? ? ? T = = = T = = ? G = T ? ? 0 P081 C G = T ? ? A T C = = G = ? T T = C ? ? G C G = = T = ? 0 P082 C G = T = C A T ? = = G = = T T = C = T G C ? = = T = = 0 P083 ? G ? = = C ? = C = A G = ? ? T ? = = T ? = G = G T = ? 0 P084 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P085 = = = = = = = = ? = = = C ? = = = = = = = = ? = = = A ? 0 P086 = = = = = = = = = = = = C = = = = = = = = = = = = = A = 0 P087 ? = T = = = ? T = = G = = ? ? = C = = = ? C = = A = = ? 0 P088 ? G C = T C ? = ? = A G = ? ? T T = A T ? = ? = G T = ? 0 P089 C G = = ? ? = = C = = G ? ? T T = = ? ? = = G = = T ? ? 0 P090 C G = T = C A T ? ? ? G ? ? T T = C = T G C ? ? ? T ? ? END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? 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END PHASEPROBS