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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

From: Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms

Term Estimates of coefficients Std error χ 2 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***
  1. MQS: SNP mapping quality score; RMD: read mapping depth; FVF: folded variant frequency. *** represents statistical significance at a 0.001 probability level.