How to judge some unassigned evidence in my experiment

[Gia1120]

I'm a PhD student studying long-term evolution, and I'm using breseq for genetic sequencing. I have read your literature and tried to analyze false negative results and structural variation using unassigned evidence. However, due to my poor knowledge reserve, I roughly changed the output.gd file and manually added the mutation types I judged by myself, but the results of re-analysis produced different unassigned evidence. I would like to ask you to help me judge whether my manual analysis was correct and where the problem occurred. I know it takes a lot of time. But I am now stuck with this problem for a long time, very much like asking you to help me!
Secondly, I have another problem that has been plaguing me for a long time. Do I have to change the mutation type in the output.gd file again and again according to the unassigned evidence until there are no mutations in the output result that we analyze? Or do we just analyze the structural variation that we want?
The last question is that most of my mutation types are point mutations, such as SNP,DEL, and rarely MOB, etc. I saw that output.gd in the attachment of your literature has mutation types such as MOB, did you add these manually after judging that there was no recognized evidence? I read your article on structural variation, but I was also wondering, can breseq identify the mutation types of structural variation? Or do we mostly have to go with the evidence.
Thank you very much for reading my letter and answering questions for me as a beginner! Wish you all the best in life.

I look forward to hearing from you!
Sincerely,
Gia
A19aE1_1007.zip