**3. Materials and Methods**

#### *3.1. Species and Databases*

A total of 4250 mycobacterial species genomes (permanent draft) available at the Joint Genome Institute (JGI)/Integrated Microbial Genomes and Microbes (IMG/M) database (from February 2019 to March 2019) were used in this study [42]. Species were grouped in six different mycobacterial categories, as described elsewhere [22,31]. The six categories included MTBC (2350 species), MCAC (1391 species), MAC (130 species), MCL (7 species), NTM (361 species), and SAP (11 species). Mycobacterial species along with their genome IDs and their mycobacterial categories were presented in Supplementary Dataset 1.
