[40 (link), 42 (link)]. For each of the seven main phylogenetic lineages of human-associated MTBC, plus the Mycobacterium bovis/M. caprae lineage, we included three redundant canonical SNPs as markers for the corresponding lineage. Previously published SNPs were complemented with SNPs obtained as described before
[40 (link)] for cases where less than three SNPs per phylogenetic clade were available. The extraction of these additional SNPs was based on 172 genomes described by
[41 (link)]. For Lineage 2, we additionally included known polymorphisms to discriminate the so-called “Beijing” lineage from non-Beijing Lineage 2 strains. An overview of the phylogenetically informative SNPs included in KvarQ is shown in Additional file
[46 (link)], and additionally compensatory mutations from
[47 (link)]. High-confidence mutations for the most important anti-tuberculosis drugs were selected (isoniazid, rifampicin, ethambutol, streptomycin, fluoroquinolones and second-line injectable drugs). Pyrazinamide-resistance conferring mutations were excluded. Mutations in TBDReamDB are listed as codon changes, therefore we generated the corresponding nucleotide changes for inclusion in KvarQ. For rifampicin- and fluoroquinolone-resistance conferring mutations, we included the rifampicin-resistance determining region (RRDR)
[34 (link)] and the quinolone resistance determining region (QRDR)
[48 (link)], respectively, rather than specific positions. The codon 315 of katG was also treated as a region of three base pairs. All included mutations and regions associated with drug resistance mutations are listed in Additional file
[44 (link), 49 (link), 50 (link)].