*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/home/qyi/lib/phase/PHASE2 -d1 fbgng.phase.inp fbgng.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
fbgng.phase.out_freqs : haplotype frequency estimates
fbgng.phase.out_pairs : most likely haplotype pairs for each individual
fbgng.phase.out_recom : estimates of recombination parameters
fbgng.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 47
Number of Loci: 10
Positions of loci: 129 902 5729 5836 7874 9340 9595 9615 9765 10034
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file fbgng.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 AAAGGCCCTC 20.000000
2 AAAGGCTCTC 2.000000
3 AAAGGTCCTC 9.000000
4 AAAGGTCCAC 5.000000
5 AGAGGCCCTC 1.000000
6 AGAGGTCCTC 29.000000
7 AGAGGTCTTT 1.000000
8 AGAAGTCCTC 5.000000
9 TAAGGTCCTC 1.000000
10 TAAGGTCTTT 1.000000
11 TAAGATCTTT 17.000000
12 TAGGATCTTT 3.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
D001: (1,7)
D002: (6,3)
D003: (3,6)
D004: (1,12)
D005: (3,11)
D006: (1,6)
D007: (11,12)
D008: (1,4)
D009: (3,4)
D010: (1,6)
D011: (1,10)
D012: (3,11)
D013: (4,11)
D014: (6,11)
D015: (3,3)
D016: (1,2)
D033: (2,11)
D034: (3,11)
D035: (3,6)
D036: (4,11)
D037: (1,1)
D038: (1,4)
D039: (11,12)
D040: (5,11)
E001: (6,6)
E002: (1,11)
E003: (1,11)
E004: (6,8)
E005: (6,6)
E006: (6,6)
E007: (6,6)
E008: (6,11)
E009: (6,8)
E010: (6,8)
E011: (6,11)
E012: (1,6)
E013: (1,1)
E014: (1,6)
E015: (6,8)
E016: (1,6)
E017: (1,11)
E018: (1,6)
E019: (6,11)
E020: (8,11)
E021: (1,6)
E022: (6,6)
E023: (6,9)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 D001
A (A) A G G (C) C C T C
A (G) A G G (T) C T T T
0 D002
A [G] A G G T C C T C
A [A] A G G T C C T C
0 D003
A A A G G T C C T C
A G A G G T C C T C
0 D004
A A A G G C C C T C
T A G G A T C T T T
0 D005
A A A G G T C C T C
T A A G A T C T T T
0 D006
A A A G G C C C T C
A G A G G T C C T C
0 D007
T A A G A T C T T T
T A G G A T C T T T
0 D008
A A A G G C C C T C
A A A G G T C C A C
0 D009
A A A G G T C C T C
A A A G G T C C A C
0 D010
A A A G G C C C T C
A [G] A G G T C C T C
0 D011
(A) A A G G (C) C C T C
(T) A A G G (T) C T T T
0 D012
A A A G G T C C T C
T A A G A T C T T T
0 D013
A A A G G T C C A C
T A A G A T C T T T
0 D014
A G A G G T C C T C
T A A G A T C T T T
0 D015
A A A G G T C C T C
A A A G G T C C T C
0 D016
A A A G G C C C T C
A A A G G C T C T C
0 D033
A A A G G C T C T C
T A A G A T C T T T
0 D034
A A A G G T C C [T] C
T A A G A T C T T T
0 D035
A A A G G T C C T C
A G A G G T C C T C
0 D036
A A A G G T C C A C
T A A G A T C T T T
0 D037
A A A G G C C C T C
A A A G G C C C T C
0 D038
A A A G G C C C T C
A A A G G T C C A C
0 D039
T A A G A T C T T T
T A G G A T C T T T
0 D040
A (G) A G G (C) C C T C
T (A) A G A (T) C T T T
0 E001
A G A G G T C C T C
A G A G G T C C T C
0 E002
A A A G G C C C T C
T A A G A T C T T T
0 E003
A A A G G C C C T C
T A A G A T C T T T
0 E004
A G A G G T C C T C
A G A A G T C C T C
0 E005
A G A [G] G T C C T C
A G A G G T C C T C
0 E006
A G A G G T C C T C
A G A G G T C C T C
0 E007
A G A G G T C C T C
A G A G G T C C T C
0 E008
A G A G G T C C T C
T A A G A T C T T T
0 E009
A [G] A G G T C C T C
A G A A G T C C T C
0 E010
A G A G G T C C T C
A G A A G T C C T C
0 E011
A G A G G T C C T C
T A A G A T C T T T
0 E012
A A A G G C C C T C
A G A G G T C C T C
0 E013
A A A G G C C C T C
A A A G G C C C T C
0 E014
A A A G G C C C T C
A G A G G T C C T C
0 E015
A G A G G T C C T C
A G A A G T C C T C
0 E016
A A A G G C C C T C
A G A G G T C C T C
0 E017
A A A G G C C C T C
T A A G A T C T T T
0 E018
A A A G G C C C T C
A G A G G T C C T C
0 E019
A G A G G T C C T C
T A A G A T C T T T
0 E020
A G A A G T C C T C
T A A G A T C T T T
0 E021
A A A G G C C C T C
A G A G G T C C T C
0 E022
A G A G G T C C T C
A G A G G T C C T C
0 E023
(A) G A G G T C C T C
(T) A A G G T C C T 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
= (A) = = = (C) = C = C
= (G) = = = (T) = T = T
0 D002
? ? ? = = = = = ? =
? ? ? = = = = = ? =
0 D003
? A = = = = = = = =
? G = = = = = = = =
0 D004
A = A = G C = C = C
T = G = A T = T = T
0 D005
A = ? = G = = C = C
T = ? = A = = T = T
0 D006
= A = = = C = = = =
= G = = = T = = = =
0 D007
= = A = = = = = = =
= = G = = = = = = =
0 D008
= = = = = C = = T =
= = = = = T = = A =
0 D009
= = = = = = ? = T =
= = = = = = ? = A =
0 D010
? ? ? = = C = ? ? ?
? ? ? = = T = ? ? ?
0 D011
(A) = = = = (C) = C = C
(T) = = = = (T) = T = T
0 D012
A = = = G = = C = C
T = = = A = = T = T
0 D013
A = = = G = = C A C
T = = = A = = T T T
0 D014
A G = = G = ? ? ? C
T A = = A = ? ? ? T
0 D015
= = = = = = = = = =
= = = = = = = = = =
0 D016
= = = = = = C = = =
= = = = = = T = = =
0 D033
A = = = G C T C = C
T = = = A T C T = T
0 D034
A = = = G = ? ? ? ?
T = = = A = ? ? ? ?
0 D035
= A = = = = = = = =
= G = = = = = = = =
0 D036
A = = = G = = C A C
T = = = A = = T T T
0 D037
= = ? ? = = ? ? ? ?
= = ? ? = = ? ? ? ?
0 D038
= = = = = C = = T =
= = = = = T = = A =
0 D039
= = A = = = = = = =
= = G = = = = = = =
0 D040
A (G) = = G (C) = C = C
T (A) = = A (T) = T = T
0 E001
= = = = ? = = = = =
= = = = ? = = = = =
0 E002
A = = = G C ? ? ? ?
T = = = A T ? ? ? ?
0 E003
A = = = G C = C = C
T = = = A T = T = T
0 E004
= = = G = = = = = =
= = = A = = = = = =
0 E005
= = ? ? = = = = = =
= = ? ? = = = = = =
0 E006
= = = = = = ? ? ? ?
= = = = = = ? ? ? ?
0 E007
= = = = = = = = = =
= = = = = = = = = =
0 E008
A G = = G = = C = C
T A = = A = = T = T
0 E009
= ? = G ? = = = = =
= ? = A ? = = = = =
0 E010
= = = G = = = = = =
= = = A = = = = = =
0 E011
A G = = ? = = C = C
T A = = ? = = T = T
0 E012
= A = = = C = = ? ?
= G = = = T = = ? ?
0 E013
= = = = = = = = = =
= = = = = = = = = =
0 E014
= A = = = C = = = ?
= G = = = T = = = ?
0 E015
= = = G = = = = = =
= = = A = = = = = =
0 E016
= A = = = C = = = =
= G = = = T = = = =
0 E017
A = = = G C ? ? ? ?
T = = = A T ? ? ? ?
0 E018
= A = = = C = = = =
= G = = = T = = = =
0 E019
A G = = G = = C = C
T A = = A = = T = T
0 E020
? ? = A ? = = C = C
? ? = G ? = = T = T
0 E021
= A = = = C = = = =
= G = = = T = = = =
0 E022
= = ? = ? = = = ? =
= = ? = ? = = = ? =
0 E023
(A) G = = = = = = ? =
(T) A = = = = = = ? =
END BESTPAIRS2
Phase probabilities at each site
with phase known positions indicated by =
and missing data positions indicated by ?
BEGIN PHASEPROBS
= 0.59 = = = 0.64 = 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
= 0.98 = = = 1.00 = = = =
= = 1.00 = = = = = = =
= = = = = 0.99 = = 1.00 =
= = = = = = ? = 1.00 =
? ? ? = = 1.00 = ? ? ?
0.78 = = = = 0.77 = 1.00 = 1.00
1.00 = = = 1.00 = = 1.00 = 1.00
1.00 = = = 1.00 = = 1.00 0.98 1.00
1.00 0.99 = = 1.00 = ? ? ? 1.00
= = = = = = = = = =
= = = = = = 1.00 = = =
1.00 = = = 1.00 1.00 0.96 1.00 = 1.00
1.00 = = = 1.00 = ? ? ? ?
= 1.00 = = = = = = = =
1.00 = = = 1.00 = = 1.00 0.99 1.00
= = ? ? = = ? ? ? ?
= = = = = 0.99 = = 1.00 =
= = 1.00 = = = = = = =
1.00 0.85 = = 1.00 0.78 = 1.00 = 1.00
= = = = ? = = = = =
1.00 = = = 1.00 0.98 ? ? ? ?
1.00 = = = 1.00 0.99 = 1.00 = 1.00
= = = 1.00 = = = = = =
= = ? ? = = = = = =
= = = = = = ? ? ? ?
= = = = = = = = = =
1.00 0.99 = = 1.00 = = 1.00 = 1.00
= ? = 1.00 ? = = = = =
= = = 1.00 = = = = = =
1.00 0.99 = = ? = = 1.00 = 1.00
= 0.97 = = = 1.00 = = ? ?
= = = = = = = = = =
= 0.98 = = = 1.00 = = = ?
= = = 1.00 = = = = = =
= 0.98 = = = 1.00 = = = =
1.00 = = = 1.00 0.98 ? ? ? ?
= 0.98 = = = 1.00 = = = =
1.00 0.99 = = 1.00 = = 1.00 = 1.00
? ? = 1.00 ? = = 1.00 = 1.00
= 0.98 = = = 1.00 = = = =
= = ? = ? = = = ? =
0.80 1.00 = = = = = = ? =
END PHASEPROBS