A curated catalogue of human genomic structural variation




Variant Details

Variant: essv28455



Internal ID9598985
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr6:29890290..29945298hg38UCSC Ensembl
Outerchr6:29890252..29945375hg38UCSC Ensembl
Innerchr6:29858067..29913075hg19UCSC Ensembl
Outerchr6:29858029..29913152hg19UCSC Ensembl
Innerchr6:29966046..30021054hg18UCSC Ensembl
Outerchr6:29966008..30021131hg18UCSC Ensembl
Cytoband6p21.33
Allele length
AssemblyAllele length
hg3855124
hg1955124
hg1855124
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv6014
Supporting Variants
Samples
Known GenesHCG4B, HLA-A, HLA-H
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)essv28455
Frequency
Sample Size1
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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