I annotated a bunch of genomes with snpeff. And although the original reads' qualities and the matches with the reference genomes were quite high, I see the above mentioned warning in almost every variant in my vcf file. Thus, I wonder how this could happen. Since I'm using bacterial genomes with a manually built database (from these reference genomes) and there are quite some genes (especially in gene clusters) that have the alternative start codon GTG, I suspect this causing the warning. Any idea how to test if this is really the reason for the warning?
Thanks a lot in advance!