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Genome Browser

Standard Tracks

The Genes and Transcripts tracks are displayed by default.

Genes

Shows C. elegans genes.

Transcripts

Shows transcripts of genes.

phyloP

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

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

Transposons

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.

Variants

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

Reference  
Alternate

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.

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

Annotations

Two types of variant annotations are avaiable.