StrainFinder Gene Content Differences

[cliffbueno]

Hello, I had a question about gene content differences between the reference genome and the identified strain. StrainFinder identifies strains based on read mapping to a reference genome. It generates complete genomes for each strain. I ran some tests to compare the strain output and the reference genome. I noticed that the strain genome contains some genes that are missing in the reference genome. What would be the mechanism, bioinformatically speaking, for this result? Is it due to the mapping parameters being loose enough to enable that big of a difference between the strain and the reference genome? Thanks, Cliff