Fig. 2

Locus-based GWAS results a Manhattan plot for locus-based GWAS for lineage 2. b Manhattan plot for locus-based GWAS for lineage 4 c Manhattan plot for locus-based GWAS for lineages 2 and 4 combined. P-value threshold <1E-21. Phenotypes with which loci were found to be significantly associated are given in brackets next to locus name. AMK = Amikacin-resistance, AG = Aminoglycoside-resistance, CAP = Capreomycin-resistance, CIP = Ciprofloxacin-resistance, EMB = Ethambutol-resistance, ETH = Ethionamide-resistance, FQ = Fluoroquinolone-resistance, INH = Isoniazid-resistance, KAN = Kanamycin-resistance, MDR = Multidrug-resistant, OFL = Ofloxacin-resistance, PAN = pan-susceptible (no known drug-resistance), PZA = Pyrazinamide-resistance, RMP = Rifampicin-resistance, STM = Streptomycin-resistance, XDR = Extensively drug-resistant