Trace Data Window Toolbar

Note: This topic is not applicable to BAM-based projects.

The following tools are available on the left side of the Trace Data window.

Button Name	Icon	Description
Zoom In		Zooms in on the view horizontally to enlarge the Trace Data view by 50% increments.
Zoom Out		Zooms out on the view horizontally to reduce the Trace Data view by 50% increments.
Quality Buttons	The quality buttons let you choose whether you wish to view individual or averaged quality scores or no scores at all. Clicking the Quality icon causes three auxiliary buttons to appear in a horizontal row. Whichever button you select determines the quality score display:
		Does not display quality scores.
		Displays individual quality scores. The quality score (Q) of a peak is calculated based on the shape and height of each peak and is adjusted relative to the maximum height of any peak in the entire sequence. Taller, sharper peaks receive the highest quality scores. The heights of any underlying peaks are subtracted from the highest peak’s score. For .fas files, SeqMan Pro automatically checks for .qual files with the same name in the same folder. These .qual files may come from SeqMan Pro or Phred, among other sources. If found, the quality values are displayed. Note that gaps are not assigned quality scores.
		Displays quality scores averaged over a defined window. This mode is useful for examining trimming (see Trimming and Restoring Sequence Ends Manually. Note that gaps are not assigned quality scores.

Note 1: If you are viewing an older project, a dialog may prompt you to update quality scores. To do so, click the Update button provided.

Note 2: When bases with very high quality scores (>99% of the 95^th percentile) are displayed, two asterisks (**) will be shown in place of the usual numerical subscripts. Example: G₅₂ A₈₄ G** C₈₅.