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.

You et al.

You et al. BMC Genomics 2012 13:354   doi:10.1186/1471-2164-13-354

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