Variant Browser

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Variant Browser

Standard Tracks

The genome browser provides five tracks.

Genes

Shows C. elegans genes.

Transcripts

Shows transcripts of genes.

Conservation Tracks

The UCSC genome browser provides a good explanation of the phyloP and phastCons tracks and how to interpret them.

phyloP

phyloP (phylogenetic P-values) are designed to detect lineage-specific selection. Positive scores indicate conserved sites (slower evolution than expected under drift) whereas negative scores indicate acceleration (faster evolution than expected under drift).

  • Caenorhabditis elegans
  • Caenorhabditis brenneri
  • Caenorhabditis japonica
  • Caenorhabditis remanei
  • Caenorhabditis briggsae
  • Strongyloides ratti
  • Onchocerca volvulus
  • Brugia malayi
phastCons

phastCons scores range from 0-1 and represent the probability that each nucleotide belongs to a conserved element.

Variants

The variants track shows variation across the species for all isotypes sequenced. Variants are colored according to the legend:

Reference  
Alternate

Variant Effects

There are three tracks (LOW, MODERATE, HIGH) that can be used to show variants and their predicted impacts as annotated by SnpEff. The tracks are color coded based on severity as follows:

  

These annotations can be used to assess what functional affects a given variant may have and are grouped into LOW, MODERATE, and HIGH impact variants. More information on variant predictions is available on the Variant Prediction page.

Strain Specific Tracks

The variants for individual isotypes can be viewed by selecting tracks from the strain list:

strain_selection

Isotypes can also be filtered using the search box. Like the variant track for the entire species, reference and alternate genotypes are colored as follows:

Reference  
Alternate

Missing genotypes are excluded.




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