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SNP and Trait Data at MaizeGDB
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SNPversity 2 creates a VCF file based on a given region of the B73 genome and a subset from thousands of diverse maize accessions.
SNPversity 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 (a USDA-maintained set of maize lines representing wide genetic variation in Ames, Iowa) 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 GEO, SRA, and other repositories.
- Genetic maps.
Downloads
- Whole genome resequencing project from James Schnable lab (Grzybowski et al. 2023)
- HapMap3 from CyVerse (Contact: Qi Sun, Cornell):
- The Hapmap3 BAM files
- Genotyping VCF files Raw
- Genotyping VCF files Imputed
- HapMap1 and HapMap2 from Panzea.
- GBS v2.7 (Genotyping by Sequencing) from Panzea.
- Search trait values (download all data as text)