TABLE 3.

Filterable characteristics Variant Output File

Characteristic	Feature	Resource	Example row Variant Output
Genome	Chromosome	hg19	chr10
	Position of variant	hg19	17171656
	Variant ID	dbSNP	rs76788243
	Reference allele	hg19	T
	Alternative allele	GATK unified	G
	Quality of variant	GATK unified	9485.04
	Gene name	HUGO	CUBN
	Effect of variant	SnpEff	Nonsynonymous change
	MAF	dbSNP	0.034
	Rare Module	Custom	Pass
Protein	Biotype	Ensembl	Protein coding
	Amino acid change	SnpEff	I37L
	Protein feature	UniProt	Mature (processed) chain
	UniProt accession	UniProt	O60494
Pathway	KEGG pathway	KEGG	Organismal systems
Disease	Gene associated with disease	UniProt	Recessive hereditary megaloblastic anemia 1 MIM:261100
	Genetic inheritance pattern	Custom	Recessive
Patient-specific	Genotype probands	GATK unified	G/G
	Confidence module	Custom	Pass
	allele depth	GATK unified	101

KEGG, Kyoto Encyclopedia of Genes and Genomes.