Numeric tracks (Coverage, Phase consistency)

If data is available, you can choose to display a numeric track in the body of the Analysis view. The available numeric tracks are Coverage and Phase consistency.

For detailed information about applying tracks, see Work with Tracks.

Sources of data for numeric tracks:

• Numeric data of any type imported via a Wiggle file (.wig) using File > Add Track (see Add tracks).

• Coverage tracks imported with a SeqMan NGen .assembly package (see Add assemblies). This track displays a plot of values along one or more sequences in the session. Values are obtained automatically from assemblies added to the session. When the Coverage track is visible, it consists of a graph showing the depth of sequence coverage for each nucleotide position along the Analysis view.

• Phase consistency tracks imported with a SeqMan NGen .assembly package that used a specific variant analysis workflow and long-read data. This track shows phase block regions (regions of the reference that could be phased into two haplotypes) and is a graphical representation of the Phase Consistency column in the Variants view.

To change Numeric track options:

To change track options, select a numeric track in the Tracks panel and then click the Options tab to expand the Options section.

You can also select a numeric track in the Analysis view to cause an Options toolbar to pop up to the top-left of the track. You can use your mouse to grab the popup on its left end and drag it to any desired location in the Analysis view. Options provided in the popup are a subset of all options available in the Options section.

In the main Options section:

• Select from three different Graph types (Line, Skyline, Bar) by clicking on the corresponding icon.

• By default, numeric graphs are displayed in green with a pale yellow background. To choose another graph color, click on the box to the right of Color to make a selection from a color chart. To choose another background color, click the color box to the right of the Background checkbox. To turn off the background color, uncheck the checkbox.

• Use the first Gridlines drop-down menu to select which grid-lines to display: Both (horizontal & vertical), Horizontal (only) or None. Use the second drop-down menu to choose whether grid-lines should be visible above (Over graph) or below (Under graph) other parts of the graph.

• Check the Smooth box if you wish to average the values over a specified number of residues. Smoothing is computed by averaging values in a sliding window of the specified number of residues. Enter the number of residues in the adjacent text box (maximum=5000). Inputting a high value will smooth the graph curves, while a low value will highlight local differences.

• Check the Logarithmic scale box if you want to use a logarithmic, rather than a linear scale. The log of 0 is not defined. Therefore, log values for the track are calculated as follows: For y > 0, y’ = log(y); otherwise, it is displayed as a 0.

• If the default display range is not be suitable for a numeric track, you may see an empty graph or a graph with the peaks cut off. To correct this, check the Maximum box and enter an integer into the associated text box. You may need to try several values before finding the ideal one.

• Click if you wish to return to the default values.

To 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.