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Table 2 Summary description of the annotations provided by SNPdat

From: Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

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