Table 2.

Summary description of the annotations provided by SNPdat

Column Number	Description	Example
1	The queried SNPs chromosome ID	CHR25
2	The queried SNPs genomic location	286966
3	Whether or not the SNP was within a feature	Y
4	Region containing the SNP; either exonic, intronic, or intergenic	Exonic
5	Distance to nearest feature	NA
6	Either the closest feature to the SNP or the feature containing the SNP	CDS
7	The number of different features that the SNP is annotated to	2
8	The number of annotations of the current feature	[1/1]
9	Start of feature (bp)	286859
10	End of feature (bp)	287050
11	The gene ID for the current feature	ENSBTAG00000016571
12	The gene name for the current feature	ITFG3_BOVIN
13	The transcript ID for the current feature	ENSBTAT00000022045
14	The transcript name for the current feature	ITFG3_BOVIN
15	The exon that contains the current feature and the total number of annotated exons for the gene containing the feature	[3/11]
16	The strand sense of the feature	+
17	The annotated reading frame (when contained in GTF)	2
18	The reading frame estimated by SNPdat	NA
19	The estimated number of stop codons in the estimated reading frame	0
20	The codon containing the SNP, position in the codon and reference base and mutation	C[C/G]T
21	The amino acid for the reference codon and new amino acid with mutation in place	[P/R]
22	Whether or not the mutation is synonymous	N
23	The protein ID for the current feature	ENSBTAP00000022045
24	The RS identifier for queries that map to known SNPs	rs134558771
25	Error messages, warnings etc.	NA