A curated catalogue of human genomic structural variation




Variant Details

Variant: esv5974



Internal ID9603242
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr10:52224501..52274177hg38UCSC Ensembl
Outerchr10:52224289..52274256hg38UCSC Ensembl
Innerchr10:53984261..54033937hg19UCSC Ensembl
Outerchr10:53984049..54034016hg19UCSC Ensembl
Innerchr10:53654267..53703943hg18UCSC Ensembl
Outerchr10:53654055..53704022hg18UCSC Ensembl
Cytoband10q21.1
Allele length
AssemblyAllele length
hg3849968
hg1949968
hg1849968
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsessv28415
Samples
Known GenesPRKG1
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)esv5974
Frequency
Sample Size1
Observed Gain0
Observed Loss0
Observed Complex0
Frequencyn/a


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