different result with mito annotation

[tanpham15]

Dear Marcela Uliano-Silva,

After running mitohifi (in both v3.2 and 3.2.1), I used final mitogenome with mitos (on https://usegalaxy.eu/) to get annotation in bed.

Here is the list parameter I used in:

• mitohifi: genetic code (-o) 5
• mitos (usegalaxy) genetic code 5, Reference data: Refseq39+MiTFi tRNA model
• mitos2 (usegalaxy) genetic code 5, Reference data: Refseq63 Metazoa/ Reference data: Refseq89 Metazoa

Finally, comparation with mitos I saw a slightly different between results of mitohifi and mitos:

1, Mitohifi is better when found all 37 genes, in mitos2 (with both refseq63 and refseq89), they missed "trnH" - translational exceptions: cox1,-1,3375,4910 (CGA, None), with mitos (refseq39) they also found all 37 genes
2, In mitohifi (png), it indicate "tRNA-Ser2", but in all three results with mitos, they found "trnS1(act)".

Could you please let me know how can I get a report for gene length (in bed file)? and can mitohifi make a circle for final mitogenome annotation?

Thank you very much in advance!

Best regards