NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels
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
