Table 2.

Accuracy comparison with PacBio simulated reads.

MAPQ_T	minimap2		minimap2-fpga
			Intel FPGA-based system		Xilinx FPGA-based system
	No. reads with MAPQ > $=$ MAPQ_T	No. wrong mappings	No. reads with MAPQ > $=$ MAPQ_T	No. wrong mappings	No. reads with MAPQ > $=$MAPQ_T	No. wrong mappings
With base-level alignment
60	1167692	0	1167691	0	1167691	0
1	1499	70	1500	70	1500	70
0	961	549	961	549	961	549
Unmapped	64		64		64
Without base-level alignment
60	1164914	0	1166460	0	1166460	0
1	1549	1
0	3738	795	3741	793	3741	792

Differences are highlighted in bold.