Optimizing genotype quality metrics for individual exomes and cohort analysis

BMC Proceedings

Table 1 Quality metrics reported in the literature, and the optimized colorspace genotyping results.

	Ideal	Colorspace exome average
Protein coding	0.048% [6]	0.052
Non-coding	>coding	0.056
Non-synonymous	45% [7]	46.2
Homozygous	37-40% [8]	38.7
Coding SNP transitions:transversions	2.8-3.0:1 [9]	3.2:1
Non-coding SNP transitions:transversions	2.0-2.2:1 [9]	2.3:1
CDS novel (versus dbSNP135)	N/A	0.58

ISSN: 1753-6561