While building snpEff database for Mitochondrial DNA using Revised Cambridge Reference Sequence genbank(NC_012920.1) file the tool was unable to read protein sequence data and was displaying following error message.
Protein check: NC_012920.1 OK: 0 Not found: 0 Errors: 13 Error percentage: 100.0%
Using the verbose mode I observed the error was caused by the mismatch between SnpEff predicted protein sequence and the Reference protein sequence in genbank file. Has anyone faced a similar issue? Also looking for other alternatives for annotating( to genes & amino acid changes) mitochondrial variants.