A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv3352020



Internal ID19782998
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr13:40879697..40879746hg38UCSC Ensembl
chr13:41453833..41453882hg19UCSC Ensembl
Cytoband13q14.11
Allele length
AssemblyAllele length
hg3850
hg1950
Variant TypeCNV herv deletion
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv14716692, nssv14718739, nssv14727235, nssv14722500, nssv14731055, nssv14717290
SamplesHG02106, HG04217, HG00268, NA12878, HG02059, HG00733
Known GenesTPTE2P5
MethodSequencing
AnalysisRead and contig alignments were done with BLASR. The Celera assembler (8.3rc2) was used to assemble RS II samples (CHM1, CHM13, HG00514, HG00733, NA19240, HG02818, NA19434, HG01352, HG02059, NA12878, and HG04217, and Canu (1.7) was used for Sequel samples (HG02106 and HG00268). Variant calling was performed with SMRT-SV (10.1101/gr.214007.116).
PlatformPacBio RS II P6C4, PacBio Sequel v2.1
CommentsAbsence of a HERV insertion that is present in the reference
ReferenceAudano_et_al_2019
Pubmed ID30661756
Accession Number(s)nsv3352020
Frequency
Sample Size14
Observed Gain0
Observed Loss6
Observed Complex0
Frequencyn/a


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