A curated catalogue of human genomic structural variation

Variant Details

Variant: essv31517

Internal ID9602048
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr6:29864747..29909006hg38UCSC Ensembl
Outerchr6:29864662..29909161hg38UCSC Ensembl
Innerchr6:29832524..29876783hg19UCSC Ensembl
Outerchr6:29832439..29876938hg19UCSC Ensembl
Innerchr6:29940503..29984762hg18UCSC Ensembl
Outerchr6:29940418..29984917hg18UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv9076
Supporting Variants
Known GenesHLA-H
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
Pubmed ID19470904
Accession Number(s)essv31517
Sample Size1
Observed Gain0
Observed Loss1
Observed Complex0

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