Additionally, an intronic 289 base pair homozygous AluY deletion (scaffold_20:26715781-26716070, overlapping with ACE gene) (Additional file 2: Fig. S12C), a 538 base pair homozygous deletion (scaffold_37:2324216-2324754, overlapping with GNG7 gene) (Additional file 2: Fig. S12D), and a 1672 base pair homozygous deletion (scaffold_8:42055418-42057090, overlapping with JAG2 gene) (Additional file 2: Fig. S12E) were detected in the tumor cell line when using HCC1395BL_v1.0 reference, but not when using GRCh38. Here, ACE is linked to neoplasm.