Hi,

I am using Freebayes for some variant calling analysis, ultimately to detect drug resistance mutations. I have scoured the internet and perhaps I am not phrasing things in the correct way to get an answer but there is one thing I still don't understand about the output.

If I have the following output as an example:

• Position 4 - ref = A - alt = G
• Position 6 - ref = G - alt = C

And lets say that the WT codon covering these regions (4-6) is ATG.

Can I assume that the variant at position 4 will have WT for some bases each side and the variant at position 6 will have WT at each side? In other words, can I assume I have a mix of GTG, ATC (and possibly WT depending on frequencies) but NOT GTC?

From my BAM I can see for some examples this is the case but I want an absolute guarantee that I won't misinterpret these results if I assume at least 2 nucleotides upstream and downstream from a single nucleotide variant are WT.

I am also confused as to why sometimes by variants are displayed as longer sequences and sometimes they are split into single nucleotides like the example above if anyone knows why this is as well.

I hope this makes sense and thank you in advance to anyone who responds!