[chr10:123543388-123543603][DEL][SVLEN=215bp]

[jzook]

chr10 123543388 Minda_14 N <DEL> . PASS SVLEN=215;SVTYPE=DEL;SUPP_VEC=PB_ID_17547_2,PB_d_43,ONT_d_19,ILL_MantaDEL:175085:0:0:1:0:0,PB_severus_DEL879,ONT_severus_DEL937,ILL_2186766853:2,ILL_gridss180fb_991h,PB_Sniffles2.DEL.3AFM9,ONT_Sniffles2.DEL.3C2M9

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr10:123543388#ribbon

[Maryamjehangir77]

• A true deletion, likely located within a region of LOH, as indicated by the 120x coverage detected via SplitThreader.
• The left-side breakpoint is consistently observed at chr10:123,543,389 in HiFi and ONT reads, while in Illumina reads, it appears at chr10:123,543,390. The right-side breakpoint is correctly identified.
• The region contains L1 repeats, suggesting a possible transposition event.

left-side breakpoint

Right-side breakpoint

clonal

The deletion seems to be clonal, present in approximately 70-80% of reads, though absent in others.