What styles are available for the data tracks in the Genome Browser?

Source: modified from Ensembl, http://www.ensembl.org/Help/Faq?id=335

To turn ON and OFF data along a genomic region and to choose from different visualization styles when they are ON, use the access points shown in these six images.


Some tracks will only give you the option to turn them on or off (such as %GC, Contigs, and Structural variants). However, other data types give you more options. Below is a list of the track types available for different data types. Try them out by clicking in their name/links to see if they suit your needs.

Genes ESTs, protein alignments and oligo probes
  • Normal - The standard, expanded format, showing a maximum of 7 features aligned against the genome with no names or IDs (click on the image to see the name or ID).
  • Labels - As 'Normal', with labels added underneath each feature alignment.
  • Half height - A maximum of 20 features are drawn, showing each alignment with a thinner bar than 'Normal'.
  • Stacked - The features are shown very thin, and the differentiation between each one is lost.
  • Stacked unlimited - All features in the region are shown (rather than 7 or 20).
  • Ungrouped - Feature ends will not be connected. Only the ends will be shown, aligned to the genome.
GENSCAN and SNAP predictions
  • No labels - Individual predictions are shown aligned to the genome, with exons and introns clearly marked, with no names shown (click for more information).
  • With labels - As above, with labels below.
SNPs and INDELs variants

In all styles, variants are shown with consequences indicated by a colour code. Insertions are shown as a small arrow underneath.

  • Normal (collapsed over a window if 200kb) - In a window greater than 200kb, variants are shown in the 'collapsed' style. In a window smaller than 200kb, variants are shown in the 'expanded without name' style.
  • Collapsed - All variants are shown in a single line. Click on a variant to find out more.
  • Expanded without name - Variants are spaced between multiple lines to show each one individually. Click on a variant to find out more.
  • Expanded with name (hidden over a window of 10kb) - Variants are spaced between multiple lines to show each one individually. In a window less than 10kb, name labels are also shown.
Structural variants

This track is currently only available for An. gambiae, and they are on chromosome arms 2L and 2R. For more details about these types of tracks please follow this link

  • Compact - The presence of SVs is indicated in black bars in a single. Click on the bar to see how many SVs there are at the region.
  • Expanded - Individual SVs are shown over multiple lines. Colour codes indicate the type of SV.
RNA-Seq alignments

All tracks are of equal height but not all frequency counts (depth of coverage), hence the red number is indicative of the maximum count for that region.

  • Normal - BAM files from RNA-Seq experiments. A maximum of 50 reads are shown at each position. A histogram showing summarising the number of reads at each base position is shown above. If you zoom in, the sequence is shown on both the BAM reads and histogram, with mismatches between the read and the genomic sequences hightlighted in red.
  • Unlimited - Similar to the 'Normal' view, but with a maximum of 500 reads.
  • Coverage only - The histogram only is shown.
BLAST and translated BLAT alignments
  • Compact - Alignments are shown on a single line with no links between them.
  • Normal- Alignments are spread between multiple strands and alignment structures are shown, with empty boxes indicating gaps in the alignment and gaps indicating gaps in the assembly.
  • No labels - The position of the feature without labels.
  • Normal - This is the default setting which varies depending on the track.
  • Labels - The position of the feature with labels underneath.

To organize the tracks there are two options:

Option 1:

Select, with a click, the light green bar of the track of interest and move it to your preferred location.

Option 2:

  • Click on 'Configure this page' or 'Configure this image'
  • Click on track order, on the left hand side menu
  • Click on each track that you want to move around and drag it to a new position