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:
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:
- blue:
- duplication
- gain
- insertion
- violet:
- light violet:
- light azure:
- brown:
- grey:
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 |
208096 |
1185 |
10KB to 100KB |
557575 |
2297 |
Over 1MB |
40578 |
57 |
Under 10KB |
4730303 |
7520 |
Total |
5536552 |
11059 |
Discovery Method Type
Value |
normal_healthy |
normal_phenotype |
Curated |
42795 |
0 |
Merging |
288817 |
395 |
Multiple |
37855 |
0 |
Oligo aCGH |
67504 |
80 |
Optical mapping |
30497 |
1342 |
SNP array |
371326 |
1759 |
Sequencing |
4697676 |
7482 |
other |
82 |
1 |
Total |
5536552 |
11059 |
Range of Reciprocal Overlap with Pathogenic Variant
Value |
normal_healthy |
normal_phenotype |
10 to 25 |
59702 |
302 |
25 to 50 |
31271 |
145 |
50 to 75 |
17084 |
173 |
75 to 90 |
7787 |
186 |
90 to 100 |
6719 |
150 |
none |
5413989 |
10103 |
Total |
5536552 |
11059 |
Population Code derived from Sample or Sampleset
Value |
normal_healthy |
normal_phenotype |
AFR |
45546 |
1 |
AMR |
31245 |
0 |
EAS |
16329 |
0 |
EUR |
138967 |
67 |
OTH |
3530 |
0 |
SAS |
3771 |
0 |
mixed |
19846 |
0 |
multiple |
443779 |
2 |
none |
4833249 |
10989 |
unknown |
290 |
0 |
Total |
5536552 |
11059 |
Variant Type
Value |
normal_healthy |
normal_phenotype |
alu deletion |
15230 |
0 |
alu insertion |
269869 |
1 |
complex substitution |
19726 |
93 |
copy number gain |
179987 |
856 |
copy number loss |
294925 |
1349 |
copy number variation |
153448 |
0 |
copy-neutral loss of heterozygosity |
26 |
0 |
deletion |
2627293 |
6099 |
delins |
687 |
0 |
duplication |
359303 |
1197 |
herv deletion |
228 |
0 |
herv insertion |
229 |
0 |
insertion |
1393622 |
165 |
inversion |
108450 |
390 |
line1 deletion |
3080 |
0 |
line1 insertion |
46006 |
0 |
mobile element deletion |
1340 |
0 |
mobile element insertion |
9379 |
1 |
novel sequence insertion |
12630 |
0 |
sequence alteration |
14326 |
908 |
sva deletion |
1118 |
0 |
sva insertion |
22028 |
0 |
tandem duplication |
3622 |
0 |
Total |
5536552 |
11059 |
Data Access
Data for this track can be downloaded from the following locations:
- interactively using the UCSC Table Browser
- as BED files from the dbVar Track Hub
Methods
Generating the Presumed Normal Track consists of the following:
References
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