Definetly you are right (thanks for the figure)!!!!! Let me add more info to the discussion. The two genomes have been assembled from the same input pacbio dataset (RSII). The only difference is that one was assembled 3 years ago and the other yesterday with Flye.
WOuld there be any explanation why the genome have been rotated. The first one was generated by another person but i don´t have the info. I was thinking they rotated the genome according to the ori but i cannot understand it is reverse complemented compared to my assembly. Do you see any particular reason ???
Thanks Alex, these are complete genomes.
A quick blast shows that the longer fragment matches plus/minus to the reference. And the small fragment also blast in plus/minus compared to the reference. However i would expect a single fragment and not two. This suggests that the small fragment is also reversed and at the wrong place compared to the reference?
Not sure ?