************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 ccnd3.phase.inp ccnd3.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ccnd3.phase.out_freqs : haplotype frequency estimates ccnd3.phase.out_pairs : most likely haplotype pairs for each individual ccnd3.phase.out_recom : estimates of recombination parameters ccnd3.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 13 Positions of loci: 376 2583 3777 3911 5163 5264 6655 6656 7432 7784 7928 8087 8676 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ccnd3.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCTICACTAGIGG 22.000000 2 GCTICTCGAGIGG 4.000000 3 GCTICTCGGGIGG 12.000000 4 GCTICTCGGGDGG 35.000000 5 GCTICTCGGAIGG 3.000000 6 GCTICTCGGAIGA 1.000000 7 GCTICTCTAGIGG 1.000000 8 GCTICTCTGGIGG 1.000000 9 GCTICTTGGGIGG 18.000000 10 GCTITTCGGGIGG 1.000000 11 GCTITTCGGGDGG 2.000000 12 GGTDTTCGGAIGA 36.000000 13 ACTICTCTGGIAG 1.000000 14 ACCICTCTAGIGG 17.000000 15 ACCICTCTGGIAG 25.000000 16 ACCICTTGGGIGG 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,4) P002: (12,14) P003: (12,15) P004: (3,9) P005: (1,15) P006: (4,15) P007: (4,15) P008: (2,16) P009: (12,15) P010: (1,12) P011: (4,5) P012: (4,12) P013: (9,9) P014: (1,4) P015: (1,4) P016: (1,4) P017: (5,15) P018: (3,4) P019: (4,12) P020: (14,15) P021: (3,4) P022: (9,9) P023: (3,9) P024: (1,14) P025: (4,14) P026: (12,14) P027: (12,12) P028: (4,12) P029: (4,12) P030: (4,12) P031: (4,9) P032: (3,4) P033: (1,12) P034: (12,14) P035: (14,14) P036: (12,15) P037: (12,12) P038: (1,3) P039: (4,12) P040: (4,6) P041: (3,4) P042: (4,9) P043: (4,12) P044: (4,4) P045: (12,14) P046: (4,15) P047: (4,12) P048: (14,15) P049: (9,15) P050: (11,12) P051: (1,2) P052: (1,9) P053: (4,15) P054: (4,15) P055: (1,2) P056: (3,5) P057: (4,4) P058: (1,1) P059: (3,15) P060: (4,12) P061: (3,10) P062: (15,15) P063: (9,12) P064: (9,15) P065: (3,12) P066: (7,12) P067: (9,14) P068: (1,9) P069: (14,14) P070: (9,14) P071: (1,15) P072: (1,12) P073: (9,15) P074: (14,14) P075: (12,15) P076: (1,13) P077: (1,12) P078: (4,12) P079: (3,9) P080: (9,11) P081: (12,12) P082: (12,12) P083: (1,12) P084: (4,15) P085: (2,15) P086: (1,15) P087: (8,12) P088: (1,15) P089: (4,15) P090: (4,14) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 G C T I C A C T A G I G G G C T I C T C G G G D G G 0 P002 G G T D T T C G G A I G A A C C I C T C T A G I G G 0 P003 G G T D T T C G G A I G A A C C I C T C T G G I A G 0 P004 G C T I C T C G G G I G G G C T I C T T G G G I G G 0 P005 G C T I C A C [T] A G I G G A C C I C T C T G G I A G 0 P006 G C T I C T C G G G D G G A C C I C T C T G G I A G 0 P007 G C T I C T C G G G D G G A C C I C T C T G G I A G 0 P008 G C T I C T C [G] A G I G G A C C I C T T G G G I G G 0 P009 G G T D T T C G G A I G A A C C I C T C T G G I A G 0 P010 G C T I C A C T A G I G G G G T D T T C G G A I G A 0 P011 G C T I C T C G G G D G G G C T I C T C G G A I G G 0 P012 G C T I C T C G G G D G G G G T D T T C G G A I G A 0 P013 G C T I C T T G G G I G G G C T I C T T G G G I G G 0 P014 G C T I C A C T A G I G G G C T I C T C G G G D G G 0 P015 G C T I C A C T A G I G G G C T I C T C G G G D G G 0 P016 G C T I C A C T A G I G G G C T I C T C G G G D G G 0 P017 G C T I C T C G G A I G G A C C I C T C T G G I A G 0 P018 G C T I C T C G G G I G G G C T I C T C G G G D G G 0 P019 G C T I C T C G G G D G G G G T D T T C G G A I G A 0 P020 A C C I C T C T A G I G G A C C I C T C T G G I A G 0 P021 G C T I C T C G G G I G G G C T I C T C G G G D G G 0 P022 G C T I C T T G G G I G G G C T I C T T G G G I G G 0 P023 G C T I C T C G G G I G G G C T I C T T G G G I G G 0 P024 G C T I C A C T A G I G G A C C I C T C T A G I G G 0 P025 G C T I C T C G G G D G G A C C I C T C T A G I G G 0 P026 G G T D T T C G G A I G A [A] C [C] I C T C T A G I G G 0 P027 G G T D T T C G G A I G A G G T D T T C G G A I G A 0 P028 G C T I C T C G G G D G G G G T D T T C G G A I G A 0 P029 G C T I C T C G G G D G G G G T D T T C G G A I G A 0 P030 G C T I C T C G G G D G G G G T D T T C G G A I G A 0 P031 G C T I C T C G G G D G G G C T I C T T G G G I G G 0 P032 G C T I C T C G G G I G G G C T I C T C G G G D G G 0 P033 G C T I C A C T A G I G G G G T D T T C G G A I G A 0 P034 G G T D T T C G G A I G A A C C I C T C T A G I G G 0 P035 A C C I C T C T A G I G G A C C I C T C T A G I G G 0 P036 G G T D T T C G G A I G A A C C I C T C T G G I A G 0 P037 G G T D T T C G G A I G A G G T D T T C G G A I G A 0 P038 G C T I C A C T A G I G G G C T I C T C G G G I G G 0 P039 G C T I C T C G G G D G G G G T D T T C G G A I G A 0 P040 G C T I C T C G G G D G G G C T I C T C G G A I G A 0 P041 G C T I C T C G [G] G I G G G C T I C T C G G G D G G 0 P042 G C T I C T C G G G D G G G C T I C T T G G G I G G 0 P043 G C T I C T C G G G D G G G G T D T T C G G A I G A 0 P044 G C T I C T C G G G D G G G C T I C T C G G G D G G 0 P045 G G T D T T C G G A I G A A C C I C T C T A G I G G 0 P046 G C T I C T C G G G D G G A C C I C T C T G G I A G 0 P047 G C T I C T C G G G D G G G G T D T T C G G A I G A 0 P048 A C C I C T C T A G I G G A C C I C T C T G G I A G 0 P049 G C T I C T T G G G I G G A C C I C T C T G G I A G 0 P050 G C T I T T C G G G D G G G G T D T T C G G A I G A 0 P051 G C T I C A C T A G I G G G C T I C T C G A G I G G 0 P052 G C T I C A C T A G I G G G C T I C T T G G G I G G 0 P053 G C T I C T C G G G D G G A C C I C T C T G G I A G 0 P054 G C T I C T C G G G D G G A C C I C T C T G G I A G 0 P055 G C T I C A C T A G I G G G C T I C T C G A G I G G 0 P056 G C T I C T C G G G I G G G C T I C T C G G A I G G 0 P057 G C T I C T C G G G D G G G C T I C T C G G G D G G 0 P058 G C T I C A C T A G I G G G C T I C A C T A G I G G 0 P059 G C T I C T C G G G I G G A C C I C T C T G G I A G 0 P060 G C T I C T C G G G D G G G G T D T T C G G A I G A 0 P061 G C T I C T C G G G I G G G C T I T T C G G G I G G 0 P062 A C C I C T C T G G I A G A C C I C T C T G G I A G 0 P063 G C T I C T T G G G I G G G G T D T T C G G A I G A 0 P064 G C T I C T T G G G I G G A C C I C T C T G G I A G 0 P065 G C T I C T C G G G I G G G G T D T T C G G A I G A 0 P066 G C T I C T C (T) A G I G G G G T D T T C (G) G A I G A 0 P067 G C T I C T T G G G I G G A C C I C T C T A G I G G 0 P068 G C T I C A C T A G I G G G C T I C T T G G G I G G 0 P069 A C C I C T C T A G I G G A C C I C T C T A G I G G 0 P070 G C T I C T T G G G I G G A C C I C T C T A G I G G 0 P071 G C T I C A C T A G I G G A C C I C T C T G G I A G 0 P072 G C T I C A C T A G I G G G G T D T T C G G A I G A 0 P073 G C T I C T T G G G I G G A C C I C T C T G G I A G 0 P074 A C C I C T C T A G I G G A C C I C T C T A G I G G 0 P075 G G T D T T C G G A I G A A C C I C T C T G G I A G 0 P076 G C T I C A C T A G I G G A C T I C T C T G G I A G 0 P077 G C T I C A C T A G I G G G G T D T T C G G A I G A 0 P078 G C T I C T C G G G D G G G G T D T T C G G A I G A 0 P079 G C T I C T C G G G I G G G C T I C T T G G G I G G 0 P080 G C T I C T T G G G I G G G C T I T T C G G G D G G 0 P081 G G T D T T C G G A I G A G G T D T T C G G A I G A 0 P082 G G T D T T C G G A I G A G G T D T T C G G A I G A 0 P083 G C T I C A C T A G I G G G G T D T T C G G A I G A 0 P084 G C T I C T C G G G D G G A C C I C T C T G G I A G 0 P085 G C T I C T C G A G I G G A C C I C T C T G G I A G 0 P086 G C T I C A C T A G I G G A C C I C T C T G G I A G 0 P087 G C T I C T C (T) G G I G G G G T D T T C (G) G A I G A 0 P088 G C T I C A C T A G I G G A C C I C T C T G G I A G 0 P089 G C T I C T C G G G D G G A C C I C T C T G G I A G 0 P090 G C T I C T C G G G D G G [A] C [C] I C T C T A G I G 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 = ? = = = A = T A = I ? ? = ? = = = T = G G = D ? ? 0 P002 G ? ? D T = ? ? ? ? ? = ? A ? ? I C = ? ? ? ? ? = ? 0 P003 G ? T D T = ? ? = A = G ? A ? C I C = ? ? = G = A ? 0 P004 = ? = = = = C = = = = = ? = ? = = = = T = = = = = ? 0 P005 G ? T ? ? ? ? ? A = = G ? A ? C ? ? ? ? ? G = = A ? 0 P006 G = T = = = = G = = D G ? A = C = = = = T = = I A ? 0 P007 G = ? = ? ? = ? = = D G ? A = ? = ? ? = ? = = I A ? 0 P008 G = T = = = C ? A = = = ? A = C = = = T ? G = = = ? 0 P009 G G T D T = = G = A = G ? A C C I C = = T = G = A ? 0 P010 = C ? I ? ? = T A G = = ? = G ? D ? ? = G G A = = ? 0 P011 = = = = ? ? = = = G D = = = = = = ? ? = = = A I = = 0 P012 = C = I C = = = = G D = G = G = D T = = = = A I = A 0 P013 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P014 = = = ? = A = T A = I = = = = = ? = T = G G = D = = 0 P015 = = ? = ? ? = T A = I = = = = ? = ? ? = G G = D = = 0 P016 = = ? = = A = T A = I = ? = = ? = = T = G G = D = ? 0 P017 G ? T = = = = G = A = G = A ? C = = = = T = G = A = 0 P018 = = = = = = = = = = I = ? = = = = = = = = = = D = ? 0 P019 = C = I C = = = = G D = G = G = D T = = = = A I = A 0 P020 = = = = = = = = A = = G = = = = = = = = = G = = A = 0 P021 = = = = = = = = = = I = = = = = = = = = = = = D = = 0 P022 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P023 = = = = = = C = = = = = = = = = = = = T = = = = = = 0 P024 G = T = ? ? = = = = = = = A = C = ? ? = = = = = = = 0 P025 G = T = = = = G G = D = = A = C = = = = T A = I = = 0 P026 ? G ? D T = = G G A = = ? ? C ? I C = = T A G = = ? 0 P027 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P028 = C = I C = = = = G D = G = G = D T = = = = A I = A 0 P029 = C = I C = = = = G D = G = G = D T = = = = A I = A 0 P030 = C = I C = = = = G D = G = G = D T = = = = A I = A 0 P031 = = = = = = C = = = D = = = = = = = = T = = = I = = 0 P032 = = = = = = = = = = I = = = = = = = = = = = = D = = 0 P033 = C ? I C A = T A G = = G = G ? D T T = G G A = = A 0 P034 ? G T D T = = G G A = = A ? C C I C = = T A G = = G 0 P035 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P036 G G T D T = = G = A = G A A C C I C = = T = G = A G 0 P037 = = = = = = = = ? = = = = = = = = = = = = ? = = = = 0 P038 ? = = = ? ? = T A = = = = ? = = = ? ? = G G = = = = 0 P039 = C = I C = = = = G D = G = G = D T = = = = A I = A 0 P040 = = = = = = = = = G D = G = = = = = = = = = A I = A 0 P041 = = = = = = = = ? = I ? ? = = = = = = = = ? = D ? ? 0 P042 ? = = = = = C = = = D = ? ? = = = = = T = = = I = ? 0 P043 = C = I C = = = = G D = G = G = D T = = = = A I = A 0 P044 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P045 G G T D T = = G G A = = A A C C I C = = T A G = = G 0 P046 G = T = = = = G = = D G = A = C = = = = T = = I A = 0 P047 = C = I C = = = = G D = G = G = D T = = = = A I = A 0 P048 = = = = = = = = A = = G = = = = = = = = = G = = A = 0 P049 G ? T = = = T G = = = G = A ? C = = = C T = = = A = 0 P050 ? C ? I = = = = = G D = G ? G ? D = = = = = A I = A 0 P051 = = = = ? ? = T = = = = = = = = = ? ? = G = = = = = 0 P052 = = = = ? ? C T A = = = = = = = = ? ? T G G = = = = 0 P053 G = T = = = = G = = D G ? A = C = = = = T = = I A ? 0 P054 G = T = = = = G = = D G = A = C = = = = T = = I A = 0 P055 = = = = = A = T = = = = = = = = = = T = G = = = = = 0 P056 = = ? = = = = = = G = = = = = ? = = = = = = A = = = 0 P057 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P058 ? = = = = = = = = = = = = ? = = = = = = = = = = = = 0 P059 G = T = = = = G = = = G = A = C = = = = T = = = A = 0 P060 = C = I ? ? = = = G D = G = G = D ? ? = = = A I = A 0 P061 ? = = = C = = = = = = = = ? = = = T = = = = = = = = 0 P062 ? = = = = = = = = = = = = ? = = = = = = = = = = = = 0 P063 = C ? I C = T = = G = = G = G ? D T = C = = A = = A 0 P064 G = ? = = = T G = = = G = A = ? = = = C T = = = A = 0 P065 = C = I C = = = = G = = G = G = D T = = = = A = = A 0 P066 ? C = I C = = (T) A G = = G ? G = D T = = (G) G A = = A 0 P067 G = T = = = T G G = = = = A = C = = = C T A = = = = 0 P068 = = = = = A C T A = = = = = = = = = T T G G = = = = 0 P069 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P070 G = ? = = = T G G = = = = A = ? = = = C T A = = = = 0 P071 G = ? = = A = = A = = G = A = ? = = T = = G = = A = 0 P072 = C ? I ? ? = T A G = = G = G ? D ? ? = G G A = = A 0 P073 G = T = = = T G = = = G = A = C = = = C T = = = A = 0 P074 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P075 G G T D T = = G = A = G A A C C I C = = T = G = A G 0 P076 G = = = = A = = A = = G = A = = = = T = = G = = A = 0 P077 = C = I C A = T A G = = G = G = D T T = G G A = = A 0 P078 ? C = I C = = = = G D = G ? G = D T = = = = A I = A 0 P079 = = = = = = C = = = = = = = = = = = = T = = = = = = 0 P080 = = = = C = T = = = I = = = = = = T = C = = = D = = 0 P081 = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P082 = = ? = = = = = = = = = = = = ? = = = = = = = = = = 0 P083 = C = I C A = T A G = = G = G = D T T = G G A = = A 0 P084 ? = T = ? ? = G = = D G = ? = C = ? ? = T = = I A = 0 P085 G = ? = = = = G A = = G = A = ? = = = = T G = = A = 0 P086 ? = T = = A = = A = = G = ? = C = = T = = G = = A = 0 P087 = ? ? I C = = (T) = G = = G = ? ? D T = = (G) = A = = A 0 P088 G = T = = A = = A = = G = A = C = = T = = G = = A = 0 P089 G = T = = = = G = = D G = A = C = = = = T = = I A = 0 P090 ? = ? = = = = G G = D = = ? = ? = = = = T A = I = = 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 ? ? 1.00 ? ? 1.00 1.00 = ? ? ? ? ? = ? 1.00 ? 1.00 1.00 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 ? 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 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 = 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 = ? ? = = = = = = = 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 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 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 = = = = = = = = ? = = = = ? = = = ? ? = 1.00 0.99 = = = = = 1.00 = 1.00 1.00 = = = = 1.00 1.00 = 1.00 = = = = = = = = = 1.00 1.00 = 0.95 = = = = = = = = ? = 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 = 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 = = = = = 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 = = = = = = = ? = = = = = = 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 1.00 = = = 1.00 = = 1.00 = 1.00 1.00 = = = = 1.00 = = 1.00 ? 1.00 = 1.00 1.00 = = 0.90 1.00 1.00 = = 1.00 0.99 = 0.99 = = = 1.00 1.00 1.00 = = = = = = = = = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = 0.99 = ? = = = 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 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 1.00 0.98 = = = = 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 = = = = = = = = = = 0.95 = 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 0.99 = = 0.99 = ? = 1.00 = = 1.00 = = 1.00 = = 1.00 = = ? ? 1.00 1.00 = = 0.55 = 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 = = END PHASEPROBS