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

BMC Bioinformatics

Table 1 Atlas2 Suite SOLiD model variables

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

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.

ISSN: 1471-2105