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Figure 1 | Genome Biology

Figure 1

From: Improved base calling for the Illumina Genome Analyzer using machine learning strategies

Figure 1

Intensity values for one tile of a 51-cycle PhiX 174 RF1 run before and after correction by Bustard. On this tile 115,288 clusters were identified by the image analysis software Firecrest. Shown are the 95th percentile for the signal intensities in each channel and cycle. The raw intensities are shown with dashed lines, the intensities after transformation by Bustard are shown with solid lines. Intensities for A, C, and G decline over the run while the intensities for T stay nearly constant. Both effects can be explained by degradation of the fluorophores or non-reversible termination of sequences over the run as well as the accumulation of T fluorophores on the synthesized strand. Intensities for the first cycle are lower than in other cycles due to dimming and bleaching caused by longer handling times before imaging of the first cycle. Corrected intensities for the last and first cycle do not follow the normal trend, since full phasing correction cannot be applied.

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