For your downstream analyses you probably want to know how many exons (targets) are above a certain coverage threshold. In other words, you want to plot the fraction of targets >= X and then iterate X from 1x, 2x, ..., 50x coverage. In addition, you want to look at the on-target rate, i.e., how efficient your enrichment worked. Among other tools, our method Alfred is generating these metrics.

alfred qc -r genom.fa -j out.json.gz -o out.tsv.gz -b exome.targets.bed input.bam

You can view an example here, just select the exome data set from the reference data set collection.