Fig. 3

DU1 duplication detection in BCG strains. Tiling array data (a) from Leung et al. 2008 [15] and Illumina sequencing data (b) for BCG Danish 1331 (this study) as well as published genome data from Pan et al. 2011 [16,17,18,19], Abdallah et al. 2015 [12] and Festjens et al. 2019 [20] were reanalyzed for the presence of a DU1 in the region of the oriC. These references were chosen as they contain BCG Danish or BCG Pasteur genome sequencing data. The graphs in (a) depict the ratio of the reference (M. tb H37Rv) probe intensity (Cy5) divided by the test (BCG strain) probe intensity as originally presented in Leung et al. 2008 [14]. The graphs in (b) depict the ratio of mean whole genome read coverage divided by the mean read coverage in 500 bp window size. Detection of a DU1-like duplication in BCG Pasteur 1173P2 [15], Birkhaug [12, 15], Danish 1331 07/270 (this study) [21] and BCG China [15, 16] sequencing data, indicated in grey. No detection of DU1-duplication for other BCG Pasteur [12, 20], Danish [12, 17] and China [12] sequencing data