Analysis of a single tile using plotQTile and cycleplot. Here we see three distinct views of tile 47 from Figure 1b. Similar to Figure 1, Figures 2a–2c were generated using the function plotQTile. Figure 2a uses the color-by category option to display the position of the reads color-coded according to their Eland category. In Figure 2b, the gray intensity values are generated by taking the mean across the first 32 cycles and then normalizing. Figure 2c is similar to 2b, but uses the minimum value across those 32 cycles instead of the mean. Figure 2c shows that some bubbles are visible from a QAG-score perspective, but the contrast between 2b and 2c shows that one must be careful to choose the proper aggregating function. Figure 2d was generated using the cycleplot function. It displays the mean QAG-score for cycles 1–32 on tile 47, and showcases the ability to detect the source of an error by decomposing the data according to cycle. Here we see the drop in average intensity that occurred during cycle 28.