************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 rps3x.phase.inp rps3x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST rps3x.phase.out_freqs : haplotype frequency estimates rps3x.phase.out_pairs : most likely haplotype pairs for each individual rps3x.phase.out_recom : estimates of recombination parameters rps3x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 12 Positions of loci: 366 1037 1683 1758 1849 1956 2121 3306 4723 5240 7658 8130 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file rps3x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ITCATCAGIAGA 47.000000 2 ITCATCAAIAGA 3.000000 3 ITCACCGGIAGA 1.000000 4 DTCACCAAIAGG 32.000000 5 DTCACCGAIAGG 51.000000 6 DTCACCGAIACG 17.000000 7 DTTACGAAIAGG 7.000000 8 DTTACGAAIGGG 5.000000 9 DCCGCCAADGGG 17.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,1) P002: (4,5) P003: (1,1) P004: (1,7) P005: (5,5) P006: (4,4) P007: (5,5) P008: (6,6) P009: (1,4) P010: (4,5) P011: (1,1) P012: (1,4) P013: (5,6) P014: (1,9) P015: (5,9) P016: (4,4) P017: (8,9) P018: (5,8) P019: (4,5) P020: (5,5) P021: (1,7) P022: (1,5) P023: (5,5) P024: (1,6) P025: (5,9) P026: (1,1) P027: (6,9) P028: (1,4) P029: (1,5) P030: (4,5) P031: (5,6) P032: (1,1) P033: (5,9) P034: (1,1) P035: (4,5) P036: (1,9) P037: (1,5) P038: (2,2) P039: (5,5) P040: (1,4) P041: (4,5) P042: (5,7) P043: (4,6) P044: (4,6) P045: (3,5) P046: (1,5) P047: (4,5) P048: (5,6) P049: (9,9) P050: (1,1) P051: (1,5) P052: (6,9) P053: (1,4) P054: (4,5) P055: (1,4) P056: (2,8) P057: (1,5) P058: (1,4) P059: (7,8) P060: (4,4) P061: (4,7) P062: (1,9) P063: (5,5) P064: (1,5) P065: (1,7) P066: (1,5) P067: (1,9) P068: (5,9) P069: (5,9) P070: (1,5) P071: (5,9) P072: (5,6) P073: (1,6) P074: (1,4) P075: (1,9) P076: (5,5) P077: (1,4) P078: (4,5) P079: (1,5) P080: (4,8) P081: (5,6) P082: (1,6) P083: (5,6) P084: (6,6) P085: (4,9) P086: (4,4) P087: (1,5) P088: (1,4) P089: (1,7) P090: (5,5) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 I T C A T C A G I A G A I T C A T C A G I A G A 0 P002 D T C A C C A A I A G G D T C A C C G A I A G G 0 P003 I T C A T C A G I A G A I T C A T C A G I A G A 0 P004 I T C A T C A G I A G A D T T A C G A A I A G G 0 P005 D T C A C C G A I A [G] G D T C A C C G A I A G G 0 P006 D T C A C C A A I A G G D T C A C C A A I A G G 0 P007 D T C A C C G A I A G G D T C A C C G A I A G G 0 P008 D T C A C C G A I A C G D T C A C C G A I A C G 0 P009 I T C A T C A G I A G A D T C A C C A A I A G G 0 P010 D T C A C C A A I A G G D T C A C C G A I A G G 0 P011 I T C A T C A G I A G A I T C A T C A G I A G A 0 P012 I T C A T C A G I A G A D T C A C C A A I A G G 0 P013 D T C A C C G A I A G G D T C A C C G A I A C G 0 P014 I T C A T C A G I A G A D C C G C C A A D G G G 0 P015 D T C A C C G A I A G G D C C G C C A A D G G G 0 P016 D T C A C C A A I A G G D T C A C C A A I A G G 0 P017 D T T A C G A A I G G G D C C G C C A A D G G G 0 P018 D T C A C C G A I A G G D T T A C G A A I G G G 0 P019 D T C A C C A A I A G G D T C A C C G A I A G G 0 P020 D T C A C C G A I A G G D T C A C C G A I A G G 0 P021 I T C A T C A G I A G A D T T A C G A A I A G G 0 P022 I T C A T C A G I A G A D T C A C C G A I A G G 0 P023 D T C A C C G A I A G G D T C A C C G A I A G G 0 P024 I T C A T C A G I A G A D T C A C C G A I A C G 0 P025 D T C A C C G A I A G G D C C G C C A A D G G G 0 P026 I T C A T C A G I A G A I T C A T C A G I A G A 0 P027 D T C A C C G A I A C G D C C G C C A A D G G G 0 P028 I T C A T C A G I A G A D T C A C C A A I A G G 0 P029 I T C A T C A G I A G A D T C A C C G A I A G G 0 P030 D T C A C C A A I A G G D T C A C C G A I A G G 0 P031 D T C A C C G A I A G G D T C A C C G A I A C G 0 P032 I T C A T C A G I A G A I T C A T C A G I A G A 0 P033 D T C A C C G A I A G G D C C G C C A A D G G G 0 P034 I T C A T C A G I A G A I T C A T C A G I A G A 0 P035 D T C A C C A A I A G G D T C A C C G A I A G G 0 P036 I T C A T C A G I A G A D C C G C C A A D G G G 0 P037 I T C A T C A G I A G A D T C A C C G A I A G G 0 P038 I T C A T C A A I A G A I T C A T C A A I A G A 0 P039 D T C A C C G A I A G G D T C A C C G A I A G G 0 P040 I T C A T C A G I A G A D T C A C C A A I A G G 0 P041 D T C A C C A A I A G G D T C A C C G A I A G G 0 P042 D T C A C C G A I A G G D T T A C G A A I A G G 0 P043 D T C A C C A A I A G G D T C A C C G A I A C G 0 P044 D T C A C C A A I A G G D T C A C C G A I A C G 0 P045 (I) T C A C C G G I A G A (D) T C A C C G A I A G G 0 P046 I T C A T C A G I A G A D T C A C C G A I A G G 0 P047 D T C A C C A A I A G G D T C A C C G A I A G G 0 P048 D T C A C C G A I A G G D T C A C C G A I A C G 0 P049 D C C G C C A A D G G G D C C G C C A A D G G G 0 P050 I T C A T C A G I A G A I T C A T C A G I A G A 0 P051 I T C A T C A G I A G A D T C A C C G A I A G G 0 P052 D T C A C C G A I A C G D C C G C C A A D G G G 0 P053 I T C A T C A G I A G A D T C A C C A A I A G G 0 P054 D T C A C C A A I A G G D T C A C C G A I A G G 0 P055 I T C A T C A G I A G A D T C A C C A A I A G G 0 P056 I T C A T C A A I A G A D T T A C G A A I G G G 0 P057 I T C A T C A G I A G A D T C A C C G A I A G G 0 P058 I T C A T C A G I A G A D T C A C C A A I A G G 0 P059 D T T A C G A A I A G G D T T A C G A A I G G G 0 P060 D T C A C C A A I A G G D T C A C C A A I A G G 0 P061 D T C A C C A A I A G G D T T A C G A A I A G G 0 P062 I T C A T C A G I A G A D C C G C C A A D G G G 0 P063 D T C A C C G A I A G G D T C A C C G A I A G G 0 P064 I T C A T C A G I A G A D T C A C C G A I A G G 0 P065 I T C A T C A G I A G A D T T A C G A A I A G G 0 P066 I T C A T C A G I A G A D T C A C C G A I A G G 0 P067 I T C A T C A G I A G A D C C G C C A A D G G G 0 P068 D T C A C C G A I A G G D C C G C C A A D G G G 0 P069 D T C A C C G A I A G G D C C G C C A A D G G G 0 P070 I T C A T C A G I A G A D T C A C C G A I A G G 0 P071 D T C A C C G A I A G G D C C G C C A A D G G G 0 P072 D T C A C C G A I A G G D T C A C C G A I A C G 0 P073 I T C A T C A G I A G A D T C A C C G A I A C G 0 P074 I T C A T C A G I A G A D T C A C C A A I A G G 0 P075 I T C A T C A G I A G A D C C G C C A A D G G G 0 P076 D T C A C C G A I A G G D T C A C C G A I A G G 0 P077 I T C A T C A G I A G A D T C A C C A A I A G G 0 P078 D T C A C C A A I A G G D T C A C C G A I A G G 0 P079 I T C A T C A G I A G A D T C A C C G A I A G G 0 P080 D T C A C C A A I A G G D T T A C G A A I G G G 0 P081 D T C A C C G A I A G G D T C A C C G A I A C G 0 P082 I T C A T C A G I A G A D T C A C C G A I A C G 0 P083 D T C A C C G A I A G G D T C A C C G A I A C G 0 P084 D T C A C C G A I A C G D T C A C C G A I A C G 0 P085 D T C A C C A A I A G G D C C G C C A A D G G G 0 P086 D T C A C C A A I A G G D T C A C C A A I A G G 0 P087 I T C A T C A G I A G A D T C A C C G A I A G G 0 P088 I T C A T C A G I A G A D T C A C C A A I A G G 0 P089 I T C A T C A G I A G A D T T A C G A A I A G G 0 P090 D T C A C C G A I A G G D T C A C C G A I A 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 = = = = = = = = = = = = = = = = = = = = = = = = 0 P002 = = = = = = A = = = = = = = = = = = G = = = = = 0 P003 = = = = = = = = = = = = = = = = = = = = = = = = 0 P004 I = C = T C = G = = = A D = T = C G = A = = = G 0 P005 = = = = = = = = = = ? = = = = = = = = = = = ? = 0 P006 = = = = = = = = = = = = = = = = = = = = = = = = 0 P007 = = = = = = = = = = = = = = = = = = = = = = = = 0 P008 = = ? = = = = = = = = = = = ? = = = = = = = = = 0 P009 I = = = T = = G ? = = A D = = = C = = A ? = = G 0 P010 = = = = = = A = = = = = = = = = = = G = = = = = 0 P011 = = = = = = = = = = = ? = = = = = = = = = = = ? 0 P012 I = = = T = = G ? = = A D = = = C = = A ? = = G 0 P013 = = = = = = = = = = G = = = = = = = = = = = C = 0 P014 I T = A T = = G I A = A D C = G C = = A D G = G 0 P015 = T = A = = G = I A ? = = C = G = = A = D G ? = 0 P016 = = = = = = = = = = = = = = = = = = = = = = = = 0 P017 = T T A = G = ? I = = = = C C G = C = ? D = = = 0 P018 = = C = = C G = = A = = = = T = = G A = = G = = 0 P019 = = = = = = A = = = = = = = = = = = G = = = = = 0 P020 = = = = = = = = = = = = = = = = = = = = = = = = 0 P021 I = C = T C = G = = = A D = T = C G = A = = = G 0 P022 I = = = T = A G = = = A D = = = C = G A = = = G 0 P023 = = = = = = = = = = = = = = = = = = = = = = = = 0 P024 I = = = T = A G = = G A D = = = C = G A = = C G 0 P025 = T = A = = G = I A = = = C = G = = A = D G = = 0 P026 = = ? = = = = = = = = = = = ? = = = = = = = = = 0 P027 = T = A = = G = I A C = = C = G = = A = D G G = 0 P028 I = = = T = = G ? = = A D = = = C = = A ? = = G 0 P029 I = = = T = A G = = = A D = = = C = G A = = = G 0 P030 = = = = = = A = = = = = = = = = = = G = = = = = 0 P031 = = = = = = = = ? = G = = = = = = = = = ? = C = 0 P032 = = = = = = = = = = = = = = = = = = = = = = = = 0 P033 = T = A = = G = I A = = = C = G = = A = D G = = 0 P034 = = = = = = = = = = = = = = = = = = = = = = = = 0 P035 = = = = = = A = = = = = = = = = = = G = = = = = 0 P036 I T = A T = = G I A = A D C = G C = = A D G = G 0 P037 I ? = = T = A G = = = A D ? = = C = G A = = = G 0 P038 = = = = = = = = = = = = = = = = = = = = = = = = 0 P039 = = = = = = = = = = = = = = = = = = = = = = = = 0 P040 I = = = T = = G ? = = A D = = = C = = A ? = = G 0 P041 = = = = = = A = = = = = = = = = = = G = = = = = 0 P042 = = C = = C G = = = ? = = = T = = G A = = = ? = 0 P043 = = = = = = A = = = G = = = = = = = G = = = C = 0 P044 = = = = = = A = = = G = = = = = = = G = = = C = 0 P045 (I) = = = = = = G = = = A (D) = = = = = = A = = = G 0 P046 I = = = T = A G = = = ? D = = = C = G A = = = ? 0 P047 = = = = = = A = = = = = = = = = = = G = = = = = 0 P048 = = = = = = = = = = G ? = = = = = = = = = = C ? 0 P049 = = = = = = = = = = = = = = = = = = = = = = = = 0 P050 = = = = = = = = = = = = = = = = = = = = = = = = 0 P051 I = = = T = A G = = = A D = = = C = G A = = = G 0 P052 = T = A = = G = I A C = = C = G = = A = D G G = 0 P053 I = = = T = = G ? = = A D = = = C = = A ? = = G 0 P054 = = = = = = A = = = ? ? = = = = = = G = = = ? ? 0 P055 I = = = T = = G = = = A D = = = C = = A = = = G 0 P056 I = C = T C = = = A = A D = T = C G = = = G = G 0 P057 I = = = T = A G = = ? A D = = = C = G A = = ? G 0 P058 I = = = T = = G ? = ? A D = = = C = = A ? = ? G 0 P059 = = = = = = = = = A = = = = = = = = = = = G = = 0 P060 = = = = = = = = = = = ? = = = = = = = = = = = ? 0 P061 = = C = = C = = = = = ? = = T = = G = = = = = ? 0 P062 I T = A T = = G I A = A D C = G C = = A D G = G 0 P063 = = = = = = = = = = = = = = = = = = = = = = = = 0 P064 I ? = = T = A G = = = A D ? = = C = G A = = = G 0 P065 I = C = T C = G = = = A D = T = C G = A = = = G 0 P066 I = = = T = A G = = = A D = = = C = G A = = = G 0 P067 I T = A T = = G I A = ? D C = G C = = A D G = ? 0 P068 = T = A = = G = I A = = = C = G = = A = D G = = 0 P069 = T = A = = G = I A = = = C = G = = A = D G = = 0 P070 I = = = T = A G = = = A D = = = C = G A = = = G 0 P071 = T = A = = G = I A = ? = C = G = = A = D G = ? 0 P072 = = = = = = = = = = G = = = = = = = = = = = C = 0 P073 I = = = T = A G ? = G A D = = = C = G A ? = C G 0 P074 I = = = T = = G = = = A D = = = C = = A = = = G 0 P075 I T = A T = = G I A = A D C = G C = = A D G = G 0 P076 = = = = = = = = = = = = = = = = = = = = = = = = 0 P077 I = = = T = = G = = ? A D = = = C = = A = = ? G 0 P078 = = = = = = A = = = ? ? = = = = = = G = = = ? ? 0 P079 I = = = T = A G = = = A D = = = C = G A = = = G 0 P080 = = C = = C = = = A ? ? = = T = = G = = = G ? ? 0 P081 = = = = = = = = = = G = = = = = = = = = = = C = 0 P082 I = = = T = A G ? = G A D = = = C = G A ? = C G 0 P083 = = = = = = = = = = G = = = = = = = = = = = C = 0 P084 = = = = = = = = = = = = = = = = = = = = = = = = 0 P085 = T = A = = = = I A = = = C = G = = = = D G = = 0 P086 = = = = = = = = = = ? = = = = = = = = = = = ? = 0 P087 I = = = T = A G = = = A D = = = C = G A = = = G 0 P088 I = = = T = = G = = = A D = = = C = = A = = = G 0 P089 I = C = T C = G = = = A D = T = C G = 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 1.00 = 1.00 = = = 1.00 = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = 1.00 = = = 1.00 = = 1.00 ? = = 1.00 = = = = = = 1.00 = = = = = = = = = = = = = = = = ? 1.00 = = = 1.00 = = 1.00 ? = = 1.00 = = = = = = = = = = 1.00 = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 1.00 ? = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 = ? 1.00 = = = = = 1.00 = = 1.00 1.00 = = 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = 1.00 = 1.00 = 1.00 1.00 = 1.00 = = = 1.00 1.00 = = = 1.00 = 1.00 1.00 = = = 1.00 = = = = = = = = = = = = 1.00 = = = 1.00 = 1.00 1.00 = = 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 = = = ? = = = = = = = 0.99 = = = 1.00 = = = = = = = 0.99 = = = 1.00 = 0.60 = = = = = = 1.00 = = = 1.00 1.00 = = = 1.00 = 1.00 1.00 = = = ? = = = = = = 1.00 = = = = = = = = = = = = = = = 1.00 ? = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 = = = 1.00 = = 1.00 ? = = 1.00 = = = = = = 1.00 = = = ? ? 1.00 = = = 1.00 = = 1.00 = = = 1.00 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 1.00 = = ? 1.00 1.00 = = = 1.00 = = 1.00 ? = ? 1.00 = = = = = = = = = 1.00 = = = = = = = = = = = = = ? = = 1.00 = = 1.00 = = = = = ? 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = 1.00 ? = = 1.00 = 1.00 1.00 = = = 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = = = 1.00 1.00 = = = 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 = ? = 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = = = 1.00 = 1.00 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 ? = = = = = = = = = = = END PHASEPROBS