I am doing amplicon sequencing, so i'm only probing particular regions of the human genome 150bp at a time. I would like to know and display where my variants are coming from within my amplicons.

So for instance if my first amplicon spans chr1:100-200 is there a good way to plot this region out and display where each variant in my vcf files are located along this 100bp segment?

I have seen lollipop plots in the past that essentially do this but I'm not sure how to implement this in R.