help finding percentage of insertion present

[tatresi]

I have some paired end reads that were aligned to a reference using an in-house pipeline. There was a big coverage dip in at a certain point on the reference. Looking at the bam alignment in geneious, we could see there was an insertion relative to the reference. After creating a new reference with the insertion included, the coverage looks great.

Now I need to find out what percentage of the reads have this insertion relative to the reference. It sounds like a pretty simple task, but I'm having trouble figuring it out. Any advice?