************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 fancg.phase.inp fancg.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST fancg.phase.out_freqs : haplotype frequency estimates fancg.phase.out_pairs : most likely haplotype pairs for each individual fancg.phase.out_recom : estimates of recombination parameters fancg.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 9 Positions of loci: 676 1481 1495 1533 1594 2146 4071 4309 6595 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file fancg.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AAGDACACA 46.000000 2 GAGDAAGCA 1.000000 3 GAGDAAGCG 57.000000 4 GAGDAAGTA 20.000000 5 GAGDACGCA 15.000000 6 GAGIACGCA 7.000000 7 GATIGCGCA 24.000000 8 GTGDAAGTA 9.000000 9 GTGDAAGTG 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,5) P002: (1,3) P003: (1,5) P004: (1,1) P005: (1,3) P006: (3,3) P007: (3,3) P008: (3,7) P009: (1,3) P010: (3,4) P011: (1,5) P012: (3,4) P013: (5,7) P014: (1,7) P015: (7,7) P016: (1,7) P017: (1,3) P018: (3,6) P019: (4,8) P020: (1,8) P021: (5,6) P022: (3,4) P023: (1,3) P024: (3,4) P025: (3,7) P026: (1,7) P027: (8,8) P028: (3,8) P029: (6,7) P030: (3,3) P031: (1,8) P032: (1,7) P033: (3,4) P034: (3,7) P035: (1,3) P036: (1,7) P037: (1,7) P038: (6,6) P039: (3,7) P040: (3,3) P041: (1,6) P042: (1,3) P043: (1,3) P044: (1,1) P045: (1,1) P046: (1,3) P047: (5,7) P048: (1,7) P049: (3,4) P050: (3,5) P051: (1,5) P052: (4,7) P053: (1,3) P054: (4,7) P055: (4,7) P056: (1,4) P057: (3,5) P058: (1,3) P059: (5,6) P060: (3,4) P061: (1,5) P062: (1,3) P063: (3,3) P064: (1,2) P065: (4,5) P066: (1,3) P067: (3,4) P068: (4,4) P069: (3,4) P070: (3,3) P071: (1,1) P072: (1,4) P073: (5,8) P074: (4,4) P075: (1,5) P076: (1,1) P077: (3,3) P078: (1,3) P079: (3,3) P080: (7,7) P081: (1,3) P082: (3,3) P083: (3,7) P084: (3,9) P085: (8,8) P086: (3,3) P087: (3,7) P088: (3,5) P089: (1,1) P090: (3,7) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 A A G D A C A C A G A G D A [C] G C A 0 P002 A A G D A C A C A G A G D A A G C G 0 P003 A A G D A C A C A G A G D A C G C A 0 P004 A A G D A C A C A A A G D A C A C A 0 P005 A A G D A C A C A G A G D A A G C [G] 0 P006 G A G D A A G C G G A G D A A G C G 0 P007 G A G D A A G C G G A G D A A G C G 0 P008 G A G D A A G C G G A T I G C G C A 0 P009 A A G D A C A C A G A G D A A G C G 0 P010 G A G D A A G C G G A G D A A G T A 0 P011 A A G D A C A C A G A G D A C G C A 0 P012 G A G D A A G C G G A G D A A G T A 0 P013 G A G D A C G C A G A T I G C G C A 0 P014 A A G D A C A C A G A T I G C G C A 0 P015 G A T I G C G C A G A T I G C G C A 0 P016 A A G D A C A C A G A T I G C G C A 0 P017 A A G D A C A C A G A G D A A G C G 0 P018 G A G D A A G C G G A G I A C G C A 0 P019 G A G D A A G T A G T G D A A G T A 0 P020 A A G D A C A C A G T G D A A G T A 0 P021 G A G D A C G C A G A G I A C G C A 0 P022 G A G D A A G C G G A G D A A G T A 0 P023 A A G D A C A C A G A G D A A G C G 0 P024 G A G D A A G C G G A G D A A G T A 0 P025 G A G D A A G C G G A T I G C G C A 0 P026 A A G D A C A C A G A T I G C G C A 0 P027 G T G D A A G T A G T G D A A G T A 0 P028 G A G D A A G C G G T G D A A G T A 0 P029 G A G I A C G C A G A T I G C G C A 0 P030 G A G D A A G C G G A G D A A G C G 0 P031 A A G D A C A C A G T G D A A G T A 0 P032 A A G D A C A C A G A T I G C G C A 0 P033 G A G D A A G C G G A G D A A G T A 0 P034 G A G D A A G C G G A T I G C G C A 0 P035 A A G D A C A C A G A G D A A G C G 0 P036 A A G D A C A C A G A T I G C G C A 0 P037 A A G D A C A C A G A T I G C G C A 0 P038 G A G I A C G C A G A G I A C G C A 0 P039 G A G D A A G C G G A T I G C G C A 0 P040 G A G D A A G C G G A G D A A G C G 0 P041 A A G D A C A C A G A G I A C G C A 0 P042 A A G D A C A C A G A G D A A G C G 0 P043 A A G D A C A C A G A G D A A G C G 0 P044 A A G D A C A C A A A G D A C A C A 0 P045 A A G D A C A C A A A G D A C A C A 0 P046 A A G D A C A C A G A G D A A G C G 0 P047 G A G D A C G C A G A T I G C G C A 0 P048 A A G D A C A C A G A T I G C G C A 0 P049 G A G D A A G C G G A G D A A G T A 0 P050 G A G D A A G C G G A G D A [C] G C A 0 P051 A A G D A C A C A G A G [D] A C G C A 0 P052 G [A] G D A A G T A G A T I G C G C A 0 P053 A A G D A C A C A G A G D A A G C G 0 P054 G [A] G D A A G T A G A T I G C G C A 0 P055 G [A] G D A A G T A G A T I G C G C A 0 P056 A A G D A C A C A G A G D A A G [T] A 0 P057 G A G D A A G C G G A G [D] A [C] G C A 0 P058 A A G D A C A C A G A G D A A G C G 0 P059 G A G D A C G C A G A G I A C G C A 0 P060 G A G D A A G C G G A G D A A G T A 0 P061 A A G D A C A C A G A G D A C G C A 0 P062 A A G D A C A C A G A G D A A G C G 0 P063 G A G D A A G C G G A G D A A G C G 0 P064 A A G D A C A C A G A G D A A G C A 0 P065 G A G D A A G [T] A G A G D A C G C A 0 P066 A A G D A C A C A G A G D A A G C G 0 P067 G A G D A A G C G G A G D A A G T A 0 P068 G A G D A A G T A G A G D A A G T A 0 P069 G A G D A A G C G G A G D A A G T A 0 P070 G A G D A A G C G G A G D A A G C G 0 P071 A A G D A C A C A A A G D A C A C A 0 P072 A A G D A C A C A G A G D A A G T A 0 P073 G A G D A C G C A G T G D A A G T A 0 P074 G A G D A A G T A G A G D A A G T A 0 P075 [A] A G D A [C] [A] C A [G] A [G] [D] [A] [C] [G] C A 0 P076 A A G D A C A C A A A G D A C A C A 0 P077 G A G D A A G C G G A G D A A G C G 0 P078 A A G D A C A C A G A G D A A G C [G] 0 P079 G A G D A A G C G G A G D A A G C G 0 P080 G A T I G C G C A G A T I G C G C A 0 P081 A A G D A C A C A G A G D A A G C G 0 P082 G A G D A A G C G G A G D A A G C G 0 P083 G A G D A A G C G G A T I G C G C A 0 P084 G A G D A A G C G G T G D A A G T G 0 P085 G T G D A A G T A G T G D A A G T A 0 P086 G A G D A A G C G G A G D A A G C G 0 P087 G A G D A A G C G G A T I G C G C A 0 P088 G A G D A A G C G G A G D A C G C A 0 P089 A A G D A C A C A A A G D A C A C A 0 P090 G A G D A A G C G G A T I G C G 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 A = = = = ? ? = = G = = = = ? ? = = 0 P002 A = = = = C ? = ? G = = = = A ? = ? 0 P003 A = = = = = ? = = G = = = = = ? = = 0 P004 = = = = = = = = ? = = = = = = = = ? 0 P005 A = = = = ? A ? ? G = = = = ? G ? ? 0 P006 = = = = = = = = = = = = = = = = = = 0 P007 = = = = = = = = = = = = = = = = = = 0 P008 = = G ? ? A = = G = = T ? ? C = = A 0 P009 A = = = = C A = A G = = = = A G = G 0 P010 = = = = = = = C G = = = = = = = T A 0 P011 A = = = = = ? = = G = = = = = ? = = 0 P012 = = = = = = = C G = = = = = = = T A 0 P013 = ? ? D A = = = = = ? ? I G = = = = 0 P014 A = G D A = A = = G = T I G = G = = 0 P015 = = = = = = = = = = = = = = = = = = 0 P016 A = G D A = ? ? = G = T I G = ? ? = 0 P017 A = = = = C ? = A G = = = = A ? = G 0 P018 = ? ? D = A = = ? = ? ? I = C = = ? 0 P019 = A = = = = = = = = T = = = = = = = 0 P020 A A = = = C A C = G T = = = A G T = 0 P021 = ? ? D = = = = = = ? ? I = = = = = 0 P022 = = = = = ? = C G = = = = = ? = T A 0 P023 A = = = = C A = A G = = = = A G = G 0 P024 = = = = = = = C G = = = = = = = T A 0 P025 = ? ? D A A = = G = ? ? I G C = = A 0 P026 A ? G D A = A = = G ? T I G = G = = 0 P027 = = = = = = = ? = = = = = = = = ? = 0 P028 = A = = = = = C G = T = = = = = T A 0 P029 = = G = A = = = = = = T = G = = = = 0 P030 = = = = = = = = = = = = = = = = = = 0 P031 A A = = = C A ? = G T = = = A G ? = 0 P032 A = G D A = A = = G = T I G = G = = 0 P033 = = = = = = = C G = = = = = = = T A 0 P034 = ? G D A A = = G = ? T I G C = = A 0 P035 A = = = = ? A = A G = = = = ? G = G 0 P036 A ? ? D A = A = = G ? ? I G = G = = 0 P037 A ? ? D A = A = = G ? ? I G = G = = 0 P038 = = = = = = = = = = = = = = = = = = 0 P039 = ? ? D A A = = G = ? ? I G C = = A 0 P040 = = = = = ? = = = = = = = = ? = = = 0 P041 A ? ? D = = A = = G ? ? I = = G = = 0 P042 A = = = = C A = A G = = = = A G = G 0 P043 A = = = = C A = A G = = = = A G = G 0 P044 = = = = = = = = = = = = = = = = = = 0 P045 = = = = = = = = = = = = = = = = = = 0 P046 A = = = = C A = A G = = = = A G = G 0 P047 = ? ? D A = = = = = ? ? I G = = = = 0 P048 A ? ? D A = A = = G ? ? I G = G = = 0 P049 = = = = = = = C G = = = = = = = T A 0 P050 = = = = = ? = = G = = = = = ? = = A 0 P051 A ? ? ? = = A ? = G ? ? ? = = G ? = 0 P052 = ? ? ? A A = ? = = ? ? ? G C = ? = 0 P053 A = = = = C A = A G = = = = A G = G 0 P054 = ? G ? A A = T = = ? T ? G C = C = 0 P055 = ? ? D A ? = T = = ? ? I G ? = C = 0 P056 A = = = = C A ? = G = = = = A G ? = 0 P057 = ? = ? = ? = = G = ? = ? = ? = = A 0 P058 A = = = = ? A ? A G = = = = ? G ? G 0 P059 = ? = D = = = = = = ? = I = = = = = 0 P060 = = = = = = = C G = = = = = = = T A 0 P061 A = = = = = A = = G = = = = = G = = 0 P062 A ? ? ? ? ? A = A G ? ? ? ? ? G = G 0 P063 = = = = = = = = = = = = = = = = = = 0 P064 A = = = = C A = = G = = = = A G = = 0 P065 = = = = = A = ? = = = = = = C = ? = 0 P066 A = = = = C A = A G = = = = A G = G 0 P067 = = = = = = = C G = = = = = = = T A 0 P068 = = = = = = = = = = = = = = = = = = 0 P069 = = = = = = = C G = = = = = = = T A 0 P070 = = = = = = = = = = = = = = = = = = 0 P071 = = = = = = = = = = = = = = = = = = 0 P072 A = = = = C A C = G = = = = A G T = 0 P073 = A = = = C = C = = T = = = A = T = 0 P074 = = = = = ? = = = = = = = = ? = = = 0 P075 ? ? ? ? ? ? ? ? = ? ? ? ? ? ? ? ? = 0 P076 = = = = = = = = = = = = = = = = = = 0 P077 = = = = = = = = = = = = = = = = = = 0 P078 A = = = = ? A = ? G = = = = ? G = ? 0 P079 = = = = = = = = = = = = = = = = = = 0 P080 = = = = = ? = = = = = = = = ? = = = 0 P081 A = = = = ? A = A G = = = = ? G = G 0 P082 = = = = = = = = = = = = = = = = = = 0 P083 = ? G D A A = = G = ? T I G C = = A 0 P084 = A = = = = = C = = T = = = = = T = 0 P085 = = = = = = = = = = = = = = = = = = 0 P086 = = = = = = = = = = = = = = = = = = 0 P087 = ? ? D A A = = ? = ? ? I G C = = ? 0 P088 = = = = = A = = ? = = = = = C = = ? 0 P089 = = = = = ? = = = = = = = = ? = = = 0 P090 = ? G ? A A = = G = ? T ? G C = = A 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 1.00 1.00 = = = = = ? = = = = = = = = = 1.00 1.00 = ? ? 1.00 1.00 = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = ? ? = 1.00 = = = = 1.00 ? = 1.00 = ? ? 1.00 = 1.00 = = ? = 1.00 = = = = = = = 1.00 1.00 = = = 1.00 1.00 1.00 = = ? ? 1.00 = = = = = = = = = = ? = 1.00 1.00 1.00 = = = = 1.00 1.00 = 1.00 = = = = = = = 1.00 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 = = = = ? 1.00 = 1.00 1.00 ? ? 1.00 1.00 = 1.00 = = 1.00 ? ? 1.00 1.00 = 1.00 = = = = = = = = = = = = ? ? 1.00 1.00 1.00 = = 1.00 = = = = = ? = = = 1.00 ? ? 1.00 = = 1.00 = = 1.00 = = = = 1.00 1.00 = 1.00 1.00 = = = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 1.00 = 1.00 = ? ? 1.00 1.00 = = = = 1.00 ? ? 1.00 1.00 = 1.00 = = = = = = = = = 1.00 1.00 = = = = = ? = = 1.00 1.00 ? ? ? = = 1.00 ? = = ? ? ? 1.00 1.00 = ? = 1.00 = = = = 1.00 1.00 = 1.00 = ? 1.00 ? 1.00 1.00 = 1.00 = = ? ? 1.00 1.00 ? = 1.00 = 1.00 = = = = 1.00 1.00 ? = = ? = ? = ? = = 1.00 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 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 END PHASEPROBS