Table 1: Summary of differential breakpoints in the merged callset.

Variants in unique regions (No TR/SD) have the fewest breakpoint offsets, which grows as SVs in more complex loci are included. TR: Tandem Repeat, SD: Segmental Duplication, N: Number of variants, Diff: Variants with different offsets in at least one haplotype, Med: Median breakpoint offset.

	Insertions				Deletions
	N	Diff	Diff %	Med bp	N	Diff	Diff %	Med bp
No TR/SD	14,961	882	5.9%	2.2	5,804	180	3.1%	4.9
SD No TR	2,609	440	16.9%	3.5	1,922	402	20.9%	5.0
All	60,716	19,589	32.3%	19.4	38,442	10,641	27.7%	22.0