A curated catalogue of human genomic structural variation




Variant Details

Variant: esv9518



Internal ID9606786
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:46085564..46085814hg38UCSC Ensembl
Outerchr2:46085431..46085925hg38UCSC Ensembl
Innerchr2:46312703..46312953hg19UCSC Ensembl
Outerchr2:46312570..46313064hg19UCSC Ensembl
Innerchr2:46166207..46166457hg18UCSC Ensembl
Outerchr2:46166074..46166568hg18UCSC Ensembl
Cytoband2p21
Allele length
AssemblyAllele length
hg38495
hg19495
hg18495
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsessv31959
Samples
Known GenesPRKCE
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)esv9518
Frequency
Sample Size1
Observed Gain0
Observed Loss0
Observed Complex0
Frequencyn/a


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