Fig. 3

Analysis of the read alignment results of BWA-MEM (without clipped alignments) and Nexus (\(K=4\)) for mapping 100 000 Illumina reads of length 101 bp as well as their reverse complement to the pan-genome graph of 10 human genomes. Left: upset plot that shows the average number of occurrences per read reported by both tools, or exclusively by one tool. Middle: distribution of the reported number of occurrences (on logarithmic scale) in function of the corresponding edit distance. We distinguish occurrences reported by both tools (plotted in function of the edit distance reported by Nexus), and those reported uniquely by only one of the tools. Right: scatter plot visualizing the common occurrences where the edit distance reported by Nexus does not match that of BWA-MEM. In total, 2 258 such occurrences are observed, 9 of which are reported at an edit distance of 23 and 3 by BWA-MEM and Nexus, respectively (not shown in the scatter plot). Additional file 1: Table S2 lists the same information