Hello, I find the function to map Sanger sequencing reads to reference really great. The only problem I have is how to edit apparent insertions of an additional base caused by one read with low quality. I know I can use the edit function to remove the additional base from the low quality read, then do the same for the introduced '-' in reads showing the correct sequence. However, this procedure will also shift the consensus vs. reference by one base. Afterwards, scanning for additional ambiguous positions using the 'Jump to next variation' button will no longer work as most bases now will differ between consensus and reference.

I guess there is a more clever way to do this?

Thank you,
Lennart

I'm not sure that I get what you want. You can replace low-quality bases with gaps, for example, and consensus won't be shifted. Of what result do you want to have?

Thank you for your reply. What I was looking for was the 'Remove all columns of gaps' function. Now it works  :).