Flow Cell Chart
The Flow Cell Chart shows color-coded quality metrics per tile for the entire flow cell.
Use the Flow Cell Chart to judge local differences per cycle, per lane, or per read in sequencing metrics on a flow cell. It is also an easy way to see the %≥Q30 metric, which is an excellent single metric to evaluate a run. Do not use the Flow Cell Chart to look at downstream analysis metrics.
The Flow Cell chart has the following features:
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You can select the displayed metric, surface (if your system scans multiple surfaces), cycle, and channel (base) using the drop-down lists. |
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The color bar to the right of the chart indicates the values that the colors represent. |
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The chart is displayed with tailored scaling by default, or you can fix the Y-axis scale by selecting the Fix Scale checkbox. |
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Some metrics (% ≥Q20 and % ≥Q30) are monitored for a single cycle by default, or you can monitor the cumulative metrics (up to that cycle) by selecting the Accum checkbox. |
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Tiles that have not been measured or are not monitored are gray. |
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You can focus on an area of interest by dragging to pan the view or using the mouse wheel to zoom in. |
The following table details the possible metrics displayed in this chart. The available options vary by run.
Flow Cell Chart Options
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Intensity
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This chart shows the intensity by color and cycle of the 90% percentile of the data for each tile.
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FWHM
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The average full width of clusters at half maximum (in pixels). Used to display focus quality.
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% Base
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The percentage of clusters for which the selected base (A, C, T, or G) has been called.
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% NoCall
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The percentage of clusters that have no call.
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% ≥Q20 and% ≥Q30
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The percentage of bases with a quality score of > 20 or > 30, respectively. These charts are generated after the 25th cycle, and the values represent the current scored cycle.
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Median Q-Score
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The median Q-score for each tile over all bases for the current cycle. These charts are generated after cycle 25. Use this setting to examine the Q-scores of your run as it progresses. Because it relies on a single threshold, the %≥Q30 plot can be oversimplified.
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Density
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The density of clusters for each tile (in thousands per mm2).
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Density PF
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The density of clusters passing filter for each tile (in thousands per mm2).
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Clusters
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The number of clusters for each tile (in millions).
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Clusters PF
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The number of clusters passing filter for each tile (in millions).
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Error Rate
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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
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The estimated 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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Legacy Phasing Rate, Legacy Prephasing Rate
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The estimated percentage of molecules in a cluster for which sequencing falls behind (phasing) or jumps ahead (prephasing) the current cycle within a read.
Legacy rates consider only the first 25 cycles.
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% Aligned
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The percentage of reads from clusters in each tile that aligned to the PhiX genome.
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Occupied Count (K)
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The total number of wells (in thousands) on the flow cell containing clusters with DNA usable for sequencing. Wells with at least nine G bases called in the first 10 cycles are considered empty. Low occupancy rate combined with low %PF may indicate the loading concentration is too low. High occupancy rate combined with suboptimal %PF may indicate the loading concentration is too high.
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% Occupied
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The percentage of wells (for patterned flow cells) or nonduplicated spots (for nonpatterned flow cells) on the flow cell containing clusters. Wells with at least nine G bases called in the first 10 cycles are considered empty.
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Corrected Intensity
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The intensity corrected for cross talk between the color channels by the matrix estimation and phasing and prephasing.
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Called Intensity
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The intensity for the called base.
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Signal to Noise
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The signal to noise ratio is calculated as mean called intensity divided by standard deviation of noncalled intensities.
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Note the variable scales used on these different parameters.