The knownGene database is based on the UCSC Genome Browser knownGene track. knownGene shows gene predictions based on data from RefSeq, Genbank, CCDS and UniProt. If you would like to annotate your variants to these genes, you can use the simpler knownGene database. If you would like to determine the exons that your variants are in, use the knownGene_exon database. See the available annotation fields for each database below.
% vtools show annotation knownGene -v2
Annotation database knownGene (version hg19_20130904)
Description: Gene predictions based on data from RefSeq, Genbank,
CCDS and UniProt, from the UCSC KnownGene track.
Database type: range
Number of records: 82,960
Distinct ranges: 60,726
Reference genome hg19: chr, txStart, txEnd
Field: name
Type: string
Comment: Name of gene such as uc001aaa.3
Missing entries: 0
Unique Entries: 82,960
Field: chr
Type: string
Missing entries: 0
Unique Entries: 60
Field: strand
Type: string
Comment: which DNA strand contains the observed alleles
Missing entries: 0
Unique Entries: 2
Field: txStart
Type: integer
Comment: Transcription start position
Missing entries: 0
Unique Entries: 48,720
Range: 1 - 249211537
Field: txEnd
Type: integer
Comment: Transcription end position
Missing entries: 0
Unique Entries: 48,713
Range: 368 - 249213345
Field: cdsStart
Type: integer
Comment: Coding region start
Missing entries: 0
Unique Entries: 51,789
Range: 1 - 249211537
Field: cdsEnd
Type: integer
Comment: Coding region end
Missing entries: 0
Unique Entries: 51,745
Range: 0 - 249212562
Field: exonCount
Type: integer
Comment: Number of exons
Missing entries: 0
Unique Entries: 119
Range: 1 - 5065
% vtools show annotation knowGene_exon -v2
Annotation database knownGene_exon (version hg19_20130904)
Description: Gene predictions based on data from RefSeq, Genbank,
CCDS and UniProt, from the UCSC KnownGene track. This database contains all
exome regions of the UCSC known gene database.
Database type: range
Number of records: 742,493
Distinct ranges: 289,953
Reference genome hg19: chr, exon_start, exon_end
Field: chr
Type: string
Missing entries: 0
Unique Entries: 60
Field: strand
Type: string
Comment: which DNA strand contains the observed alleles
Missing entries: 0
Unique Entries: 2
Field: txStart
Type: integer
Comment: Transcription start position
Missing entries: 0
Unique Entries: 48,720
Range: 1 - 249211537
Field: txEnd
Type: integer
Comment: Transcription end position
Missing entries: 0
Unique Entries: 48,713
Range: 368 - 249213345
Field: cdsStart
Type: integer
Comment: Coding region start
Missing entries: 0
Unique Entries: 51,789
Range: 1 - 249211537
Field: cdsEnd
Type: integer
Comment: Coding region end
Missing entries: 0
Unique Entries: 51,745
Range: 0 - 249212562
Field: exonCount
Type: integer
Comment: Number of exons
Missing entries: 0
Unique Entries: 119
Range: 1 - 5065
Field: exon_start
Type: integer
Comment: exon start position
Missing entries: 0
Unique Entries: 276,580
Range: 1 - 249211537
Field: exon_end
Type: integer
Comment: exon end position
Missing entries: 0
Unique Entries: 276,718
Range: 368 - 249213345