[chr16:89166442-89166520][DEL][SVLEN=78bp]

[jzook]

chr16 89166442 Minda_51 N <DEL> . PASS SVLEN=78;SVTYPE=DEL;SUPP_VEC=PB_ID_29443_2,ONT_ID_63605_2,PB_severus_DEL2591,PB_Sniffles2.DEL.2CEMF,ONT_Sniffles2.DEL.2D0MF,ONT_severus_DEL2900,PB_d_154

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr16:89166442#ribbon

[aganezov]

Too small of a variant to see in SplitThreader on coverage levels.

Visible in ribbon:

Variant location is in the repeat region, making mapping challenging even for long reads. Across consistently mapped deletion signatures the chr16:89,166,442 appears indeed the most consistent.

Most likely del length is indeed 78bp, and mapping inconsistencies within technologies and across them can be explained by the repetitive nature of the underlying genomic context.

From the fraction of affected reads with deletion signature in both PB and ONT data, as well as partial read phasing, it appears that the deletion is clonal (i.e., affecting all reads coming from a single haplotype).