StrainPhlAn Usage for Bacterial SNP Annotation

Hello everyone,

I have some questions regarding the analysis outputs. Concerning the .fna files located in the output/tmp/clean_dna directory, do these files encompass all the reads mapped to the markers and classified to the species? I am specifically looking for files that contain the reads mapped to the reference genome of the species and exclude reads assigned with the same likelihood to more than one species. Additionally, I am interested in using StrainPhlAn to annotate bacterial SNPs.