| | | |
Haplotype frequencies (rounded to 5 decimal places)
|
Haplotype numbers (rounded to nearest haplotype)
|
|---|
|
Example
|
SNP pair
|
Haplotype
|
REAL frequency
|
PHASE frequency
|
MIDAS frequency
|
CUBEX alpha
|
CUBEX beta
|
CUBEX gamma
|
REAL number
|
PHASE number
|
MIDAS number
|
CUBEX alpha
|
CUBEX beta
|
CUBEX gamma
|
|
1
|
Pair1_2
|
AC
|
0.0875
|
0.08689
|
0.0875
|
na
|
0.0875
|
na
|
14
|
14
|
14
|
na
|
14
|
na
|
| |
Pair1_2
|
AT
|
0.725
|
0.72561
|
0.725
|
na
|
0.725
|
na
|
116
|
116
|
116
|
na
|
116
|
na
|
| |
Pair1_2
|
TC
|
0
|
0.00061
|
0
|
na
|
0
|
na
|
0
|
0
|
0
|
na
|
0
|
na
|
| |
Pair1_2
|
TT
|
0.1875
|
0.18689
|
0.1875
|
na
|
0.1875
|
na
|
30
|
30
|
30
|
na
|
30
|
na
|
|
2
|
Pair1_5
|
AG
|
0.75
|
0.75318
|
0.75478
|
0.75478
|
na
|
0.75
|
120
|
121 *
|
121 *
|
121 *
|
na
|
120
|
| |
Pair1_5
|
AA
|
0.0625
|
0.05932
|
0.05772
|
0.05772
|
na
|
0.0625
|
10
|
9 *
|
9 *
|
9 *
|
na
|
10
|
| |
Pair1_5
|
TG
|
0.1875
|
0.18432
|
0.18272
|
0.18272
|
na
|
0.1875
|
30
|
29 *
|
29 *
|
29 *
|
na
|
30
|
| |
Pair1_5
|
TA
|
0
|
0.00318
|
0.00478
|
0.00478
|
na
|
0
|
0
|
1 *
|
1 *
|
1 *
|
na
|
0
|
|
3
|
Pair1_9
|
AT
|
0.05625
|
0.06477
|
0.05633
|
na
|
0.0563
|
0.075
|
9
|
10 *
|
9
|
na
|
9
|
12 *
|
| |
Pair1_9
|
AC
|
0.75625
|
0.74773
|
0.75617
|
na
|
0.7562
|
0.7375
|
121
|
120 *
|
121
|
na
|
121
|
118 *
|
| |
Pair1_9
|
TT
|
0.01875
|
0.01023
|
0.01867
|
na
|
0.0187
|
0
|
3
|
2 *
|
3
|
na
|
3
|
0 *
|
| |
Pair1_9
|
TC
|
0.16875
|
0.17727
|
0.16883
|
na
|
0.1688
|
0.1875
|
27
|
28 *
|
27
|
na
|
27
|
30 *
|
|
4
|
Pair2_3
|
CG
|
0.05625
|
0.04724
|
0.0465
|
0.0465
|
na
|
na
|
9
|
8 *
|
7 *
|
7 *
|
na
|
na
|
| |
Pair2_3
|
CT
|
0.03125
|
0.04026
|
0.041
|
0.041
|
na
|
na
|
5
|
6 *
|
7 *
|
7 *
|
na
|
na
|
| |
Pair2_3
|
TG
|
0.48125
|
0.49026
|
0.491
|
0.491
|
na
|
na
|
77
|
78 *
|
79 *
|
79 *
|
na
|
na
|
| |
Pair2_3
|
TT
|
0.43125
|
0.42224
|
0.4215
|
0.4215
|
na
|
na
|
69
|
68 *
|
67 *
|
67 *
|
na
|
na
|
|
5
|
pair5_9
|
GT
|
0.075
|
0.07313
|
0.06664
|
na
|
0.0666
|
0.075
|
12
|
12
|
11 *
|
na
|
11 *
|
12
|
| |
pair5_9
|
GC
|
0.8625
|
0.86437
|
0.87086
|
na
|
0.8709
|
0.8625
|
138
|
138
|
139 *
|
na
|
139 *
|
138
|
| |
pair5_9
|
AT
|
0
|
0.00187
|
0.00836
|
na
|
0.0084
|
0
|
0
|
0
|
1 *
|
na
|
1 *
|
0
|
| |
pair5_9
|
AC
|
0.0625
|
0.06063
|
0.05414
|
na
|
0.0541
|
0.0625
|
10
|
10
|
9 *
|
na
|
9 *
|
10
|
- A selection of comparisons using direct haplotyped APOE data [25]. Full data are present as a additional table. For haplotype numbers (rounded to the nearest number) incorrect answers are marked '*', correct answers are unmarked. Examples: (1) Phase, MIDAS and CubeX (1 solution) give correct answer. (2) Only CubeX gives the correct answer as one of its two solutions. (3) MIDAS and CubeX give the correct answer, PHASE and the other CubeX solution are wrong. (4) All three approaches are wrong. (5) PHASE and CubeX give the correct answer, MIDAS and the other CubeX solution are wrong.
