Table 4.

Read mapping quality comparisons

Dataset	Tool	Average depth of Cov. (×)	Breadth of coverage (%)	Aligned reads (#)	Properly paired (%)
CHM13	BLEND	16.58	99.991	3 171 916	NA
(HiFi)	minimap2	16.58	99.991	3 172 261	NA
	LRA	16.37	99.064	3 137 631	NA
	Winnowmap2	16.58	99.990	3 171 313	NA
HG002	BLEND	51.25	92.245	11 424 762	NA
(HiFi)	minimap2	53.08	92.242	12 407 589	NA
	LRA	52.48	92.275	13 015 195	NA
	Winnowmap2	53.81	92.248	12 547 868	NA
D. ananassae	BLEND	57.37	99.662	1 223 388	NA
(HiFi)	minimap2	57.57	99.665	1 245 931	NA
	LRA	57.06	99.599	1 235 098	NA
	Winnowmap2	57.40	99.663	1 249 575	NA
E. coli	BLEND	99.14	99.897	39 048	NA
(HiFi)	minimap2	99.14	99.897	39 065	NA
	LRA	99.10	99.897	39 063	NA
	Winnowmap2	99.14	99.897	39 036	NA
CHM13	BLEND	29.34	99.999	10 322 767	NA
(ONT)	minimap2	29.33	99.999	10 310 182	NA
	LRA	28.84	99.948	9 999 432	NA
	Winnowmap2	28.98	99.936	9 958 402	NA
Yeast	BLEND	195.87	99.980	270 064	NA
(PacBio)	minimap2	195.86	99.980	269 935	NA
	LRA	194.65	99.967	267 399	NA
	Winnowmap2	192.35	99.977	259 073	NA
Yeast	BLEND	97.88	99.964	134 919	NA
(ONT)	minimap2	97.88	99.964	134 885	NA
	LRA	97.25	99.952	132 862	NA
	Winnowmap2	97.04	99.963	130 978	NA
Yeast	BLEND	79.92	99.975	6 493 730	95.88
(Illumina)	minimap2	79.91	99.974	6 492 994	95.89
	Strobealign	79.92	99.970	6 498 380	97.59
E. coli	BLEND	97.51	100	83 924	NA
(PacBio)	minimap2	97.29	100	85 326	NA
	LRA	93.61	100	80 802	NA
	Winnowmap2	89.78	100	69 884	NA

Best results are highlighted with bold text.

Properly paired rate is only available for paired-end Illumina reads.