A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv436370



Internal ID8347838
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Outerchr3:189644124..189653177hg38UCSC Ensembl
Outerchr3:189361913..189370966hg19UCSC Ensembl
Outerchr3:190844607..190853660hg18UCSC Ensembl
Cytoband3q28
Allele length
AssemblyAllele length
hg389054
hg199054
hg189054
Variant TypeCNV deletion
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv466050
SamplesNA18505
Known GenesTP63
MethodSequencing
AnalysisThe best placements of paired-ends were used for identifying several different categories of SV: (i) deletions (size sd=3 kb) were identified from two or more overlapping discordant paired-ends with paired-end span >cutoff (with the condition that both putative breakpoints are spanned); (ii) simple insertions (3 kb > ssi > 2 kb) were identified from two or more overlapping discordant paired-ends with paired-end span < cutoff; (iii) mated insertions were identified from two unpaired SVs that lie in nearby (i.e. 6 kb) genomic regions and had =2 paired-ends linking to a common, distant genomic region <100 kb; mated insertions may involve tandem duplications or events related to transpositions. (iv) Inversions were called when =2 paired-ends matched different strands. (v) Unmated insertions were predicted from =2 paired ends that support a rearrangement of a genomic region in which loci change relative order without changing the relative orientation (i.e., the strand). (These events are similar to mated insertions; however, unmated insertions have only one assigned breakpoint.) In each case we required at least two paired-ends to support a predicted SV. Furthermore, at least one paired-end had to match the human reference genome at sequence identity =97%. In addition, ends were required to yield best-scoring sequence alignments genome-wide to their respective region as assessed by Blat.
Platform454
Comments
ReferenceKorbel_et_al_2007
Pubmed ID17901297
Accession Number(s)nsv436370
Frequency
Sample Size2
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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