[chr9:21952492-21972343][DEL][SVLEN=19851bp]

[jzook]

chr9 21952492 Minda_145 N <DEL> . PASS SVLEN=19851;SVTYPE=DEL;SUPP_VEC=PB_ID_33516_2,PB_d_449,ONT_ID_52188_2,ONT_d_213,ILL_MantaDEL:154624:0:1:0:0:0,PB_severus_DEL7417,ONT_severus_DEL8539,PB_Sniffles2.DEL.73M8,ONT_Sniffles2.DEL.78M8,ILL_497701932:2,ILL_gridss156fb_360h

https://v2.genomeribbon.com/?session=https://42basepairs.com/download/s3/giab-data/ribbon-json/ribbon-hg008-cov-bedpe.json&locus=chr9:21952492#ribbon

[chunlinxiao]

It appears this DEL is true, as clearly supported by HiFi and ONT read evidence, located in the region with 100x read coverage (in fact chr9 just one copy from verkko). Basedd on IGV HiFi winnowmap alignments, correct Left breakpoint should be chr9:21952498 (6 bps down from the prediction). However, ONT_UL in-read deletion supports the predicted Left breakpoint. The predicted right breakpoint chr9:21972343 was correct. So overall, the prediction was correct! There seems a true DUP (chr9:22631432-22939870) downstream.

[chunlinxiao]

Ribbon image1

[chunlinxiao]

Ribbon image2

[chunlinxiao]

IGV image for Left breakpoint and Right breakpoint (above)

Now adding ONT in-reads DEL evidence here:

[jzook]

Likely exact breakpoint witih sequence homology. Also a biologically interesting del that removes part of the remaining copy of CDKN2A (p16) gene

[jzook]