The appearance of the Alignment and Strategy views is controlled via the Style panel, which is composed of three expandable sections.

Sequence section:

To access options affecting the sequence font and background/foreground color, click on the Style panel expand bar entitled Sequence, or choose View > Style > Sequence.

Task How to…
Select font options for sequence names Select a font from the Font drop-down menu. Recently selected fonts (if any) appear at the top of the menu, and other available fonts appear below the row of dashes. Enter the preferred font size by typing a number between 4-72 in the box at right, or by using the corresponding up and down arrows ( ).
Select font options for tracks Check the box next to Track names font, then use the corresponding drop-down menu to change the font from the current value. Enter the preferred font size by typing a number between 4-72 in the box at right, or by using the corresponding up and down arrows ( ).
Change the sequence color scheme in the Alignment view To change the letter color in the Alignment view, check the Color sequence foreground box. To change the background color (boxes around each letter), check the Color sequence background box. Then make selections from the corresponding drop-down menus. Color schemes are described in Available color schemes. To specify which parts of the sequence should be colored, see Alignment coloring in the Alignment section below.

Alignment section:

To access options affecting the Alignment view, click on the Style panel expand bar entitled Alignment, or choose View > Style > Alignment.

Task How to…
Specify the type(s) of editing allowed in an .sqd assembly Make a selection from the Editing drop-down menu. Choices are:

  • All editing allowed – Allows you to type in new nucleotides or gaps into the consensus sequence, or to delete the same. To add gaps, use dashes (-).

  • Only gap editing allowed – Allows you to add gaps using dashes (-) or to remove gap-indicating dashes. Does not allow nucleotide characters to be added or deleted.

  • No editing allowed – Disallows adding or removing nucleotides or gaps in the Alignment view. If you choose this option and attempt to edit the consensus, you will receive a warning message asking if you would like to allow editing. If you respond with Yes, the Editing menu will be switched to All editing allowed.

  • No editing allowed permanently – This option is similar to No editing allowed. However, the only way to override the option is to manually make a different selection from the Editing menu.
Limit color-coding to the targeted coverage region only Check the Color only in targeted coverage regions box to cause coloring options selected elsewhere in this section to only be applied to nucleotides in the targeted region of the assembly.
Display quality scores To display quality scores as subscripts next to each nucleotide, check the Quality box and then make a selection from the drop-down menu to the right:

  • Show scores – Causes quality scores to be displayed as a subscript next to the base. When bases with very high quality scores (>99% of the 95th percentile) are displayed, two asterisks (**) will be shown in place of the usual numerical subscripts. Example: G52 A84 G** C85.The quality score 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. Illumina data will typically have higher scores than Sanger data. For .fas files, SeqMan NGen automatically checks for .qual files with the same name in the same folder. If found, the quality values are displayed. Note that gaps are not assigned quality scores.

  • Show averaged scores – Displays quality scores averaged over a defined window. This mode is useful for examining trimming. Note that gaps are not assigned quality scores.
Specify where background and foreground coloring should be applied To show where background and/or foreground coloring should be applied, make a selection from the Alignment coloring drop-down menu. This option is only active if at least one of the Color sequence foreground or Color sequence background boxes are checked in the Sequence section described above. Options include: No special coloring, Color only differences from consensus, Color only matches to consensus, Show only differences from consensus, and Color matches and differences. The last option will apply the foreground and/or background colors to all nucleotides.
Display negated weights or trimmed sequence with a custom font color or highlighter Check the corresponding font color box (left) or highlight box (right) to enable color choosing. Then click on the “A” and/or Color “highlighter” icons to open their color choosers.

Strategy section:

To access options affecting the visibility of reads in the Strategy view, click on the Style panel expand bar entitled Strategy, or choose View > Style > Strategy.

Task How to…
Show or hide specific types of paired reads in the Strategy view Choose an option from the Show drop-down menu or manually check or uncheck the individual boxes: Unpaired, Inconsistent (single contig, Inconsistent (multi contig), Consistent (single contig), Consistent (multi contig), Consistent if regrouped, Split. If your group of checked/unchecked boxes does not match any of the presets, the Show menu will automatically change to Custom.

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