Fig. 3
Detection of potential RDs for sublineage classification in Lineage 4 Mtb isolates. In the detection of potential RDs for a certain sublineage, isolates belong to this sublineage constitute the experiment group while other isolates constitute the control group. For each sublineage, the p-values reflecting the difference in the read depth between the experiment group and the control groups were calculated for each position and translated into –log10 (p-value) to be plotted on the y-axis of the plot, where the x-axis is grouped by the studied sublineage and the values indicate the genomic positions along the reference genome. Extremely low p-values are indicative of significant difference in read depth between the two groups. Regions with consecutive positions having –log10 (p-value) larger than 60 were regarded as candidate RD markers. Those sublineages with well-defined RD makers are shaded gray in the background