#Gene_ID	Gene_name	No of mutations needed	Codon_pos	Ref_nuc	Ref_codon	Res_codon	Resistance	PMID
penA	penA	1	501	GCG	A	V,T,P	Cephalosporins	24982323,24982323,27432602
penA	penA	1	542	GGC	G	S	Cephalosporins, note: only statistically associated with enhanced resistance	20511367
penA	penA	1	551	CCG	P	S,L	Cephalosporins, note: only statistically associated with enhanced resistance	20511367,20511367
penA	penA	1 	346	---	ins	D	Cephalosporins, note: mutation often denoted 'D345a' or 'D345 insertion'	24982323
penA	mosaic penA	1	311	GCA	A	V	Cephalosporins, note: this mutation indicates mosaic penA gene	24982323
penA	mosaic penA	1	312	ATC	I	M	Cephalosporins, note: this mutation indicates mosaic penA gene	24982323
penA	mosaic penA	1	316	GTG	V	T	Cephalosporins, note: this mutation indicates mosaic penA gene	24982323
penA	mosaic penA	1	483	ACC	T	S	Cephalosporins, note: this mutation indicates mosaic penA gene	24982323
penA	mosaic penA	1	512	AAC	N	Y	Cephalosporins, note: this mutation indicates mosaic penA gene	24982323
penA	mosaic penA	1	545	GGC	G	S	Cephalosporins, note: this mutation indicates mosaic penA gene	24982323
penA	mosaic penA	1	546	GGC	G	S	Cephalosporins, note: this mutation indicates mosaic penA gene	24982323
mtrR	mtrR	1	45	GGC	G	D	Penicillins, Tetracyclines, Cephalosporins, and Macrolides	7773394
pilQ	pilQ	1	666	GAA	E	K	Penicillins, Tetracyclines, and ciprofloxacin, only effective in the presents of the mtrR and penB (porB mutation) resistance determinants	24982323
rpsJ	rpsJ	1	57	GTG	V	M,L,Q	Tetracyclines	16189114,16189114,16189114
rpsE	rpsE	1	27	GTT	V	del	Spectinomycin	23183436
rpsE	rpsE	1	28	AAA	K	E	Spectinomycin, Mutation seen together with V27 deletion 	23183436
rpsE	rpsE	1	24	ACC	T	P	Spectinomycin, low-level resistance	23183436
gyrA	gyrA	1	91	TCC	S	F	Quinolones, Mutation ofthen seen together with D95N/G mutation (PMID: 23347339) 	12529019
gyrA	gyrA	1	95	GAC	D	N,G	Quinolones, Mutation seen together with D95N/G mutation 	12529019,12529019
parC	parC	1	91	GAG	E	G,Q,K	Quinolones, high-level resistance when additional to gyrA S91P and gyrA D95N/G mutation	24982323,24982323,24982323
parC	parC	1	88	TCC	S	P	Quinolones, high-level resistance when additional to gyrA S91P and gyrA D95N/G mutation	24982323
porB	porB	1	120	GGC	G	D	Penicillins, Tetracyclines, and Cephalosporins when additional to porB A121D mutation, alone only partial resistance 	12183233
porB	porB	1	121	GCC	A	D	Penicillins, Tetracyclines, and Cephalosporins when additional to porB G120D mutation, alone only partial resistance 	12183233
porB	porB	1	120	GGC	G	R	Penicillins, Tetracyclines, and Cephalosporins when additional to porB A121H mutation	12183233
porB	porB	1	121	GCC	A	H	Penicillins, Tetracyclines, and Cephalosporins when additional to porB G120R mutation 	12183233
porB	porB	1	120	GGC	G	P	Penicillins, Tetracyclines, and Cephalosporins when additional to porB A121P mutation	12183233
porB	porB	1	121	GCC	A	P	Penicillins, Tetracyclines, and Cephalosporins when additional to porB G120P mutation 	12183233
porB	porB	1	120	GGC	G	K	Penicillins, Tetracyclines, and Cephalosporins	12183233
ponA	ponA	1	421	CTG	L	P	Penicillins, mutation mediates transformation of intermediate-level penicillin-resistant transformants to high-level penicillin resistance	11850260
16S_rRNA	16S_rRNA	1	1192	C	C	T	Spectinomycin	24982323
23S_rRNA	23S_rRNA	1	2604	C	C	T	Macrolides, note: C2611T mutation (Escherichia coli numbering)	12183262
23S_rRNA	23S_rRNA	1	2603	C	C	T	Macrolides, note: C2611T mutation (Escherichia coli numbering)	12183262
23S_rRNA	23S_rRNA	1	2603	C	C	T	Macrolides, note: C2611T mutation (Escherichia coli numbering)	12183262
23S_rRNA	23S_rRNA	1	2610	C	C	T	Macrolides, note: C2611T mutation (Escherichia coli numbering)	12183262
23S_rRNA	23S_rRNA	1	2051	A	A	G	Macrolides	12183262,20585125
23S_rRNA	23S_rRNA	1	2050	A	A	G	Macrolides	12183262,20585125
23S_rRNA	23S_rRNA	1	2050	A	A	G	Macrolides	12183262,20585125
23S_rRNA	23S_rRNA	1	2054	A	A	G	Macrolides	12183262,20585125
mtrC_promoter_size_174bp	mtr120 promoter	1	-120	C	C	T	Penicillins,Tetracyclines,Cephalosporins,Macrolides,Rifampin,Erythromycin, note: -10 hexamer (TATAAC->TATAAT) is created as an alternative transcription start point	21933917
macAB_promoter_size_225bp	macAB promoter	1	-48	G	G	T	Macrolides	16162665
#Indels
#Gene_ID	Gene_name	No of mutations needed	Codon_pos	Ref_nuc	Ref_codon	Res_codon	Resistance	PMID
penA	penA	1	1038	-	ins	D	Cephalosporins, note: mutation often denoted 'D345a' or 'D345 insertion (Not sure about position!)	24982323
mtrR_promoter_size_66bp	mtrR promoter	1	-57	-	del	A	Penicillins,Tetracyclines,Cephalosporins,Macrolides, note: deletion in 13bp inverted repeat	24982323
