plot the number of variations within a certain window

Question

[Sara]

we have used crispr-cas9 technology which was followed by whole genome sequencing. I have got the SNPs and INDELs frequency and now trying to plot how many variations are within 10 bp of a NGG or NAG sequence in the geome. do you have any suggestion about how the plot should look like? or how to make such plot?

[German.M.Demidov]

I suppose they should look like at Fig1 from here https://www.nature.com/articles/nature14221 (if they are not super-rare, otherwise I question the usefullness of such visualization). I would not analyse indels because for me it is totally unclear how to count their frequencies within your provided sequences. As I answered in another thread, you can count your occurences, create SEG file and visualize in IGV - https://software.broadinstitute.org/software/igv/SEG - otherwise I'd recommend to use R - but! - it is impossible to see anything in a human genome with 10bp resolution, you will just get a total mess (of course if your plot will not be of width of 1 million of pixels)