Table 1. The top genes or intergenic regions ranked by their most significant oligopeptides per drug, up to a maximum of 20 (more only when the 20th was tied).

Genes are highlighted in bold if they were catalogued for that drug by [11,17]. Gene names separated by colons indicate intergenic regions. Genes or intergenic regions capturing repeat regions are highlighted with the superscript ^R. Alphabetic characters following gene names are used to cross-reference with the corresponding Manhattan plots in Fig 3.

Drug	Top significant genes and intergenic regions
First-line
Ethambutol	embB, rpoB (A), katG (B), embA, pncA (C), gyrA (D), rpsL (E), Rv1565c (F), Rv2478c:Rv2481c (G), Rv1752 (H), Rv3183:Rv3188 R (I), dxs2:Rv3382c R (J), rpsA/coaE (K), ctpI (L), guaA (M), moaC3:Rv3327 R (N), lprF:Rv1371 R (O), fabG1 (P), spoU (Q), glpK (R)
Isoniazid	katG, proA:ahpC, fabG1, rpoB (A), inhA, embB (B), Rv1139c:Rv1140 (C), Rv1158c (D), rpsL (E), Rv1219c (F), ftsK/Rv2749 (G), gid (H)
Rifampicin	rpoB, katG (A), embB (B), Rv1565c (C), guaA (D), ctpI (E), spoU (F), dxs2:Rv3382c R (G), Rv3183:Rv3188 R (H), relA (I), proA:ahpC (J), fabG1 (K), moaC3:Rv3327 R (L), Rv0810c (M), fadD9 (N), Rv3779 (O), rpsL (P), rpoC (Q), Rv2190c:Rv2191 (R)
Second-line
Amikacin	rrs, gyrA (A), rpoB (B), echA8 (C), Rv2896c (D), Rv0078A (E), Rv1830 (F), Rv0792c/Rv0793 (G), PPE54 (H), Rv2041c (I), PPE42 (J), cyp141:Rv3122 (K), Rv1765cR (L), lprF:Rv1371R (M), espA:ephA (N), narU (O), rne (P), Rv1393c (Q), Rv1362c (R), Rv0579 (S), glnE (T), ethA (U), Rv0208c:Rv0209 (V)
Ethionamide	fabG1, ethA (A), rpoB (B), gyrA (C), inhA (D), whiB7 (E), PPE3 (F), mpt53 (G), embB (H), eccA1 (I), embA (J), Rv0565c (K), fadB4 (L), plsC (M), Rv0920c (N), Rv3698 (O), rrs (P), pncA (Q), PPE56 (R), Rv2019 (S), lprF:Rv1371 R (T)
Kanamycin	rrs, eis, gyrA (A), rpoB (B), ethA (C), fabG1 (D), Rv1830 (E), ptbB (F), PPE42 (G), echA8 (H), lprF:Rv1371 R (I), Rv2348c:plcC (J), narU (K), pgi (L), mmaA4 (M), pncA (N), viuB (O), lprC (P), murA (Q), Rv1393c (R), Rv0579 (S), glnE (T), rne (U), Rv1362c (V), Rv0208c:Rv0209 (W)
Levofloxacin	gyrA, rrs (A), gyrB, embB (B), rpoB (C), vapC36 (D), mce2F (E), fabG1 (F), katG (G), folC (H), tlyA (I), ethA (J), Rv0228 (K)
Moxifloxacin	gyrA, rrs (A), rpoB (B), gyrB (C), embB (D), katG (E)
Rifabutin	rpoB, embB (A), katG (B), rpoC (C), Rv0810c (D), Rv2478c:Rv2481c R (E), Rv2647:Rv2650c R (F), rplP (G), Rv2797c (H), cpsY (I), lysA (J), mprB (K), mprA (L), Rv3228 (M), Rv1290c (N), pncA (O), Rv2277c:pitB R (P), Rv0726c (Q), cysA3/cysA2 (R), Rv0914c (S)
New and repurposed
Bedaquiline	Rv0678, rpoB (A), rrs (B), atpE (C), pgi (D), mmaA4 (E), rplC (F), Rv0078A (G), era/amiA2 (H), viuB (I), pncA (J), murA (K), Rv0792c/Rv0793 (L), dnaB (M), Rv2665:clpC2 (N), PPE54 (O), Rv0332 (P), Rv2019 (Q), vapC22 (R), Rv2896c (S)
Clofazimine	Rv0678, fabG1 (A), cyp142 (B), Rv3183:Rv3188 R (C), moaC3:Rv3327 R (D), dxs2:Rv3382c R (E), mmsA (F), Rv3723:Rv3725 (G), gid (H), rpoB (I), pks1 (J), mmaA2:mmaA1 (K), Rv3273 (L), mce3R/yrbE3A (M), Rv3796 (N), mez (O), Rv2390c (P), yrbE3B (Q), Rv0207c (R), argS (S)
Delamanid	ddn, fadE22 (A), fba (B), Rv2180c (C), gap (D), lprF:Rv1371 R (E), Rv0914c (F), Rv1200 (G), fadE10 (H), dinP (I), mmpL8 (J), cut1 R (K), PPE39 R (L), Rv3430a:gadB (M), Rv1429 (N), Rv3847 (O), pknH (P), plsC (Q), agpS (R), Rv3263 (S)
Linezolid	rplC, rpoB (A), emrB (B), Rv3552 (C), add (D), vapC33 (E), ppgK (F), pncB1:Rv1331 (G), lprA (H), pafA (I), PE_PGRS6 (J), vapB20 (K), Rv0061c (L), PE_PGRS4 (M), Rv1049 (N), lprF:Rv1371 R (O), Rv3183:Rv3188 R (P), dxs2:Rv3382c R (Q), Rv0556 (R), Rv0514 (S)