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

From: Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens)

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 7739b Single reads 86x ND ND ND ND SB0155 Germany (zoo) [5]
M. pinnipedii 7011b 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 Unknownc Australia [20]
  1. 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]