Presumed Normal SV Track Settings

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Presumed Normal Structural Variants in dbVar

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Variant Length Range	Discovery Method Type	Pathogenic Reciprocal Overlap	Population Code	Variant Type

Display data as a density graph:

List subtracks: only selected/visible all
	pack Configure	Presumed Normal SVs	Presumed Normal SVs	Schema
	pack Configure	Structural Variants with Phenotype	Structural Variants with Phenotype	Schema

Description

Structural variants in dbVar excluding the following:

common variants in Common SV track

variants with somatic origin in Somatic SV track

clinical variants in ClinVar SV track

variants with clinical significance that were not submitted to ClinVar

variants of these types:

short tandem repeat
interchromosomal translocation
intrachromosomal translocation

variants from these dbVar studies:

variants discovered using these methods:

BAC aCGH
FISH
Karyotyping
MassSpec
Microsatellite genotyping
Multiple complete digestion
Not provided
ROMA
Southern
Western

Data Updates

This track is updated with every dbVar monthly release.

Subtracks

The Presumed Normal Structural variants are separated into the following subtracks:

Presumed Normal SVs

Structural variants in dbVar with no reported phenotype, excluding common and somatic variants.

Structural Variants with Phenotype

Structural variants in dbVar with a reported phenotype, excluding clinical and somatic variants.

Non-Redundant

This track is non-redundant with respect to placement, variant type, and discovery method type. The label and detail fields contain the lists of unique values for each field of the redundant variant calls.

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
List of unique phenotypes of the redundant calls (for phenotype subtrack)
List of unique populations derived from samples or samplesets of the redundant calls (if available)
Total number of redundant calls

Detail Page

The detail page contains the following:

Link to the Variant Page in dbVar .

Discovery Method Type (NOTE: other includes ddPCR,qPCR,PCR,MLPA)

Variant Type

Variant Length Range

Mouseover Label

dbVar study containing the variant

Range of Reciprocal Overlap with Pathogenic Variant

Link to the dbVar Page of the pathogenic variant with the highest reciprocal overlap

Population Code derived from Sample or Sampleset

List of dbVar Variant calls with the same placement, variant type, and discovery method

Track Hub date last updated

Variant Colors

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

red:

deletion
delins
loss

blue:

duplication
gain
insertion

violet:

copy number variation

light violet:

inversion

light azure:

complex substitution

brown:

tandem duplication

grey:

sequence alteration

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
Population Code derived from Sample or Sampleset
Variant Type

Statistics

Counts per subtrack for each filter value:

Variant Length Range

Value	normal_healthy	normal_phenotype
100KB to 1MB	0	113029
10KB to 100KB	0	221748
Over 1MB	0	7202
Under 10KB	0	71771
Total	0	413750

Discovery Method Type

Value	normal_healthy	normal_phenotype
Merging	0	395
Oligo aCGH	0	80
Optical mapping	0	1344
SNP array	0	404363
Sequencing	0	7567
other	0	1
Total	0	413750

Range of Reciprocal Overlap with Pathogenic Variant

Value	normal_healthy	normal_phenotype
10 to 25	0	305
25 to 50	0	145
50 to 75	0	165
75 to 90	0	190
90 to 100	0	149
none	0	412796
Total	0	413750

Population Code derived from Sample or Sampleset

Value	normal_healthy	normal_phenotype
EUR	0	65
multiple	0	2
none	0	413683
Total	0	413750

Variant Type

Value	normal_healthy	normal_phenotype
alu insertion	0	1
complex substitution	0	93
copy number gain	0	126481
copy number loss	0	278359
deletion	0	6132
duplication	0	1211
insertion	0	164
inversion	0	400
mobile element insertion	0	1
sequence alteration	0	908
Total	0	413750