*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 apexx.phase.inp apexx.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
apexx.phase.out_freqs : haplotype frequency estimates
apexx.phase.out_pairs : most likely haplotype pairs for each individual
apexx.phase.out_recom : estimates of recombination parameters
apexx.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 4
Positions of loci: 567 1853 2573 4119
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file apexx.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 GTGA 20.000000
2 GTGG 4.000000
3 GTTA 38.000000
4 GTTG 5.000000
5 GCGA 35.000000
6 GCGG 2.000000
7 GCTA 1.000000
8 TTGA 9.000000
9 TTTA 62.000000
10 TTTG 3.000000
11 TCGA 1.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
P001: (3,9)
P002: (3,5)
P003: (3,9)
P004: (4,5)
P005: (3,5)
P006: (1,5)
P007: (3,9)
P008: (1,9)
P009: (3,9)
P010: (5,8)
P011: (3,9)
P012: (3,3)
P013: (3,9)
P014: (9,9)
P015: (1,3)
P016: (1,1)
P017: (3,5)
P018: (4,5)
P019: (9,9)
P020: (9,9)
P021: (9,9)
P022: (3,3)
P023: (5,9)
P024: (9,9)
P025: (5,9)
P026: (8,9)
P027: (3,5)
P028: (3,5)
P029: (3,9)
P030: (5,8)
P031: (1,5)
P032: (2,9)
P033: (1,9)
P034: (5,9)
P035: (8,9)
P036: (1,5)
P037: (1,3)
P038: (2,4)
P039: (3,9)
P040: (5,7)
P041: (1,9)
P042: (1,9)
P043: (5,9)
P044: (1,9)
P045: (3,3)
P046: (5,9)
P047: (3,9)
P048: (5,9)
P049: (9,9)
P050: (5,6)
P051: (3,9)
P052: (5,5)
P053: (3,9)
P054: (3,3)
P055: (3,9)
P056: (1,9)
P057: (3,9)
P058: (1,9)
P059: (5,8)
P060: (3,9)
P061: (4,10)
P062: (1,5)
P063: (8,9)
P064: (1,2)
P065: (3,3)
P066: (9,9)
P067: (5,5)
P068: (9,9)
P069: (5,9)
P070: (9,10)
P071: (1,9)
P072: (3,9)
P073: (3,3)
P074: (3,9)
P075: (1,9)
P076: (9,9)
P077: (5,9)
P078: (5,8)
P079: (9,9)
P080: (2,5)
P081: (5,5)
P082: (1,5)
P083: (3,9)
P084: (3,5)
P085: (1,8)
P086: (8,9)
P087: (6,11)
P088: (4,10)
P089: (5,9)
P090: (3,9)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 P001
G T [T] A
[T] T [T] A
0 P002
G T [T] A
G C G A
0 P003
G T [T] A
[T] T [T] A
0 P004
G T T (G)
G C G (A)
0 P005
G T T A
G C G A
0 P006
[G] T G A
G C G A
0 P007
G T T A
T T T A
0 P008
(G) T G A
(T) T T A
0 P009
G T T A
T T T A
0 P010
(G) C G A
(T) T G A
0 P011
G T [T] A
T T [T] A
0 P012
G T T A
G T T A
0 P013
G T T A
T T T A
0 P014
T T T A
T T [T] A
0 P015
G T G A
G T T A
0 P016
G T G A
G T G A
0 P017
G T T A
G C G A
0 P018
G T T (G)
G C G (A)
0 P019
T T T A
T T [T] A
0 P020
T T T A
T T T A
0 P021
T T T A
T T [T] A
0 P022
G T T A
G T T A
0 P023
(G) C G A
(T) T T A
0 P024
T T T A
T T T A
0 P025
(G) C G A
(T) T T A
0 P026
T T G A
T T T A
0 P027
G T T A
G C G A
0 P028
G T T A
G C G A
0 P029
G T [T] A
T T [T] A
0 P030
(G) C G A
(T) T G A
0 P031
G T G A
G C G A
0 P032
(G) T (G) (G)
(T) T (T) (A)
0 P033
(G) T G A
(T) T T A
0 P034
(G) C G A
(T) T T A
0 P035
T T G A
T T T A
0 P036
G T G A
G C G A
0 P037
G T G A
G T T A
0 P038
G T G G
G T T G
0 P039
G T T A
T T T A
0 P040
G C G A
G C T A
0 P041
(G) T G A
(T) T T A
0 P042
G T (G) A
[T] T (T) A
0 P043
(G) C G A
(T) T T A
0 P044
(G) T G A
(T) T T A
0 P045
G T T A
G T T A
0 P046
(G) C G A
(T) T T A
0 P047
G T T A
T T T A
0 P048
G C G A
[T] T T A
0 P049
T T T A
T T [T] A
0 P050
G [C] G A
G [C] G G
0 P051
G T [T] A
T T [T] A
0 P052
G C G A
G C G A
0 P053
G T [T] A
T T [T] A
0 P054
G T T A
G T T A
0 P055
G T T A
T T T A
0 P056
G [T] (G) A
[T] T (T) A
0 P057
G T [T] A
T T [T] A
0 P058
(G) T G A
(T) T T A
0 P059
(G) C G A
(T) T G A
0 P060
G T [T] A
T T [T] A
0 P061
G T T G
T T T G
0 P062
G T G A
G C G A
0 P063
T T G A
T T T A
0 P064
[G] T G A
[G] T G G
0 P065
G T T A
G T T A
0 P066
T T T A
T T [T] A
0 P067
G C G A
G C G A
0 P068
T T T A
T T [T] A
0 P069
(G) C G A
(T) T T A
0 P070
T T T A
T T T G
0 P071
(G) T G A
(T) T T A
0 P072
G T T A
T T T A
0 P073
G T T A
G T T A
0 P074
G T T A
T T T A
0 P075
(G) T G A
(T) T T A
0 P076
T T T A
T T [T] A
0 P077
(G) C G A
(T) T T A
0 P078
(G) C G A
(T) T G A
0 P079
T T T A
T T T A
0 P080
[G] (T) G (G)
G (C) G (A)
0 P081
G C G A
G C G A
0 P082
G T G A
G C G A
0 P083
G T T A
T T T A
0 P084
G T [T] A
G C G A
0 P085
G T G A
T T G A
0 P086
T T G A
T T T A
0 P087
(G) C G G
(T) C G A
0 P088
G T T G
[T] T T G
0 P089
(G) C G A
(T) T [T] A
0 P090
[G] T T A
[T] T T 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
? = ? ?
? = ? ?
0 P002
= T ? =
= C ? =
0 P003
? = ? ?
? = ? ?
0 P004
= T T (G)
= C G (A)
0 P005
= T T =
= C G =
0 P006
? T = =
? C = =
0 P007
G = = =
T = = =
0 P008
(G) = G =
(T) = T =
0 P009
G = = ?
T = = ?
0 P010
(G) C = =
(T) T = =
0 P011
G = ? ?
T = ? ?
0 P012
= = = ?
= = = ?
0 P013
G = = =
T = = =
0 P014
= = ? ?
= = ? ?
0 P015
= = G =
= = T =
0 P016
= = = =
= = = =
0 P017
= T T =
= C G =
0 P018
= T T (G)
= C G (A)
0 P019
= = ? =
= = ? =
0 P020
= ? = =
= ? = =
0 P021
= = ? =
= = ? =
0 P022
= = = =
= = = =
0 P023
(G) C G =
(T) T T =
0 P024
= = = =
= = = =
0 P025
(G) C G =
(T) T T =
0 P026
= = G =
= = T =
0 P027
= T T =
= C G =
0 P028
= T T =
= C G =
0 P029
G = ? =
T = ? =
0 P030
(G) C = =
(T) T = =
0 P031
= T = =
= C = =
0 P032
(G) = (G) (G)
(T) = (T) (A)
0 P033
(G) = G =
(T) = T =
0 P034
(G) C G =
(T) T T =
0 P035
= = G ?
= = T ?
0 P036
= T = =
= C = =
0 P037
= = G =
= = T =
0 P038
= = G =
= = T =
0 P039
G = = =
T = = =
0 P040
? = G =
? = T =
0 P041
(G) = G =
(T) = T =
0 P042
? = (G) =
? = (T) =
0 P043
(G) C G =
(T) T T =
0 P044
(G) = G =
(T) = T =
0 P045
= = = =
= = = =
0 P046
(G) C G =
(T) T T =
0 P047
G = = =
T = = =
0 P048
? C G =
? T T =
0 P049
= = ? =
= = ? =
0 P050
= ? = A
= ? = G
0 P051
G = ? ?
T = ? ?
0 P052
= = ? =
= = ? =
0 P053
G = ? =
T = ? =
0 P054
= ? = =
= ? = =
0 P055
G = = =
T = = =
0 P056
? ? (G) =
? ? (T) =
0 P057
G = ? =
T = ? =
0 P058
(G) = G =
(T) = T =
0 P059
(G) C = =
(T) T = =
0 P060
G = ? =
T = ? =
0 P061
G ? = =
T ? = =
0 P062
= T = =
= C = =
0 P063
= = G =
= = T =
0 P064
? = = A
? = = G
0 P065
= ? = =
= ? = =
0 P066
= = ? =
= = ? =
0 P067
= = = ?
= = = ?
0 P068
= = ? =
= = ? =
0 P069
(G) C G =
(T) T T =
0 P070
= = = A
= = = G
0 P071
(G) = G =
(T) = T =
0 P072
G = = =
T = = =
0 P073
= = = =
= = = =
0 P074
G = = =
T = = =
0 P075
(G) = G ?
(T) = T ?
0 P076
= = ? =
= = ? =
0 P077
(G) C G =
(T) T T =
0 P078
(G) C = =
(T) T = =
0 P079
= ? = =
= ? = =
0 P080
? (T) = (G)
? (C) = (A)
0 P081
= = = =
= = = =
0 P082
= T = =
= C = =
0 P083
G = = ?
T = = ?
0 P084
= T ? =
= C ? =
0 P085
G = = =
T = = =
0 P086
= = G =
= = T =
0 P087
(G) = = G
(T) = = A
0 P088
? = = =
? = = =
0 P089
(G) C ? =
(T) T ? =
0 P090
? = = =
? = = =
END BESTPAIRS2
Phase probabilities at each site
with phase known positions indicated by =
and missing data positions indicated by ?
BEGIN PHASEPROBS
? = ? ?
= 0.96 ? =
? = ? ?
= 0.97 0.96 0.55
= 0.93 1.00 =
? 1.00 = =
1.00 = = =
0.57 = 1.00 =
1.00 = = ?
0.84 1.00 = =
1.00 = ? ?
= = = ?
1.00 = = =
= = ? ?
= = 1.00 =
= = = =
= 0.93 1.00 =
= 0.97 0.96 0.54
= = ? =
= ? = =
= = ? =
= = = =
0.89 0.99 0.95 =
= = = =
0.88 0.99 0.95 =
= = 1.00 =
= 0.93 1.00 =
= 0.93 1.00 =
1.00 = ? =
0.84 1.00 = =
= 1.00 = =
0.79 = 0.78 0.72
0.57 = 1.00 =
0.89 0.99 0.95 =
= = 1.00 ?
= 1.00 = =
= = 1.00 =
= = 1.00 =
1.00 = = =
? = 1.00 =
0.57 = 1.00 =
? = 0.78 =
0.89 0.99 0.95 =
0.57 = 1.00 =
= = = =
0.88 0.99 0.95 =
1.00 = = =
? 1.00 0.94 =
= = ? =
= ? = 1.00
1.00 = ? ?
= = ? =
1.00 = ? =
= ? = =
1.00 = = =
? ? 0.87 =
1.00 = ? =
0.57 = 1.00 =
0.84 1.00 = =
1.00 = ? =
1.00 ? = =
= 1.00 = =
= = 1.00 =
? = = 1.00
= ? = =
= = ? =
= = = ?
= = ? =
0.89 0.99 0.95 =
= = = 1.00
0.57 = 1.00 =
1.00 = = =
= = = =
1.00 = = =
0.57 = 1.00 ?
= = ? =
0.88 0.99 0.95 =
0.84 1.00 = =
= ? = =
? 0.70 = 0.80
= = = =
= 1.00 = =
1.00 = = ?
= 0.96 ? =
1.00 = = =
= = 1.00 =
0.51 = = 1.00
? = = =
0.84 0.96 ? =
? = = =
END PHASEPROBS