Orientation of the OH flipped in nearly identical samples

Hello,

I have two samples of the same species that have nearly identical assemblies. However, MITOS v2.1.9 flips the orientation of the OH features. See the alignment screenshot below.

Any idea what might be causing this?

I have attached assembly FASTAs and MITOS GFFs for the two samples shown in the screenshot. Happy to provide more info if needed.

Thanks for your help, Dan

403042_S291.fa 403042_S291.gff 403040_S295.fa 403040_S295.gff