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Help Home > The Genome Browser > The Genome Viewer

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The Genome Viewer

The Genome Viewer displays tracks (colored, horizontal rows of sequence data) that represent the scaffold, JGI-predicted genes (gene models), and other relevant sequences, all aligned by base position. Each track is shown in a specific color and with an identifying label.

Tracks in the Genome Viewer are displayed from top to bottom in the following order

  1. Base Position Track
  2. Custom Tracks
  3. Curve tracks
  4. Vista tracks
  5. Scaffold Track
  6. Feature Tracks

In addition to displaying tracks, the Genome Viewer allows annotators to create and edit gene models


screenshot of browser viewer

1. The Base Position Track

Beneath custom tracks in the Genome viewer you will see the Base Position track, showing the nucleotide base position along the scaffold. The Base Position track operates as the horizontal scale of the Genome viewer. To center the Genome Viewer on a specific nucleotide, click the Base Position track at the desired position. Centering behavior is determined by the Recenter Options setting in Browser Options in the Browser toolbar.

2. Custom Tracks

The top-most tracks in the Genome viewer are Custom Tracks displaying data uploaded by JGI users. Click here to learn about how to upload, manage, and share custom tracks, including Wiggle tracks.

3. Curve Tracks

Appearing below the Base Position track, Curve tracks are colored line-graphs that display three different types of information:

  1. The Read depth track displays 454 Read Depth as it varies over the scaffold. The horizontal line through the middle of the track represents the mean read depth for the displayed segment.

  2. The GC Content track displays the GC content as it varies over the scaffold.

4. Vista Tracks

  1. Vista tracks indicate the density of alignment of the displayed region with other genomes.

The VISTA curve is calculated as a windowed-average identity score for the alignment. Each "peaks and valleys" graph represents percent conservation between aligned sequences at a given coordinate on the base genome. Regions are classified as "conserved" by analyzing scores for each base pair in the genomic interval, that is "Minimum Conserved Width" (default value 100 bp) and "Conservation Identity" (default value 70%). A region is considered conserved if the conservation over this region is greater than or equal to the "Conservation Identity" and has the minimum length of "Minimum Conserved Width". Regions of high conservation are colored according to the annotation as exons (dark blue), UTRs (light blue) or non-coding (pink). For more detailed information about Vista Curves and VISTA tools see here.

5. The Scaffold Track

The scaffold under observation in the Genome Viewer is represented by the Scaffold Track, a black and red bar underneath the curve tracks. When viewed in full mode (the default), black areas indicate contigs, and red lines or rectangles indicate gaps. The track label shows the scaffold number (e.g., "Scaffold_1"). Small gaps may not be evident when zoomed out.

When zoomed in to a shorter range on the browser, the scaffold track also includes the 3-frame amino acid translation (AA) or at a closer range, the 3-frame amino acid translation with nucleotide bases (NA).

6. Feature Tracks

The majority of the tracks in the Genome Viewer represent collections of features.

Quick Tips: What is a Feature?

  1. A feature is a general term for any designation given to a location on the genome, such as a predicted gene model, an EST, or a repeat sequence.

Display and manipulation of feature tracks

Tracks can appear in one of three viewing modes with respect to how features are displayed: full (or "expanded"), condensed, or packed. To the left of the label for each track, a set of icons allows the user to select among theses modes and to shift the position of the track up and down in the browser window:

  • pack Displays a track in pack mode. In this mode, a track is represented by multiple rows, each of which contains multiple features in the track. Pack mode minimizes the number of rows necessary to show the track by collecting non-overlapping features together within each row.

  • plus Expands a track to full mode, in each feature of the track is displayed in a separate row. (The track will not expand if more than five hundred features are present.)

  • minus Collapses a track to dense mode, summarizing the data in one row.

  • up arrow Moves a track up one row.

  • down arrowMoves a track down one row.

  • i Displays information (such as methodology) about a track, if available.

Tracks can also be switched between full and collapsed modes by clicking on the label that appears above each track, or by using the Browser Toolbar.

When visible (when viewed in pack or full mode), features are shown as rectangles joined by lines, with arrowheads indicating the read direction of the feature.

Quick Tips

  • To toggle a track between full and dense mode, click on the track, the track label, or the + or - button to the left of the track. If the track does not appear to expand, try zooming in.
  • To view descriptive information about a feature, expand the track, then place your cursor over the feature row. Information should appear in the Feature text box of the Navigation Controls or in a pop-up window.
  • To move a track up or down in the Genome Viewer, click the up or down arrow to the left of the track.

Previous/Next arrows

When you expand a track, the track label will include black arrows to the left and right of the label name (as shown in the image above on either side of "Contigs in Scaffolds"). These arrows allow you to navigate to the previous and next features for the current track and on the current scaffold/chromosome only.

The left-side arrow moves you to the previous feature, and the right-side arrow moves you to the next feature. The previous or next track feature will be centered in the browser along with a 20% padding on each side, causing the zoom to automatically adjust.

If you are currently viewing the first feature in a track, using the previous feature icon will result in recentering around the same feature. Similarly, using the next feature icon when viewing the last feature in a track will cause the browser to recenter around the same feature.

Quick Tips

  • To view scaffold information, click anywhere along the scaffold track or its label. The Scaffold Info page shows contigs and gaps and allows you to retrieve scaffold and contig sequences in FASTA format.
  • To view the 3-frame translation of the scaffold, click the Zoom +3x button several times until the 3-frame translation is visible, OR select either the NA or AA button in the Browser Navigation Controls frame.

Gene Model Tracks

JGI-predicted genes appear in a track below the scaffold track, usually labeled "Gene Models" or "Filtered Models." User-created gene models may be shown further down the list of tracks.

On Gene Model tracks, each feature represents a single gene model. Rectangles represent exons, and the connecting lines represent introns.

Quick Tips

  • To view the Protein Page for a gene model of interest, click on a gene model track to expand it into feature rows, then click the feature row that corresponds to the gene model and select "Feature Web Page" from the popup menu.

Loci Tracks

For some organisms, loci are shown in a "Loci" track. Each feature in such a track represents a locus. To view the annotation area for a locus, click the Loci track to expand it to full mode, then click the feature row for the locus of interest.

Nucleotide/Alignment Tracks

Tracks for nucleotide sequences are shown below the gene models. These can for include, for instance, ESTs, clones, reads, PFAM domain alignments or BLAT or BLAST data for related organisms.

On nucleotide tracks, each feature generally represents an alignment. Rectangles represent high-scoring pairs (HSPs), and connecting lines represent gaps in the alignment.

Repeat Tracks

In repeat sequence tracks (usually shown in black near the bottom of the screen), each feature represents a repetitive region on the scaffold.

Quick Tip

  • To view a feature of interest (of any type), click on the containing track to view it in full mode, then click on the row that corresponds to the feature and select"Feature Web Page".

Other Feature Tracks

Other tracks may describe the location of SNPs, user-loaded features, or other data along the scaffold.