Table 1 Assembly statistics, genotyping and demographics of modern Mycobacterium pinnipedii strains used in this study

Strains	Assembly statistics						Genotyping	Demographics
	Available data	Coverage	Number of contigs	N50	Contig size (range)	Software	Spoligotypes	Source (species, country)^a	Ref.
M. pinnipedii MP1	Paired-end reads and draft genome	228x	102	61,148	1020-184,975	CLC Genomics Workbench 11	SB0155	Otaria flavescens, Brazil	This study
M. pinnipedii MP2	Paired-end reads and draft genome	220x	106	60,933	1010- 184,294	CLC Genomics Workbench 11	SB2455	Otaria flavescens, Brazil	This study
M. pinnipedii G01222	Paired-end reads	32x	138	38,346	1020-121,089	CLC Genomics Workbench 11	SB0155	Argentina	[5]
M. pinnipedii G01491	Paired-end reads	242x	194	45,251	1135–150,198	SPAdes 3.13.0	SB0155	Australia	[5]
M. pinnipedii G01492	Paired-end reads	484x	128	64,538	1146–193,250	SPAdes 3.13.0	SB0155	Australia	[5]
M. pinnipedii G01498	Paired-end reads	113x	201	42,094	1026-122,203	SPAdes 3.13.0	SB0155	Australia	[5]
M. pinnipedii 7739^b	Single reads	86x	ND	ND	ND	ND	SB0155	Germany (zoo)	[5]
M. pinnipedii 7011^b	Single reads	87x	ND	ND	ND	ND	SB0155	Germany (zoo)	[5]
M. pinnipedii ATCC BAA-688	Draft genome	NA	162	113,505	500–281,603	Velvet 1.2.10	Unknown^c	Australia	[20]

ND: not done. NA: not available. ^awhere animal species are not listed, it is because they were not informed by the authors. ^bReads of M. pinnipedii 7739 and 7011 were not assembled because they were available as single reads. These reads were only used in the phylogenomic analysis. ^cSpoligotype pattern not found in Mbovis.org database (Bincode: 0000001000000000000000010100010001000000000). Sequencing coverage was calculated by the number of bases (after adaptors removal and quality trimming) divided by the average size of an MTBC genome (i.e. 4.3 Mb). Spoligotypes were defined using SpoTyping [40]

ISSN: 1471-2164