Genetic Marker

The genetic marker page is currently a customized feature page. Stored in the Chado Feature table broken out by type_id.

Overview

• Meta-data

  • Name
  • Marker technology
  • Species
  • @todo Gene name and location in gene (if within gene)
  • @todo any additional meta-data helpful for running the marker (e.g. primers)

Marker Locations

• marker locations by assembly (@todo not yet by assembly)

Genotypic Data

• pie chart summarizing the known alleles
• @todo Genotype look-up field: mini genotype matrix for a single variant. Germplasm are the rows.
• @todo Genotypes Matrix Link: Redirects to the genotype matrix pre-filtered for the current marker.

Sequence

• Variant Marked-up Sequence (FASTA format) (@todo -state assembly?) for all locations

Genome View

• @todo JBrowse field located on this marker

Genetic Maps

• @todo List all the genetic maps containing this marker

QTL

• @todo List of all QTL this marker falls within?