Alignment tracks

If you are viewing an assembly created in SeqMan NGen, you can add a track to the Analysis view showing each of the aligned reads in the selected experiment using the method described in Work with Tracks. Briefly, you can display an Alignment track by opening the Tracks panel and checking one or more of the boxes to the left of Analysis body > Alignment > (sample names).

The look of the track varies by project type and zoom level.

Scenario	Appearance of track
Non-phased assembly, zoomed in	Base codes are displayed in gray. Letters in contrasting colors indicate variants of different types.
Phased assembly, zoomed in	Base codes are displayed in green or blue, corresponding with the phase blocks in the Genome view. Letters in contrasting colors indicate variants of different types.
Non-phased assembly, zoomed out	Displays green and red arrows representing forward and reverse reads, respectively.
Phased assembly, zoomed out	By default, displays phased reads as alternating bands of green or blue and unphased reads as bands of gray. (Reads are defined as “unphased” if they do not have heterozygous sites or if the pattern of sites does not match the other reads.) Variants of different types are indicated by vertical bars. The following image is a single screenshot of a small portion of an alignment track for a phased assembly. The track has been expanded to full height by pulling down on the “grab bar” in the bottom center of the track. Labels have been added to the image to show how the default colors are used to indicate membership in a phase block and association with a particular allele (parent). Note that the assignment to one allele or the other is random from one phase block to the next. Colors used to indicate alternating phase blocks and the two alleles for each can be customized using the procedure described below this table.

Tasks related to Alignment tracks in the Analysis view:

Task	How To
View a tool tip with details about a position or phase block in the alignment	Hover over the position or phase block with the mouse. Click on the position or phase block to view information about it in the Details panel.
Resize the track vertically	Use the slider that appears if you hover over the bottom middle of the track data. You can also resize the track and change the amount of white space above/below the track using sliders in the Layout section.
Display a popup toolbar	Select an Alignment track in the Analysis view. The toolbar will pop up at the top-left of the track. All tools referred to below this row are located in the popup toolbar. You can use your mouse to grab the popup on its left end and drag it to any desired location in the view.
Close the popup toolbar	Use the Close popup tool ().
Display quality score information	Click the Quality scores tool () and choose between Don’t show scores and Show scores. This option is only available for assemblies created using Sanger (.abi) reads. An option for displaying averaged quality scores is available in the track options section (see last row in this table).
Export the alignment consensus	Click on the Export data tool (). See Export data to a file for detailed instructions.
Open the Tracks panel	Click the “hamburger menu” () and choose Tracks.
Open the Layout section for the Alignment track.	Click the “hamburger menu” () and choose Options.
Change Alignment track options	Select the Alignment track in the Tracks panel and then click the Options tab to expand the Options section. The first two options below are available for all Alignment tracks. The full set of options is only available for phased assemblies created using long-read data in SeqMan NGen. Use the Read Layout drop-down menu to choose One sequence per line or One or more per line. If you choose One sequence per line, only one sequence will appear in each line, preceded or followed by blank space before and after the sequence. If you choose One or more per line, GenVision Pro saves vertical space by putting any sequences that do not interfere/overlap with another sequence on the same row as another sequence. These sequences are placed in areas that would otherwise have consisted only of blank space. Use the Quality Score drop-down menu to choose Don’t show scores, Show scores, or Show averaged scores. Use the Mismatch Presentation drop-down menu to select how mismatches in reads are drawn when zoomed out. Options are Scale by length and Draw as ticks. Color A is used to indicate reads associated with one allele (parent), while Color B indicates they are from the other parent. By default, alleles in odd blocks are represented by two shades of blue; alleles in odd blocks are represented by two shades of green. If desired, click on any of the four colors to select a different color from the color picker. Click if you wish to return to the default values.