*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 rftc2.phase.inp rftc2.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
rftc2.phase.out_freqs : haplotype frequency estimates
rftc2.phase.out_pairs : most likely haplotype pairs for each individual
rftc2.phase.out_recom : estimates of recombination parameters
rftc2.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 12
Positions of loci: 983 1634 4546 4790 5029 6849 13622 14132 17044 18697 18970 19437
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file rftc2.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 ACAICTGATGGA 61.000000
2 ACAICTGATGAA 1.000000
3 ACAICTGGTGGA 53.000000
4 ACAIATGATGGA 13.000000
5 ACGICTGACGAA 1.000000
6 ACGICTGACGAG 3.000000
7 AGGICTGACGGG 3.000000
8 AGGDCAAACGAG 1.000000
9 AGGDCAAACTGG 1.000000
10 AGGDCAAACTAG 9.000000
11 GCAICTGATGGA 32.000000
12 GCAICTGGTGGA 2.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
P001: (1,11)
P002: (4,11)
P003: (1,3)
P004: (6,11)
P005: (3,12)
P006: (1,11)
P007: (11,11)
P008: (3,3)
P009: (1,10)
P010: (1,1)
P011: (1,11)
P012: (3,11)
P013: (1,3)
P014: (4,11)
P015: (1,3)
P016: (1,2)
P017: (3,11)
P018: (1,10)
P019: (1,4)
P020: (3,4)
P021: (7,7)
P022: (3,3)
P023: (1,3)
P024: (1,1)
P025: (1,3)
P026: (1,11)
P027: (1,10)
P028: (1,3)
P029: (1,11)
P030: (3,11)
P031: (1,3)
P032: (7,8)
P033: (1,3)
P034: (3,11)
P035: (1,11)
P036: (4,9)
P037: (1,3)
P038: (1,11)
P039: (10,11)
P040: (1,3)
P041: (1,3)
P042: (3,6)
P043: (3,3)
P044: (1,11)
P045: (1,3)
P046: (1,10)
P047: (1,10)
P048: (1,3)
P049: (1,1)
P050: (1,3)
P051: (1,3)
P052: (3,12)
P053: (1,10)
P054: (3,3)
P055: (4,4)
P056: (11,11)
P057: (3,6)
P058: (1,3)
P059: (1,1)
P060: (1,11)
P061: (1,11)
P062: (3,10)
P063: (1,11)
P064: (3,11)
P065: (11,11)
P066: (1,3)
P067: (3,4)
P068: (1,4)
P069: (3,3)
P070: (3,3)
P071: (1,1)
P072: (1,3)
P073: (1,11)
P074: (1,3)
P075: (1,1)
P076: (1,4)
P077: (1,3)
P078: (1,4)
P079: (3,4)
P080: (1,11)
P081: (3,11)
P082: (1,1)
P083: (11,11)
P084: (3,3)
P085: (3,4)
P086: (3,11)
P087: (1,5)
P088: (1,10)
P089: (3,3)
P090: (1,3)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 P001
A C A I C T G A T G G A
[G] C A I C T G A T G G A
0 P002
A C A I A T G A T G G A
G C A I C T G A T G G A
0 P003
[A] C A I C T G A T G G A
A C A I C T G G T G G A
0 P004
A C G I C T G A C G A G
G C A I C T G A T G G A
0 P005
A C A I C T G G T G G A
G C A I C T G G T G G A
0 P006
A C A I C T G A T G G A
G C A I C T G A T G G A
0 P007
G C A I C T G A T G G A
G C A I C T G A T G G A
0 P008
A C A I C T G G T G G A
A C A I C T G G T G G A
0 P009
A C A I C T G [A] T G G A
A G G D C A A A C T A G
0 P010
A C A I C T G A T G G A
A C A I C T G A T G G A
0 P011
A C A I C T G [A] T G G A
G C A I C T G A T G G A
0 P012
(A) C A I C T G G T G G A
(G) C A I C T G A T G G A
0 P013
A C A I C T G A T G G A
A C A I C T G G T G G A
0 P014
A C A I A T G A T G G A
G C A I C T G A T G G A
0 P015
[A] C A I C T G A T G G A
A C A I C T G [G] T G G A
0 P016
[A] C A I C T G A T G G A
[A] C A I C T G A T G A A
0 P017
(A) C A I C T G G T G G A
(G) C A I C T G A T G G A
0 P018
[A] C A I C T G A T G G A
A G G D C A A A C T A G
0 P019
A C A I C T G [A] T G G A
A C A I A T G A T G G A
0 P020
A C A I C T G G T G G A
A C A I A T G A T G G A
0 P021
A G G I C T G A C G G G
A G G I C T G A C G G G
0 P022
A C A I C T G G T G G A
A C A I C T G G T G G A
0 P023
A C A I C T G A T G G A
A C A I C T G G T G G A
0 P024
A C A I C T G A T G G A
A C A I C T G A T G G A
0 P025
A C A I C T G A T G G A
A C A I C T G G T G G A
0 P026
A C A I C T G A T G G A
G C A I C T G A T G G A
0 P027
A C A I C T G A T G G A
A G G D C A A A C T A G
0 P028
A C A I C T G A T G G A
A C A I C T G [G] T G G A
0 P029
A C A I C T G A T G G A
G C A I C T G A T G G A
0 P030
(A) C A I C T G G T G G A
(G) C A I C T G A T G G A
0 P031
A C A I C T G A T G G A
A C A I C T G [G] T G G A
0 P032
A G G I C T G A C G (G) G
A G G D C A A A C G (A) G
0 P033
A C A I C T G A T G G A
A C A I C T G [G] T G G A
0 P034
(A) C A I C T G G T G G A
(G) C A I C T G A T G G A
0 P035
A C A I C T G [A] T G G A
G C A I C T G A T G G A
0 P036
A C A I A T G A T G G A
A G G D C A A A C T G G
0 P037
[A] C A I C T G A T G G A
A C A I C T G [G] T G G A
0 P038
A C A I C T G A T G G A
[G] C A I C T G A T G G A
0 P039
A G G D C A A A C T [A] G
G C A I C T G A T G G A
0 P040
[A] C A I C T G A T G G A
A C A I C T G G T G G A
0 P041
A C A I C T G A T G G A
A C A I C T G [G] T G G A
0 P042
A C A I C T G G T G G A
A C G I C T G A C G A [G]
0 P043
A C A I C T G G T G G A
A C A I C T G G T G G A
0 P044
A C A I C T G A T G G A
G C A I C T G A T G G A
0 P045
A C A I C T G A T G G A
A C A I C T G G T G G A
0 P046
A C A I C T G A T G G A
A G G D C A A A C T A G
0 P047
A C A I C T G A T G G A
A G G D C A A A C T A G
0 P048
[A] C A I C T G A T G G A
A C A I C T G G T G G A
0 P049
A C A I C T G A T G G A
A C A I C T G A T G G A
0 P050
A C A I C T G A T G G A
A C A I C T G G T G G A
0 P051
[A] C A I C T G A T G G A
A C A I C T G [G] T G G A
0 P052
A C A I C T G G T G G A
G C A I C T G G T G G A
0 P053
A C A I C T G A T G G A
A G G D C A A A C T [A] G
0 P054
A C A I C T G G T G G A
A C A I C T G G T G G A
0 P055
A C A I A T G A T G G A
A C A I A T G A T G G A
0 P056
G C A I C T G A T G G A
G C A I C T G A T G G A
0 P057
A C A I C T G G T G G A
A C G I C T G A C G A G
0 P058
A C A I C T G A T G G A
A C A I C T G G T G G A
0 P059
A C A I C T G A T G G A
A C A I C T G A T G G A
0 P060
A C A I C T G A T G G A
G C A I C T G A T G G A
0 P061
A C A I C T G [A] T G G A
G C A I C T G A T G G A
0 P062
A C A I C T G G T G G A
A G G D C A A A C T A G
0 P063
A C A I C T G A T G G A
G C A I C T G A T G G A
0 P064
(A) C A I C T G G T G G A
(G) C A I C T G A T G G A
0 P065
G C A I C T G A T G G A
G C A I C T G A T G G A
0 P066
A C A I C T G A T G G A
A C A I C T G G T G G A
0 P067
A C A I C T G G T G G A
A C A I A T G A T G G A
0 P068
A C A I C T G [A] T G G A
A C A I A T G A T G G A
0 P069
A C A I C T G G T G G A
A C A I C T G G T G G A
0 P070
A C A I C T G G T G G A
A C A I C T G G T G G A
0 P071
A C A I C T G A T G G A
A C A I C T G A T G G A
0 P072
[A] C A I C T G A T G G A
A C A I C T G [G] T G G A
0 P073
A C A I C T G A T G G A
G C A I C T G A T G G A
0 P074
A C A I C T G A T G G A
A C A I C T G G T G G A
0 P075
A C A I C T G A T G G A
A C A I C T G A T G G A
0 P076
A C A I C T G A T G G A
A C A I A T G A T G G A
0 P077
A C A I C T G A T G G A
A C A I C T G G T G G A
0 P078
[A] C A I C T G A T G G A
A C A I A T G A T G G A
0 P079
A C A I C T G G T G G A
A C A I A T G A T G G A
0 P080
A C A I C T G [A] T G G A
G C A I C T G A T G G A
0 P081
(A) C A I C T G G T G G A
(G) C A I C T G A T G G A
0 P082
A C A I C T G A T G G A
A C A I C T G A T G G A
0 P083
G C A I C T G A T G G A
G C A I C T G A T G G A
0 P084
A C A I C T G G T G G A
A C A I C T G G T G G A
0 P085
A C A I C T G G T G G A
A C A I A T G A T G G A
0 P086
(A) C A I C T G G T G G A
(G) C A I C T G A T G G A
0 P087
A C A I C T G A T G G A
A C G I C T G A C G A A
0 P088
A C A I C T G A T G G A
A G G D C A A A C T A G
0 P089
A C A I C T G G T G G A
A C A I C T G G T G G A
0 P090
[A] C A I C T G A T G G A
A C A I C T G [G] T G G 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
A = = = A = = ? = = = =
G = = = C = = ? = = = =
0 P003
? = ? = = = ? A = = = =
? = ? = = = ? G = = = =
0 P004
A = G = = = = = C = A G
G = A = = = = = T = G A
0 P005
A = = = = = = = = = = ?
G = = = = = = = = = = ?
0 P006
A = ? = = = = = = = = =
G = ? = = = = = = = = =
0 P007
= = ? = = = ? = = = = =
= = ? = = = ? = = = = =
0 P008
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P009
= ? A I = T G ? T G G ?
= ? G D = A A ? C T A ?
0 P010
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P011
A = = = = = = ? = = = ?
G = = = = = = ? = = = ?
0 P012
(A) = = = = = = G = = = =
(G) = = = = = = A = = = =
0 P013
= = = = = = = A ? = = =
= = = = = = = G ? = = =
0 P014
A = = = A = = = = = ? =
G = = = C = = = = = ? =
0 P015
? = = = = = = ? = = = =
? = = = = = = ? = = = =
0 P016
? = = ? = = = = = = G =
? = = ? = = = = = = A =
0 P017
(A) = ? ? = = = G = = = =
(G) = ? ? = = = A = = = =
0 P018
? C A ? ? T G = T G G A
? G G ? ? A A = C T A G
0 P019
= = = = C = = ? = = = ?
= = = = A = = ? = = = ?
0 P020
= = = = C = = G = = = =
= = = = A = = A = = = =
0 P021
= = = = = = = = = = ? =
= = = = = = = = = = ? =
0 P022
= = = = = = = = = = ? =
= = = = = = = = = = ? =
0 P023
= = = = = = ? A = = = ?
= = = = = = ? G = = = ?
0 P024
= = = = = = = = = = = ?
= = = = = = = = = = = ?
0 P025
= = = = = = = A = = = =
= = = = = = = G = = = =
0 P026
A = = = = = = = = = = ?
G = = = = = = = = = = ?
0 P027
= C A I = T G = T G G A
= G G D = A A = C T A G
0 P028
= = ? = = = ? ? = = = =
= = ? = = = ? ? = = = =
0 P029
A = ? = = = = = = = = =
G = ? = = = = = = = = =
0 P030
(A) = = = = = = G = = = =
(G) = = = = = = A = = = =
0 P031
= = = = = = = ? = = = =
= = = = = = = ? = = = =
0 P032
? = = I = T G ? = = (G) =
? = = D = A A ? = = (A) =
0 P033
= = ? ? ? = = ? = = = =
= = ? ? ? = = ? = = = =
0 P034
(A) = = = = = = G = = = =
(G) = = = = = = A = = = =
0 P035
A = = = = = = ? = = = =
G = = = = = = ? = = = =
0 P036
= C A I A T G = T G = A
= G G D C A A = C T = G
0 P037
? = = = = = = ? = = = =
? = = = = = = ? = = = =
0 P038
? = = = = = = = = = = =
? = = = = = = = = = = =
0 P039
A G G D = A ? = C T ? G
G C A I = T ? = T G ? A
0 P040
? = = = = = = A = = = =
? = = = = = = G = = = =
0 P041
= = ? ? ? = = ? = = ? ?
= = ? ? ? = = ? = = ? ?
0 P042
? = A = = = = G T = ? ?
? = G = = = = A C = ? ?
0 P043
= = ? = = = = = = = ? =
= = ? = = = = = = = ? =
0 P044
A = = = = = = = = = ? =
G = = = = = = = = = ? =
0 P045
= = = = = = = A = = = =
= = = = = = = G = = = =
0 P046
= C A I = T G = T G G A
= G G D = A A = C T A G
0 P047
= C ? I = T G = T G G A
= G ? D = A A = C T A G
0 P048
? = = = = = = A = = = =
? = = = = = = G = = = =
0 P049
= = ? = = = = = = = ? =
= = ? = = = = = = = ? =
0 P050
= = = = = = = A = = ? =
= = = = = = = G = = ? =
0 P051
? = = = = = = ? = = = =
? = = = = = = ? = = = =
0 P052
A = = = = = = = = = = =
G = = = = = = = = = = =
0 P053
= C A I = T G = T G ? A
= G G D = A A = C T ? G
0 P054
= = ? = = = = = = = = =
= = ? = = = = = = = = =
0 P055
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P056
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P057
= = ? = = = = G T = G A
= = ? = = = = A C = A G
0 P058
= = = = = = = A = = = =
= = = = = = = G = = = =
0 P059
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P060
A = = = = = = = = = = =
G = = = = = = = = = = =
0 P061
A = = = = = = ? = = = =
G = = = = = = ? = = = =
0 P062
= C A I = T G G T G G A
= G G D = A A A C T A G
0 P063
A = = = = = ? = = = = ?
G = = = = = ? = = = = ?
0 P064
(A) = = = = = = G = = = =
(G) = = = = = = A = = = =
0 P065
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P066
= = = = = = = A = = = =
= = = = = = = G = = = =
0 P067
= = = = C = = G = = = ?
= = = = A = = A = = = ?
0 P068
? = = = C = = ? = = = =
? = = = A = = ? = = = =
0 P069
= = = = = = = = = = = ?
= = = = = = = = = = = ?
0 P070
? = = = = = ? = = = = =
? = = = = = ? = = = = =
0 P071
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P072
? = = = = = = ? = = = =
? = = = = = = ? = = = =
0 P073
A = = = = = = = = = = =
G = = = = = = = = = = =
0 P074
= = = = = = = A = = = =
= = = = = = = G = = = =
0 P075
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P076
= = ? = C = ? = = = = =
= = ? = A = ? = = = = =
0 P077
= = = = = = = A = = = =
= = = = = = = G = = = =
0 P078
? = = = C = ? = = = = =
? = = = A = ? = = = = =
0 P079
= = = = C = = G = = = =
= = = = A = = A = = = =
0 P080
A = = = = = ? ? = = = =
G = = = = = ? ? = = = =
0 P081
(A) = = = = = = G = ? = =
(G) = = = = = = A = ? = =
0 P082
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P083
= = = = = = = = = = = =
= = = = = = = = = = = =
0 P084
= ? = = = = = = = = = =
= ? = = = = = = = = = =
0 P085
= = ? = C = = G = = = =
= = ? = A = = A = = = =
0 P086
(A) = = ? = = = G = = = =
(G) = = ? = = = A = = = =
0 P087
= = A = = = = = T = G =
= = G = = = = = C = A =
0 P088
= C A I = T G = T G G A
= G G D = A A = C T A G
0 P089
= = = ? ? = = = = = = =
= = = ? ? = = = = = = =
0 P090
? = ? ? ? = = ? = = = =
? = ? ? ? = = ? = = = =
END BESTPAIRS2
Phase probabilities at each site
with phase known positions indicated by =
and missing data positions indicated by ?
BEGIN PHASEPROBS
? = = = = = = = = = = =
0.98 = = = 1.00 = = ? = = = =
? = ? = = = ? 1.00 = = = =
0.96 = 0.99 = = = = = 1.00 = 1.00 0.97
1.00 = = = = = = = = = = ?
1.00 = ? = = = = = = = = =
= = ? = = = ? = = = = =
= = = = = = = = = = = =
= ? 1.00 1.00 = 1.00 1.00 ? 1.00 1.00 1.00 ?
= = = = = = = = = = = =
1.00 = = = = = = ? = = = ?
0.88 = = = = = = 1.00 = = = =
= = = = = = = 1.00 ? = = =
0.98 = = = 1.00 = = = = = ? =
? = = = = = = ? = = = =
? = = ? = = = = = = 1.00 =
0.87 = ? ? = = = 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 = ? = = = = = = = = =
0.88 = = = = = = 1.00 = = = =
= = = = = = = ? = = = =
? = = 1.00 = 1.00 1.00 ? = = 0.89 =
= = ? ? ? = = ? = = = =
0.88 = = = = = = 1.00 = = = =
1.00 = = = = = = ? = = = =
= 1.00 1.00 1.00 0.99 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
= = ? = = = = = = = = =
= = = = = = = = = = = =
= = = = = = = = = = = =
= = ? = = = = 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 = = = = = ? = = = = ?
0.88 = = = = = = 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 = = = = = ? ? = = = =
0.88 = = = = = = 1.00 = ? = =
= = = = = = = = = = = =
= = = = = = = = = = = =
= ? = = = = = = = = = =
= = ? = 0.98 = = 1.00 = = = =
0.88 = = ? = = = 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
= = = ? ? = = = = = = =
? = ? ? ? = = ? = = = =
END PHASEPROBS