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 |