Cloud-based Annotated Variations Table
Overview
The Annotated Variations Table contains variants identified relative to the SARS-CoV-2 RefSeq record (NC_045512.2) for each processed run, along with VIGOR3 annotation. More detailed information on the generation of these variants can be found here: https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/sra/docs/sars-cov-2-variant-calling/.
Linking to other tables
- to Metadata Table by run/acc column
- to Taxonomy Analysis Information Table by run/acc column
- to Taxonomy Analysis Table by run/acc column
Description of fields
| Column name | Type | Description |
|---|---|---|
| RUN | STRING | SRA Accession |
| CHR | STRING | Reference Sequence Accession |
| POS | INTEGER | Genomic Position |
| REF | STRING | reference base(s) |
| ALT | STRING | alternate base(s) |
| DP | INTEGER | read depth |
| G_AD_2 | INTEGER | alt allele depth |
| EFFECT | STRING | Type of variation |
| FUNCLASS | STRING | The effect of the variation |
| CODON | STRING | Codon nucleotide sequence change |
| variation | STRING | amino acid change |
| AA_LEN | INTEGER | amino acid length |
| protein_name | STRING | protein name, if any |
| ref_aa | STRING | reference amino acid |
| alt_aa | STRING | alternate amino acid |
| protein_position | INTEGER | position of the associated amino acid if any |
| ver | STRING | runtime version stamp |
| updated | TIMESTAMP | Time of variation analysis |
Example query for Athena UI
SELECT distinct Run, variation
FROM "<db_name>"."annotated_variations"
WHERE variation = 'E484K'
FROM "<db_name>"."annotated_variations"
WHERE variation = 'E484K'
Contact SRA
Contact SRA staff for assistance at sra@ncbi.nlm.nih.gov