I've been working with a bacterial genome assembly. The initial stats look pretty good (3 main pieces, depth ~50x [20x - 100x] if I calculated it right). I'd expect this to be a virtually complete genome apart from some low-complexity regions.
However, when I use CheckM to estimate completeness / redundancy, I get ~99% completion, <2% redundancy. (out of 579 expected single-copy marker genes, 563 were present once, and 11 were present twice). I am especially concerned about the missing genes.
I can think of several possibilities: a) Limits of CheckM. This software uses a sample of 82 genomes to select marker genes for this phylum: however, there are no available genomes in the same genus as the one I'm working with. It might be possible that this is natural variation.
b) The "single-copy" genes present twice might be due to misassembly. But while the sample was not axenic, the organism of interest was majoritary, and long reads were used as well, so this shouldn't be an issue?
c) The genes were somehow missed by sequencing. (but the depth is pretty good?)
I don't know how likely a) is, so it's difficult for me to assess whether what I have is a normal result, or something that requires additional sequencing in order to make sense. I would appreciate your thoughts!