A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv819550



Internal ID8551240
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Outerchr19:33458789..33458830hg38UCSC Ensembl
Outerchr19:33949695..33949736hg19UCSC Ensembl
Outerchr19:38641535..38641576hg18UCSC Ensembl
Cytoband19q13.11
Allele length
AssemblyAllele length
hg381058
hg191058
hg181058
Variant TypeCNV insertion
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv1418902
SamplesAK1
Known GenesPEPD
MethodSequencing
AnalysisCNV insertion could be detected in Long Insert sized Paired End (LIPE) data on the basis of compressed pairs which indicated insertion of certain sequence between pair reads. The average insert size of the LIPE library was 2,700 bp and the standard deviation (SD) was about 300 bp. Based on these figures, a compressed pair was defined as one with insert size shorter than 2,000 bp (< mean - 2 SD). Similar to method used to detect deletion, compressed pairs were defined to be clustered if one compressed pair was within 3,300 bp (mean + 2 SD) to neighboring compressed pair. To remove redundant pairs present in LIPE library, two or more pairs with both reads aligned to exactly the same position of reference genome were defined as one pair and named de-redundant. If 10 or more deredundant compressed pairs were found in one cluster, we defined this region as a candidate region for amplification.
PlatformGPL10329
Comments
ReferenceKim_et_al_2009
Pubmed ID19587683
Accession Number(s)nsv819550
Frequency
Sample Size2
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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