Charts Tab

The Flow Cell chart shows color-coded quality metrics per tile for the entire flow cell and has the following features:

•

Select the displayed metric, surface (if your system scans multiple surfaces), cycle, and channel using the drop-down lists.

•

The color bar slider at the bottom of the chart indicates the values that each color represents.

–

Move the slider to adjust the scale values and change color contrast.

–

The chart is displayed with auto scaling by default or can be fixed by selecting the Fix Scale checkbox. To reset the slider values, right-click and then select Reset zoom. To enter specific scale values, right-click and then select Manual scale.

–

For some metrics (% Q ≥ 20 and % Q ≥ 30), you can monitor the metrics for a single cycle by default. Alternatively, you can monitor the metrics for the entire run (up to that cycle) by selecting the (accumulated) metric option.

•

Tiles that have not been measured or are not monitored appear gray.

•

Hover over the tile to view the lane and tile number.

•

Select a tile to view more detailed information for that tile on the Imaging tab. Refer to Imaging Tab for more information.

•

Right-click the chart to copy it to the clipboard.

•

Switch to full-screen view by selecting the icon in the upper-right corner of the chart.

The Data by Cycle chart allows you to follow the progress of quality metrics during a run. The chart has the following features:

•

Select the displayed metric, lane, surface, and channel using the drop-down lists.

•

Hover over a data point to view the exact value according to the cycle number.

•

The chart is displayed with auto-scaling by default or can be fixed by selecting the Fix Scale checkbox.

–

For some metrics (% Q ≥ 20 and % Q ≥ 30), you can monitor the metrics for a single cycle by default.

–

Alternatively, you can monitor the metrics for the entire run (up to that cycle) by selecting the (accumulated) metric option.

•

To zoom in on a data point, hover over the data point, and then use the mouse wheel. To zoom in on a specific axis, hover over the axis, and then use the mouse wheel. To reset, right-click and then select Reset zoom. To enter specific zoom values, right-click and then select Manual scale.

•

Right-click the chart to copy it to the clipboard.

•

Switch to full-screen view by selecting the icon in the upper-right corner of the chart.

The Data by Lane pane shows quality metrics per lane. The chart has the following features:

•

Select the displayed metric, surface, and read (when applicable) using the drop-down lists.

•

Zoom in and out using the mouse wheel. To reset, right-click and then select Reset zoom. To enter specific zoom values, right-click and then select Manual scale.

•

Right-click the chart to copy it to the clipboard.

•

Switch to full-screen view by selecting the icon in the upper-right corner of the chart.

•

For some metrics (Density and Clusters), each lane has two box plots.

–

Blue boxes—Represent the raw cluster metric.

–

Green boxes—Represent the equivalent PF cluster metric.

The plots share various characteristics:

•

The red line indicates the median tile value.

•

The box outlines the interquartile range (the middle 50% of the data) for the tiles analyzed for the data point.

•

The error bars delineate the minimum and maximum without outliers.

•

The outliers are values that exceed 1.5 times the interquartile range below the 25th percentile, or exceed 1.5 times the interquartile range above the 75th percentile. Outliers are indicated as dots.

•

The numbers above the X-axis indicate the number of analyzed tiles used for the data point.

Use the Q-score Distribution chart to view the number of reads by quality score. The quality score is cumulative for current cycle and previous cycles, and only reads that pass the chastity filter are included. On most systems, quality scores are binned in groups.

The Q-score is based on the Phred scale. The following table lists Q-scores and the corresponding estimated base call error rate at that Q-score.

Q-score	Chance of Wrong Base Call
Q10	10%
Q20	1%
Q30	0.1%
Q40	0.01%

The chart has the following features:

•

Select the displayed lane, surface, read, and cycle using the drop-down lists.

•

The Read drop-down list selects the first cycle for calculating the histogram.

•

The Cycle drop-down list determines the last cycle used for calculating the histogram.

•

The cutoff slider determines how many bases have a minimum Q-score or higher. Move the slider to the minimum Q-score. The software calculates how many bases have that Q-score or higher.

•

To zoom in on a specific axis, hover over the axis, and then use the mouse wheel. To reset, right-click and then select Reset zoom. To enter specific zoom values, right-click and then select Manual scale.

•

Right-click the chart to copy it to the clipboard.

•

Switch to full-screen view by selecting the icon in the upper-right corner of the chart.

The Q-score heat map shows the Q-score by cycle. The chart has the following features:

•

Select the displayed lane and surface using the drop-down lists.

•

The quality score values are binned in groups.

•

The color bar at the bottom of the chart indicates the values that each color represents. The charts are displayed with auto scaling. The scale is always 0–100% of maximum value. Right-click to change the color scheme.

•

Right-click the chart to copy it to the clipboard.

•

Switch to full-screen view by selecting the icon in the upper-right corner of the chart.