SIFTDbColumns: SIFTDb Columns

In Bioconductor/VariantAnnotation: Annotation of Genetic Variants

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

Bioconductor/VariantAnnotation documentation built on Nov. 2, 2024, 7:22 a.m.