Reads Tab Features and Functionalities

3.7.1

The Reads tab contains many features with the functionalities described below (see Figure 37):

•	The Options area (on the top left area of the tab):

◦	Read Attributes: choice of data type to display:

▪	Read length

▪	Base Quality

◦	Well Categories: choice of reads to display (only passed filter reads):

▪	GACT (rapid library) or TCAG (standard library)

▪	CATG and/or ATGC (control) - see Section 7.1 for details

•

Navigation and data capture buttons: All the buttons on this tab have common functions: setting and adjusting the zoom level of the main image display or allowing a user to save the data as a text file or snapshot image. See Section 3.3.4 for a description of the navigation and data capture button functions.

•	Plot display:

◦	Graphic display of the data, as selected in the Options area for a single region or for the whole PTP Device, as selected on the Summary.

◦	Each selection on the options area refreshes the plot (and Summary) with a different set of data, so there are four possible combinations of plot displays to choose from.

◦	For read length, the “count” (y-axis) corresponds to the number of reads at a given length. For read quality, the “count” (y-axis) corresponds to the number of bases at a given quality score (PHRED equivalent; see Section 6.6).

◦	The plot shares the common scrolling and zooming functions of the other GS Run Browser plots. See Section 3.3.3 for a description of the plot functions.

◦	When the mouse pointer is over the plot, the usual mouse tracker shows the x-axis signal value and the number of reads having that attribute value, in the selected region or entire PTP Device.

•

Summary:

◦	This displays a text version of the data shown in the plot (choice of 4 kinds of sets of data), for each of the regions and for the entire PTP Device, plus additional intermediate data.

◦

A blue rectangle identifies the set of data (single region or “Total” column) currently displayed on the plot. When the mouse is moved over the data in another column, the highlight moves to this column; left-clicking the mouse selects the highlighted column (blue rectangle) for display in the plot.