Hello question about insertions and deletions

[nousiaso]

Hello ! I used your very nice pipeline for my project concerning some plant genomes. Wanted to ask you : I have 5 genomes I run 5 times the pipeline. Every result, for each reference genome there are insertion results and deletion results. The Insertion at the resulting "info" file, has just start coordinates, the deletion has both start and end. I would like to understand, how this works. For instance, I did a strict blast of the insertion sequence to see if I will get unique hits between the reference and the queries ymthat were reported to have it from the results (indeed I verified Thales unique hit). Concerning the deletion now : you give start and end coordinates of the reference for the deletion. For example reference "A" has a deletion sequence D1A , and only one of the queries is reported to have it query "B" (for simplicity). Does this mean that in the aligned region of the "A" and query "B" , "B" has a TE insertion while A does not?

Happy holidays!