Table 6. Read based support of assembly calls.

Assembly	SV type	total	filtered	supported	fraction
Haplotype 1 lra	DEL	6101	5874	5767	0.982
Haplotype 1 minimap2	DEL	6078	5924	5841	0.986
Haplotype 2 lra	DEL	6287	6061	5963	0.984
Haplotype 2 minimap2	DEL	6267	6107	6033	0.989
Haplotype 1 lra	INS	9736	9354	9275	0.992
Haplotype 1 minimap2	INS	9882	9619	9587	0.997
Haplotype 2 lra	INS	10032	9651	9568	0.991
Haplotype 2 minimap2	INS	10183	9890	9859	0.997

The two haplotype assemblies are considered separately to avoid complications of merging into a diploid callset. Calls are produced by lra and minimap2, with only deletion and insertion SV classes considered. The total calls are the original calls produced by each method, and filtered are calls excluding centromeres and 50kb of flanking sequence. The supported SV have at least four reads supporting the call from either lra or minimap2 alignments.