************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 cyr61.phase.inp cyr61.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST cyr61.phase.out_freqs : haplotype frequency estimates cyr61.phase.out_pairs : most likely haplotype pairs for each individual cyr61.phase.out_recom : estimates of recombination parameters cyr61.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 11 Positions of loci: 175 628 1166 1412 2448 2835 5347 5601 6224 6489 6771 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file cyr61.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ACACAGCGCCT 47.000000 2 ACACAGCGCCC 1.000000 3 ACACAGTGCTC 3.000000 4 ACGAAGTGTTC 1.000000 5 ACGAGGTGCCC 3.000000 6 ACGAGCTGCTC 1.000000 7 ATGCGGTGCTC 3.000000 8 ATGAAGCGCCT 3.000000 9 ATGAGGCCCCT 4.000000 10 ATGAGGCCCCC 18.000000 11 ATGAGGTGCTC 12.000000 12 ATGAGGTGTTC 1.000000 13 ATGAGCCGCCT 2.000000 14 ATGAGCTGCTC 20.000000 15 ATGAGCTGTTC 5.000000 16 GTGAAGCGCCT 1.000000 17 GTGAAGCCCCC 1.000000 18 GTGAAGTGCTC 2.000000 19 GTGAAGTGTTC 30.000000 20 GTGAACTGCTC 1.000000 21 GTGAGGCCCCC 9.000000 22 GTGAGGTGCTC 1.000000 23 GTGAGGTGTTC 11.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,1) P002: (10,19) P003: (10,19) P004: (11,11) P005: (14,23) P006: (13,19) P007: (11,21) P008: (1,1) P009: (14,19) P010: (10,21) P011: (14,19) P012: (13,21) P013: (15,15) P014: (14,23) P015: (1,14) P016: (7,12) P017: (10,11) P018: (1,19) P019: (10,11) P020: (19,19) P021: (5,19) P022: (10,10) P023: (15,19) P024: (1,14) P025: (1,1) P026: (1,19) P027: (1,1) P028: (19,19) P029: (11,11) P030: (1,14) P031: (14,19) P032: (11,20) P033: (19,21) P034: (1,1) P035: (1,10) P036: (9,23) P037: (1,23) P038: (11,23) P039: (8,14) P040: (19,21) P041: (14,19) P042: (2,5) P043: (1,14) P044: (1,1) P045: (10,23) P046: (14,22) P047: (7,19) P048: (1,1) P049: (3,19) P050: (1,21) P051: (1,19) P052: (1,1) P053: (1,19) P054: (6,7) P055: (1,8) P056: (1,3) P057: (1,19) P058: (10,23) P059: (11,11) P060: (17,21) P061: (19,23) P062: (14,16) P063: (15,19) P064: (1,4) P065: (14,21) P066: (1,10) P067: (1,15) P068: (1,10) P069: (10,23) P070: (10,14) P071: (9,9) P072: (1,23) P073: (1,1) P074: (1,1) P075: (9,10) P076: (1,14) P077: (18,21) P078: (14,19) P079: (1,14) P080: (19,23) P081: (19,19) P082: (1,1) P083: (10,14) P084: (1,10) P085: (1,18) P086: (14,19) P087: (5,11) P088: (1,3) P089: (8,19) P090: (1,10) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 A C A C A G C G C C T A C A C A G C G C C T 0 P002 A T G A G G C C C C C G T G A [A] G T G T T C 0 P003 (A) T G A G G C C C C C (G) T G A [A] G T G [T] T C 0 P004 A T G A G G T G C T C A T G A G G T G C T C 0 P005 A T G A G C T G C T C G T G A G G T G T T C 0 P006 (A) T G A (G) (C) C G C C T (G) T G A (A) (G) T G T T C 0 P007 (A) T G A G G T G C T C (G) T G A G G C C C C C 0 P008 A C A C A G C G C C T A C A C A G C G C C T 0 P009 A T G A G C T G C T C G T G A A G T G T T C 0 P010 A T G A G G C C C C C G T G A G G C C C C C 0 P011 A T G A G [C] T G C T C G T G A [A] G T G T T C 0 P012 (A) T G A G C C G C C T (G) T G A G G C C C C C 0 P013 A T G A G C T G T T C A T G A G C T G T T C 0 P014 A T G A G C T G C T C G T G A G G T G T T C 0 P015 A C A C A G C G C C T A T G A G [C] T G C T C 0 P016 A T G (C) G G T G C T C A T G (A) G G T G T T C 0 P017 A T G A G G C C C C C A T G A G G T G C T C 0 P018 A C A C A G C G C C T G T G A A G T G T T C 0 P019 A T G A G G C C C C C A T G A G G T G C T C 0 P020 G T G A A G T G T T C G T G A A G T G T T C 0 P021 A C G A G G T G C C C G T G A A G T G T T C 0 P022 A T G A G G C C C C C A T G A G G C C C C C 0 P023 A T G A G C T G T T C G T G A A G T G T T C 0 P024 A C A C A G C G C C T A T G A G C T G C T C 0 P025 A C A C A G C G C C T A C A C A G C G C C T 0 P026 A C A C A G C G C C T G T G A A G T G T T C 0 P027 A C A C A G C G C C T A C A C A G C G C C T 0 P028 G T G A [A] G T G T T C G T G A A G T G T T C 0 P029 A T G A G G T G C T C A T G A G G T G C T C 0 P030 A C A C A G C G C C T A T G A G C T G C T C 0 P031 A T G A G C T G C T C G T G A A G T G T T C 0 P032 A T G A (G) G T G C T C G T G A (A) C T G C T C 0 P033 G T G A A G T G T T C G T G A G G C C C C C 0 P034 A C A C A G C G C C T A C A C A G C G C C T 0 P035 A C A C A G C G C C T A T G A G G C C C C C 0 P036 A T G A G G C C C C T G T G A G G T G T T C 0 P037 A C A C A G C G C C T G T G A G G T G T T C 0 P038 A T G A G G T G C T C G T G A G G T G T T C 0 P039 A T G A A G C G C C T A T G A G C T G C T C 0 P040 G T G A A G T G T T C G T G A G G C C C C C 0 P041 A T G A G C T G C T C G T G A A G T G T T C 0 P042 A C A C A G C G C C C A C G A G G T G C C C 0 P043 A C A C A G C G C C T A T G A G C T G C T C 0 P044 A C A C A G C G C C T A C A C A G C G C C T 0 P045 (A) T G A G G C C C C C (G) T G A G G T G T T C 0 P046 (A) T G A G C T G C T C (G) T G A G G T G C T C 0 P047 A T G C G G T G (C) T C G T G A A G T G (T) T C 0 P048 A C A C A G C G C C T A C A C A G C G C C T 0 P049 A C A C A G [T] G C T C G T G A A G T G T T C 0 P050 A C A C A G C G C C T G T G A G G C C C C C 0 P051 A C A C A G C G C C T G T G A A G T G T T C 0 P052 A C A C A G C G C C T A C A C A G C G C C T 0 P053 A C A C A G C G C C T G T G A A G T G [T] T C 0 P054 A (C) G A G C T G C T C A (T) G C G G T G C T C 0 P055 A C A C A G C G C C T A T G A A G C G C C T 0 P056 A C A C A G C G C C T A C A C A G [T] G C T C 0 P057 A C A C A G C G C C T G T G A A G T G T T C 0 P058 (A) T G A G G C C C C C (G) T G A G G T G T T C 0 P059 A T G A G G T G C T C A T G A G G T G C T C 0 P060 G T G A A G C [C] C C C G T G A G G C C C C C 0 P061 G T G A A G T G T T C G T G A G G T G T T C 0 P062 (A) T G A (G) (C) T G C T C (G) T G A (A) (G) C G C C T 0 P063 A T G A G C T G T T C G T G A A G T G T T C 0 P064 A C A C A G C G C C T A C G A A G T G T T C 0 P065 (A) T G A G [C] T G C T C (G) T G A G G C C C C C 0 P066 A C A C A G C G C C T A T G A G G C C C C C 0 P067 A C A C A G C G C C T A T G A G C T G T T C 0 P068 A C A C A G C G C C T A T G A G G C C C C C 0 P069 (A) T G A G G C C C C C (G) T G A G G T G T T C 0 P070 A T G A G G C C C C C A T G A G C T G C T C 0 P071 A T G A G G C C C C T A T G A G G C C C C T 0 P072 A C A C A G C G C C T G T G A G G T G T T C 0 P073 A C A C A G C G C C T A C A C A G C G C C T 0 P074 A C A C A G C G C C T A C A C A G C G C C T 0 P075 A T G A G G C C C C T A T G A G G C C C C C 0 P076 A C A C A G C G C C T A T G A G C T G C T C 0 P077 G T G A (A) G T G C T C G T G A (G) G C C C C C 0 P078 A T G A G C T G C T C G T G A A G T G T T C 0 P079 A C A C A G C G C C T A T G A G C T G C T C 0 P080 G T G A A G T G T T C G T G A G G T G T T C 0 P081 G T G A A G T G T T C G T G A A G T G T T C 0 P082 A C A C A G C G C C T A C A C A G C G C C T 0 P083 A T G A G G C C C C C A T G A G C T G C T C 0 P084 A C A C A G C G C C T A T G A G G C C C C C 0 P085 A C A C A G C G C C T G T G A A G T G C T C 0 P086 A T G A G C T G C T C G T G A A G T G T T C 0 P087 A C G A G G T G C C C A T G A G G T G C T C 0 P088 A C A C A G C G C C T A C A C A G [T] G C T C 0 P089 [A] T G A [A] G C G C C T [G] T G A [A] G T G T T C 0 P090 A C A C A G C G C C T A T G A G G C C C 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 A = = = ? = C C C C = G = = = ? = T G T T = 0 P003 (A) = ? = ? ? C C ? C = (G) = ? = ? ? T G ? T = 0 P004 = = = = = = = = = = = = = = = = = = = = = = 0 P005 A = = = = C = = C = = G = = = = G = = T = = 0 P006 (A) = = = (G) (C) C = C C T (G) = = = (A) (G) T = T T C 0 P007 (A) = = = = = T G = T = (G) = = = = = C C = C = 0 P008 = = = = = ? = = = = = = = = = = ? = = = = = 0 P009 A = ? = G C = = C = = G = ? = A G = = T = = 0 P010 A = = = = = = = = = = G = = = = = = = = = = 0 P011 A = ? = ? ? = = C = = G = ? = ? ? = = T = = 0 P012 (A) = = = = C = G = = T (G) = = = = G = C = = C 0 P013 = = ? = = = = = = = = = = ? = = = = = = = = 0 P014 A = = = = C = = C = = G = = = = G = = T = = 0 P015 = C A C ? ? C = = C T = T G A ? ? T = = T C 0 P016 = = ? (C) = = ? ? C = = = = ? (A) = = ? ? T = = 0 P017 = = ? = = = C C = C = = = ? = = = T G = T = 0 P018 A C A C = = C = C C T G T G A = = T = T T C 0 P019 = = = = = = C C = C = = = = = = = T G = T = 0 P020 = = ? = = = = = = = = = = ? = = = = = = = = 0 P021 A C ? = G = = = C C = G T ? = A = = = T T = 0 P022 = = ? = = = = = = = = = = ? = = = = = = = = 0 P023 A = ? = G C = = = = = G = ? = A G = = = = = 0 P024 = C A ? A G ? = = C T = T G ? G C ? = = T C 0 P025 = = = = = = = = = = = = = = = = = = = = = = 0 P026 A C A C = = C = C C T G T G A = = T = T T C 0 P027 = = = = = = = = = = = = = = = = = = = = = = 0 P028 = = = = ? = = = = = = = = = = ? = = = = = = 0 P029 = = = = = = = = = = = = = = = = = = = = = = 0 P030 = C A C A G C = = C T = T G A G C T = = T C 0 P031 A = = = G C = = C = = G = = = A G = = T = = 0 P032 A = = = (G) G ? ? = = = G = = = (A) C ? ? = = = 0 P033 = = ? = A = T G T T = = = ? = G = C C C C = 0 P034 = = = = = = = = = = = = = = = = = = = = = = 0 P035 = C A C A = = G = = T = T G A G = = C = = C 0 P036 A = = = = = C C C C T G = = = = = T G T T C 0 P037 A C A C A = C = C C T G T G A G = T = T T C 0 P038 A = = = = = = = C = = G = = = = = = = T = = 0 P039 = = = = A G C = = C T = = = = G C T = = T C 0 P040 = = ? = A = T G T T = = = ? = G = C C C C = 0 P041 A = = = G C = = C = = G = = = A G = = T = = 0 P042 = = A C A = C = = = = = = G A G = T = = = = 0 P043 = C A C A G C = = C T = T G A G C T = = T C 0 P044 = = = = = = = = = = = = = = = = = = = = = = 0 P045 (A) = = = = = C C C C = (G) = = = = = T G T T = 0 P046 (A) = = = = C = = = = = (G) = = = = G = = = = = 0 P047 A = = C G = ? ? (C) = = G = = A A = ? ? (T) = = 0 P048 = = = = = = = = = = = = = = = = = = = = = = 0 P049 A C A C = = ? ? C = = G T G A = = ? ? T = = 0 P050 A C A C A = = G = = T G T G A G = = C = = C 0 P051 A C A C = = C = C C T G T G A = = T = T T C 0 P052 = = = = ? = = = = = = = = = = ? = = = = = = 0 P053 A C A C = = C = ? C T G T G A = = T = ? T C 0 P054 = (C) = A = C = = = = = = (T) = C = G = = = = = 0 P055 = C A C = = ? ? = = = = T G A = = ? ? = = = 0 P056 = = = = = = ? ? = C T = = = = = = ? ? = T C 0 P057 A C A C = = C = C C T G T G A = = T = T T C 0 P058 (A) = = = = = C C C C = (G) = = = = = T G T T = 0 P059 = = = = = = = = = = = = = = = = = = = = = = 0 P060 = = = = A = ? ? = = = = = = = G = ? ? = = = 0 P061 = = = = A = = = = = = = = = = G = = = = = = 0 P062 (A) = = = (G) (C) T = = T C (G) = = = (A) (G) C = = C T 0 P063 A = = = G C = = = = = G = = = A G = = = = = 0 P064 = = A C = = C = C C T = = G A = = T = T T C 0 P065 (A) = ? = = ? T G = T = (G) = ? = = ? C C = C = 0 P066 = C A C A = = G = = T = T G A G = = C = = C 0 P067 = C A C A G C = C C T = T G A G C T = T T C 0 P068 = C A C A = = G = = T = T G A G = = C = = C 0 P069 (A) = = = = = C C C C = (G) = = = = = T G T T = 0 P070 = = = = = G C C = C = = = = = = C T G = T = 0 P071 = = = = = = = = = = = = = = = = = = = = = = 0 P072 A C A C A = C = C C T G T G A G = T = T T C 0 P073 = = = = = = = = = = = = = = = = = = = = = = 0 P074 = = ? ? = = = = = = = = = ? ? = = = = = = = 0 P075 = = = = = = = = = = T = = = = = = = = = = C 0 P076 = C A C A G C = = C T = T G A G C T = = T C 0 P077 = = = = (A) = T G = T = = = = = (G) = C C = C = 0 P078 A = = = G C = = C = = G = = = A G = = T = = 0 P079 = C A C A G C = = C T = T G A G C T = = T C 0 P080 = = = = A = = = = = = = = = = G = = = = = = 0 P081 = = = = = = = = = = = = = = = = = = = = = = 0 P082 = = = = = = = = = = = = = = = = = = = = = = 0 P083 = = = = = G C C = C = = = = = = C T G = T = 0 P084 = C A C A = = G = = T = T G A G = = C = = C 0 P085 A C A C = = ? ? = C T G T G A = = ? ? = T C 0 P086 ? = = = G C = = C = = ? = = = A G = = T = = 0 P087 = C = = = = = = = C = = T = = = = = = = T = 0 P088 = = = = = = ? ? = C T = = = = = = ? ? = T C 0 P089 ? = ? = ? ? C = C C T ? = ? = ? ? T = T T C 0 P090 = C ? C A = = G = = T = T ? A G = = C = = C END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = = = = = = = = = 0.93 = = = ? = 1.00 1.00 1.00 1.00 = 0.67 = ? = ? ? 1.00 1.00 ? 1.00 = = = = = = = = = = = = 0.98 = = = = 0.98 = = 0.94 = = 0.73 = = = 0.72 0.72 1.00 = 1.00 1.00 1.00 0.76 = = = = = 1.00 1.00 = 1.00 = = = = = = ? = = = = = 0.99 = ? = 0.99 1.00 = = 0.95 = = 1.00 = = = = = = = = = = 0.96 = ? = ? ? = = 0.95 = = 0.87 = = = = 0.97 = 1.00 = = 1.00 = = ? = = = = = = = = 0.98 = = = = 0.98 = = 0.93 = = = 0.99 0.99 0.99 ? ? 0.99 = = 0.99 0.99 = = ? 0.62 = = ? ? 1.00 = = = = ? = = = 1.00 1.00 = 1.00 = 0.99 0.99 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 ? = = 0.98 0.98 = = = = = = = = = = = 0.99 0.99 0.99 0.99 = = 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 0.99 = = 0.99 0.99 0.99 = = = 0.99 1.00 = = 0.95 = = 0.95 = = = 0.82 1.00 ? ? = = = = = ? = 0.92 = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = = 1.00 = = 0.99 0.98 = = = = = 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 0.96 = = = = = = = 1.00 = = = = = = 0.96 0.96 1.00 = = 1.00 1.00 = = ? = 0.92 = 1.00 1.00 1.00 1.00 = 0.99 = = = 0.99 1.00 = = 0.95 = = = = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 1.00 1.00 0.99 = = 0.99 0.99 = = = = = = = = = = = 0.88 = = = = = 1.00 1.00 1.00 1.00 = 0.68 = = = = 1.00 = = = = = 0.99 = = 0.94 0.97 = ? ? 0.84 = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = = ? ? 0.92 = = 0.97 1.00 1.00 1.00 1.00 = = 1.00 = = 0.99 0.99 0.99 0.99 0.99 = = 1.00 = 1.00 1.00 1.00 = = = = ? = = = = = = 0.99 0.99 0.99 0.99 = = 0.99 = ? 0.99 0.99 = 0.61 = 0.91 = 0.92 = = = = = = 1.00 1.00 1.00 = = ? ? = = = = = = = = = ? ? = 1.00 1.00 0.99 0.99 0.99 0.99 = = 1.00 = 1.00 1.00 1.00 0.88 = = = = = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = 1.00 = ? ? = = = = = = = 1.00 = = = = = = 0.72 = = = 0.79 0.81 1.00 = = 1.00 1.00 1.00 = = = 1.00 1.00 = = = = = = = 0.96 0.96 = = 1.00 = 1.00 1.00 1.00 0.80 = ? = = ? 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 0.98 = 0.98 0.98 0.98 = 1.00 1.00 1.00 1.00 = = 1.00 = = 0.99 0.88 = = = = = 1.00 1.00 1.00 1.00 = = = = = = 0.98 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 0.99 = = 0.99 0.99 = = = = 0.87 = 1.00 1.00 = 1.00 = 0.99 = = = 0.99 1.00 = = 0.95 = = = 1.00 1.00 1.00 1.00 1.00 0.99 = = 0.99 0.99 = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.98 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 = = 0.99 0.94 0.94 0.94 0.94 = = ? ? = 0.94 0.94 ? = = = 0.98 0.99 = = 0.94 = = = 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 END PHASEPROBS