Somatic SV Track Settings
 
Somatic Structural Variants in dbVar

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Variant Length Range Discovery Method Type Pathogenic Reciprocal Overlap Variant Type


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 Somatic Structural Variants in dbVar  Somatic Structural Variants in dbVar   Schema 

Description

Structural variants in dbVar with somatic origin.

Data Updates

This track is updated with every dbVar monthly release.

This track contains data from the following studies:

Subtracks

There is only one subtrack:

Display Conventions and Configuration

Labels

The variant label is the dbVar variant call accession (nssv) of the variant in dbVar.

Mouseover

The mouseover (displayed when the mouse is hovered over a variant) shows the following:

  • List of Affected Genes
  • Position
  • Size
  • Variant Type
  • dbVar study containing the variant
  • Discovery Method Type

Detail Page

The detail page contains the following:

Variant Colors

The colors indicate variant type of the variant, and are based on the dbVar colors described in the dbVar Overview page.

Placements

For simplicity, the BED files and tracks only contain the variants' outer-most start and stop placements. The actual variant placements may consist of exact start/stop with breakpoint resolution, inner-placements only, outer-placements-only, or some combination. For full details of variant placements, follow the links to the variant pages in dbVar.

Filters

The track can be filtered by the following:

  • Variant Length Range
  • Discovery Method Type
  • Range of Reciprocal Overlap with Pathogenic Variant
  • Variant Type

Statistics

Counts per subtrack for each filter value:

Variant Length Range

Value somatic_sv
100KB to 1MB 6952
10KB to 100KB 8386
Over 1MB 6075
Under 10KB 45492
Total 66905

Discovery Method Type

Value somatic_sv
Curated 65572
Multiple 274
SNP array 214
Sequencing 845
Total 66905

Range of Reciprocal Overlap with Pathogenic Variant

Value somatic_sv
10 to 25 25
25 to 50 16
50 to 75 30
75 to 90 35
90 to 100 89
none 66710
Total 66905

Variant Type

Value somatic_sv
complex substitution 42
copy number gain 233
copy number loss 169
copy-neutral loss of heterozygosity 8
deletion 29737
duplication 8
insertion 45
inversion 18597
mobile element insertion 845
tandem duplication 17221
Total 66905

Data Access

Data for this track can be downloaded from the following locations:

Methods

Generating the Somatic Track consists of the following:

References