A curated catalogue of human genomic structural variation




Variant Details

Variant: esv7072



Internal ID9604340
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:94773945..94774246hg38UCSC Ensembl
Innerchr10:47088405..47088709hg19UCSC Ensembl
Outerchr10:47088316..47088975hg19UCSC Ensembl
Innerchr10:46508411..46508715hg18UCSC Ensembl
Outerchr10:46508322..46508981hg18UCSC Ensembl
Cytoband10q11.22
Allele length
AssemblyAllele length
hg38302
hg19660
hg18660
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsessv29513
Samples
Known GenesNPY4R
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)esv7072
Frequency
Sample Size1
Observed Gain0
Observed Loss0
Observed Complex0
Frequencyn/a


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