Help Variant Browser
Transcripts tracks are displayed by default.
Shows C. elegans genes.
Shows transcripts of genes.
The UCSC genome browser provides a good explanation of the
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.
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:
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.
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:
DL238 - A passing alternative variant
Two types of variant annotations are avaiable.