. 2020 Apr 21;6:100040. doi: 10.1016/j.tcsw.2020.100040

Table 3.

Whole genome sequencing results of M. bovis BCG spontaneous resistant mutants raised against HTB-03 and HTB-04. High frequency single nucleotide polymorphisms resulting in changes in the amino acid sequence are reported. Genomic positions of the SNP are relative to M. bovis BCG strain Pasteur 1173P2. The base changes (deletions, insertions or substitutions) are capitalized. The amino acid changes are documented, where *¹, *², *³ and *⁴ represent the generation of a stop codon, amino acid deletions, insertion of a base leading to an amino acid change and a subsequent frameshift, and amino acid insertions. Spontaneous resistant mutants are numbered and the MIC at which they were generated is shown. Dots represent areas where sequence coverage was not sufficient for analysis. Blank spaces indicate the absence of a base change relative to the reference strain.

Gene	Genome position of SNP	Codon change	Amino acid changes	Frequency of SNP	HTB-03 Mutants					HTB-04 Mutants
					50 × MIC		100 × MIC			20 × MIC
					1	2	1	2	3	1	2	3
BCG_0220	244,283	taT/taG	Y99*¹	98.86				G
	244,393	GTGGCGGCACAGgac/gac	VAAQD137D*²	97.09	GTGGCGGCACAG		GTGGCGGCACAG			GTGGCGGCACAG		GTGGCGGCACAG
	244,500	Tct/Cct	S172P	100							C
BCG_0404c	475,202	Gcc/Acc	A143T	100	A	A	A		A	A		A
Non-coding region	1,344,671	C/G	–	100	G	G	G	G	G	G	G	G
	1,344,672	G/C	–	100	C	C	C	C	C	C	C	C
PE_PGRS28	1,661,298	Gcc/Acc	A651T	100	.	A	.	.	.	A	.	.
	1,661,300	gTc/gGc	V650G	100	.	G	.	.	.	G	.	.
	1,661,303	aTc/aAc	I649N	100	.	A	.	.	.	A	.	.
	1,661,304	Atc/Gtc	I649V	100	.	G	.	.	.	G	.	.
	1,661,306	aTc/aGc	I648S	100	.	G	.	.	.	G	.	.
	1,661,307	Atc/Gtc	I648V	100	.	G	.	.	.	G	.	.
	1,661,309	gAc/gGc	D647G	100	.	G	.	.	.	G	.	.
pks12	2,282,655	Ggt/Agt	G2662S	100
	2,282,656	tgG/tgA	W2661*¹	100
proB	2,702,724	Gcc/Tcc	A232S	100							T
fadD28	3,237,397	ttt/ttAt	F25L*³	100	TA	TA	TA		TA	TA		TA
BCG_3499c	3,833,488	gcc/gcGGCc	A433AA*⁴	100	GGC	GGC	GGC	GGC	GGC	GGC	GGC
cut3	3,854,969	ggc/gGTCgc	G261GR*⁴	100	GTC	GTC	GTC	GTC	GTC	GTC		GTC
PE_PGRS53	3,907,860	Aac/Gac	N599D	100	G	G	G	G	G	G	G	G
PE_PGRS57	3,927,720	Acc/Gcc	T598A	100	G	.	.	.	.	G	.	.
BCG_3742	4,098,093	gaC/gaA	D188E	100	A	A	A		A	A		A
glpK	4,111,717	ttG/ttC	L385F	100	C	C	C		C	C		C