I have a follow-up question regarding my ONT data set, after my first question here. I have used minimap2 to map my sample against the reference genome and converted the results sam into bam file. I have than ran pycoQC with the addition of the bam files to check the alignments. I have attached below a few of the additional images added with the bam file QC run.

When I look at the pie chart I get only 0.14% unmapped reads, which would have been great, but when I look at the plot below, which shows the bases alignment rate, it shows ~70% reads unmapped. How do these two results fit together?

thanks