On the interpretation of visualized *.fastg file about getorganelle HOT 1 CLOSED

Hi @Jiny000

All those three results are perfect. You can take a look at the get_org.log.txt file. It must have told you successful and complete.
It's very common that there are mitochondria segments attached, which basically dues to the similarity between mitogenome and plastome or the horizontal transfer. Similar case could be found here.
If you take a look at the flowchart of GetOrganelle here, you would understand that GetOrganelle would automatically clean the assembly_graph.fastg, and pick the plastome graph and store it as a gfa file. In your three results, the final resulting -- fasta and gfa files should be identical, too. You can load gfa file with Bandage, you will see.
It's also fine to manually remove those contigs in Bandage and export the circular path. But this is not suggested because many users make mistakes in exporting the final result.

Let me know if you have further questions!
Good luck with your study!
J

from getorganelle.