Fig. 4

X-Mapper exhibits higher alignment accuracy with a lower suboptimal alignment rate (percentage of reads reported with suboptimal alignments) than other aligners, when applied to a a bacterial metagenome and b a human transcriptome. Optimal alignments were identified as those with the lowest penalty (highest alignment scores) reported by all aligners. Each sample was tested using four different penalty settings, including the default settings of (1) Bowtie2, (2) BWA (referring to BWA MEM in this study), (3) X-Mapper, and (4) Minimap2 (x-axis). Reads where local aligners, such as Minimap2, reported soft clips in the middle of the contigs were removed from downstream analysis (“alignments without middle soft clips”)