Help Variant Browser


Variant Browser

Standard Tracks

The Genes and Transcripts tracks are displayed by default.


Shows C. elegans genes.


Shows transcripts of genes.


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

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


The transposons track shows transposon calls from Laricchia et al. 2017. Each call lists the transposon type and isotype.

Divergent Regions

Hyper-divergent regions are genomic intervals that contain sequences not found in the N2 reference strain. They were identified by high levels of variation and low coverage from read alignments. For a complete description, please see Lee et al. 2020.

Two divergent tracks are available:

  • Divergent Regions Summary - Divergent region intervals and their observed frequency across wild isolate strains.
  • Divergent Regions Strain - Divergent region intervals for individual strains.

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


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:


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:


Missing genotypes are excluded.

Variant filters

Variants displayed on the genome browser are 'hard-filtered', meaning that filters have been applied, and poor-quality variants and genotypes have been removed or set to missing.

Genotypes are displayed as follows:

CB4856 - A passing reference variant
DL238 - A passing alternative variant


Two types of variant annotations are avaiable.