15 Promoter SNPs | Error Rate Based on # of Heterozygous Sites (N) | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Error Rate | ||||||||||
Algorithm | MSE | IH # correct/# wrong | IF | Overall | Ambiguous Individuals | 2 (13) | 3 (32) | 4 (24) | 5 (28) | 6 (11) |
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% | ||||||||||
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 |