A curated catalogue of human genomic structural variation




Variant Details

Variant: esv5554



Internal ID9602771
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr9:132199790..132199876hg38UCSC Ensembl
Outerchr9:132199734..132199926hg38UCSC Ensembl
Innerchr9:135075177..135075263hg19UCSC Ensembl
Outerchr9:135075121..135075313hg19UCSC Ensembl
Innerchr9:134064998..134065084hg18UCSC Ensembl
Outerchr9:134064942..134065134hg18UCSC Ensembl
Cytoband9q34.13
Allele length
AssemblyAllele length
hg38193
hg19193
hg18193
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsessv27995
Samples
Known GenesNTNG2
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)esv5554
Frequency
Sample Size1
Observed Gain0
Observed Loss0
Observed Complex0
Frequencyn/a


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