Table 2.

Details of the regions of difference (RD) of lengths greater than 500 bp in the sequenced strains from Uruguay, as well as deletions found in PE/PPE-coding genes. Each RD is defined by an ID, and all deletions show the number of ORFs that cover, starting and ending coordinates, length, strains presenting these deletions and spoligotypes associated with them. Marked in bold are the RDs with more robust association to a given spoligotype

ID		Genes covered	Start	End	Length	Strains (MbURU-)	Spoligotypes associated
Previously described	RD3	14, Mb 1598-Mb1611c	1,764,652	1,773,872	9221	001, 002, 003, 005, 007, 0010, 012, 014, 016	SB0145, SB0130
	RDbov145a	2, Mb0026-Mb0027	29,475	30,078	604	001, 003, 005, 014, 016, 019, 020	SBO145
	RDbovI 31	5, Mb0677c-Mb0681c	756,105	757,654	1550	010	X
	RDbov145b	1, serA2	824,054	824,599	546	001, 003, 005, 014, 016, 019, 020	SB0145
	RDbov145c	2, Mb0930-Mb0931	1,009,480	1,010,927	1448	001, 003, 005, 014, 016, 019, 020	SB0145
	RDbovI 072	7, Mb1908-Mb1914c	2,116,213	2,122,816	6604	006	SB1072
	RDbovI 32	1, rmlB2	3,832,661	3,833,913	1253	007	X
	RDbov133	2, bisC-Mb1478c	1,616,260	1,619,455	3196	012	X
	RDbov134	1, Mb3756	4,115,825	4,116,744	920	012	X
	RDbov130a	1, Mb3923c	4,310,701	4,311,694	994	002, 007, 010, 012, 017, 018	SB0130
PE/PPE		1, PE_PGRS19	1,189,852	1,190,034	183	001, 003, 005, 014, 016, 019, 020	SB0145
		1, PE_PGRS20	1,192,321	1,192,742	422	001, 003, 005, 014, 016, 019, 020	SB0145
		1, PE_PGRS24	1,486,342	1,486,528	187	001, 003, 005, 014, 016, 019, 020	SB0145
		1, PPE30	2,033,505	2,033,624	120	002, 007, 010, 012, 017, 018	SB0130
		1, PE_PGRS42d	2,762,816	2,762,980	165	004, 008, 009, 011, 013, 015, 021, 022, 023	SB0140, SB0274
		1, PE_PGRS50b	3,691,479	3,691,697	219	004, 006, 008, 009, 011, 013, 015, 021, 022, 023	SB0140, SB0274, SB1072
		1, PE_PGRS50b	3,694,231	3,694,311	81	006	SB1072
		1, PE_PGRS51	3,733,072	3,733,247	176	001, 003, 005, 014, 016, 019, 020	SB1045