Query regarding contigs order by Mauve contig mover

[neha]

Hello Everyone,

I have around 300 contigs from a newly sequenced bacterial strain and MCM does four iteration. In fourth iteration it produces a .tab file which contains all information about the reverse contigs, ordered Contigs and Contigs with conflicting order. In my output file , I see that all 300 Contigs are being ordered, out of these 300 only some are also in the reverse category and some are also in Contigs with conflicting information. How to decide what is the best order of the contig? Can we confidently rely on this ordering process?

Thanks in advance,
Neha