Inconsistant transfer

[gdroc]

Hi,

I want to compare 4 genomes, and I use liftoff to transfer annotations from one genome to another. In the vast majority of cases, it works very fine, but in the example in attachment, I have the impression that it does not keep the expected gene.
In the JBrowse, the track "C. micrantha" matches the original annotations, and we found CITMI_009t013070 (expected to be on chromosome 9).
In the track "C. micrantha remove CITMI_009t013070", I simply deleted this gene from the original GFF3, and I find the expected gene CITMI_001t000040, which also seems to have a much better coverage than CITMI_009t013070. When I look at the output of minimap2, I find the same alignments.
I tried to play with several liftoff parameters without success (-polish, -s)
Do you have any idea where this could be coming from?
Regards
Gaetan