************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 ptge4.phase.inp ptge4.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ptge4.phase.out_freqs : haplotype frequency estimates ptge4.phase.out_pairs : most likely haplotype pairs for each individual ptge4.phase.out_recom : estimates of recombination parameters ptge4.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 22 Positions of loci: 1410 1479 1600 1701 1757 2876 3166 4462 5479 6588 9381 9949 9977 10470 10918 11914 14858 16072 16715 16884 16988 17118 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ptge4.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CCGTGCCTACCAAATGGTCACD 16.000000 2 CCGTGCCTACCAAATGACCCTI 1.000000 3 CTGTGCCTACCAAATGGTCACD 1.000000 4 TCGCACCCGTCGAGGAGTTATD 1.000000 5 TCGCACCTGCCAAATGGCCATD 4.000000 6 TCGCACCTGCCAAATGGCCCTI 1.000000 7 TCGCACCTGCTAGATGGCCCTI 12.000000 8 TCGCACCTGCTAGATGACCCTI 5.000000 9 TCGCACCTGTCAAATGGCCATD 1.000000 10 TCGCGGTTACTAGATGGCCCTI 8.000000 11 TCGTGGTTATCAAATGGTCATD 1.000000 12 TCGTGGTTATCAAGGAGTCATD 1.000000 13 TTGCACCCGCTAGATGGCCCTI 3.000000 14 TTGCACCCGTCAAGGAGTTATD 2.000000 15 TTGCACCCGTCGAGGAGTTATD 16.000000 16 TTGCACCTGTCAAGGAGTCATD 1.000000 17 TTACACCCGTCGAGGAGTTATD 18.000000 18 TTACACCCGTCGAGGGGTTATD 1.000000 19 TTACACCTACCAAATGACCCTI 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,15) DY02: (15,15) DY03: (4,15) DY04: (7,15) DY05: (7,7) DY06: (5,16) DY07: (15,15) DY08: (7,15) DY09: (14,15) DY10: (12,15) DY11: (1,15) DY12: (7,15) DY13: (1,7) DY14: (7,11) DY15: (10,13) DY16: (7,9) DY17: (7,13) DY18: (5,10) DY19: (6,14) DY20: (7,15) DY21: (7,10) DY22: (1,5) DY23: (1,10) DY24: (5,7) E101: (10,17) E102: (17,17) E103: (17,17) E104: (10,17) E105: (1,2) E106: (1,17) E107: (8,17) E108: (8,17) E109: (8,15) E110: (1,8) E111: (1,17) E112: (1,10) E113: (1,17) E114: (1,13) E115: (3,17) E116: (17,18) E117: (1,1) E118: (10,15) E119: (15,17) E120: (1,1) E121: (8,17) E122: (17,17) E123: (17,19) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 C C G T G C C T A C C A A A T G G T C A C D T T G C A C C C G T C G A G G A G T T A T D 0 DY02 T T G C A C C C G T C G A G G A G T T A T D T T G C A C C C G T C G A G G A G T T A T D 0 DY03 T C G C A C C C G T C G A G G A G T T A T D T T G C A C C C G T C G A G G A G T T A T D 0 DY04 T C G C A C C T G C T A G A T G G C C C T I T T G C A C C C G T C G A G G A G T T A T D 0 DY05 T C G C A C C T G C T A G A T G G C C C T I T C G C A C C T G C T A G A T G G C C C T I 0 DY06 T (C) G C A C C T G C C A A A T G G C C A T D T (T) G C A C C T G T C A A G G A G T C A T D 0 DY07 T T G C A C C C G T C G A G G A G T T A T D T T G C A C C C G T C G A G G A G T T A T D 0 DY08 T C G C A C C T G C T A G A T G G C C C T I T T G C A C C C G T C G A G G A G T T A T D 0 DY09 T T G C A C C C G T C A A G G A G T T A T D T T G C A C C C G T C G A G G A G T T A T D 0 DY10 T C G T G G T T A T C A A G G A G T C A T D T T G C A C C C G T C [G] A G G A G T T A T D 0 DY11 C C G T G C C T A C C A A A T G G T C A C D T T G C A C C C G T C [G] A G G A G T T A T D 0 DY12 T C G C A C C T G C T A G A T G G C C C T I T T G C A C C C G T C G A G G A G T T A T D 0 DY13 C C G T G C C T A C C A A A T G G T C A C D T C G C A C C T G C T A G A T G G C C C T I 0 DY14 T C G C (A) (C) (C) T (G) (C) (T) A (G) A T G G C C (C) T (I) T C G T (G) (G) (T) T (A) (T) (C) A (A) A T G G T C (A) T (D) 0 DY15 T C G C G G T T A C T A G A T G G C C C T I T T G C A C C C G C T A G A T G G C C C T I 0 DY16 T C G C A C C T G (C) T A G A T G G C C C T I T C G C A C C T G (T) C A A A T G G C C A T D 0 DY17 T C G C A C C T G C T A G A T G G C C C T I T T G C A C C C G C T A G A T G G C C C T I 0 DY18 T C G C A C C T G C C A A A T G G C C A T D T C G C G G T T A C T A G A T G G C C C T I 0 DY19 T C G C A C C T G C C A A A T G G C C C T I T T G C A C C C G T C A A G G A G T T A T D 0 DY20 T C G C A C C T G C T A G A T G G C C C T I T T G C A C C C G T C G A G G A G T T A T D 0 DY21 T C G C A C C T G C T A G A T G G C C C T I T C G C G G T T A C T A G A T G G C C C T I 0 DY22 C C G T G C C T A C C A A A T G G T C A C D T C G C A C C T G C C A A A T G G C C A T D 0 DY23 C C G T G C C T A C C A A A T G G T C A C D T C G C G G T T A C T A G A T G G C C C T I 0 DY24 T C G C A C C T G C C A A A T G G C C A T D T C G C A C C T G C T A G A T G G C C C T I 0 E101 T C G C G G T T A C T A G A T G G C C C T I T T A C A C C C G T C G A G G A G T T A T D 0 E102 T T A C A C C C G T C G A G G A G T T A T D T T A C A C C C G T C G A G G A G T T A T D 0 E103 T T A C A C C C G T C G A G G A G T T A T D T T A C A C C C G T C G A G G A G T T A T D 0 E104 T C G C G G T T A C T A G A T G G C C C T I T T A C A C C C G T C G A G G A G T T A T D 0 E105 C C G T G C C T A C C A A A T G G T C A C D C C G T G C C T A C C A A A T G A C C C T I 0 E106 C C G T G C C T A C C A A A T G G T C A C D T T A C A C C C G T C G A G G A G T T A T D 0 E107 T C G C A C C T G C T A G A T G A C C C T I T T A C A C C C G T C G A G G A G T T A T D 0 E108 T C G C A C C T G C T A G A T G A C C C T I T T A C A C C C G T C G A G G A G T T A T D 0 E109 T C G C A C C T G C T A G A T G A C C C T I T T G C A C C C G T C G A G G A G T T A T D 0 E110 C C G T G C C T A C C A A A T G G T C A C D T C G C A C C T G C T A G A T G A C C C T I 0 E111 C C G T G C C T A C C A A A T G G T C A C D T T A C A C C C G T C G A G G A G T T A T D 0 E112 C C G T G C C T A C C A A A T G G T C A C D T C G C G G T T A C T A G A T G G C C C T I 0 E113 C C G T G C C T A C C A A A T G G T C A C D T T A C A C C C G T C G A G G A G T T A T D 0 E114 C C G T G C C T A C C A A A T G G T C A C D T T G C A C C C G C T A G A T G G C C C T I 0 E115 C T G T G C C T A C C A A A T G G T C A C D T T A C A C C C G T C G A G G A G T T A T D 0 E116 T T A C A C C C G T C G A G G A G T T A T D T T A C A C C C G T C G A G G G G T T A T D 0 E117 C C G T G C C T A C C A A A T G G T C A C D C C G T G C C T A C C A A A T G G T C A C D 0 E118 T C G C G G T T A C T A G A T G G C C C T I T T G C A C C C G T C G A G G A G T T A T D 0 E119 T T G C A C C C G T C G A G G A G T T A T D T T [A] C A C C C G T C G A G G A G T T A T D 0 E120 C C G T G C C T A C C A A A T G G T C A C D C C G T G C C T A C C A A A T G G T C A C D 0 E121 T C G C A C C T G C T A G A T G A C C C T I T T A C A C C C G T C G A G G A G T T A T D 0 E122 T T A C A C C C G T C G A G G A G T T A T D T T A C A C C C G T C G A G G A G T T A T D 0 E123 T T A C A C C C G T C G A G G A G T T A T D T T A C A C C T A C C A A A T G A C C C T I 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 DY01 C C = T G = = T A C = A = A ? G = = C = C = T T = C A = = C G T = G = G ? A = = T = T = 0 DY02 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY03 = C = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = 0 DY04 = C = = = = = T = C T A G A T ? = C C C = I = T = = = = = C = T C G A G G ? = T T A = D 0 DY05 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY06 = (C) = = = = = = = C = = = A T ? = C = = = = = (T) = = = = = = = T = = = G G ? = T = = = = 0 DY07 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY08 = C = = = = = T = C T A G A T ? = ? C C = I = T = = = = = C = T C G A G G ? = ? T A = D 0 DY09 = = = = = = = = = = ? A = = = = = = = = = = = = = = = = = = = = ? G = = = = = = = = = = 0 DY10 = C = T G G T T A = = ? ? = = ? = = C = = = = T = C A C C C G = = ? ? = = ? = = T = = = 0 DY11 C C = T G = = T A C = ? ? ? T G = = C = C = T T = C A = = C G T = ? ? ? G A = = T = T = 0 DY12 = C = = = = = T = C T A G A T G = C C C = I = T = = = = = C = T C G A G G A = T T A = D 0 DY13 C = = T G = = = A = C = A = = = = T = A C D T = = C A = = = G = T = G = = = = C = C T I 0 DY14 = = = C (A) (C) (C) = (G) (C) (T) = (G) = = = = C = (C) = (I) = = = T (G) (G) (T) = (A) (T) (C) = (A) = = = = T = (A) = (D) 0 DY15 = C = = G G T T A = = = = = = = = = = = = = = T = = A C C C G = = = = = = = = = = = = = 0 DY16 = = = = = = = = = (C) T = G = = = = = = C = I = = = = = = = = = (T) C = A = = = = = = A = D 0 DY17 = C = = = = = T = = = = = = = = = = = = = = = T = = = = = C = = = = = = = = = = = = = = 0 DY18 = = = = A C C = G ? C = A = = = = = = A = D = = = = G G T = A ? T = G = = = = = = C = I 0 DY19 = C = = = = = T = C = = = A T G = C C C = I = T = = = = = C = T = = = G G A = T T A = D 0 DY20 = C = = = = = T = C T A G A T G = C C C = I = T = = = = = C = T C G A G G A = T T A = D 0 DY21 = = = = A C C = G = ? = = = = = = = = = = = = = = = G G T = A = ? = = = = = = = = = = = 0 DY22 C = = T G = = = A = = = = = ? = = T = = C = T = = C A = = = G = = = = = ? = = C = = T = 0 DY23 C = = T = C C = = = C = A = ? = = T = A C D T = = C = G T = = = T = G = ? = = C = C T I 0 DY24 = = = = = = = = = = C = A = = = = ? = A = D = = = = = = = = = = T = G = = = = ? = C = I 0 E101 = C G = G G T T A C T A G A T G = C C C = I = T A = A C C C G T C G A G G A = T T A = D 0 E102 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E103 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E104 = C G = G G T T A C T A G A T G = C C C = I = T A = A C C C G T C G A G G A = T T A = D 0 E105 = = = = = = = = = = = = = = = = G T = A C D = = = = = = = = = = = = = = = = A C = C T I 0 E106 C C G T G = = T A C = A = A T G = = C = C = T T A C A = = C G T = G = G G A = = T = T = 0 E107 = C G = = = = T = C T A G A T G A C C C = I = T A = = = = C = T C G A G G A G T T A = D 0 E108 = C G = = = = T = C T A G A T G A C C C = I = T A = = = = C = T C G A G G A G T T A = D 0 E109 = C = = = = = T = C T A G A T G A C C C = I = T = = = = = C = T C G A G G A G T T A = D 0 E110 ? ? ? ? ? = = = A = C = A = = = G T = A C D ? ? ? ? ? = = = G = T = G = = = A C = C T I 0 E111 C C G T G = = T A C = A = A T G = = C = C = T T A C A = = C G T = G = G G A = = T = T = 0 E112 C = = T = C C = = = C = A = = = = T = A C D T = = C = G T = = = T = G = = = = C = C T I 0 E113 C C G T G = = T A C = A = A T G = = C = C = T T A C A = = C G T = G = G G A = = T = T = 0 E114 C C = T G = = T A = C = A = = = = ? = A C D T T = C A = = C G = T = G = = = = ? = C T I 0 E115 C = G T G = = T A C = A = A T G = = C = C = T = A C A = = C G T = G = G G A = = T = T = 0 E116 = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = G = = = = = = 0 E117 = = = = = = = ? = = = = = ? = = = = = = = = = = = = = = = ? = = = = = ? = = = = = = = = 0 E118 = C = ? G G T T A C T A G A T G = C C C = I = T = ? A C C C G T C G A G G A = T T A = D 0 E119 ? ? ? ? ? = = = = = = = = = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = 0 E120 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E121 = C G = = = = T = C T A G A T G A C C C = I = T A = = = = C = T C G A G G A G T T A = D 0 E122 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E123 = = = = = = = C G T = G = G G A G T T A = D = = = = = = = T A C = A = A T G A C C C = I END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS 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 = = = = = = = = = = = = = = = = = = = = = = = 0.83 = = = = = = = 0.92 = = = 1.00 1.00 ? = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 ? = ? 1.00 1.00 = 1.00 = = = = = = = = = = ? 1.00 = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = ? ? = = ? = = 1.00 = = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 = ? ? ? 1.00 1.00 = = 1.00 = 1.00 = = 1.00 = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = = = 1.00 = 1.00 = 1.00 = = = = 1.00 = 1.00 1.00 1.00 = = = 0.91 0.68 0.68 0.68 = 0.68 0.78 0.85 = 0.85 = = = = 0.93 = 0.85 = 0.85 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = 0.63 1.00 = 1.00 = = = = = = 1.00 = 1.00 = 1.00 = = = = = 1.00 = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 ? 1.00 = 1.00 = = = = = = 1.00 = 1.00 = 1.00 = = = = = 1.00 = 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = 1.00 1.00 1.00 = 1.00 = ? = = = = = = = = = = = 1.00 = = 1.00 1.00 = = = 1.00 = = = = = ? = = 1.00 = = 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 = ? = = 1.00 = 1.00 1.00 1.00 = = = = = = = = = = 1.00 = 1.00 = = = = ? = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = 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 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 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 = 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 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 END PHASEPROBS