Table 6.
Logistic regression model of polymorphism of SNPs (true-positive and false-positive) and several related SNP filtering criteria: log (p/(1-p)) = b0 + b1*X1 + b2*X2 + b3*X3, where p is the probability of an SNP belonging to a false-positive
| Term | Estimates of coefficients | Std error | χ2 | Prob > χ2 |
|---|---|---|---|---|
| Intercept |
10.3976899 (b0) |
0.7025 |
219.05 |
<0.0001*** |
|
MQS (X1) |
−0.3077982 (b1) |
0.0197 |
244.83 |
<0.0001*** |
|
RMD (X2) |
0.07896269 (b2) |
0.003 |
699.67 |
<0.0001*** |
| FVF (X3) | −5.2585503 (b3) | 0.3871 | 184.57 | <0.0001*** |
MQS: SNP mapping quality score; RMD: read mapping depth; FVF: folded variant frequency. *** represents statistical significance at a 0.001 probability level.