text: user4401: NCBI has several labels for assembly completeness - Complete, Scaffold, Chromosome and Contig. Complete would be a circularized genome (or linear, rarely)
  For a Complete genome it's fairly straightforward - if not present, a gene can safely assumed to be missing (or possibly present on plasmids, if those aren't available in the database).
  But what about the others? With Contig-level genomes, I'd feel uncertain about making any statements (especially since some of these projects are split into thousands of contigs). But what about Scaffold, or Chromosome? Are they expected to be complete in terms of genes, but just missing repetitive sequences?
  
  user2108: I would suggest that in the absence of "Complete" no very confident assertion can be made about gene presence/absence in a genome assembly. You need to actually  have the chromosome sequence to make strong statements.
  I think that most people (me included) would reluctantly accept that genomes with very good BUSCO or CheckM numbers (depending on your organism's taxonomy) are probably more or less accurate in terms of presence/absence. For metagenomics, I would extend that to the MIMAG criteria, which are pretty stringent.
  These criteria are of course independent of the NCBI categories, which are pretty coarse-grained.
  That said, I think that you can make stronger arguments about gene presence/absence from the sequencing reads from which the genome assembly is derived. Find all the reads for your genome, map them to the genome assembly and also to the closest related ortholog of the gene in question. How well is the gene covered? How do the alignments look? Harder for metagenomics, but there are still probably tricks one could use.
  
original_text: 4401: <p>NCBI has several labels for assembly completeness - Complete, Scaffold, Chromosome and Contig. Complete would be a circularized genome (or linear, rarely)</p>
  <p>For a Complete genome it's fairly straightforward - if not present, a gene can safely assumed to be missing (or possibly present on plasmids, if those aren't available in the database).</p>
  <p>But what about the others? With Contig-level genomes, I'd feel uncertain about making any statements (especially since some of these projects are split into thousands of contigs). But what about Scaffold, or Chromosome? Are they expected to be complete in terms of genes, but just missing repetitive sequences?</p>
   2108: <p>I would suggest that in the absence of &quot;Complete&quot; no very confident assertion can be made about gene presence/absence in a genome assembly. You need to actually  have the chromosome sequence to make strong statements.</p>
  <p>I think that most people (me included) would reluctantly accept that genomes with very good BUSCO or CheckM numbers (depending on your organism's taxonomy) are probably more or less accurate in terms of presence/absence. For metagenomics, I would extend that to the <a href="https://www.nature.com/articles/nbt.3893" rel="nofollow noreferrer">MIMAG</a> criteria, which are pretty stringent.</p>
  <p>These criteria are of course independent of the NCBI categories, which are pretty coarse-grained.</p>
  <p>That said, I think that you can make stronger arguments about gene presence/absence from the sequencing reads from which the genome assembly is derived. Find all the reads for your genome, map them to the genome assembly and also to the closest related ortholog of the gene in question. How well is the gene covered? How do the alignments look? Harder for metagenomics, but there are still probably tricks one could use.</p>
  