Table 1.

List of variations. Name and description of all variation classes used in NovelSNPer. A cross (X) indicates that a variation class can be assigned to an SNP, MNP, or InDel, respectively.

Name	SNP	MNP	InDel	Description
Intergenic	X	X	X	More than 5000 bp away from any gene
Upstream	X	X	X	Upstream the nearest gene and this gene is closer than 5000 bp
Downstream	X	X	X	Downstream the nearest gene and this gene is closer than 5000 bp
Within noncoding transcript	X	X	X	In the exon or intron of a noncoding gene
Intronic	X	X	X	In the intron of a coding gene
5′ UTR	X	X	X	In the exonic 5′ UTR
3′ UTR	X	X	X	In the exonic 3′ UTR
Synonymous coding	X	X		Variation in a coding region without changing the amino acid
Nonsynonymous coding	X	X		Variation in a coding region with changing a single amino acid
Framekeep			X	Insertion or deletion of some amino acids
Frameshift			X	Changing the reading frame in coding region
Stop gained	X	X	X	Generates a new stop codon in the coding region
Stop lost	X	X	X	Deletion of an existing stop codon at the end of coding region
Potential start gained	X	X	X	Generates a potential start codon
				in 5′ UTR or in an exon of noncoding transcript
Start lost	X	X	X	Deletion of an existing start codon at the beginning of coding region
Delete exon			X	Deletion of a whole exon
Merge exon			X	Deletion of a whole intron
Acceptor		X	X	Deletion of the exonic and intronic splice site upstream of an exon
Donor		X	X	Deletion of the exonic and intronic splice site downstream of an exon
Splice site	X	X	X	Variation near the exon-intron boundary
Essential splice site	X	X	X	Intronic variation within 3 bp range of an exon-intron boundary