Scatter plot. The panel shows the scatter plots of the A-C and G-T pairs, constructed from the raw data alone. The y axis and the x axis in the left panel represent the C and A channels respectively. Similarly, the y and the x axes in the right panel denotes the T and G channels. The top panel consists of smoothed density plots of A intensities versus C intensities, and G intensities versus T intensities. The four colors in the figures of the bottom panel represent the estimated base calls from the proposed BM-BC method: black- A, red - C-green G, blue-T. The intensity values shown in the figure are normalized by subtracting from the overall minimum intensity and then dividing by the standard deviation.