[chrX:125899652-125899715][INS][SVLEN=63bp]

jzook / testHG008curation

This repository is primarily for the Genome in a Bottle Consortium to curate structural variants in HG008

https://www.nist.gov/programs-projects/cancer-genome-bottle

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[chrX:125899652-125899715][INS][SVLEN=63bp] #301

Open jzook opened 1 month ago

jzook commented 1 month ago

chrX 125899652 Minda_155 N <INS> . PASS SVLEN=63;SVTYPE=INS;SUPP_VEC=ONT_severus_INS22084,ONT_Sniffles2.INS.313M16,ONT_i_414,ONT_ID_50518_1,PB_severus_INS19445,PB_Sniffles2.INS.2F0M16,PB_i_950,PB_ID_51051_1

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chrX:125899652#ribbon

jo-mc commented 1 month ago

Sequence: ATTTTTTTTTTTTTTTTTTTTTTTTTATTCTTCTTTGTTTTATTTTTCTTTTTTTTTTTTTTTTTT with varying T counts, after A at start and at end. Deletion of 4bp at insertions site TAAG.

Unknown.

Looks clonal. (see igv and snps to right align to read without insertion) Coverage ~160? maybe just lower than 200 here. chromosome pairs about even coverage.

Possible subclonal deletion of 121 bp (5 reads) at 124213876. (~2500 bp to right)

IGV: