SIFTDbColumns {VariantAnnotation} | R Documentation

## SIFTDb Columns

### Description

Description of the SIFT Sqlite Database Columns

### Column descriptions

These column names are displayed when `columns` is called on a `SIFTDb` object.

- RSID : rsid

- PROTEINID : NCBI RefSeq protein ID

- AACHANGE : amino acid substitution; reference aa is preceeding, followed by the position and finally the snp aa

- METHOD : method of obtaining related sequences using PSI-BLAST

- AA : either the reference or snp residue amino acid

- PREDICTION : SIFT prediction

- SCORE : SIFT score (range 0 to 1)

  - TOLERATED : score is greater than 0.05

  - DAMAGING : score is less than or equal to 0.05

  - NOT SCORED : no prediction is made if there are less than 2 homologous sequences that have an amino acid at the position of the given SNP or if the SIFT prediction is not available

- MEDIAN : diversity measurement of the sequences used for prediction (range 0 to 4.32)

- POSITIONSEQS : number of sequences with an amino acide at the position of prediction

- TOTALSEQS : total number of sequences in alignment

### Author(s)

Valerie Obenchain

### See Also

`?SIFTDb`

[Package VariantAnnotation version 1.30.1 Index]