Roary will filter out some locus tags when calculating the pan genome. I was lazy and was counting on the locus tags to only be removed when filtering out the core genome. This can cause a string of consecutive locus tags to look like they are interrupted by a missing locus tag or two, when those locus tags never existed in the pan-genome in the first place.
Roary will filter out some locus tags when calculating the pan genome. I was lazy and was counting on the locus tags to only be removed when filtering out the core genome. This can cause a string of consecutive locus tags to look like they are interrupted by a missing locus tag or two, when those locus tags never existed in the pan-genome in the first place.