Flow Cell Chart

Flow Cell Chart

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You can select the surface, read, and cycle 1 or the current cycle (C1 and CN) through the buttons above the graph, where appropriate.

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The color bar to the right of the chart indicates the values that the colors represent. The color bar is also a slider: you can adjust the scale values by right-clicking; change the contrast using the mouse-wheel.

You can monitor the following quality metrics with this chart:

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Cluster Density—The number of clusters for each tile (k/mm2).

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Cluster Density PF—The number of clusters passing filter for each tile (k/mm2). These charts are generated after the 25th cycle.

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Intensity—This chart displays the intensity by color and cycle of the 90% percentile of the data for each tile.

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% Resynthesis—The intensity of cycle 1 in the subsequent read relative to the intensity of cycle 1 in read 1.

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% Int at C 20—The corresponding intensity at cycle 20 as a percentage of that at the first cycle.

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Error Rate—The calculated error rate, as determined by a spiked in PhiX control sample. If no PhiX control sample is run in the lane, this chart is not available.

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%Q>30—The percentage of bases with a quality score of 30 or higher, respectively. This chart is generated after the 25th cycle, and the values represent the current cycle.