Table 2 Inferred frequencies of haplotypes.
SNP | Haplotype Frequency | ||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
-476 | -339 | -308 | -301 | -278 | -168 | -75 | -57 | -31 | -6 | -1 | 3 | 16 | 25 | 59 | Empirical | Phase, no LD | Phase, with LD | Haplotyper | PL-EM | SNPHAP | |
Empirical Haplotypes | |||||||||||||||||||||
1 | G | G | G | G | G | T | A | T | G | A | A | G | A | A | T | 0.334 | 0.312 | 0.321 | 0.325 | 0.333 | 0.326 |
2 | G | G | G | G | T | T | A | G | G | G | A | G | A | A | T | 0.162 | 0.166 | 0.162 | 0.166 | 0.181 | 0.171 |
3 | G | G | T | T | G | T | A | G | G | A | A | G | A | A | T | 0.091 | 0.097 | 0.097 | 0.101 | 0.098 | 0.102 |
4 | G | G | T | T | G | T | A | G | - | A | A | G | A | A | T | 0.052 | 0.055 | 0.055 | 0.049 | 0.047 | 0.050 |
5 | G | G | G | G | T | T | G | G | G | G | A | G | A | A | T | 0.042 | 0.052 | 0.052 | 0.052 | 0.049 | 0.050 |
6 | G | G | T | T | G | T | A | G | - | A | A | G | A | A | G | 0.029 | 0.032 | 0.032 | 0.032 | 0.030 | 0.030 |
7 | G | G | G | G | T | T | A | G | G | G | T | G | A | A | T | 0.026 | 0.032 | 0.032 | 0.032 | 0.028 | 0.029 |
8 | G | G | T | T | G | T | A | G | G | G | A | G | A | A | T | 0.019 | 0.016 | 0.016 | 0.013 | 0.016 | 0.018 |
9 | G | G | G | G | T | T | A | T | G | G | A | G | A | A | T | 0.019 | 0.013 | 0.013 | 0.013 | 0.011 | 0.011 |
10 | G | G | T | T | G | T | A | G | - | G | A | G | A | A | T | 0.019 | 0.023 | 0.026 | 0.023 | 0.025 | 0.025 |
11 | G | G | G | G | T | T | G | G | G | G | A | G | G | C | T | 0.016 | 0.016 | 0.016 | 0.016 | 0.014 | 0.014 |
12 | G | G | G | G | T | T | A | G | G | A | A | G | A | A | T | 0.016 | 0.010 | 0.006 | 0.006 | 0.008 | 0.008 |
13 | G | - | G | G | T | T | G | G | G | G | A | G | A | A | T | 0.016 | 0.016 | 0.016 | 0.013 | 0.010 | 0.013 |
14 | G | G | G | G | T | C | A | G | G | G | T | G | A | A | T | 0.016 | 0.016 | 0.016 | 0.016 | 0.016 | 0.016 |
15 | G | G | T | T | G | T | A | G | G | G | T | G | A | A | T | 0.013 | 0.010 | 0.010 | 0.010 | 0.006 | 0.009 |
16 | G | G | G | G | T | T | G | G | G | A | A | G | A | A | T | 0.013 | 0.013 | 0.013 | 0.016 | 0.008 | 0.008 |
17 | G | - | G | G | T | T | A | G | G | G | A | G | A | A | T | 0.013 | 0.013 | 0.013 | 0.013 | 0.011 | 0.011 |
18 | G | G | G | G | T | T | A | G | - | G | A | G | A | A | T | 0.010 | - | 0.006 | 0.010 | 0.007 | 0.008 |
19 | A | G | G | G | T | T | A | G | G | G | A | G | A | A | T | 0.010 | 0.013 | 0.013 | 0.010 | 0.005 | 0.010 |
20 | G | G | G | G | G | T | A | G | - | A | A | G | A | A | T | 0.010 | - | 0.003 | 0.010 | 0.006 | 0.005 |
21 | G | G | G | G | T | T | G | G | G | G | A | G | A | A | G | 0.010 | 0.010 | 0.010 | 0.010 | 0.011 | 0.011 |
22 | G | G | T | T | G | T | A | T | G | A | A | G | A | A | T | 0.010 | 0.013 | 0.010 | 0.013 | 0.007 | 0.007 |
23 | G | G | G | G | G | T | A | G | G | A | A | G | A | A | T | 0.006 | 0.016 | 0.013 | 0.006 | 0.006 | 0.008 |
24 | G | G | T | T | G | T | G | G | - | A | A | G | A | A | T | 0.006 | - | - | - | - | - |
25 | G | G | T | T | G | T | A | G | G | A | A | G | A | A | G | 0.003 | - | - | - | 0.004 | 0.004 |
26 | G | G | G | G | T | T | G | G | G | G | T | G | A | A | T | 0.003 | 0.006 | 0.006 | 0.006 | 0.007 | 0.007 |
27 | G | G | G | G | T | T | A | T | G | A | A | G | A | A | T | 0.003 | 0.003 | 0.003 | - | - | - |
28 | G | G | G | G | T | T | A | G | - | A | A | G | A | A | T | 0.003 | - | - | - | - | - |
29 | A | G | G | G | T | T | A | G | G | A | A | G | A | A | T | 0.003 | - | - | - | - | - |
30 | G | - | G | G | T | T | A | G | G | A | A | G | A | A | T | 0.003 | 0.003 | 0.003 | 0.003 | 0.003 | 0.003 |
31 | G | G | G | G | T | T | G | G | - | G | A | G | A | A | T | 0.003 | 0.010 | - | - | - | - |
32 | G | G | T | T | G | T | G | G | G | G | A | G | A | A | G | 0.003 | - | - | - | 0.002 | - |
33 | G | G | G | G | T | T | A | G | G | G | A | G | G | C | T | 0.003 | 0.003 | 0.003 | 0.003 | 0.004 | 0.004 |
34 | G | - | G | G | T | C | A | G | G | G | T | G | A | A | T | 0.003 | 0.003 | 0.003 | 0.003 | 0.003 | 0.003 |
35 | G | G | G | G | G | T | A | G | G | A | C | C | A | A | T | 0.003 | - | - | 0.003 | 0.003 | 0.003 |
36 | G | G | G | G | T | T | A | G | G | G | T | G | A | A | G | 0.003 | - | - | - | 0.003 | 0.003 |
Incorrect Haplotypes | |||||||||||||||||||||
1 | G | - | G | G | T | T | G | G | G | G | A | G | G | C | T | - | - | - | 0.002 | 0.002 | |
2 | G | G | G | G | T | T | G | G | - | A | A | G | A | A | T | - | 0.006 | - | 0.009 | 0.008 | |
3 | G | G | G | G | T | T | G | T | - | G | A | G | A | A | T | - | - | - | - | 0.002 | |
4 | G | - | G | G | T | T | G | T | G | A | A | G | A | A | T | - | - | 0.003 | - | - | |
5 | G | - | G | G | T | T | G | T | G | G | A | G | A | A | T | - | - | - | 0.003 | 0.002 | |
6 | G | G | G | G | T | T | G | T | G | G | A | G | A | A | T | - | 0.003 | - | - | - | |
7 | G | G | G | G | T | T | G | T | G | A | A | G | A | A | T | - | - | - | - | 0.004 | |
8 | A | G | G | G | T | T | A | T | G | A | A | G | A | A | T | - | - | 0.003 | 0.003 | 0.003 | |
9 | G | G | G | G | T | T | A | G | G | G | C | C | A | A | T | 0.003 | 0.003 | - | - | - | |
10 | A | G | T | T | G | T | A | G | - | A | A | G | A | A | T | - | - | - | 0.002 | - | |
11 | A | G | T | T | G | T | A | G | G | G | T | G | A | A | T | - | - | - | 0.003 | - | |
12 | G | G | T | T | T | T | G | G | - | G | A | G | A | A | T | - | - | 0.006 | 0.004 | - | |
13 | G | G | T | T | T | T | G | G | G | A | A | G | A | A | T | - | - | - | 0.003 | - | |
14 | G | G | G | G | G | T | A | T | - | A | A | G | A | A | T | 0.010 | - | - | - | - | |
15 | G | G | G | G | G | T | A | T | G | G | A | G | A | A | T | 0.006 | 0.006 | 0.006 | 0.008 | 0.008 | |
16 | G | G | G | G | G | T | A | T | G | A | A | G | A | A | G | 0.006 | 0.006 | 0.006 | - | - | |
Minor Allele Frequency | |||||||||||||||||||||
0.013 | 0.036 | 0.247 | 0.247 | 0.399 | 0.019 | 0.114 | 0.367 | 0.133 | 0.412 | 0.065 | 0.003 | 0.019 | 0.019 | 0.049 | |||||||