************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 tnfxx.phase.inp tnfxx.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST tnfxx.phase.out_freqs : haplotype frequency estimates tnfxx.phase.out_pairs : most likely haplotype pairs for each individual tnfxx.phase.out_recom : estimates of recombination parameters tnfxx.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 8 Positions of loci: 707 876 882 1431 1501 2228 3049 4902 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file tnfxx.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CCCGAGAG 3.000000 2 CCCGAGGC 9.000000 3 CCCGAGGG 1.000000 4 CCCGGGAG 2.000000 5 CACGGGAG 18.000000 6 CATGGAAG 7.000000 7 TCCGGGAG 109.000000 8 TCCGGGGG 4.000000 9 TCCGGAAG 1.000000 10 TCCAGGAG 15.000000 11 TCTGGAAG 11.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (4,8) P002: (2,7) P003: (6,7) P004: (7,7) P005: (7,11) P006: (7,7) P007: (6,7) P008: (5,8) P009: (6,7) P010: (1,7) P011: (4,7) P012: (5,7) P013: (7,7) P014: (5,7) P015: (6,7) P016: (7,11) P017: (7,7) P018: (5,5) P019: (7,7) P020: (5,7) P021: (7,7) P022: (5,7) P023: (2,7) P024: (7,7) P025: (7,7) P026: (7,7) P027: (2,9) P028: (8,10) P029: (5,7) P030: (7,7) P031: (6,7) P032: (5,5) P033: (7,7) P034: (7,7) P035: (7,7) P036: (7,7) P037: (7,7) P038: (7,7) P039: (7,10) P040: (10,10) P041: (2,7) P042: (7,10) P043: (7,7) P044: (7,7) P045: (7,7) P046: (7,7) P047: (7,7) P048: (7,7) P049: (7,10) P050: (7,7) P051: (2,11) P052: (6,7) P053: (7,10) P054: (7,10) P055: (7,11) P056: (5,7) P057: (7,7) P058: (2,7) P059: (7,11) P060: (7,7) P061: (7,10) P062: (5,8) P063: (2,7) P064: (7,10) P065: (7,7) P066: (7,7) P067: (5,7) P068: (6,7) P069: (5,7) P070: (11,11) P071: (5,7) P072: (10,11) P073: (5,7) P074: (5,7) P075: (7,11) P076: (7,7) P077: (2,10) P078: (7,7) P079: (7,11) P080: (7,7) P081: (7,7) P082: (5,7) P083: (3,7) P084: (1,7) P085: (1,7) P086: (10,10) P087: (7,7) P088: (7,10) P089: (2,11) P090: (7,7) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 C C C G [G] G A G T C C G G G G G 0 P002 (C) C C G (A) G (G) (C) (T) C C G (G) G (A) (G) 0 P003 C A T G G A A G T C C G G G A G 0 P004 T C C G G G A G T C C G G G A [G] 0 P005 T C (C) G G G A G T C (T) G G A A G 0 P006 T C C G G G A G T C C G G G A [G] 0 P007 (C) (A) T G G (A) A G (T) (C) C G G (G) A G 0 P008 (C) [A] C G G G (A) G (T) C C G [G] G (G) G 0 P009 (C) (A) T G G (A) A G (T) (C) C G G (G) A G 0 P010 C C C G A G A G T C C G G G A G 0 P011 C C C G [G] G A G T C C G G G A G 0 P012 C A C G G G A G T C C G G G A G 0 P013 T C C G G G A G T C C G G G A G 0 P014 C A C G G G A G T C C G G G A G 0 P015 (C) (A) T G G (A) A G (T) (C) C G G (G) A G 0 P016 T C C G G G A G T C T G G A A G 0 P017 T C C G G G A G T C C G G G A [G] 0 P018 C A C G G G A G C A C G G G A G 0 P019 T C C G G G A G T C C G G G A G 0 P020 C A C G G G A G T C C G G G A G 0 P021 T C C G G G A G T C C G G G A G 0 P022 C A C G G G A G T C C G G G A G 0 P023 (C) C C G (A) G (G) (C) (T) C C G (G) G (A) (G) 0 P024 T C C G G G A G T C C G G G A G 0 P025 T C C G G G A G [T] C C G G G A G 0 P026 T C C G G G A G T C C G G G A G 0 P027 (C) C C G (A) (G) (G) (C) (T) C C G (G) (A) (A) (G) 0 P028 T C C (G) G G G G T C C (A) G G A G 0 P029 C A C G G G A G T C C G G G A G 0 P030 T C C G G G A G T C C G G G A [G] 0 P031 (C) (A) T G G (A) A G (T) (C) C G G (G) A G 0 P032 C A C G G G A G C A C G G G A G 0 P033 T C C G G G A G [T] C C G G G A G 0 P034 T C C G G G A G T C C G G G A G 0 P035 T C C G G G A G T C C G G G A G 0 P036 T C C G G G A G T C C G G G A G 0 P037 T C C G G G A G [T] C C G G G A G 0 P038 T C C G G G A G T C C G G G A [G] 0 P039 T C C G G G A G T C C A G G A G 0 P040 T C C A G G A G T C C A G G A [G] 0 P041 [C] C C G (A) G (G) (C) T C C G (G) G (A) (G) 0 P042 T C C G G G A G T C C A G G A G 0 P043 T C C G G G A G [T] C C G G G A G 0 P044 T C C G G G A G T C C G G G A G 0 P045 T C C G G G A G T C C G G G A G 0 P046 T C C G G G A G T C C G G G A G 0 P047 T C C G G G A G T C C G G G A G 0 P048 T C C G G G A G T C C G G G A G 0 P049 T C C G G G A G T C C A G G A G 0 P050 T C C G G G A G T C C G G G A G 0 P051 C C C G A (G) (G) (C) T C T G G (A) (A) (G) 0 P052 (C) (A) T G G (A) A G (T) (C) C G G (G) A G 0 P053 T C C G G G A G T C C A G G A G 0 P054 T C C G G G A G T C C A G G A G 0 P055 T C C G G G A G T C T G G A A G 0 P056 C A C G G G A G T C C G G G A G 0 P057 T C C G G G A G T C C G G G A G 0 P058 (C) C C G (A) G (G) (C) (T) C C G (G) G (A) (G) 0 P059 T C (C) G G G A G T C (T) G G A A G 0 P060 T C C G G G A G T C C G G G A G 0 P061 T C C G G G A G T C C A G G A G 0 P062 C A C G G G (A) G T C C G G G (G) G 0 P063 (C) C C G (A) G (G) (C) (T) C C G (G) G (A) (G) 0 P064 T C C G G G A G T C C A G G A G 0 P065 T C C G G G A G T C C G G G A G 0 P066 T C C G G G A G T C C G G G A G 0 P067 C A C G G G A G T C C G G G A G 0 P068 (C) (A) T G G (A) A G (T) (C) C G G (G) A G 0 P069 C A C G G G A G T C C G G G A G 0 P070 T C T G G A A G T C T G G A A G 0 P071 C A C G G G A G T C C G G G A G 0 P072 T C C A G (G) A G T C T G G (A) A G 0 P073 C A C G G G A G T C C G G G A G 0 P074 C A C G G G A G T C C G G G A G 0 P075 T C (C) G G G A G T C (T) G G A A G 0 P076 T C C G G G A G T C C G G G A G 0 P077 C C C G A G (G) (C) T C C A G G (A) (G) 0 P078 T C C G G G A G T C C G G G A G 0 P079 T C (C) G G G A G T C (T) G G A A G 0 P080 T C C G G G A G T C C G G G A G 0 P081 T C C G G G A G T C C G G G A G 0 P082 C A C G G G A G T C C G G G A G 0 P083 C C C G A G (G) [G] T C C G G G (A) G 0 P084 C C C G A G A G T C C G G G A G 0 P085 (C) C C G A G A G (T) C C G G G A G 0 P086 T C C A G G A G T C C A G G A G 0 P087 T C C G G G A G T C C G G G A G 0 P088 T C C G G G A G T C C A G G A G 0 P089 C C C G A (G) (G) (C) T C T G G (A) (A) (G) 0 P090 T C C G G G A G T C C G G G A G 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 = = = ? = A ? T = = = ? = G ? 0 P002 (C) = = = (A) = (G) (C) (T) = = = (G) = (A) (G) 0 P003 C A T = = A = ? T C C = = G = ? 0 P004 ? = = = = = = ? ? = = = = = = ? 0 P005 = = (C) = = G = ? = = (T) = = A = ? 0 P006 = = = = = = = ? = = = = = = = ? 0 P007 (C) (A) T = = (A) = = (T) (C) C = = (G) = = 0 P008 (C) ? = ? ? = (A) ? (T) ? = ? ? = (G) ? 0 P009 (C) (A) T = = (A) = = (T) (C) C = = (G) = = 0 P010 C = = = A ? = = T = = = G ? = = 0 P011 C = = = ? = = ? T = = = ? = = ? 0 P012 C A = = = = = = T C = = = = = = 0 P013 = = = ? ? = = ? = = = ? ? = = ? 0 P014 C A = = = ? = = T C = = = ? = = 0 P015 (C) (A) T = = (A) = = (T) (C) C = = (G) = = 0 P016 = = C = = G = ? = = T = = A = ? 0 P017 = = = = = = = ? = = = = = = = ? 0 P018 = = = = = = = = = = = = = = = = 0 P019 = = = = = = = = = = = = = = = = 0 P020 C A = = = = = = T C = = = = = = 0 P021 = = = = = ? = = = = = = = ? = = 0 P022 C A = = = = = = T C = = = = = = 0 P023 (C) = = = (A) = (G) (C) (T) = = = (G) = (A) (G) 0 P024 = = = = = = = = = = = = = = = = 0 P025 ? ? ? = = ? = = ? ? ? = = ? = = 0 P026 = = = = = = = = = = = = = = = = 0 P027 (C) = ? = (A) (G) (G) (C) (T) = ? = (G) (A) (A) (G) 0 P028 = = = (G) = = G = = = = (A) = = A = 0 P029 C A = = = = = = T C = = = = = = 0 P030 = = = = = = = ? = = = = = = = ? 0 P031 (C) (A) T = = (A) = = (T) (C) C = = (G) = = 0 P032 = = = = = = = = = = = = = = = = 0 P033 ? ? ? = = ? = = ? ? ? = = ? = = 0 P034 = = = = = = = = = = = = = = = = 0 P035 = = = = = = = = = = = = = = = = 0 P036 = = = = = ? = = = = = = = ? = = 0 P037 ? ? ? = = = = = ? ? ? = = = = = 0 P038 = = = = = = = ? = = = = = = = ? 0 P039 = = = G = = = = = = = A = = = = 0 P040 = = = = = = = ? = = = = = = = ? 0 P041 ? ? ? = (A) = (G) (C) ? ? ? = (G) = (A) (G) 0 P042 = = = G = = = = = = = A = = = = 0 P043 ? ? ? = = = = = ? ? ? = = = = = 0 P044 = = = = = = = = = = = = = = = = 0 P045 = = = = = = = = = = = = = = = = 0 P046 = = = = = = = = = = = = = = = = 0 P047 = = = = = = = = = = = = = = = = 0 P048 = = = ? ? = = ? = = = ? ? = = ? 0 P049 ? ? ? G = = = = ? ? ? A = = = = 0 P050 = = = = = = = = = = = = = = = = 0 P051 C = C = A (G) (G) (C) T = T = G (A) (A) (G) 0 P052 (C) (A) T = = (A) = = (T) (C) C = = (G) = = 0 P053 ? ? ? G = = = ? ? ? ? A = = = ? 0 P054 = = = G = = = = = = = A = = = = 0 P055 = = C = = G = ? = = T = = A = ? 0 P056 C A = = = = = = T C = = = = = = 0 P057 = = = = = = = = = = = = = = = = 0 P058 (C) = = = (A) = (G) (C) (T) = = = (G) = (A) (G) 0 P059 = = (C) = = G = = = = (T) = = A = = 0 P060 = ? ? = = = = = = ? ? = = = = = 0 P061 = ? ? G = = = = = ? ? A = = = = 0 P062 C A = = = = (A) = T C = = = = (G) = 0 P063 (C) = = = (A) = (G) (C) (T) = = = (G) = (A) (G) 0 P064 = = = G = = = = = = = A = = = = 0 P065 = = = = = = = = = = = = = = = = 0 P066 = = = = = = = = = = = = = = = = 0 P067 C A = = = = = = T C = = = = = = 0 P068 (C) (A) T = = (A) = = (T) (C) C = = (G) = = 0 P069 C A = = = = = = T C = = = = = = 0 P070 = = = = = = = = = = = = = = = = 0 P071 C A = = = = = = T C = = = = = = 0 P072 = = C A = (G) = ? = = T G = (A) = ? 0 P073 C A = = = = = = T C = = = = = = 0 P074 C A = = = = = = T C = = = = = = 0 P075 = = (C) = = G = = = = (T) = = A = = 0 P076 = = = = = = = = = = = = = = = = 0 P077 C = = G A = (G) (C) T = = A G = (A) (G) 0 P078 = = = = = = = = = = = = = = = = 0 P079 = = (C) = = G = = = = (T) = = A = = 0 P080 = = ? = = = = = = = ? = = = = = 0 P081 = = = = = = = = = = = = = = = = 0 P082 C A = = = = = = T C = = = = = = 0 P083 C = = = A = (G) ? T = = = G = (A) ? 0 P084 C = = = A ? = = T = = = G ? = = 0 P085 (C) ? = = A ? = = (T) ? = = G ? = = 0 P086 = = = = ? ? = = = = = = ? ? = = 0 P087 = = = = = = = = = = = = = = = = 0 P088 = = = G = = = = = = = A = = = = 0 P089 C = C = A (G) (G) (C) T = T = G (A) (A) (G) 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 ? 0.77 = = = 0.81 = 0.87 0.79 1.00 1.00 1.00 = = 1.00 = ? ? = = = = = = ? = = 0.79 = = 1.00 = ? = = = = = = = ? 0.71 0.72 0.92 = = 0.87 = = 0.64 ? = ? ? = 0.74 ? 0.71 0.71 0.92 = = 0.87 = = 0.94 = = = 1.00 ? = = 1.00 = = = ? = = ? 0.99 1.00 = = = = = = = = = ? ? = = ? 0.99 1.00 = = = ? = = 0.70 0.71 0.92 = = 0.87 = = = = 1.00 = = 1.00 = ? = = = = = = = ? = = = = = = = = = = = = = = = = 0.99 1.00 = = = = = = = = = = = ? = = 0.99 1.00 = = = = = = 0.77 = = = 0.81 = 0.87 0.79 = = = = = = = = ? ? ? = = ? = = = = = = = = = = 0.87 = ? = 0.88 0.75 0.79 0.71 = = = 0.51 = = 1.00 = 0.99 1.00 = = = = = = = = = = = = = ? 0.71 0.72 0.92 = = 0.87 = = = = = = = = = = ? ? ? = = ? = = = = = = = = = = = = = = = = = = = = = = = ? = = ? ? ? = = = = = = = = = = = = ? = = = 1.00 = = = = = = = = = = = ? ? ? ? = 0.89 = 0.83 0.89 = = = 1.00 = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = ? ? ? ? 1.00 = = = = = = = = = = = = 0.91 = 0.93 = 0.93 0.87 0.76 0.66 0.71 0.71 0.92 = = 0.87 = = ? ? ? 1.00 = = = ? = = = 1.00 = = = = = = 1.00 = = 1.00 = ? 0.99 1.00 = = = = = = = = = = = = = = 0.78 = = = 0.81 = 0.88 0.79 = = 0.79 = = 1.00 = = = ? ? = = = = = = ? ? 1.00 = = = = 0.99 1.00 = = = = 0.52 = 0.78 = = = 0.81 = 0.87 0.79 = = = 1.00 = = = = = = = = = = = = = = = = = = = = 0.99 1.00 = = = = = = 0.71 0.71 0.92 = = 0.87 = = 0.99 1.00 = = = = = = = = = = = = = = 0.99 1.00 = = = = = = = = 1.00 0.94 = 0.84 = ? 0.99 1.00 = = = = = = 0.99 1.00 = = = = = = = = 0.79 = = 1.00 = = = = = = = = = = 0.96 = = 0.98 0.98 = 0.70 0.61 = = = = = = = = = = 0.79 = = 1.00 = = = = ? = = = = = = = = = = = = = 0.99 1.00 = = = = = = 1.00 = = = 1.00 = 0.69 ? 0.95 = = = 1.00 ? = = 0.86 ? = = 1.00 ? = = = = = = ? ? = = = = = = = = = = = = = 1.00 = = = = 0.91 = 0.93 = 0.93 0.86 0.76 0.66 = = = = = = = = END PHASEPROBS