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

BMC Genomics

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	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***

MQS: SNP mapping quality score; RMD: read mapping depth; FVF: folded variant frequency. *** represents statistical significance at a 0.001 probability level.

ISSN: 1471-2164