Diversity, SNP, and Trait Data at MaizeGDB

About diversity, SNP, and trait data at MaizeGDB

MaizeGDB is working with the Schnable lab, the Panzea project, The Genome Reference Consortium, and iPlant Collaborative to create a plan for archiving, dessiminating, visualizing, and analyzing diversity data.

Please contact us if you are preparing a proposal for a project that will generate diversity data.

Search

SNPversity is a new tool which allows you to compare SNPs across a diverse selection of inbred lines.
Search genotype data at Panzea.
Search GBS data at Panzea.
TYPSimSelector: Sort lines from the Ames Diversity Panel based on IBS (Identity by State) score.

Types of variation data

  • Single Nucleotide Polymorphisms (SNPs), including insertions and deletions.
  • Copy Number Variations (CNVs).
  • Presence/Absence Variations (PAVs).
  • Complex alleles. (also called "alternative loci")
  • Sequences which do not align to the reference genome.
  • Inversion break points.
  • Phenotypes.
  • Germplasm via GRIN.
  • Transcript assemblies and exome contigs alignments.
  • Transcript assemblies and exome contigs sequences at GenBank.
  • Expression data at PLEXdb, GEO, SRA, and other repositories.
  • Genetic maps.
  • Haplotypes? Pre-computed analyses?

Information for contributers

If you wish to submit diversity, SNP, or trait data to MaizeGDB, contact us.

Downloads

Genome browser tracks

Aligned data is available as tracks on the MaizeGDB Genome Browser. These tracks are available:
  • HapMap1 and HapMap2 from Panzea
  • Mo17 SNPs and Indels from JGI
  • Palomero toluqueño contigs
  • GBS v2.7

Projects

A list of projects and resources related to maize diversity is available here.