With the insert option in make.contigs, if a base is compared to a gap, its score needs to be above or equal to the threshold or it is eliminated.
With the deltaq option, when there is a mismatch between two bases, the difference of there scores must be of at least “deltaq” for a base to be chosen over the other, or a consensus base (N) is put at this position.
Now, if deltaq=6, but the two bases’ scores are respectively 10 and 16, the last one would be chosen… And we would agree that a score of 16 is a poor score. So, it would be interesting to implement a threshold for the mismatches, in addition to what already exists for “base vs gap” - insert option. I think it is also a good thing to specify that this option should not impact the matches, for if two bases with a poor score match, it is more likely that the base at this position is the right one. I think this could eliminate false positives and increase the total quality of the sequence. Thank you for your constant help, it is appreciated.