Novel duplications identified in BCG-Birkhaug and BCG-Tice by NimbleGen tiling array. Sections of the ratio plot are shown. The ratio of the reference (M. tb H37Rv) probe intensity (Cy5) was divided by the test (BCG strain) probe intensity (Cy3). Reference probes and test probes that do not span a mutation should represent full-length perfect match hybridization, and thus should have similar intensities, with a reference/test ratio near 1. If the test genome contains an amplification event (increased copy number when compared to the reference), then the reference/test ratio will shift below 1. (A) Novel duplication (DU-Birkhaug) identified in BCG-Birkhaug, which is analogous to the DU-Pasteur (DU1) but has different borders. The same genomic region of BCG-Sweden, which is closely related to BCG-Birkhaug, is shown for comparison. (B) Novel duplication (DU-Tice) identified in BCG-Tice. Three other BCG strains belonging to the same group (DU2-IV) are shown for comparison. (C) The precise border of DU-Tice is mapped by PCR amplification using primers specific to the junction. The two copies are immediately adjacent to each other and overlap by 1 bp.