Flow Cell Chart
The Flow Cell Chart displays color-coded quality metrics per tile for the entire flow cell, and has the following features:
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You can select the displayed metric, cycle, and base through the dropdown lists. |
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The color bar to the right of the chart indicates the values that the colors represent. |
The chart is displayed with tailored scaling by default, or can be fixed by checking the Fix Scale checkbox.
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Tiles that have not been measured or are not monitored are gray. |
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By right-clicking an image you can copy it to the clipboard. |
You can monitor the following quality metrics with this chart:
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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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% Base—The percentage of clusters for which the selected base has been called. |
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%Q>20, %Q>30—The percentage of bases with a quality score of 20 or 30 or higher, respectively. These charts are generated after the 25th cycle, and the values represent the current cycle. A check box appears that lets you toggle between cumulative (include previous cycles) or not (just display current cycle). |
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Median Q-Score—The median Q-Score over all basesfor the current cycle. These charts are generated after the 25th cycle. |
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Density—The density of clusters for each tile (in thousands per mm2). |
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Density PF—The density of clusters passing filter for each tile (in thousands per mm2). |
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Clusters—The number of clusters for each tile (in millions). |
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Clusters PF—The number of clusters passing filter for each tile (in millions). |
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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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% Phasing, % Prephasing—The percentage of molecules in a cluster for which sequencing falls behind (phasing) or jumps ahead (prephasing) the current cycle within a read. |
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% Aligned—The percentage of the sample that aligned to the PhiX genome. |
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% Perfect Reads—The percentage of reads that align perfectly, 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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Corrected Intensity—The intensity corrected for cross-talk between the color channels and phasing and prephasing. |
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Called Intensity—The intensity for the called base. |
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Signal to Noise—The signal to noise ratio is calculated as mean called intensity divided by standard deviation of non called intensities.
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