The Wells Tab

3.5	The Wells Tab

3.5.1 Wells Tab Features and Functionalities

3.5.2 Well Flowgrams (for Wells Generating Library Reads)

3.5.3 Well Tri-Flowgrams (for Wells Generating Control DNA Reads)

3.5.4 Location Flowgrams

3.5.5 Subtraction Raw Flowgrams

The Wells tab (Figure 23) displays information about the wells identified during data processing; this information is overlaid on the raw images if they are available. The main display features include the following:

•	Well indicators, shown as colored circles (where the color scheme can indicate a number of read type and quality attributes described below) overlaid on the image of the PTP Device for each base flow

•	Access to the fully processed well flowgrams generated by the data processing software

Additionally, well density statistics are displayed for each region of the PTP Device and for the whole PTP Device, below the image area.

Figure 23: The GS Run Browser application’s Wells tab

For the Well data to be displayed, the region.cwf file(s) [or, for data sets processed with software v. 1.1.03 or earlier, the region.wells file(s)], located in the “regions” sub-folder of the “D_” data processing folder of the sequencing Run, must exist. If no region.cwf (or region.wells) files exist for the Run, the Wells tab will only display the images and the Flows selector, if available.

For the images to be displayed, there must be a rawImages directory (containing at least one .png or legacy .pif file) for the sequencing Run being viewed. The information on which reagent was flowed at each step comes from the imageLog.parse file.

Data sets from past sequencing Runs may or may not contain the images, since images may be removed or archived to save storage space. All the tabs in the GS Run Browser will still be available even if the images are not present.