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  1. 1. ccdsGene
  2. 2. ccdsGene_exon

This database contains high-confidence human gene annotations from the Consensus Coding Sequence (CCDS) project. It was constructed from the UCSC Genome Browser ccdsGene track. If you would like to annotate your variants to these genes, you can use the simpler ccdsGene database. If you would like to determine the exons that your variants are in, use the ccdsGene_exon database. See the available annotation fields for each database below.

1.  ccdsGene

% vtools show annotation ccdsGene -v2
Annotation database ccdsGene (version hg19_20130904)
Description:            High-confidence human gene annotations from the
  Consensus Coding Sequence (CCDS) project.
Database type:          range
Number of records:      27,762
Distinct ranges:        23,393
Reference genome hg19:  chr, cdsStart, cdsEnd

Field:                  name
Type:                   string
Comment:                Gene name (usually a CCDS transcript ID)
Missing entries:        0
Unique Entries:         27,731

Field:                  chr
Type:                   string
Missing entries:        0
Unique Entries:         24

Field:                  strand
Type:                   string
Comment:                which DNA strand contains the observed alleles
Missing entries:        0
Unique Entries:         2

Field:                  cdsStart
Type:                   integer
Comment:                Coding region start
Missing entries:        0
Unique Entries:         20,946
Range:                  41608 - 249211537

Field:                  cdsEnd
Type:                   integer
Comment:                Coding region end
Missing entries:        0
Unique Entries:         21,000
Range:                  46385 - 249212562

Field:                  exonCount
Type:                   integer
Comment:                Number of exons
Missing entries:        0
Unique Entries:         107
Range:                  1 - 362

Field:                  score
Type:                   integer
Comment:                Score
Missing entries:        0
Unique Entries:         1
Range:                  0 - 0

Field:                  name2
Type:                   string
Comment:                Alternate name
Missing entries:        0
Unique Entries:         1

Field:                  cdsStartStat
Type:                   string
Comment:                cds start stat, can be 'non', 'unk', 'incompl', and
                        'cmp1'
Missing entries:        0
Unique Entries:         1

Field:                  cdsEndStat
Type:                   string
Comment:                cds end stat, can be 'non', 'unk', 'incompl', and
                        'cmp1'
Missing entries:        0
Unique Entries:         1

2.  ccdsGene_exon

% vtools show annotation ccdsGene_exon -v2
Annotation database ccdsGene_exon (version hg19_20130904)
Description:            High-confidence human gene annotations from the
  Consensus Coding Sequence (CCDS) project. This database contains all exon
  regions of the CCDS genes.
Database type:          range
Number of records:      291,746
Distinct ranges:        192,096
Reference genome hg19:  chr, exon_start, exon_end

Field:                  name
Type:                   string
Comment:                CCDS gene name
Missing entries:        0
Unique Entries:         27,731

Field:                  chr
Type:                   string
Missing entries:        0
Unique Entries:         24

Field:                  strand
Type:                   string
Comment:                which DNA strand contains the observed alleles
Missing entries:        0
Unique Entries:         2

Field:                  cdsStart
Type:                   integer
Comment:                Coding region start
Missing entries:        0
Unique Entries:         20,946
Range:                  41608 - 249211537

Field:                  cdsEnd
Type:                   integer
Comment:                Coding region end
Missing entries:        0
Unique Entries:         21,000
Range:                  46385 - 249212562

Field:                  exonCount
Type:                   integer
Comment:                Number of exons
Missing entries:        0
Unique Entries:         107
Range:                  1 - 362

Field:                  exon_start
Type:                   integer
Comment:                exon start position
Missing entries:        0
Unique Entries:         189,635
Range:                  41608 - 249211537

Field:                  exon_end
Type:                   integer
Comment:                exon end position
Missing entries:        0
Unique Entries:         189,690
Range:                  41627 - 249212562

Field:                  score
Type:                   integer
Comment:                Score
Missing entries:        0
Unique Entries:         1
Range:                  0 - 0

Field:                  name2
Type:                   string
Comment:                Alternative name
Missing entries:        0
Unique Entries:         1

Field:                  cdsStartStat
Type:                   string
Comment:                cds start stat, can be 'non', 'unk', 'incompl', and
                        'cmp1'
Missing entries:        0
Unique Entries:         1

Field:                  cdsEndStat
Type:                   string
Comment:                cds end stat, can be 'non', 'unk', 'incompl', and
                        'cmp1'
Missing entries:        0
Unique Entries:         1