[chr7:68922689-68930586][BND][JoinedTo=chr7:68930585]]

[jzook]

chr7 68922689 Minda_135 N N]chr7:68930585] . PASS SVLEN=7896;SVTYPE=BND;SUPP_VEC=PB_severus_INV6737,PB_r_320_1,ONT_severus_INV7748,ONT_r_211_1,ILL_gridss130ff_2083h,ILL_MantaBND:131944:0:1:0:0:0:0,PB_ID_26961_2

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr7:68922689#ribbon

[mikolmogorov]

• Appears to be a subclonal cluster with multiple rearrangements. Hard to tell exact structure in part because there are very few reads that have the variant, and only a few UL ONT reads.
• Minda is likely missing one breakpoint, which have the similar coordinates to one of the culstered breakpoint, but the opposite direction (as a balanced translocation).
• Looks like there are two deleted segments of 3-5kb length as a part of the rearrangement. But otherwise seems balanced wrt to chromosome structure. Looks a bit like INVDEL, but seems more complex.
• It could be that there are 2 overlapping events on different clones/haplotypes, need to carefully thread UL reads to understand.
• On chromosome scale, seems to be a part of LOH region and close to pericentromere. Thus CNA calls may be uncertain.

[jzook]

Also looks subclonal in LOH region in UL-ONT and HiFi data. Only one UL read traverses the region, which supports a del followed by a small inverted region followed by a larger inverted region. Also interesting that this haplotype has many small variants relative to GRCh38, but no evidence of SV in germline. I think there's probably only one subclonal event and HiFi just has different alignments of it, but hard to tell for sure without more UL data