Table 3 |
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|
Accuracy of computational inferences of haplotype structure of the GH1 gene promoter. |
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|
15 Promoter SNPs |
Error Rate Based on # of Heterozygous Sites (N) |
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|
|
|
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|
Error Rate |
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|
|
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|
Algorithm |
MSE |
IH # correct/# wrong |
IF |
Overall |
Ambiguous Individuals |
2 (13) |
3 (32) |
4 (24) |
5 (28) |
6 (11) |
|
|
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|
Phase v2, no LD |
3.6 × 10-5 |
0.81 27/4 |
0.91 |
0.11 |
0.15 |
0.08 |
0.09 |
0.25 |
0.11 |
0.27 |
|
Phase v2, with LD |
2.2 × 10-5 |
0.81 28/5 |
0.93 |
0.10 |
0.13 |
0 |
0.09 |
0.17 |
0.14 |
0.27 |
|
Haplotyper 1.0 |
2.0 × 10-5 |
0.81 28/5 |
0.93 |
0.09 |
0.13 |
0 |
0.06 |
0.13 |
0.18 |
0.27 |
|
PL-EM 1.0 |
2.5 × 10-5 |
0.82 31/9 |
0.92 |
0.11 |
0.15 |
0 |
0.09 |
0.13 |
0.21 |
0.36 |
|
SNPHAP 1.0 |
2.0 × 10-5 |
0.82 30/7 |
0.93 |
0.09 |
0.13 |
0 |
0.09 |
0.13 |
0.14 |
0.27 |
|
8 SNPs with Minor Allele Frequency ≥ 5% |
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|
|
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|
Phase v2, no LD |
4.8 × 10-5 |
0.79 19/3 |
0.92 |
0.11 |
0.15 |
|||||
|
Phase v2, with LD |
4.1 × 10-5 |
0.80 20/4 |
0.92 |
0.11 |
0.15 |
|||||
|
Haplotyper 1.0 |
3.8 × 10-5 |
0.81 19/2 |
0.93 |
0.10 |
0.14 |
|||||
|
PL-EM 1.0 |
2.3 × 10-5 |
0.85 22/4 |
0.94 |
0.08 |
0.11 |
|||||
|
SNPHAP 1.0 |
3.3 × 10-5 |
0.85 22/4 |
0.93 |
0.08 |
0.11 |
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|
|
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|
Adkins BMC Genetics 2004 5:22 doi:10.1186/1471-2156-5-22 |
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