Table 2.

SVs called from HCC1395 and HCC1395BL cell lines. The somatic SV and germline SV raw calls are the number of SVs counted after Survivor software tool merge of all replicate call sets for each platform. The total merged somatic SV raw calls contain the merged tumor-only calls from tumor-normal paired subtraction analysis. The total merged germline SV calls contain the merged germline SV calls from all replicates from HCC1398BL cell line

NGS Technologies	Initial SVs call set		High-confidence SVs call set
	HCC1395 (tumor cell line)	HCC1395BL (normal cell line)	HCC1395 (tumor cell line)
	Somatic SVs (raw calls)	Germline SVs (raw calls)	Deletions	Duplications	Insertions	Inversions	Translocations	BNDs
Illumina WGS	9155	105,732	375	226	4	82	143	10
10x GenomicsWGS	16,886	37,059	42	86	N/A	78	119	5
PacBio WGS	9574	27,069	643	138	549	94	99	10
HiC WGS	137	1	8	6	N/A	9	5	1
Oxford NanoporeWGS	21,245	63,061	664	180	549	65	96	4
Total Merged SVs	46,284	168,401	717	230	551	133	146	11