*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/home/qyi/lib/phase/PHASE2 -d1 fbgna.phase.inp fbgna.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
fbgna.phase.out_freqs : haplotype frequency estimates
fbgna.phase.out_pairs : most likely haplotype pairs for each individual
fbgna.phase.out_recom : estimates of recombination parameters
fbgna.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 47
Number of Loci: 12
Positions of loci: 251 841 1176 2224 3655 3807 3845 5498 6534 8834 9205 9659
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file fbgna.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 GAGGGTATGCCC 1.000000
2 GAGGGTGTGCCC 3.000000
3 GATGATGTACTC 11.000000
4 GATGGTATACCC 1.000000
5 GATGGTGTACCC 25.000000
6 GATGGTGTGCCC 1.000000
7 GATGGCATACCC 2.000000
8 GATGGCGTACCC 11.000000
9 AAGGGTGTACCC 1.000000
10 AAGGGTGTGCCC 9.000000
11 AAGAGTGTGCCC 16.000000
12 AAGAGTGTGTCT 4.000000
13 AGGAGTGCACCC 9.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
D001: (1,3)
D002: (5,12)
D003: (5,7)
D004: (3,10)
D005: (2,5)
D006: (3,5)
D007: (9,12)
D008: (3,10)
D009: (5,10)
D010: (11,13)
D011: (11,13)
D012: (5,10)
D013: (10,12)
D014: (11,11)
D015: (5,8)
D016: (3,5)
D033: (3,11)
D034: (5,11)
D035: (5,11)
D036: (10,12)
D037: (2,13)
D038: (2,13)
D039: (10,10)
D040: (7,10)
E001: (5,5)
E002: (11,13)
E003: (11,13)
E004: (5,8)
E005: (5,8)
E006: (8,11)
E007: (5,5)
E008: (4,11)
E009: (5,5)
E010: (6,8)
E011: (5,11)
E012: (3,8)
E013: (3,13)
E014: (3,5)
E015: (5,5)
E016: (3,8)
E017: (11,13)
E018: (8,13)
E019: (5,11)
E020: (5,11)
E021: (3,5)
E022: (8,8)
E023: (8,11)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 D001
G A G G G T (A) T G C C C
G A T G A T (G) T A C T C
0 D002
G A T G G [T] G T A C C C
A A G A G T G T [G] T C T
0 D003
G A T G G (T) G T A C C C
G A T G G (C) A T A C C C
0 D004
G A T G A T G T A C T C
[A] A G G G T G T G C C C
0 D005
G A G G G T G T G C C C
G A T G G T G T A C C C
0 D006
G A T G A T G T A C T C
G A T G G T G T A C C C
0 D007
A A G (G) G T G T (A) C C C
A A G (A) G T G T (G) T C T
0 D008
G A T G A T G T A C T C
A A G G G T G T G C C C
0 D009
G A T G G T G T A C C C
A A G G G T G T G C C C
0 D010
A A G A G T G T G C C C
A G G A G T G C A C C C
0 D011
A A G A G T G T G C C C
A G G A G T G C A C C C
0 D012
G A T G G T G T A C C C
A A G G G T G T G C C C
0 D013
A A G (G) G T G T G C C C
A A G (A) G T G T [G] T C T
0 D014
A A G A G T G T G C C C
A A G A G T G T G C C C
0 D015
G A T G G T G T A C C C
G A T G G C G T A C C C
0 D016
G A T G A T G T A C T C
G A T G G T G T A C C C
0 D033
G A T G A T G T A C T C
A A G A G T G T G C C C
0 D034
G A T G G T G T A C C C
A A G A G T G T G C C C
0 D035
G A T G G T G T A C C C
A A G A G T G T G C C C
0 D036
A A G G G T G T G C C C
A A G A G T G T G T C T
0 D037
(G) A G G G T G T G C C C
(A) G G A G T G C A C C C
0 D038
(G) A G G G T G T G C C C
(A) G G A G T G C A C C C
0 D039
A A G G G T G T G C C C
A A G G G T G T G C C C
0 D040
G A T G G C (A) T A C C C
A A G G G T (G) T G C C C
0 E001
G A T G G T G T A C C C
G A T G G T G T A C C C
0 E002
A A G A G T G T G C C C
A G G A G T G C A C C C
0 E003
A A G A G T G T G C C C
A G G A G T G C A C C C
0 E004
G A T G G T G T A C C C
G A T G G C G T A C C C
0 E005
G A T G G T G T A C C C
G A T G G C G T A C C C
0 E006
G A T G G C G T A C C C
A A G A G T G T G C C C
0 E007
G A T G G T G T A C C C
G A T G G T G T A C C C
0 E008
G A T G G T (A) T A C C C
A A G A G T (G) T G C C C
0 E009
G A T G G T G T A C C C
G A T G G T G T A C C C
0 E010
G A T G G (T) G T G C C C
G A T G G (C) G T A C C C
0 E011
G A T G G T G T A C C C
A A G A G T G T G C C C
0 E012
G A T G A T G T A C T C
G A T G G C G T A C C C
0 E013
G A T G A T G T A C T C
A G G A G T G C A C C C
0 E014
G A T G A T G T A C T C
G A T G G T G T A C C C
0 E015
G A T G G T G T A C C C
G A T G G T G T A C C C
0 E016
G A T G A T G T A C T C
G A T G G C G T A C C C
0 E017
A A G A G T G T G C C C
A G G A G T G C A C C C
0 E018
G A T G G C G T A C C C
A G G A G T G C A C C C
0 E019
G A T G G T G T A C C C
A A G A G T G T G C C C
0 E020
G A T G G T G T A C C C
A A G A G T G T G C C C
0 E021
G A T G A T G T A C T C
G A T G G T G T A C C C
0 E022
G A T G G C G T A C C C
G A T G G C G T A C C C
0 E023
G A T G G C G T A C C C
A A G A G T G T G C C C
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 D001
= = G = G = (A) = G = C =
= = T = A = (G) = A = T =
0 D002
? = T G ? ? ? = ? C = C
? = G A ? ? ? = ? T = T
0 D003
= = = = = (T) G = = = = =
= = = = = (C) A = = = = =
0 D004
? = T = A = = = A = T =
? = G = G = = = G = C =
0 D005
= = G ? = = = = G = = =
= = T ? = = = = A = = =
0 D006
? = = = A = = = ? = T =
? = = = G = = = ? = C =
0 D007
= = = (G) = = = = (A) C = C
= = = (A) = = = = (G) T = T
0 D008
G = T = A = = = A = T =
A = G = G = = = G = C =
0 D009
G = T = = = = = A = = =
A = G = = = = = G = = =
0 D010
? A = = = = = T G = = =
? G = = = = = C A = = =
0 D011
= A = = = = = T G = = =
= G = = = = = C A = = =
0 D012
G = T = = = = = A = = =
A = G = = = = = G = = =
0 D013
= = = (G) = = = = ? C = C
= = = (A) = = = = ? T = T
0 D014
= ? = = = = = = = = ? ?
= ? = = = = = = = = ? ?
0 D015
= = = = = T = = = = = =
= = = = = C = = = = = =
0 D016
= = = = A = = = = = T =
= = = = G = = = = = C =
0 D033
G = T G A = = = A = T =
A = G A G = = = G = C =
0 D034
G ? T G = = = = A = = =
A ? G A = = = = G = = =
0 D035
G = T G = = = = A = = =
A = G A = = = = G = = =
0 D036
= = = G = = = = = C = C
= = = A = = = = = T = T
0 D037
(G) A = ? = = = T G = = =
(A) G = ? = = = C A = = =
0 D038
(G) A = G = = = T G = = =
(A) G = A = = = C A = = =
0 D039
= ? = = = = = = = = = =
= ? = = = = = = = = = =
0 D040
G = T = = C (A) = A = = =
A = G = = T (G) = G = = =
0 E001
= = = = = = = = = = = =
= = = = = = = = = = = =
0 E002
= A = = = = = T ? = = =
= G = = = = = C ? = = =
0 E003
= A = = = = = T G = = =
= G = = = = = C A = = =
0 E004
= = = = = T = = = = = =
= = = = = C = = = = = =
0 E005
= = = = = T = = = = = =
= = = = = C = = = = = =
0 E006
G = T G = C = = A = = =
A = G A = T = = G = = =
0 E007
= = = = = = = = = = = =
= = = = = = = = = = = =
0 E008
? = T G = = (A) = ? ? ? ?
? = G A = = (G) = ? ? ? ?
0 E009
= = = = = = = = = = ? =
= = = = = = = = = = ? =
0 E010
= = = = = (T) = = G = = =
= = = = = (C) = = A = = =
0 E011
G = T G = = = = A = = =
A = G A = = = = G = = =
0 E012
= = = = A T = = = = T =
= = = = G C = = = = C =
0 E013
G A T G A = = T = = T =
A G G A G = = C = = C =
0 E014
= = = = A = = = = = T =
= = = = G = = = = = C =
0 E015
= = = = = = = = = = = =
= = = = = = = = = = = =
0 E016
= = = = A T = = = = T =
= = = = G C = = = = C =
0 E017
= A = = = = = T G = = =
= G = = = = = C A = = =
0 E018
G ? T G = C = T = = = =
A ? G A = T = C = = = =
0 E019
G = T G = = = = A = = =
A = G A = = = = G = = =
0 E020
G = T G = = = = A = = =
A = G A = = = = G = = =
0 E021
= = = = A = = = = = T =
= = = = G = = = = = C =
0 E022
= = = = = = = = ? = = =
= = = = = = = = ? = = =
0 E023
G = T G = C = = A ? = =
A = G A = T = = G ? = =
END BESTPAIRS2
Phase probabilities at each site
with phase known positions indicated by =
and missing data positions indicated by ?
BEGIN PHASEPROBS
= = 0.99 = 1.00 = 0.55 = 1.00 = 1.00 =
? = 1.00 1.00 ? ? ? = ? 0.99 = 0.99
= = = = = 0.68 1.00 = = = = =
? = 1.00 = 1.00 = = = 1.00 = 1.00 =
= = 1.00 ? = = = = 1.00 = = =
? = = = 1.00 = = = ? = 1.00 =
= = = 0.88 = = = = 0.61 1.00 = 1.00
1.00 = 1.00 = 1.00 = = = 1.00 = 1.00 =
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 = = = = = =
= = = = 1.00 = = = = = 1.00 =
1.00 = 1.00 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 = = = = = 1.00 = 1.00
0.87 1.00 = ? = = = 1.00 1.00 = = =
0.88 1.00 = 1.00 = = = 1.00 1.00 = = =
= ? = = = = = = = = = =
1.00 = 1.00 = = 0.97 0.83 = 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 = = 0.64 = ? ? ? ?
= = = = = = = = = = ? =
= = = = = 0.60 = = 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 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 = 0.99 = = 1.00 ? = =
END PHASEPROBS