Extensive annotation of the selection of reconstructed CRISPRs using our pipeline (SRA, dataset #3, see Fig 2).

Legend IS6110 sheet. Column A: lineage assignation according to Coll et al., column B: Lineage and Sublineage according to Palittapongarnpim et al. for L1, Shitikov et al. for L2, Stücki et al. for L4; column C: spoligotyping-based alias name, column D: SIT nomenclature, column E: selection set, column F: Accession number, column G: common Strain name, column H: location, column I: spoligotype (old), column J to end: the first line designates the name of the gene or the spacer ID; the second title line designates the spacer ID according to the classical spoligotyping nomenclature (also visible by yellow shade). Vertical bars stand for IS6110 copies within DR, in green for copies in orientation 1 (antisense) and red for orientation 2 (sense). Color boxes are for insertions within a gene or a spacer, with the same color for the orientation than above. The number in the box indicates the position (nucleotide) where the insertion occurred in the coding sequence. Finally, a large colored tube with white squares depicts a very likely recombination event between two insertion sequences that led to the deletion of all sequences between them (thus, only one IS6110 remains). “esp” sheet: column E-AD: spacers with at least one variant in the sample set. The SRA are shown in lines in the same orders as others sheets. Crosses show samples with a variant in the corresponding spacers. When several variants were found, they are numbered. “DR” sheet: columns F to AE list the variant DRs and their bordering spacers. A black square indicates a variant, a white square corresponds to the wt version, a dot corresponds to a deletion. “Dupl” sheet: DVRs duplicating in some samples are shown in the order in which they occurred, black squares indicating actual presence of the DVR at this position, white square indicate the absence of the DVR. Red blocks identify the duplicated DVR blocks.
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