snippy-multi: Core genome length very small for clusters of closely-related intraspecies isolates

[tkiryuti]

Hello! I ran snippy-multi on a dataset of about 20 bacterial isolates (*.fasta assemblies) within the same genus (Enterobacter spp.). The core genome length (from core.aln) was around 273,000 base pairs. Based on a tree from this aligned fasta file, I detected two clusters (very closely-related). I re-ran snippy-multi on each of the two clusters (5-6 isolates each). The core genome length (core.aln) were only around 100-200 base pairs for each. However, because they are closely-related, I would expect them to be longer than 273,000. The 100-200 bp core alignment length seems very small and I'm wondering why the tool would not be working as expected. Thank you.