************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 dclre.phase.inp dclre.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST dclre.phase.out_freqs : haplotype frequency estimates dclre.phase.out_pairs : most likely haplotype pairs for each individual dclre.phase.out_recom : estimates of recombination parameters dclre.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 11 Positions of loci: 835 2248 5250 5944 7978 8283 8528 13454 14305 16204 17870 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file dclre.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TCTCAADTTIG 11.000000 2 TCTCACDTTDG 80.000000 3 TCTCACDTTIG 1.000000 4 TCTCACDTGDG 23.000000 5 TCTGACDTTDG 2.000000 6 TCTGACICTDG 1.000000 7 TTTGACDTTDG 2.000000 8 TTTGACICTDG 3.000000 9 TTTGACICTDA 14.000000 10 TTTGGCICTDA 21.000000 11 TTGGACITTDG 11.000000 12 ACTCACDTTDG 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: (4,10) P003: (2,8) P004: (5,8) P005: (1,12) P006: (2,10) P007: (2,12) P008: (2,2) P009: (2,10) P010: (2,2) P011: (7,11) P012: (10,10) P013: (2,2) P014: (2,10) P015: (1,10) P016: (2,9) P017: (2,2) P018: (2,11) P019: (4,4) P020: (2,2) P021: (2,9) P022: (1,2) P023: (4,9) P024: (2,4) P025: (1,2) P026: (2,2) P027: (2,10) P028: (2,2) P029: (6,11) P030: (2,9) P031: (4,10) P032: (2,11) P033: (4,12) P034: (1,2) P035: (1,4) P036: (2,2) P037: (2,9) P038: (4,11) P039: (2,4) P040: (2,12) P041: (9,12) P042: (2,2) P043: (1,12) P044: (4,12) P045: (2,9) P046: (2,12) P047: (4,9) P048: (4,10) P049: (2,2) P050: (2,5) P051: (2,2) P052: (2,4) P053: (2,4) P054: (2,2) P055: (2,2) P056: (2,9) P057: (10,11) P058: (2,2) P059: (2,11) P060: (2,9) P061: (2,9) P062: (2,10) P063: (1,9) P064: (2,8) P065: (9,11) P066: (2,4) P067: (2,2) P068: (2,2) P069: (2,2) P070: (4,4) P071: (3,4) P072: (2,10) P073: (2,12) P074: (2,4) P075: (2,4) P076: (10,10) P077: (10,12) P078: (2,10) P079: (2,10) P080: (2,7) P081: (2,4) P082: (2,4) P083: (2,2) P084: (2,10) P085: (10,12) P086: (1,10) P087: (2,11) P088: (2,9) P089: (11,11) P090: (2,2) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 T C T C A A D T T I G T C T C A A D T T I G 0 P002 T C T C A C D T G D G T T T G G C I C T D A 0 P003 T C T C A C D T T D G T T T G A C I C T D G 0 P004 T (C) T G A C D T T D G T (T) T G A C I C T D G 0 P005 T C T C A A D T T I G A C T C A C D T T D G 0 P006 T C T C A C D T T D G T T T G G C I C T D A 0 P007 T C T C A C D T T D G A C T C A C D T T D G 0 P008 T C T C A C D T T D G T C T C A C D T T D G 0 P009 T C T C A C D T T D G T T T G G C I C T D A 0 P010 T C T C A C D T T D G T C T C A C D T T D G 0 P011 T T T G A C D T T D G T T G G A C I T T D G 0 P012 T T T G G C I C T D A T T T G G C I C T D A 0 P013 T C T C A C D T T D G T C T C A C D T T D G 0 P014 T C T C A C D T T D G T T T G G C I C T D A 0 P015 T C T C A A D T T I G T T T G G C I C T D A 0 P016 T C T C A C D T T D G T T T G A C I C T D A 0 P017 T C T C A C D T [T] D G T C T C A C D T T D G 0 P018 T C T C A C D T T D G T T G G A C I T T D G 0 P019 T C T C A C D T G D G T C T C A C D T G D G 0 P020 T C T C A C D T T D G T C T C A C D T T D G 0 P021 T C T C A C D T T D G T T T G A C I C T D A 0 P022 T C T C A A D T T I G T C T C A C D T T D G 0 P023 T C T C A C D T G D G T T T G A C I C T D A 0 P024 T C T C A C D T T D G T C T C A C D T G D G 0 P025 T C T C A A D T T I G T C T C A C D T T D G 0 P026 T C T C A C D T T D G T C T C A C D T T D G 0 P027 T C T C A C D T T D G T T T G G C I C T D A 0 P028 T C T C A C D T T D G T C T C A C D T T D G 0 P029 T (C) T G A C I C T D G T (T) G G A C I T T D G 0 P030 T C T C A C D T T D G T T T G A C I C T D A 0 P031 T C T C A C D T G D G T T T G G C I C T D A 0 P032 T C T C A C D T T D G T T G G A C I T T D G 0 P033 T C T C A C D T G D G A C T C A C D T T D G 0 P034 T C T C A A D T T I G T C T C A C D T T D G 0 P035 T C T C A A D T T I G T C T C A C D T G D G 0 P036 T C T C A C D T T D G T C T C A C D T T D G 0 P037 T C T C A C D T T D G T T T G A C I C T D A 0 P038 T C T C A C D T G D G T T G G A C I T T D G 0 P039 T C T C A C D T T D G T C T C A C D T G D G 0 P040 T C T C A C D T T D G A C T C A C D T T D G 0 P041 T T T G A C I C T D A A C T C A C D T T D G 0 P042 T C T C A C D T T D G T C T C A C D T T D G 0 P043 T C T C A A D T T I G A C T C A C D T T D G 0 P044 T C T C A C D T G D G A C T C A C D T T D G 0 P045 T C T C A C D T T D G T T T G A C I C T D A 0 P046 T C T C A C D T T D G A C T C A C D T T D G 0 P047 T C T C A C D T G D G T T T G A C I C T D A 0 P048 T C T C A C D T G D G T T T G G C I C T D A 0 P049 T C T C A C D T [T] D G T C T C A C D T T D G 0 P050 T C T C A C D T T D G T C T G A C D T T D G 0 P051 T C T C A C D T T D G T C T C A C D T T D G 0 P052 T C T C A C D T T D G T C T C A C D T G D G 0 P053 T C T C A C D T T D G T C T C A C D T G D G 0 P054 T C T C A C D T T D G T C T C A C D T T D G 0 P055 T C T C A C D T T D G T C T C A C D T T D G 0 P056 T C T C A C D T T D G T T T G A C I C T D A 0 P057 T T T G G C I C T D A T T G G A C I T T D G 0 P058 T C T C A C D T T D G T C T C A C D T T D G 0 P059 T C T C A C D T T D G T T G G A C I T T D G 0 P060 T C T C A C D T T D G T T T G A C I C T D A 0 P061 T C T C A C D T T D G T T T G A C I C T D [A] 0 P062 T C T C A C D T T D G T T T G G C I C T D A 0 P063 T C T C A A D T T I G T T T G A C I C T D A 0 P064 T C T C A C D T T D G T [T] T G A C I C T D G 0 P065 T T T G A C I C T D A T T G G A C I T T D G 0 P066 T C T C A C D T T D G T C T C A C D T G D G 0 P067 T C T C A C D T T D G T C T C A C D T T D G 0 P068 T C T C A C D T T D G T C T C A C D T T D G 0 P069 T C T C A C D T T D G T C T C A C D T T D G 0 P070 T C T C A C D T G D G T C T C A C D T G D G 0 P071 T C T C A C D T (T) I G T C T C A C D T (G) D G 0 P072 T C T C A C D T T D G T T T G G C I C T D A 0 P073 T C T C A C D T T D G A C T C A C D T T D G 0 P074 T C T C A C D T T D G T C T C A C D T G D G 0 P075 T C T C A C D T T D G T C T C A C D T G D G 0 P076 T T T G G C I C T D A T T T G G C I C T D A 0 P077 T T T G G C I C T D A A C T C A C D T T D G 0 P078 T C T C A C D T T D G T T T G G C I C T D A 0 P079 T C T C A C D T T D G T T T G G C I C T D A 0 P080 T C T C A C D T T D G T T T [G] A C D T T D G 0 P081 T C T C A C D T T D G T C T C A C D T G D G 0 P082 T C T C A C D T T D G T C T C A C D T G D G 0 P083 T C T C A C D T T D G T C T C A C D T T D G 0 P084 T C T C A C D T T D G T T T G G C I C T D A 0 P085 T T T G G C I C T D A A C T C A C D T T D G 0 P086 T C T C A A D T T I G T T T G G C I C T D A 0 P087 T C T C A C D T T D G T T G G A C I T T D G 0 P088 T C T C A C D T T D G T T T G A C I C T D A 0 P089 T T G G A C I T T D G T T G G A C I T T D G 0 P090 T C T C A C D T T D G T C T C A C D T T D 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 = = = = = = = = = ? = = = = = = = = = = ? = 0 P002 = C = ? A = D T G = G = T = ? G = I C T = A 0 P003 = C = C = = D T = = = = T = G = = I C = = = 0 P004 = (C) = = = = D T = = = = (T) = = = = I C = = = 0 P005 T = = = = A = = = I = A = = = = C = = = D = 0 P006 = C = C A = D ? = = G = T = G G = I ? = = A 0 P007 T = = = = = = ? = = = A = = = = = = ? = = = 0 P008 = = = = = = ? = = = = = = = = = = ? = = = = 0 P009 = C = C A = D ? = ? G = T = G G = I ? = ? A 0 P010 = = = = = = = = = ? = = = = = = = = = = ? = 0 P011 ? = T = = = D = = ? = ? = G = = = I = = ? = 0 P012 = = = = = = = = = ? = = = = = = = = = = ? = 0 P013 = = = = = = = = = = = = = = = = = = = = = = 0 P014 ? C = C A ? ? T = = G ? T = G G ? ? C = = A 0 P015 = C = C A A D ? = ? G = T = G G C I ? = ? A 0 P016 = C ? C = ? ? T = = G = T ? G = ? ? C = = A 0 P017 = = = = = = = = ? = = = = = = = = = = ? = = 0 P018 = ? T C = = D = = = = = ? G G = = I = = = = 0 P019 = = = = = = = = = = = = = = = = = = = = = = 0 P020 = = = = = = = = = = = = = = = = = = = = = = 0 P021 = C = ? = = D T = = G = T = ? = = I C = = A 0 P022 = = = = = A = = = I = = = = = = C = = = D = 0 P023 = C = C = = D T G = G = T = G = = I C T = A 0 P024 = = = = = = = ? T = = = = = = = = = ? G = = 0 P025 = = = = = A = = = I = = = = = = C = = = D = 0 P026 = = = = = = = = = = = = = = = = = = = = = = 0 P027 = C = C A = D T = = G = T = G G = I C = = A 0 P028 = = = = = = = ? = = = = = = = = = = ? = = = 0 P029 = (C) T = = = = C = = = = (T) G = = = = T = = = 0 P030 = C = C = = D T = = G = T = G = = I C = = A 0 P031 ? C = C A ? ? T G = G ? T = G G ? ? C T = A 0 P032 = C T C = = D = = = = = T G G = = I = = = = 0 P033 T = = = = = = ? G = = A = = = = = = ? T = = 0 P034 = = = = = A = = = I = = = = = = C = = = D = 0 P035 = = = = = A = = T I = = = = = = C = = G D = 0 P036 = = = = = = = = = = = = = = = = = = = = = = 0 P037 = C = C = = D T = = G = T = G = = I C = = A 0 P038 = C T C = = D = G = = = T G G = = I = T = = 0 P039 = = = = = = = = T = = = = = = = = = = G = = 0 P040 T = = = = = = = = = = A = = = = = = = = = = 0 P041 T T = G = = I C = = A A C = C = = D T = = G 0 P042 = = = = = = = = = = = = = = = = = = = = = = 0 P043 T = = = = A = = = I = A = = = = C = = = D = 0 P044 T = = = = = = = G = = A = = = = = = = T = = 0 P045 = C = C = = D T = = G = T = G = = I C = = A 0 P046 T = = = = = = ? ? = = A = = = = = = ? ? = = 0 P047 = C = C = = D T G = G = T = G = = I C T = A 0 P048 = C = C A = D T G = G = T = G G = I C T = A 0 P049 = = = = = = = = ? = = = = = = = = = = ? = = 0 P050 = = = C = = = = = = = = = = G = = = = = = = 0 P051 = = = = = = = = = = = = = = = = = = = = = = 0 P052 = = = = = = = = T = = = = = = = = = = G = = 0 P053 = = = = = = = = T = = = = = = = = = = G = = 0 P054 = = = = = = = = = = = = = = = = = = = = = = 0 P055 = = = = = = = = = = = = = = = = = = = = = = 0 P056 = C = C = = D T = = G = T = G = = I C = = A 0 P057 = = T = G = = C = = A = = G = A = = T = = G 0 P058 ? = = = = = = = = = = ? = = = = = = = = = = 0 P059 = C T C = = D = = = = = T G G = = I = = = = 0 P060 = C = C = = D ? = = G = T = G = = I ? = = A 0 P061 = C = C = = D T = = ? = T = G = = I C = = ? 0 P062 = C = C A = D ? = = G = T = G G = I ? = = A 0 P063 = C = C = A D T = I G = T = G = C I C = D A 0 P064 = ? = C = = D T = = = = ? = G = = I C = = = 0 P065 = = T = = = = C = = A = = G = = = = T = = G 0 P066 = = = = = = = = T = = = = = = = = = = G = = 0 P067 = = = = = = = = = = = = = = = = = = = = = = 0 P068 = = = = = = = = = = = = = = = = = = = = = = 0 P069 = = = = = = = = = = = = = = = = = = = = = = 0 P070 = = = = = = = = = = = = = = = = = = = = = = 0 P071 = = = = = = = = (T) I = = = = = = = = = (G) D = 0 P072 = C = C A = D T = = G = T = G G = I C = = A 0 P073 T = = = = = = = = = = A = = = = = = = = = = 0 P074 = = = = = = = = T = = = = = = = = = = G = = 0 P075 = = = = = = = = T = = = = = = = = = = G = = 0 P076 = = = = = = = ? ? = = = = = = = = = ? ? = = 0 P077 T T = G G = I C = = A A C = C A = D T = = G 0 P078 = C = C A = D T = = G = T = G G = I C = = A 0 P079 = C = C A = D T = = G = T = G G = I C = = A 0 P080 ? C = ? = = = ? = ? = ? T = ? = = = ? = ? = 0 P081 = = = = = = = ? T = = = = = = = = = ? G = = 0 P082 = = = = = = = = T = = = = = = = = = = G = = 0 P083 = = = = = = = = = = = = = = = = = = = = = = 0 P084 ? C = C A = D T = = ? ? T = G G = I C = = ? 0 P085 T T = G G = I C = = A A C = C A = D T = = G 0 P086 = C = C A A D T = I G = T = G G C I C = D A 0 P087 = C T C = = D = = = = = T G G = = I = = = = 0 P088 = C = C = = D T = = G = T = G = = I C = = A 0 P089 = ? = = = ? ? ? = = = = ? = = = ? ? ? = = = 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 0.98 = 1.00 = 0.96 = 1.00 = = 1.00 1.00 = = = = 0.53 = = = = 1.00 1.00 = = = 0.96 = = = = 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 = = 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 1.00 = = 1.00 = = = = = = = ? = = = = 0.74 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 = = = = 0.97 = = = = = = ? 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 = = = = = = = = = = 0.99 1.00 = 1.00 = = 1.00 1.00 = = 1.00 = = = = = = = = = = = 0.97 = = = = 1.00 = = = 1.00 = 0.96 = = = = = = = 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 0.98 = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.61 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 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 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 = ? = = = ? ? ? = = = = = = = = = = ? = = = END PHASEPROBS