************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 igbp4.phase.inp igbp4.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST igbp4.phase.out_freqs : haplotype frequency estimates igbp4.phase.out_pairs : most likely haplotype pairs for each individual igbp4.phase.out_recom : estimates of recombination parameters igbp4.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 10 Positions of loci: 177 235 727 1097 2603 4554 5151 10192 10212 11672 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file igbp4.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ATCACGCGTA 27.000000 2 ATCACGCGTG 7.000000 3 ATCACGCACA 9.000000 4 ATCACGTGTG 38.000000 5 ATCACGTACA 1.000000 6 ATCACACGTA 2.000000 7 ATCACATGTG 1.000000 8 CCCGCGCGTA 2.000000 9 CCCGCGTGTG 5.000000 10 CCCGCACGTA 16.000000 11 CCCGCACGTG 1.000000 12 CCCGCACACA 43.000000 13 CCCGCATGTG 8.000000 14 CCCGTACGTA 1.000000 15 CCTGCACGCG 1.000000 16 CCTGTACGTA 2.000000 17 CCTGTATGTG 13.000000 18 CCTGTATATG 1.000000 19 CTCACGTGTG 2.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,4) P002: (3,8) P003: (12,14) P004: (17,17) P005: (1,3) P006: (1,1) P007: (4,7) P008: (1,9) P009: (9,12) P010: (12,19) P011: (2,13) P012: (4,10) P013: (1,4) P014: (3,12) P015: (12,13) P016: (1,4) P017: (12,17) P018: (12,12) P019: (2,17) P020: (3,12) P021: (13,17) P022: (1,4) P023: (4,4) P024: (4,13) P025: (4,5) P026: (12,12) P027: (10,12) P028: (4,12) P029: (10,16) P030: (4,10) P031: (1,4) P032: (12,12) P033: (4,13) P034: (1,4) P035: (1,1) P036: (2,12) P037: (1,2) P038: (1,17) P039: (4,4) P040: (6,10) P041: (10,17) P042: (12,17) P043: (4,10) P044: (1,4) P045: (12,12) P046: (4,10) P047: (1,4) P048: (1,12) P049: (1,3) P050: (3,4) P051: (1,12) P052: (4,10) P053: (1,12) P054: (1,3) P055: (4,4) P056: (6,12) P057: (3,18) P058: (12,12) P059: (12,13) P060: (9,10) P061: (13,17) P062: (1,4) P063: (8,12) P064: (12,17) P065: (11,17) P066: (4,4) P067: (4,12) P068: (4,10) P069: (4,4) P070: (1,4) P071: (2,4) P072: (2,12) P073: (4,4) P074: (12,12) P075: (1,12) P076: (12,12) P077: (4,19) P078: (1,12) P079: (4,12) P080: (15,17) P081: (10,10) P082: (10,10) P083: (9,10) P084: (12,13) P085: (1,3) P086: (2,12) P087: (9,17) P088: (1,12) P089: (12,16) P090: (12,12) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 A T C A C G C G T A A T C A C G T G T G 0 P002 (A) (T) C (A) C G C A C A (C) (C) C (G) C G C G T A 0 P003 C C C G (C) A C A C A C C C G (T) A C G T A 0 P004 C C T G T A T G T G C C T G T A T G T G 0 P005 A T C A C G C G T A A T C A C G C A C A 0 P006 A T C A C G C G T A A T C A C G C G T A 0 P007 A T C A C G T G T G A T C A C A T G T G 0 P008 A T C A C G (C) G T (A) C C C G C G (T) G T (G) 0 P009 C C C G C G T G T G C C C G C A C A C A 0 P010 C C C G C A C A C A C T C A C G T G T G 0 P011 A T C A C G (C) G T G C C C G C A (T) G T G 0 P012 A T C A C G (T) G T (G) C C C G C [A] (C) G T (A) 0 P013 A T C A C G C G T A A T C A C G T G T G 0 P014 A T C A C G C A C A C C C G C A C A C A 0 P015 C C C G C A C A C A C C C G C [A] T G T G 0 P016 A T C A C G C G T A A T C A C G T G T G 0 P017 C C C G C A C A C A C C T G T A T G T G 0 P018 C C C G C A C A C A C C C G C A C [A] [C] A 0 P019 A T C A C G C G T G C C T G T A T G T G 0 P020 A T C A C G C A C A C C C G C A C A C A 0 P021 C C C G C A T G T G C C T G T A T G T G 0 P022 A T C A C G C G T A A T C A C G T G T G 0 P023 A T C A C G T G T G A T C A C G T G T G 0 P024 A T C A C G T G T G C C C G C A T G T G 0 P025 A T C A C G T G T G A T C A C G T A C A 0 P026 C C C G C A C A C A C C C G C A C A C A 0 P027 C C C G C A C G T A C C C G C A C A C A 0 P028 A T C A C G T G T G C C C G C A C A C A 0 P029 C C C G C A C G T A C C T G T A C G T A 0 P030 A T C A C G (T) G T [G] C C C G C [A] (C) G T [A] 0 P031 A T C A C G C G T A A T C A C G T G T G 0 P032 C C C G C A C A C A C C C G C A C A C A 0 P033 A T C A C G T G T G C C C G C A T G T G 0 P034 A T C A C G C G T A A T C A C G T G T G 0 P035 A T C A C G C G T A A T C A C G C G T A 0 P036 A T C A C G C G T (G) C C C G C A C [A] [C] (A) 0 P037 A T C A C G C G T A A T C A C G C G T G 0 P038 A T C A C G (C) G T (A) C C T G T A (T) G T (G) 0 P039 A T C A C G T G T G A T C A C G T G T G 0 P040 A T C A C A C G T A C C C G C A C G T A 0 P041 C C C G C A (C) G T (A) C C T G T A (T) G T (G) 0 P042 C C C G C A C A C A C C T G T A T G T G 0 P043 A T C A C G (T) G T (G) C C C G C A (C) G T (A) 0 P044 A T C A C G C G T A A T C A C G T G T G 0 P045 C C C G C A C A C A C C C G C A C A C A 0 P046 A T C A C G (T) G T (G) C C C G C [A] (C) G T (A) 0 P047 A T C A C G C G T A A T C A C G T G T G 0 P048 A T C A C G C G T A C C C G C A C [A] [C] A 0 P049 A T C A C G C G T A A T C A C G C A C A 0 P050 A T C A C G C A C A A T C A C G T G T G 0 P051 A T C A C G C (G) (T) A C C C G C A C (A) (C) A 0 P052 A T C A C G (T) G T (G) C C C G C [A] (C) G T (A) 0 P053 A T C A C G C (G) (T) A C C C G C A C (A) (C) A 0 P054 A T C A C G C G T A A T C A C G C A C A 0 P055 A T C A C G T G T G A T C A C G T G T G 0 P056 A T C A C A C (G) (T) A C C C G C A C (A) (C) A 0 P057 A T C A C G (C) A (C) (A) C C [T] G T A (T) A (T) (G) 0 P058 C C C G C A C A C A C C C G C A C A C A 0 P059 C C C G C A C [A] [C] A C C C G C A T G T G 0 P060 C C C G C (G) T G T G C C C G C (A) C G T A 0 P061 C C C G C A T G T G C C T G T A T G T G 0 P062 A T C A C G C G T A A T C A C G T G T G 0 P063 C C C G C (G) C G T A C C C G C (A) C A C A 0 P064 C C C G C A C A C A C C T G T A T G T G 0 P065 C C C G C A C G T G C C T G T A T G T G 0 P066 A T C A C G T G T G A T C A C G T G T G 0 P067 A T C A C G T G T G C C C G C A C A C A 0 P068 A T C A C G (T) G T (G) C C C G C A (C) G T (A) 0 P069 A T C A C G T G T G A T C A C G T G T G 0 P070 A T C A C G C G T A A T C A C G T G T G 0 P071 A T C A C G C G T G A T C A C G T G T G 0 P072 A T C A C G C (G) (T) (G) C C C G C A C (A) (C) (A) 0 P073 [A] [T] C A C G T G T G A T C A C G T G T G 0 P074 C C C G C A C A C A C C C G C A C A C A 0 P075 A T C A C G C (G) (T) A C C C G C A C (A) (C) A 0 P076 C C C G C A C A C A C C C G C A C A C A 0 P077 A T C A C G T G T G C T C A C G T G T G 0 P078 A T C A C G C [G] [T] A C C C G C A C [A] [C] A 0 P079 A T C A C G T G T G C C C G C A C A C A 0 P080 C C T G C A C G (C) G C C T G T A T G (T) G 0 P081 C C C G C A C G T A C C C G C A C G T A 0 P082 C C C G C A C G T A C C C G C A C G T A 0 P083 C C C G C (G) T G T G C C C G C (A) C G T A 0 P084 C C C G C A C A C A C C C G C A T G T G 0 P085 A T C A C G C G T A A T C A C G C A C A 0 P086 A T C A C G C (G) (T) (G) C C C G C A C (A) (C) (A) 0 P087 C C C G C G T G T G C C T G T A T G T G 0 P088 A T C A C G C (G) (T) A C C C G C A C (A) (C) A 0 P089 [C] C C [G] (C) [A] C A C A [C] C [T] [G] (T) [A] C G T A 0 P090 C C C G C A C A C A C C C G C A C A C A 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 (A) (T) ? (A) = = = ? C = (C) (C) ? (G) = = = ? T = 0 P003 = = = ? (C) = = A C ? = = = ? (T) = = G T ? 0 P004 = = = ? = = = = = = = = = ? = = = = = = 0 P005 = = = ? = = = ? T = = = = ? = = = ? C = 0 P006 = = = ? = = = = = = = = = ? = = = = = = 0 P007 = = ? ? = G = = = = = = ? ? = A = = = = 0 P008 A T ? ? = = (C) = = (A) C C ? ? = = (T) = = (G) 0 P009 ? ? ? = = G T G T G ? ? ? = = A C A C A 0 P010 = C ? G = ? C A C A = T ? A = ? T G T G 0 P011 A T = ? = G (C) = = = C C = ? = A (T) = = = 0 P012 A T = ? = ? (T) = = (G) C C = ? = ? (C) = = (A) 0 P013 = = = ? = = C = = A = = = ? = = T = = G 0 P014 A T = ? = ? = = = ? C C = ? = ? = = = ? 0 P015 = = = ? = ? C A C A = = = ? = ? T G T G 0 P016 = = = = = = C = = A = = = = = = T = = G 0 P017 ? ? ? = C = C A C A ? ? ? = T = T G T G 0 P018 = = = = = = = ? ? = = = = = = = = ? ? = 0 P019 A T C A C G C = = = C C T G T A T = = = 0 P020 A T = ? = G = = ? ? C C = ? = A = = ? ? 0 P021 = = C ? C = = = = = = = T ? T = = = = = 0 P022 = = = ? = ? C = = A = = = ? = ? T = = G 0 P023 = = = = = ? = = = ? = = = = = ? = = = ? 0 P024 A T = A = G = ? ? = C C = G = A = ? ? = 0 P025 ? ? ? = = = = G T G ? ? ? = = = = A C A 0 P026 = = = = = ? = = = ? = = = = = ? = = = ? 0 P027 = = = ? = = = G T = = = = ? = = = A C = 0 P028 A T = ? = G T G T G C C = ? = A C A C A 0 P029 = = C ? C = = = = = = = T ? T = = = = = 0 P030 A T ? ? = ? (T) = = ? C C ? ? = ? (C) = = ? 0 P031 = = = = = = C = = A = = = = = = T = = G 0 P032 = = = = = = = = = ? = = = = = = = = = ? 0 P033 ? ? ? A = G = = = = ? ? ? G = A = = = = 0 P034 = = = = = = C = = A = = = = = = T = = G 0 P035 = = = = = = = = = = = = = = = = = = = = 0 P036 A T = ? = G = ? ? (G) C C = ? = A = ? ? (A) 0 P037 = = = ? = = = = = A = = = ? = = = = = G 0 P038 A T C ? C G (C) = = (A) C C T ? T A (T) = = (G) 0 P039 = = = = = = = = = = = = = = = = = = = = 0 P040 A T = A = = = = = = C C = G = = = = = = 0 P041 ? ? ? = C = (C) = = (A) ? ? ? = T = (T) = = (G) 0 P042 = = C = C = C A C A = = T = T = T G T G 0 P043 A T = ? = G (T) = = (G) C C = ? = A (C) = = (A) 0 P044 = = = ? = = C = = A = = = ? = = T = = G 0 P045 = = = ? = = = = = = = = = ? = = = = = = 0 P046 A T = ? = ? (T) ? = (G) C C = ? = ? (C) ? = (A) 0 P047 = = = = = = C = = A = = = = = = T = = G 0 P048 A T = A = G = ? ? = C C = G = A = ? ? = 0 P049 ? ? ? = = = = G T = ? ? ? = = = = A C = 0 P050 = = = = = = C A C A = = = = = = T G T G 0 P051 A T = ? = G = (G) (T) = C C = ? = A = (A) (C) = 0 P052 A T = ? = ? (T) = = (G) C C = ? = ? (C) = = (A) 0 P053 A T = ? = ? = (G) (T) = C C = ? = ? = (A) (C) = 0 P054 = = = ? = = = G T = = = = ? = = = A C = 0 P055 = = = = ? = = = = = = = = = ? = = = = = 0 P056 A T = ? = = = (G) (T) = C C = ? = = = (A) (C) = 0 P057 ? ? ? A C G (C) = (C) (A) ? ? ? G T A (T) = (T) (G) 0 P058 = = = = ? = = = = = = = = = ? = = = = = 0 P059 = = = ? = = C ? ? A = = = ? = = T ? ? G 0 P060 = = = ? = (G) T = = G = = = ? = (A) C = = A 0 P061 = = C ? C = = = = = = = T ? T = = = = = 0 P062 = = = ? = = C = = A = = = ? = = T = = G 0 P063 = = = = = (G) = G T = = = = = = (A) = A C = 0 P064 = = C ? C = C A C A = = T ? T = T G T G 0 P065 ? ? ? = C = C = = = ? ? ? = T = T = = = 0 P066 = = = = = = = = = = = = = = = = = = = = 0 P067 A T = ? = G T G T G C C = ? = A C A C A 0 P068 A T = ? = G (T) = = (G) C C = ? = A (C) = = (A) 0 P069 = = = ? = = = = = = = = = ? = = = = = = 0 P070 = = = ? = = C = = A = = = ? = = T = = G 0 P071 = = = = = = C = = = = = = = = = T = = = 0 P072 A T = ? = G = (G) (T) (G) C C = ? = A = (A) (C) (A) 0 P073 ? ? ? ? = = = = = = ? ? ? ? = = = = = = 0 P074 = = = ? = = = = = = = = = ? = = = = = = 0 P075 A T = ? = ? = (G) (T) = C C = ? = ? = (A) (C) = 0 P076 = = = ? = = = = = = = = = ? = = = = = = 0 P077 A = = ? = = = = = = C = = ? = = = = = = 0 P078 A T = ? ? G ? ? ? = C C = ? ? A ? ? ? = 0 P079 A T = A = ? T G T G C C = G = ? C A C A 0 P080 = = = ? C = C = (C) = = = = ? T = T = (T) = 0 P081 ? ? ? = ? = = = = = ? ? ? = ? = = = = = 0 P082 = = = ? = = ? = = = = = = ? = = ? = = = 0 P083 = = = ? = (G) T = = G = = = ? = (A) C = = A 0 P084 = = = ? = = C A C A = = = ? = = T G T G 0 P085 = = = ? = ? = G T = = = = ? = ? = A C = 0 P086 A T = ? = ? = (G) (T) (G) C C = ? = ? = (A) (C) (A) 0 P087 = = C = C G = = = ? = = T = T A = = = ? 0 P088 A T = ? = ? = (G) (T) = C C = ? = ? = (A) (C) = 0 P089 ? ? ? ? (C) ? = A C ? ? ? ? ? (T) ? = G T ? 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 0.56 0.56 ? 0.56 = = = ? 1.00 = = = = ? 0.60 = = 1.00 1.00 ? = = = ? = = = = = = = = = ? = = = ? 1.00 = = = = ? = = = = = = = = ? ? = 1.00 = = = = 0.98 0.98 ? ? = = 0.65 = = 0.65 ? ? ? = = 0.92 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 0.51 = = = 0.98 0.98 = ? = ? 0.58 = = 0.58 = = = ? = = 1.00 = = 1.00 1.00 1.00 = ? = ? = = = ? = = = ? = ? 1.00 1.00 1.00 1.00 = = = = = = 1.00 = = 1.00 ? ? ? = 0.97 = 1.00 1.00 1.00 1.00 = = = = = = = ? ? = 1.00 1.00 1.00 1.00 1.00 1.00 0.91 = = = 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 0.91 0.91 0.91 0.91 = = 0.96 ? 1.00 = = = = = 0.98 0.98 ? ? = ? 0.56 = = ? = = = = = = 1.00 = = 1.00 = = = = = = = = = ? ? ? ? 1.00 = 0.98 = = = = = = = = = = 1.00 = = 1.00 = = = = = = = = = = 0.94 0.94 = ? = 0.94 = ? ? 0.82 = = = ? = = = = = 1.00 1.00 1.00 1.00 ? 1.00 1.00 0.84 = = 0.84 = = = = = = = = = = 1.00 1.00 = 1.00 = = = = = = ? ? ? = 0.94 = 0.90 = = 0.90 = = 0.99 = 0.99 = 1.00 1.00 1.00 1.00 1.00 1.00 = ? = 0.98 0.62 = = 0.62 = = = ? = = 1.00 = = 1.00 = = = ? = = = = = = 0.98 0.98 = ? = ? 0.58 ? = 0.58 = = = = = = 1.00 = = 1.00 0.92 0.92 = 0.92 = 0.92 = ? ? = ? ? ? = = = = 1.00 1.00 = = = = = = = 0.98 1.00 1.00 1.00 1.00 1.00 = ? = 1.00 = 0.86 0.86 = 0.98 0.98 = ? = ? 0.58 = = 0.58 1.00 1.00 = ? = ? = 0.85 0.85 = = = = ? = = = 1.00 1.00 = = = = = ? = = = = = 0.98 0.98 = ? = = = 0.90 0.90 = ? ? ? 1.00 0.98 1.00 0.77 = 0.77 0.77 = = = = ? = = = = = = = = ? = = 1.00 ? ? 1.00 = = = ? = 0.70 1.00 = = 1.00 = = 1.00 ? 1.00 = = = = = = = = ? = = 1.00 = = 1.00 = = = = = 0.71 = 1.00 1.00 = = = 0.99 ? 0.99 = 1.00 1.00 1.00 1.00 ? ? ? = 0.97 = 0.90 = = = = = = = = = = = = = 1.00 1.00 = ? = 1.00 0.91 0.91 0.91 0.91 1.00 1.00 = ? = 0.98 0.62 = = 0.62 = = = ? = = = = = = = = = ? = = 1.00 = = 1.00 = = = = = = 1.00 = = = 1.00 1.00 = ? = 1.00 = 0.88 0.88 0.86 ? ? ? ? = = = = = = = = = ? = = = = = = 1.00 1.00 = ? = ? = 0.85 0.85 = = = = ? = = = = = = 1.00 = = ? = = = = = = 1.00 1.00 = ? ? 1.00 ? ? ? = 0.96 0.96 = 0.96 = ? 0.92 0.92 0.92 0.92 = = = ? 0.96 = 0.94 = 0.67 = ? ? ? = ? = = = = = = = = ? = = ? = = = = = = ? = 0.70 1.00 = = 1.00 = = = ? = = 1.00 1.00 1.00 1.00 = = = ? = ? = 1.00 1.00 = 1.00 1.00 = ? = ? = 0.89 0.89 0.86 = = 1.00 = 1.00 0.98 = = = ? 1.00 1.00 = ? = ? = 0.85 0.85 = ? ? ? ? 0.82 ? = 0.91 0.91 ? = = = = = = = = = ? END PHASEPROBS