*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 taf12.phase.inp taf12.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
taf12.phase.out_freqs : haplotype frequency estimates
taf12.phase.out_pairs : most likely haplotype pairs for each individual
taf12.phase.out_recom : estimates of recombination parameters
taf12.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 7
Positions of loci: 1478 3267 7280 25935 29633 37171 38540
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file taf12.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 CCDCGTA 2.000000
2 CCDTGTA 6.000000
3 CCDTGTC 24.000000
4 CTICGTA 86.000000
5 CTICGCA 8.000000
6 CTICATA 36.000000
7 CTDCGTA 9.000000
8 TTICATA 9.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
P001: (2,4)
P002: (4,4)
P003: (8,8)
P004: (4,4)
P005: (4,6)
P006: (2,6)
P007: (4,6)
P008: (2,4)
P009: (4,4)
P010: (2,3)
P011: (4,8)
P012: (4,4)
P013: (4,4)
P014: (4,4)
P015: (2,3)
P016: (4,4)
P017: (4,6)
P018: (6,6)
P019: (3,4)
P020: (4,5)
P021: (6,6)
P022: (3,4)
P023: (4,6)
P024: (4,4)
P025: (2,4)
P026: (4,4)
P027: (3,6)
P028: (6,6)
P029: (6,7)
P030: (4,5)
P031: (4,4)
P032: (1,8)
P033: (6,6)
P034: (4,4)
P035: (4,5)
P036: (4,6)
P037: (4,6)
P038: (1,7)
P039: (4,4)
P040: (3,6)
P041: (3,8)
P042: (4,5)
P043: (3,4)
P044: (4,6)
P045: (4,4)
P046: (3,6)
P047: (4,4)
P048: (3,6)
P049: (6,6)
P050: (4,4)
P051: (4,4)
P052: (4,4)
P053: (3,4)
P054: (4,4)
P055: (4,4)
P056: (4,8)
P057: (6,8)
P058: (4,4)
P059: (7,7)
P060: (3,3)
P061: (7,8)
P062: (3,4)
P063: (4,6)
P064: (5,7)
P065: (4,4)
P066: (4,5)
P067: (3,4)
P068: (4,4)
P069: (4,4)
P070: (4,4)
P071: (4,6)
P072: (4,4)
P073: (4,6)
P074: (3,4)
P075: (4,6)
P076: (4,6)
P077: (4,6)
P078: (3,6)
P079: (4,8)
P080: (6,7)
P081: (3,6)
P082: (3,3)
P083: (3,4)
P084: (3,4)
P085: (3,4)
P086: (3,6)
P087: (4,6)
P088: (6,7)
P089: (5,7)
P090: (4,5)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 P001
C C D T G T [A]
C T I C G T A
0 P002
C T I C G T A
C T I C G T A
0 P003
T T I C A T A
T T I C A T A
0 P004
C T I C G T A
C T I C G T A
0 P005
C T I C G T A
C T I C A T A
0 P006
C C D [T] (G) T [A]
C T I C (A) T A
0 P007
C T I C G T A
C T I C A T A
0 P008
C C D T G T [A]
C T I C G T A
0 P009
C T I C G T A
C T I C G T A
0 P010
C C D T G T A
C C D T G T [C]
0 P011
(C) T I C G T A
(T) T I C A T A
0 P012
C T I C [G] T A
C T I C G T A
0 P013
C T I C G T A
C T I C G T A
0 P014
C T I C [G] T A
C T I C G T A
0 P015
C C D T G T A
C C D T G T [C]
0 P016
C T I C G T A
C T I C G T A
0 P017
C T I C G T A
C T I C A T A
0 P018
C T I C A T A
C T I C A T A
0 P019
C C D T G T (C)
C T I C G T (A)
0 P020
C T I C G T A
C T I C G C A
0 P021
C T I C A T A
C T I C A T A
0 P022
C C D T G T (C)
C T I C G T (A)
0 P023
C T I C G T A
C T I C A T A
0 P024
C T I C G T A
C T I C G T A
0 P025
C C D T G T [A]
C T I C G T A
0 P026
C T I C [G] T A
C T I C G T A
0 P027
C C D T (G) T (C)
C T I C (A) T (A)
0 P028
C T I C A T A
C T I C A T A
0 P029
C T (I) C (A) T A
C [T] (D) C (G) T A
0 P030
C T I C G T A
C T I C G C A
0 P031
C T I C G T A
C T I C G T A
0 P032
(C) C [D] C G T A
(T) T I C [A] T A
0 P033
C T I C A T A
C T I C A T A
0 P034
C T I C G T A
C T I C G T A
0 P035
C T I C G T A
C T I C G C A
0 P036
C T I C G T A
C T I C A T A
0 P037
C T I C G T A
C T I C A T A
0 P038
C C D C G T A
C T D C G T A
0 P039
C T I C G T A
C T I C G T A
0 P040
C C D T (G) T (C)
C T I C (A) T (A)
0 P041
C C D T G T (C)
T T I C A T (A)
0 P042
C T I C [G] T A
C T I C G C A
0 P043
C C D T G T (C)
C T I C G T (A)
0 P044
C T I C G T A
C T I C A T A
0 P045
C T I C G T A
C T I C G T A
0 P046
C C D T (G) T (C)
C T I C (A) T (A)
0 P047
C T I C G T A
C T I C G T A
0 P048
C C D T (G) T (C)
C T I C (A) T (A)
0 P049
C T I C A T A
C T I C A T A
0 P050
C T I C G T A
C T I C G T A
0 P051
C T I C G T A
C T I C G T A
0 P052
C T I C G T A
C T I C G T A
0 P053
C C D T G T (C)
C T I C G T (A)
0 P054
C T I C G T A
C T I C G T A
0 P055
C T I C G T A
C T I C G T A
0 P056
(C) T I C G T A
(T) T I C A T A
0 P057
C T I C A T A
T T I C A T A
0 P058
C T I C G T A
C T I C G T A
0 P059
C T D [C] G T A
C T D C G T A
0 P060
C C D T G T C
C C D T G T C
0 P061
(C) T D C G T A
(T) T I C A T A
0 P062
C C D T G T (C)
C T I C G T (A)
0 P063
C T I C G T A
C T I C A T A
0 P064
C T (I) C G C A
C T (D) C G T A
0 P065
C T I C G T A
C T I C G T A
0 P066
C T I C G T A
C T I C G C A
0 P067
C C D T G T (C)
C T I C G T (A)
0 P068
C T I C G T A
C T I C G T A
0 P069
C T I C G T A
C T I C G T A
0 P070
C T I C G T A
C T I C G T A
0 P071
C T I C G T A
C T I C A T A
0 P072
C T I C G T A
C T I C G T A
0 P073
C T I C G T A
C T I C A T A
0 P074
C C D T G T (C)
C T I C G T (A)
0 P075
C T I C G T A
C T I C A T A
0 P076
C T I C G T A
C T I C A T A
0 P077
C T I C G T A
C T I C A T A
0 P078
C C D T (G) T (C)
C T I C (A) T (A)
0 P079
(C) T I C G T A
(T) T I C A T A
0 P080
C T (I) C A T A
C T (D) C G T A
0 P081
C C D T (G) T (C)
C T I C (A) T (A)
0 P082
C C D T G T C
C C D T G T C
0 P083
C C D T G T (C)
C T I C G T (A)
0 P084
C C D T G T (C)
C T I C G T (A)
0 P085
C C D T G T (C)
C T I C G T (A)
0 P086
C C D T (G) T (C)
C T I C (A) T (A)
0 P087
C T I C G T A
C T I C A T A
0 P088
C T (I) C A T A
C T (D) C G T A
0 P089
C T (I) C G C A
C T (D) C G T A
0 P090
C T I C G T A
C T I C G C 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
= C ? T = ? ?
= T ? C = ? ?
0 P002
= = = = = ? ?
= = = = = ? ?
0 P003
= = = = = ? =
= = = = = ? =
0 P004
= = = = = ? ?
= = = = = ? ?
0 P005
= = ? ? G ? ?
= = ? ? A ? ?
0 P006
= C D ? (G) ? ?
= T I ? (A) ? ?
0 P007
= = = = G ? ?
= = = = A ? ?
0 P008
= C D T = ? ?
= T I C = ? ?
0 P009
= ? = ? = ? ?
= ? = ? = ? ?
0 P010
= = = = = ? ?
= = = = = ? ?
0 P011
(C) = = ? G = =
(T) = = ? A = =
0 P012
= ? = ? ? = =
= ? = ? ? = =
0 P013
= = = = = ? =
= = = = = ? =
0 P014
= = ? = ? ? =
= = ? = ? ? =
0 P015
= = = = = ? ?
= = = = = ? ?
0 P016
= = = = = ? ?
= = = = = ? ?
0 P017
= ? ? ? G ? ?
= ? ? ? A ? ?
0 P018
= = = = = ? =
= = = = = ? =
0 P019
= C D T = = (C)
= T I C = = (A)
0 P020
= = = = = T =
= = = = = C =
0 P021
= = = = = = =
= = = = = = =
0 P022
= C D T = = (C)
= T I C = = (A)
0 P023
= = = = G = ?
= = = = A = ?
0 P024
= = = = = ? ?
= = = = = ? ?
0 P025
= C D T ? ? ?
= T I C ? ? ?
0 P026
= = = = ? = =
= = = = ? = =
0 P027
= C D T (G) = (C)
= T I C (A) = (A)
0 P028
= = = = = = =
= = = = = = =
0 P029
= ? (I) = (A) = =
= ? (D) = (G) = =
0 P030
= ? = = = T ?
= ? = = = C ?
0 P031
= = = = = = ?
= = = = = = ?
0 P032
(C) C ? = ? = ?
(T) T ? = ? = ?
0 P033
= = = = = ? =
= = = = = ? =
0 P034
= = = = = = =
= = = = = = =
0 P035
= = = = = T =
= = = = = C =
0 P036
= = = = G = =
= = = = A = =
0 P037
= = = = G = =
= = = = A = =
0 P038
= C = = = ? =
= T = = = ? =
0 P039
= = = = = = ?
= = = = = = ?
0 P040
= C D ? (G) = (C)
= T I ? (A) = (A)
0 P041
C C D T G = (C)
T T I C A = (A)
0 P042
= = = = ? T =
= = = = ? C =
0 P043
= C D T = = (C)
= T I C = = (A)
0 P044
= = = = G = =
= = = = A = =
0 P045
= = = = = = =
= = = = = = =
0 P046
= C D T (G) = (C)
= T I C (A) = (A)
0 P047
= = = = = = =
= = = = = = =
0 P048
= ? D T (G) = (C)
= ? I C (A) = (A)
0 P049
= = = = = = =
= = = = = = =
0 P050
= = = = = = =
= = = = = = =
0 P051
= ? = = = = =
= ? = = = = =
0 P052
= = = = = = =
= = = = = = =
0 P053
= ? D T = = (C)
= ? I C = = (A)
0 P054
= = = = = = =
= = = = = = =
0 P055
= ? = ? = = =
= ? = ? = = =
0 P056
(C) = = = G = =
(T) = = = A = =
0 P057
C = = = = = =
T = = = = = =
0 P058
= = ? = = ? =
= = ? = = ? =
0 P059
= = = ? = = =
= = = ? = = =
0 P060
= = = = = = =
= = = = = = =
0 P061
(C) = D = G ? =
(T) = I = A ? =
0 P062
= C D ? = = (C)
= T I ? = = (A)
0 P063
= = = ? G = =
= = = ? A = =
0 P064
= = (I) ? = C =
= = (D) ? = T =
0 P065
= = = = = ? =
= = = = = ? =
0 P066
= = = = = T =
= = = = = C =
0 P067
= C D T = = (C)
= T I C = = (A)
0 P068
= = = = = = =
= = = = = = =
0 P069
= = = = = = =
= = = = = = =
0 P070
= = = ? = = =
= = = ? = = =
0 P071
= = = = G = =
= = = = A = =
0 P072
= = = ? = = =
= = = ? = = =
0 P073
= = = = G = =
= = = = A = =
0 P074
= C D T = = (C)
= T I C = = (A)
0 P075
= = = = G = ?
= = = = A = ?
0 P076
= = = = G ? =
= = = = A ? =
0 P077
= = = = G = =
= = = = A = =
0 P078
= C D T (G) = (C)
= T I C (A) = (A)
0 P079
(C) = = ? G = =
(T) = = ? A = =
0 P080
= = (I) = A = =
= = (D) = G = =
0 P081
= C D T (G) = (C)
= T I C (A) = (A)
0 P082
= = = = = = =
= = = = = = =
0 P083
= C D T = = (C)
= T I C = = (A)
0 P084
= C D T = = (C)
= T I C = = (A)
0 P085
= C D T = = (C)
= T I C = = (A)
0 P086
= C D T (G) = (C)
= T I C (A) = (A)
0 P087
= = = = G ? =
= = = = A ? =
0 P088
= = (I) ? A = =
= = (D) ? G = =
0 P089
= = (I) ? = C =
= = (D) ? = T =
0 P090
= = = ? = T =
= = = ? = C =
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 ? 0.76 ? ?
= = = = 1.00 ? ?
= 1.00 1.00 1.00 = ? ?
= ? = ? = ? ?
= = = = = ? ?
0.78 = = ? 1.00 = =
= ? = ? ? = =
= = = = = ? =
= = ? = ? ? =
= = = = = ? ?
= = = = = ? ?
= ? ? ? 1.00 ? ?
= = = = = ? =
= 0.99 1.00 1.00 = = 0.85
= = = = = 1.00 =
= = = = = = =
= 0.99 1.00 1.00 = = 0.85
= = = = 1.00 = ?
= = = = = ? ?
= 1.00 1.00 1.00 ? ? ?
= = = = ? = =
= 0.99 1.00 1.00 0.89 = 0.85
= = = = = = =
= ? 0.80 = 0.84 = =
= ? = = = 1.00 ?
= = = = = = ?
0.79 0.93 ? = ? = ?
= = = = = ? =
= = = = = = =
= = = = = 1.00 =
= = = = 1.00 = =
= = = = 1.00 = =
= 1.00 = = = ? =
= = = = = = ?
= 0.97 0.98 ? 0.88 = 0.84
0.90 1.00 1.00 1.00 0.95 = 0.89
= = = = ? 1.00 =
= 0.99 1.00 1.00 = = 0.85
= = = = 1.00 = =
= = = = = = =
= 0.99 1.00 1.00 0.89 = 0.85
= = = = = = =
= ? 1.00 1.00 0.89 = 0.85
= = = = = = =
= = = = = = =
= ? = = = = =
= = = = = = =
= ? 1.00 1.00 = = 0.84
= = = = = = =
= ? = ? = = =
0.77 = = = 1.00 = =
1.00 = = = = = =
= = ? = = ? =
= = = ? = = =
= = = = = = =
0.90 = 0.93 = 0.90 ? =
= 1.00 1.00 ? = = 0.83
= = = ? 1.00 = =
= = 0.56 ? = 1.00 =
= = = = = ? =
= = = = = 1.00 =
= 0.99 1.00 1.00 = = 0.85
= = = = = = =
= = = = = = =
= = = ? = = =
= = = = 1.00 = =
= = = ? = = =
= = = = 1.00 = =
= 0.99 1.00 1.00 = = 0.85
= = = = 1.00 = ?
= = = = 1.00 ? =
= = = = 1.00 = =
= 0.99 1.00 1.00 0.89 = 0.85
0.77 = = ? 1.00 = =
= = 0.68 = 1.00 = =
= 0.99 1.00 1.00 0.89 = 0.85
= = = = = = =
= 0.99 1.00 1.00 = = 0.85
= 0.99 1.00 1.00 = = 0.85
= 0.99 1.00 1.00 = = 0.85
= 0.99 1.00 1.00 0.89 = 0.85
= = = = 1.00 ? =
= = 0.70 ? 1.00 = =
= = 0.57 ? = 1.00 =
= = = ? = 1.00 =
END PHASEPROBS