[chr11:95796274-95802108][DEL][SVLEN=5834bp]

[jzook]

chr11 95796274 Minda_20 N <DEL> . PASS SVLEN=5834;SVTYPE=DEL;SUPP_VEC=PB_ID_48786_2,PB_d_63,ONT_ID_38610_2,ONT_d_26,ILL_MantaDEL:184951:0:1:0:0:0,PB_severus_DEL1225,ONT_severus_DEL1326,PB_Sniffles2.DEL.2E5MA,ONT_Sniffles2.DEL.2E9MA,ILL_4054454279:2,ILL_gridss190fb_11787h

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr11:95796274#ribbon

[Faizal-Eeman]

• Deletion alone is observed in the region
• No complex SV or CNA observed near the region

[Faizal-Eeman]

Het SNPs are seen in and around the deletion region in both Normal and Tumor BAMs.

Het SNPs that overlap the deletion region

• Normal BAM - all SNPs are Het
• Tumor BAM - all SNPs overlapping the deletion region are Homozygous. VAF for this Hom SNP is 100% with decreased coverage, while there are reads that support the deletion event at ~50% VAF. Looks like a compound heterozygous event and the presence of Hom SNPs within the deletion region instead of Het SNPs indicates this could be a true deletion event.
• Because we see a combination of reads that support Hom SNPs and a deletion event ONLY, it maybe just a clonal event.