I have 113 human mitogenomes, which I need to get on GenBank before I can submit a manuscript for publication.

There is one set of 23 and one set of 90. I am currently working on the set of 23 with Sequin.

I was wondering, how much annotation do I actually have to do? My adviser and labmates know nothing and next-to-nothing about uploading mitogenomes to GenBank. I have the 23 aligned to rCRS in Geneious Basic, so I can convert the rCRS annotation base numbers (http://www.phylotree.org/resources/rCRS_annotated.htm) to my alignment base numbers. I am using a GenBank record (https://www.ncbi.nlm.nih.gov/nuccore/HM185251) from a previous publication from our lab as a template of everything to annotate.

I totally understand the need to annotate the base pairs for different RNAs and genes and CDSs, but do I need to annotate every miscellaneous feature of every protein? What will happen, if I do not annotate these miscellaneous features?

-Deven