Fig. 2

Example of joint-call recovery of deletion candidate and effectiveness of progressive filtering procedure. a Example of a deletion (chr7:152419400-152419715; 315 bp deletion) that was identified after applying the joint-call recovery. The deletion region is enclosed by the dashed box, and sequencing reads used by IMSindel to detect the deletion’s breakpoints are highlighted in red. For the first four samples, the deletion was detected by IMSindel using only forward or reverse reads, while both read types were used for the detection in the following two samples, leading to a higher confidence deletion call. b The true-positive rate estimation of detected deletion candidates at each processing step by comparison with deletions detected by Nanopore long-read sequencing. The processing was effective in improving the accuracy of deletion calls, with only a 45.2% consensus rate of the initial detected deletion candidates by IMSindel. Improvement in consensus rate was seen at each processing step, with a final consensus rate of 97.3% seen for the high-confidence deletion candidates