Display fraction of mutations and variants for Amplicon Sequencing sample?

Question

[Saran]

Hello,

I have several Paired-End, Amplicon Sequenced data. The amplicon is 222 base-pairs and 2x250 sequencing was done so there is heavy overlap. I already aligned these sequences to the reference amplicon using BWA and created weblogos to display any regions with mutations.

I would like to do more analysis including:

• Get fraction of mutated alignments versus wildtype
• Display all of the different variants and their fraction within the pool of reads.

I can't find information online to tackle this issue. I would like to make an allele frequency table, listing all of the variant sequences and displaying the mutations. I am not sure if I am using the correct vocabulary and that is why I can't find the solutions that I am searching for.

I created VCF files from the bam files and am trying to investigate what I can do with these.

Any guidance would be appreciated. Thank You, Sara