Table 4. Information provided by SnpEff in variant call format (VCF).

Sub-field	Notes
Effect	Effect of this variant. See details below.
Codon_Change	Codon change: old_codon/new_codon
Amino_Acid_change	Amino acid change: old_AA/new_AA
Warnings	Any warnings or errors.
Gene_name	Gene name
Gene_BioType	BioType, as reported by ENSEMBL.
Coding	[CODING | NON_CODING]. If information reported by ENSEMBL (e.g., has 'protein_id' information in GTF file).
Trancript	Transcript ID (usually ENSEMBL)
Exon	Exon ID (usually ENSEMBL)
Warnings	Any warnings or errors (not shown if empty).

The information is added to the INFO fields using an tag ‘EFF’. The format for each effect is “Effect (Effect_Impact | Codon_Change | Amino_Acid_change | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ])”