Fig. 3

Evaluation of large deletions detected by GenoMycAnalyzer and DELLY. A Venn diagram of the large deletions detected by GenoMycAnalyzer and DELLY. Large deletions confirmed as true positive by manual inspection are displayed in gray. B-D Examples of large deletions detected in gid (B), pncA (C), katG (D), and ethA (E). In each example, the top (1), middle (2), and bottom (3) panels represent large deletions detected by GenoMycAnalyzer only, both tools, and DELLY only, respectively. The x-axis represents genomic position, and the y-axis represents sequencing depth. The black arrows indicate the breakpoint of a large deletion. GenoMycAnalyzer detects large deletions at the gene level. Accession numbers for the B-1 to E-3 are SRR958195, ERR718365, SRR6824567, SRR6824340, SRR6824578, ERR040134, SRR6824287, ERR040137, ERR867540, SRR924218, ERR038737, and SRR6824300, respectively