A curated catalogue of human genomic structural variation




Variant Details

Variant: essv31108



Internal ID9601639
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr11:16039594..16039675hg38UCSC Ensembl
Outerchr11:16039531..16039737hg38UCSC Ensembl
Innerchr11:16061140..16061221hg19UCSC Ensembl
Outerchr11:16061077..16061283hg19UCSC Ensembl
Innerchr11:16017716..16017797hg18UCSC Ensembl
Outerchr11:16017653..16017859hg18UCSC Ensembl
Cytoband11p15.2
Allele length
AssemblyAllele length
hg38207
hg19207
hg18207
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv8667
Supporting Variants
Samples
Known GenesSOX6
MethodSequencing
AnalysisWe detected SVs based on span size and orientation information of each paired-end read. Paired-end reads with an anomalously long span size (more than double the average span size of each DNA library) were identified as SV candidates (deletion and inversion), especially when they had a minimum of three reads in the region, maximum 100 read depth and mapping quality (Q20). SV candidates either found in repeat regions of the genome or having more than 100 kb of genomic deletions were filtered out. For insertion detection larger than the short indels (-29 to +14 bp), the longest 300-bp span size of our paired-end libraries was used. Thus, we could fill 175-bp to 250-bp insert gaps between short inserts and large inserts. The criteria used for detecting these insertions absent from the reference genome in the range of 175-250 bp were minimum four read depth, maximum 60 read depth to filter out randomly placed hits in a repetitive structure region, and mapping quality (Q20).
PlatformIllumina Genome Analyzer
Comments
ReferenceAhn_et_al_2009
Pubmed ID19470904
Accession Number(s)essv31108
Frequency
Sample Size1
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


Hosted by The Centre for Applied Genomics
Grant support for DGV
Please read the usage disclaimer