Presumed Normal SV Track Settings
 
Presumed Normal Structural Variants in dbVar

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


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 Configure 		 Presumed Normal SVs  Presumed Normal Structural Variants in dbVar   Data format 
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 Configure 		 Structural Variants with Phenotype  Presumed Normal Structural Variants in dbVar   Data format 
Assembly: Human Feb. 2009 (GRCh37/hg19)

Description

Structural variants in dbVar excluding the following:

Data Updates

This track is updated with every dbVar monthly release.

Subtracks

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

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:

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
  • 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 210238 1211
10KB to 100KB 556903 2329
Over 1MB 42152 59
Under 10KB 4700060 7550
Total 5509353 11149

Discovery Method Type

Value normal_healthy normal_phenotype
Curated 43115 0
Merging 287504 395
Multiple 38185 0
Oligo aCGH 68320 80
Optical mapping 29730 1344
SNP array 375219 1762
Sequencing 4667198 7567
other 82 1
Total 5509353 11149

Range of Reciprocal Overlap with Pathogenic Variant

Value normal_healthy normal_phenotype
10 to 25 67618 305
25 to 50 36419 145
50 to 75 19224 165
75 to 90 9313 190
90 to 100 8701 149
none 5368078 10195
Total 5509353 11149

Population Code derived from Sample or Sampleset

Value normal_healthy normal_phenotype
AFR 45157 0
AMR 30521 0
EAS 16096 0
EUR 140037 65
OTH 3507 0
SAS 3741 0
mixed 19699 0
multiple 442612 2
none 4807690 11082
unknown 293 0
Total 5509353 11149

Variant Type

Value normal_healthy normal_phenotype
alu deletion 15102 0
alu insertion 268588 1
complex substitution 19326 93
copy number gain 182170 865
copy number loss 296899 1374
copy number variation 147408 0
copy-neutral loss of heterozygosity 26 0
deletion 2615591 6132
delins 697 0
duplication 357873 1211
herv deletion 224 0
herv insertion 223 0
insertion 1385104 164
inversion 107667 400
line1 deletion 3027 0
line1 insertion 45222 0
mobile element deletion 1279 0
mobile element insertion 9305 1
novel sequence insertion 12718 0
sequence alteration 14186 908
sva deletion 1116 0
sva insertion 21963 0
tandem duplication 3639 0
Total 5509353 11149

Data Access

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

Methods

Generating the Presumed Normal Track consists of the following:

References