I ran MUMMER4's show-diff function to identify translocations between two genomes. The feature type SEQ is supposed to correspond to a gap between alignments to two different chromosomes, representing a translocation. What's odd is that I have found several instances of SEQ features with negative lengths, such as this one:
scaffold_8 SEQ 851807 851663 -143 scaffold_9 scaffold_22
Even more concerning, most SEQ coordinates seem to overlap with actual alignments. See the corresponding region in the out.mcoords file, which shows that the 851807-851663 "gap" listed above actually overlaps with an alignment:
844366 851806 631634 624353 7441 7282 86.67 1497812 1483417 0.50 0.49 scaffold_8 scaffold_9
On the manual there is some discussion of how to interpret negative gap-diff, but I found no such discussion of negative SEQ length. I was wondering whether there is any 'official' word on how negative SEQ length should be interpreted? Is it just an error?
Thank you!
