Table 1.

Performance of MSRs, HPC, and raw mappings across different mappers and reference sequences

mapq		Whole human genome				Whole human genome				Whole Drosophila genome
		minimap2				winnowmap2				minimap2
		Fraction		error		fraction		error		fraction		error
HPC	60	0.935	+0%	1.85e-03	+0%	0.894	+0%	1.43e-03	+0%	0.957	+0%	2.27e-03	+0%
raw	60	0.921	−1%	1.86e-03	+0%	0.932	+4%	1.75e-03	+23%	0.958	+0%	2.27e-03	−0%
MSRF	50	0.938	+0%	1.29e-03	−30%	0.886	−1%	3.82e-04	−73%	0.960	+0%	1.37e-03	−39%
MSRE	50	0.936	+0%	1.17e-04	−94%	0.820	−8%	8.93e-05	−94%	0.954	−0%	0	−100%
MSRP	50	0.938	+0%	4.15e-04	−78%	0.845	−6%	1.14e-04	−92%	0.957	+0%	8.11e-04	−64%

For each reference sequence and mapper pair, we report the fraction of reads mapped (“fraction” columns) and the mapping error rate (“error” columns) reported by paftools mapeval. The percentage differences are computed w.r.t the respective HPC value. The second column indicates that for HPC and raw these metrics were obtained for alignments of mapping quality of 60; for MSRs E, F, and P, these metrics were obtained for alignments of mapping quality $\ge 50$. See also Table S1.