A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv819010



Internal ID15238293
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
OuterchrX:150417903..150417937hg38UCSC Ensembl
OuterchrX:149586177..149586211hg19UCSC Ensembl
OuterchrX:149336835..149336869hg18UCSC Ensembl
CytobandXq28
Allele length
AssemblyAllele length
hg381856
hg191856
hg181856
Variant TypeCNV insertion
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv1418909
SamplesAK1
Known GenesMAMLD1
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)nsv819010
Frequency
Sample Size2
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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