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Table 1 Atlas2 Suite SOLiD model variables

From: An integrative variant analysis suite for whole exome next-generation sequencing data

SNPs    
   Description Type z-value p-value
   Reference/variant reads ratio Numeric -34.36 < 2E-16
   Strand direction Boolean 17.57 < 2E-16
   Mean distance to 3' end Numeric 16.87 < 2E-16
   Mean neighboring base quality (NBQ) Numeric 14.83 < 2E-16
   Mean variant base quality Numeric 10.61 < 2E-16
   Mean NBQ × Mean distance 3' (interaction) Numeric -12.39 < 2E-16
   Strand direction × Mean distance 3' (interaction) Numeric -10.52 < 2E-16
INDELs    
   Description Type z-value p-value
   Mean neighbor base quality (NBQ) Numeric 9.097 < 2E-16
   Normalized variant square (NVS) Numeric 7.035 2.00E-12
   Mean variation rate Numeric -6.669 2.57E-11
   Read end ratio Numeric -4.436 9.15E-06
  1. Variables and interactions for both the SNP and INDEL models along with the variable's Wald z-statistic and p-value as estimated by the R environment's glm function. The z-values and p-values indicate the significance of the variables in the model, with the most significant variables having a z-value furthest from zero.