I have two PCR amplicons that have been multiplexed and sequenced using the nanopore minion.

I have aligned the fastq reads using minimap2 with a reference file containing both amplicon sequences and generated a bam file that I have viewed using IGV.

I am looking for a way to generate some simple summary statistics.

In particular, is there a way to extract the total number of fastq reads aligning to each amplicon reference from the bam file?