A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv3398249



Internal ID19829226
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr4:166755887..166761921hg38UCSC Ensembl
chr4:167677038..167683072hg19UCSC Ensembl
Cytoband4q32.3
Allele length
AssemblyAllele length
hg386035
hg196035
Variant TypeCNV line1 deletion
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv14775257, nssv14781120, nssv14789941, nssv14782681, nssv14788140, nssv14786427, nssv14788899, nssv14784255, nssv14789912, nssv14781967, nssv14790447, nssv14774707
SamplesHG02106, HG04217, CHM1, NA12878, HG02818, HX1, HG02059, HG01352, NA19434, NA19240, HG00733, HG00514
Known GenesSPOCK3
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 L1 insertion that is present in the reference
ReferenceAudano_et_al_2019
Pubmed ID30661756
Accession Number(s)nsv3398249
Frequency
Sample Size14
Observed Gain0
Observed Loss12
Observed Complex0
Frequencyn/a


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