Fig. 4

Comparison of the missed regions among the sequenced genomes. A circular map of the regions (Red color) missed when mapping the raw reads of the sequenced strains against the H37Rv genome (NC_000962.3). Inside track within the map displays a plot of G + C contents. In outer strain circles, from the inside out, include the following missed regions in those isolates of A1, A2, A3, A4, A5, B1, B2, B3, C1, C2, C3, C4, C5, D1, D3, D4, and D5. The circular map was constructed using Circos, which is a software package for visualizing data and information (http://circos.ca/). Genes in the main missed regions were showed (Table 3), not including those belonging to PE or PPE family that contain large, near perfect repeats that create a high likelihood of sequencing and assembly error