************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 cdk1b.phase.inp cdk1b.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST cdk1b.phase.out_freqs : haplotype frequency estimates cdk1b.phase.out_pairs : most likely haplotype pairs for each individual cdk1b.phase.out_recom : estimates of recombination parameters cdk1b.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 10 Positions of loci: 616 1020 1894 2406 3047 3158 3578 3673 4842 5391 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file cdk1b.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CGTDDCTCAA 16.000000 2 CGTDDGCTCG 1.000000 3 CGTDIGCTCA 6.000000 4 CGTIDCCTAA 2.000000 5 CGADIGCTCA 1.000000 6 CGAIDCCTCA 2.000000 7 CTTDDCTCAA 47.000000 8 CTTDDGCCCA 10.000000 9 CTTDIGCTCA 22.000000 10 CTTIDCCTAA 4.000000 11 CTTIDCCTCA 1.000000 12 CTADDGCCCA 1.000000 13 CTADIGCTCA 11.000000 14 TGTDDCCTAA 1.000000 15 TGTDDCTCAA 2.000000 16 TGTDDGCCCA 1.000000 17 TGTDDGCTCA 5.000000 18 TGTDDGCTCG 7.000000 19 TGTDIGCTCA 3.000000 20 TGTIDCCTAA 1.000000 21 TGADDGCTCG 4.000000 22 TTTDDGCCCA 6.000000 23 TTTDDGCTCA 1.000000 24 TTTDIGCTCA 2.000000 25 TTTIDCCTAA 13.000000 26 TTTIDCCTCA 5.000000 27 TTADDGCCCA 1.000000 28 TTAIDCCTAA 2.000000 29 TTAIDCCTCA 2.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,3) P002: (22,28) P003: (1,9) P004: (17,21) P005: (26,29) P006: (6,15) P007: (9,22) P008: (7,13) P009: (9,26) P010: (7,7) P011: (10,21) P012: (6,7) P013: (7,9) P014: (7,22) P015: (4,7) P016: (7,25) P017: (9,18) P018: (19,26) P019: (3,25) P020: (8,9) P021: (1,3) P022: (7,9) P023: (9,25) P024: (9,9) P025: (1,16) P026: (7,25) P027: (7,13) P028: (7,26) P029: (7,23) P030: (7,10) P031: (7,8) P032: (1,9) P033: (1,5) P034: (7,8) P035: (7,8) P036: (13,25) P037: (7,25) P038: (1,7) P039: (9,9) P040: (7,7) P041: (15,25) P042: (1,20) P043: (1,8) P044: (7,29) P045: (7,28) P046: (7,9) P047: (7,7) P048: (7,11) P049: (7,24) P050: (2,18) P051: (7,13) P052: (13,25) P053: (9,22) P054: (9,9) P055: (25,25) P056: (7,7) P057: (19,24) P058: (7,8) P059: (1,7) P060: (3,4) P061: (7,17) P062: (22,26) P063: (7,13) P064: (17,18) P065: (1,17) P066: (7,7) P067: (13,25) P068: (7,12) P069: (7,7) P070: (9,9) P071: (7,25) P072: (1,13) P073: (1,7) P074: (8,14) P075: (7,27) P076: (7,7) P077: (1,25) P078: (7,19) P079: (1,9) P080: (18,21) P081: (10,13) P082: (9,13) P083: (1,8) P084: (22,3) P085: (7,9) P086: (3,13) P087: (10,18) P088: (18,21) P089: (17,18) P090: (8,8) 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 D D C T C A A C G T D I G C T C A 0 P002 T T (T) D D G C C C A T T (A) I D C C T A A 0 P003 C (G) T D D C T C A A C (T) T D I G C T C A 0 P004 T G T D D G C T C A T G A D D G C T C G 0 P005 T T T I D C C T C A T T A I D C C T C A 0 P006 (C) G A [I] D C C T C A (T) G T D D C T C A A 0 P007 (C) T T D I G C T C A (T) T T D D G C C C A 0 P008 C T (T) D D C T C A A C T (A) D I G C T C A 0 P009 C T T D I G C T C A T T T I D C C T C A 0 P010 C T T D D C T C A A C T T D D C T C A A 0 P011 (C) T (T) I D C C T A A (T) G (A) D D G C T C G 0 P012 C (G) (A) [I] D C C T C A C (T) (T) D D C T C A A 0 P013 C T T D D C T C A A C T [T] D I G C T C A 0 P014 (C) T T D D C T C A A (T) T T D D G C C C A 0 P015 C (G) T I D C C T A A C (T) T D D C T C A A 0 P016 C T T D D C T C A A T T T I D C C T A A 0 P017 C T T D I G C T C A T G T D D G C T C G 0 P018 T G T D I G C T C A T T T I D C C T C A 0 P019 (C) (G) T D I G C T C A (T) (T) T I D C C T A A 0 P020 C T T D D G C C C A C T [T] D I G C T C A 0 P021 C G T D D C T C A A C G T D I G C T C A 0 P022 C T T D D C T C A A C T T D I G C T C A 0 P023 C T T D I G C T C A T T T I D C C T A A 0 P024 C T T D I G C T C A C T T D I G C T C A 0 P025 (C) G T D D C T C A A (T) G T D D G C C C A 0 P026 C T T D D C T C A A T T T I D C C T A A 0 P027 C T (T) D D C T C A A C T (A) D I G C T C A 0 P028 C T T D D C T C A A T T [T] I D C C T C A 0 P029 (C) T T D D C T C A A (T) T T D D G C T C A 0 P030 C T T D D C T C A A C T T I D C C T A A 0 P031 C T T D D C T C A A C T T D D G C C C A 0 P032 C (G) T D D C T C A A C (T) T D I G C T C A 0 P033 C G (T) D D C T C A A C G (A) D I G C T C A 0 P034 C T T D D C T C A A C T T D D G C C C A 0 P035 C T T D D C T C A A C T T D D G C C C A 0 P036 C T (A) D I G C T C A T T (T) I D C C T A A 0 P037 C T T D D C T C A A T T T I D C C T A A 0 P038 C G T D D C T C A A C T T D D C T C A A 0 P039 C T T D I G C T C A C T T D I G C T C A 0 P040 C T T D D C T C A A C T T D D C T C A A 0 P041 T (G) T D D C T C A A T (T) T I D C C T A A 0 P042 (C) G T D D C T C A A (T) G T I D C C T A A 0 P043 C (G) T D D C T C A A C (T) T D D G C C C A 0 P044 C T (T) D D C T C A A T T (A) I D C C T C A 0 P045 C T (T) D D C T C A A T T (A) I D C C T A A 0 P046 C T T D D C T C A A C T T D I G C T C A 0 P047 C T T D D C T C A A C T T D D C T C A A 0 P048 C T T D D C T C A A C T T [I] D C C T C A 0 P049 (C) T T D D C T C A A (T) T T D I G C T C A 0 P050 C G T D D G C T C G T G T D D G C T C G 0 P051 C T (T) D D C T C A A C T (A) D I G C T C A 0 P052 C T (A) D I G C T C A T T (T) I D C C T A A 0 P053 (C) T T D I G C T C A (T) T T D D G C C C A 0 P054 C T T D I G C T C A C T T D I G C T C A 0 P055 T T T I D C C T A A T T T I D C C T A A 0 P056 C T T D D C T C A A C T T D D C T C A A 0 P057 T G T D I G C T C A T T T D I G C T C A 0 P058 C T T D D C T C A A C T T D D G C C C A 0 P059 C G T D D C T C A A C T T D D C T C A A 0 P060 C G T D I G C T C A C G T I D C C T A A 0 P061 C T T D D C T C A A T G T D D G C T C A 0 P062 T T T D D G C C C A T T T I D C C T C A 0 P063 C T (T) D D C T C A A C T (A) D I G C T C A 0 P064 T G T D D G C T C A T G T D D G C T C G 0 P065 C G T D D C T C A A T G T D D G C T C A 0 P066 C T T D D C T C A A C T T D D C T C A A 0 P067 C T (A) D I G C T C A T T (T) I D C C T A A 0 P068 C T (T) D D C T C A A C T (A) D D G C C C A 0 P069 C T T D D C T C A A C T T D D C T C A A 0 P070 C T T D I G C T C A C T T D I G C T C A 0 P071 C T T D D C T C A A T T T I D C C T A A 0 P072 C (G) (T) D D C T C A A C (T) (A) D I G C T C A 0 P073 C G T D D C T C A A C T T D D C T C A A 0 P074 (C) (T) T D D (G) C C (C) A (T) (G) T D D (C) C T (A) A 0 P075 (C) T (T) D D C T C A A (T) T (A) D D G C C C A 0 P076 C T T D D C T C A A C T T D D C T C A A 0 P077 (C) (G) T D D C T C A A (T) (T) T I D C C T A A 0 P078 (C) (T) T D D C T C A A (T) (G) T D I G C T C A 0 P079 C (G) T D D C T C A A C (T) T D I G C T C A 0 P080 T G T D D G C T C G T G A D D G C T C G 0 P081 C T (T) I D C C T A A C T (A) D I G C T C A 0 P082 C T T D I G C T C A C T A D I G C T C A 0 P083 C (G) T D D C T C A A C (T) T D D G C C C A 0 P084 (T) (T) T D D G C C C A (C) (G) T D I G C T C A 0 P085 C T T D D C T C A A C T T D I G C T C A 0 P086 C (G) T D I G C T C A C (T) A D I G C T C A 0 P087 (C) T T I D C C T A A (T) G T D D G C T C G 0 P088 T G T D D G C T C G T G A D D G C T C G 0 P089 T G T D D G C T C A T G [T] D D G C T C G 0 P090 C T T D D G C C C A C [T] T D D G C C 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 T C A = = = = ? ? G C T C = 0 P002 = = (T) ? = G = C C = = = (A) ? = C = T A = 0 P003 = (G) = = D C T C A = = (T) = = I G C T C = 0 P004 = = T = = = = = = A = = A = = = = = = G 0 P005 = = T = = = = = = = = = A = = = = = = = 0 P006 (C) = A ? = = C T C = (T) = T ? = = T C A = 0 P007 (C) = = = I = = T = = (T) = = = D = = C = = 0 P008 = = (T) = D C T C A = = = (A) = I G C T C = 0 P009 C = = D I G = = = ? T = = I D C = = = ? 0 P010 = = = = = = = = = = = = = = = = = = = = 0 P011 (C) T (T) I = C = = A A (T) G (A) D = G = = C G 0 P012 = (G) (A) ? = = C T C = = (T) (T) ? = = T C A = 0 P013 = = ? = D C T C A = = = ? = I G C T C = 0 P014 (C) = = = = C T = A ? (T) = = = = G C = C ? 0 P015 = (G) = I = = C T = = = (T) = D = = T C = = 0 P016 C = = D = = T C = = T = = I = = C T = = 0 P017 C T = = I = = = = A T G = = D = = = = G 0 P018 = G = ? I G = = = = = T = ? D C = = = = 0 P019 (C) (G) = D I G = = C = (T) (T) = I D C = = A = 0 P020 = = ? = D = = C = = = = ? = I = = T = = 0 P021 = = ? = D C ? C A = = = ? = I G ? T C = 0 P022 = = = = D C T C A = = = = = I G C T C = 0 P023 C = = D I G = = C = T = = I D C = = A = 0 P024 = = = = = = = = = = = = = = = = = = = = 0 P025 (C) = = = = C T = A = (T) = = = = G C = C = 0 P026 C = = D = = T C = = T = = I = = C T = = 0 P027 = = (T) = D C T C A = = = (A) = I G C T C = 0 P028 C = ? D = = T C A = T = ? I = = C T C = 0 P029 (C) = = = = C T C A = (T) = = = = G C T C = 0 P030 = = = D = = T C = = = = = I = = C T = = 0 P031 = = = = = C T = A = = = = = = G C = C = 0 P032 = (G) = = D C T C A = = (T) = = I G C T C = 0 P033 = = (T) = D C T C A = = = (A) = I G C T C = 0 P034 = = = = = C T = A = = = = = = G C = C = 0 P035 = = = = = C T = A = = = = = = G C = C = 0 P036 C = (A) D I G = = C = T = (T) I D C = = A = 0 P037 C = = D = = T C = = T = = I = = C T = = 0 P038 = G = = = = = = = = = T = = = = = = = = 0 P039 = = = = = = = = = = = = = = = = = = = = 0 P040 = = = = = = = = = = = = = = = = = = = = 0 P041 = (G) = D = = T C = = = (T) = I = = C T = = 0 P042 (C) = = D = = T C = = (T) = = I = = C T = = 0 P043 = (G) = = = C T = A = = (T) = = = G C = C = 0 P044 C = (T) D = = T C A = T = (A) I = = C T C = 0 P045 C = (T) D = = T C = = T = (A) I = = C T = = 0 P046 = = = = D C T C A = = = = = I G C T C = 0 P047 = = = = = = = = = = = = = = = = = = = = 0 P048 = = = ? = = T C A = = = = ? = = C T C = 0 P049 (C) = = = D C T C A ? (T) = = = I G C T C ? 0 P050 C = = = = = = = ? = T = = = = = = = ? = 0 P051 = = (T) = D C T C A = = = (A) = I G C T C = 0 P052 C = (A) D I G = = C = T = (T) I D C = = A = 0 P053 (C) = = = I = = T ? = (T) = = = D = = C ? = 0 P054 = = = = = = = = = = = = = = = = = = = = 0 P055 = = = = = = = = = = = = = = = = = = = = 0 P056 = = = = = = = = = = = = = = = = = = = = 0 P057 = G ? = = = = = = = = T ? = = = = = = = 0 P058 = = = = = C T = A = = = = = = G C = C = 0 P059 = G ? ? = = = = = = = T ? ? = = = = = = 0 P060 = = = D I G = = C = = = = I D C = = A = 0 P061 C T = = = C T C A = T G = = = G C T C = 0 P062 = = = D = G = C = = = = = I = C = T = = 0 P063 = = (T) = D C T C A = = = (A) = I G C T C = 0 P064 = = = = = = = = = A = = = = = = = = = G 0 P065 C = = = = C T C A = T = = = = G C T C = 0 P066 = = ? = = = = = = = = = ? = = = = = = = 0 P067 C = (A) ? I G = = C = T = (T) ? D C = = A = 0 P068 = = (T) = = C T = A = = = (A) = = G C = C = 0 P069 = = = = = = = = = = = = = = = = = = = = 0 P070 = = = = = = = = = = = = = = = = = = = = 0 P071 C = = D = = T C = = T = = I = = C T = = 0 P072 = (G) (T) = D C T C A = = (T) (A) = I G C T C = 0 P073 = G = = = = = = = = = T = = = = = = = = 0 P074 (C) (T) = = = (G) = C (C) = (T) (G) = = = (C) = T (A) = 0 P075 (C) = (T) = = C T = A = (T) = (A) = = G C = C = 0 P076 = = = = = = = = = = = = = = = = = = = = 0 P077 (C) (G) = D = = T C = = (T) (T) = I = = C T = = 0 P078 (C) (T) = = D C T C A = (T) (G) = = I G C T C = 0 P079 = (G) ? = D C T C A = = (T) ? = I G C T C = 0 P080 = = T = = = = = = = = = A = = = = = = = 0 P081 = = (T) I D C = = A = = = (A) D I G = = C = 0 P082 = = T = = = = = = = = = A = = = = = = = 0 P083 = (G) ? = = C T = A = = (T) ? = = G C = C = 0 P084 (T) (T) = = D = = C = = (C) (G) = = I = = T = = 0 P085 = = = = D C T C A = = = = = I G C T C = 0 P086 = (G) T = = = = = = = = (T) A = = = = = = = 0 P087 (C) T = I = C = = A A (T) G = D = G = = C G 0 P088 = = T = = = = = = = = = A = = = = = = = 0 P089 = = ? = = = = = = 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 1.00 1.00 = = = 0.55 ? = 1.00 = 1.00 0.98 = = 0.53 = = 1.00 1.00 1.00 1.00 1.00 = = = 0.95 = = = = = = 1.00 = = 1.00 = = = = = = = 0.53 = 0.92 ? = = 1.00 1.00 1.00 = 0.71 = = = 1.00 = = 1.00 = = = = 0.90 = 1.00 1.00 1.00 1.00 1.00 = 0.95 = = 1.00 1.00 1.00 = = = ? = = = = = = = = = = 0.79 0.98 0.75 1.00 = 1.00 = = 1.00 1.00 = 0.67 0.89 ? = = 1.00 1.00 1.00 = = = ? = 1.00 1.00 1.00 1.00 1.00 = 0.85 = = = = 1.00 1.00 = 1.00 ? = 0.55 = 1.00 = = 1.00 1.00 = = 0.96 = = 1.00 = = 1.00 1.00 = = 0.93 0.97 = = 1.00 = = = = 1.00 = 0.91 = ? 0.99 1.00 = = = = 0.77 0.70 = 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 = 0.92 = = 1.00 1.00 1.00 = = 1.00 = = = = = = = = = = = 0.74 = = = = 1.00 1.00 = 1.00 = 0.97 = = 1.00 = = 1.00 1.00 = = = = 0.89 = 1.00 1.00 1.00 1.00 1.00 = 0.98 = ? 1.00 = = 1.00 1.00 0.98 = 0.84 = = = = 1.00 1.00 0.96 1.00 = = = = 1.00 = = 1.00 1.00 = = = = = = = 1.00 1.00 = 1.00 = = 0.53 = = 1.00 1.00 1.00 1.00 1.00 = = = 0.75 = 1.00 1.00 1.00 1.00 1.00 = = = = = = 1.00 1.00 = 1.00 = = = = = = 1.00 1.00 = 1.00 = 0.97 = 0.73 1.00 1.00 1.00 = = 1.00 = 0.97 = = 1.00 = = 1.00 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.87 = 1.00 = = 1.00 1.00 = = 0.57 = = 1.00 = = 1.00 1.00 = = = 0.78 = = = 1.00 1.00 = 1.00 = 0.98 = 0.87 1.00 = = 1.00 1.00 0.99 = 0.93 = 0.62 1.00 = = 1.00 1.00 = = = = = = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = ? = = 1.00 1.00 0.95 = 0.69 = = = 1.00 1.00 1.00 1.00 1.00 ? 1.00 = = = = = = = ? = = = 0.89 = 1.00 1.00 1.00 1.00 1.00 = 0.96 = 0.73 1.00 1.00 1.00 = = 1.00 = 0.70 = = = 1.00 = = 1.00 ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 ? = = = = = = = = = = = = 1.00 1.00 = 1.00 = = 1.00 ? ? = = = = = = = = = 1.00 1.00 1.00 = = 1.00 = 0.98 0.92 = = = 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 = 1.00 = = = = 0.90 = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = 1.00 0.98 = = = = 1.00 1.00 1.00 1.00 = = = ? = = = = = = = 0.96 = 0.71 ? 1.00 1.00 = = 1.00 = = = 0.51 = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = 0.97 = = 1.00 = = 1.00 1.00 = = = 0.66 0.86 = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = = = = = = = 0.63 0.80 = = = 0.72 = 0.96 0.73 = 0.76 = 0.59 = = 1.00 1.00 = 1.00 = = = = = = = = = = = 0.88 0.75 = 1.00 = = 1.00 1.00 = = 0.66 0.55 = = 1.00 1.00 1.00 1.00 1.00 = = 0.56 ? = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = = = = = = = = = 0.83 1.00 1.00 1.00 = = 1.00 = = = 1.00 = = = = = = = = 0.79 ? = = 1.00 1.00 = 1.00 = 0.58 0.66 = = 1.00 = = 1.00 = = = = = = 1.00 1.00 1.00 1.00 1.00 = = 0.66 1.00 = = = = = = = 0.61 0.96 = 1.00 = 1.00 = = 1.00 1.00 = = 1.00 = = = = = = = = = ? = = = = = = 1.00 = ? ? = = = = = = = END PHASEPROBS