About & Data

Pseudogenomes for 1135 Arabidopsis thaliana strains were generated by combining reference and variant calls including deletions, with uncalled sites represented as Ns.

Data & Downloads

The data powering SNPst☆r is published as an Annotated Research Context (ARC) — Arabidopsis thaliana GWAS & Proteotype ARC (export 2026-06-05, 38.2 GB total).

Or download individual collections directly. All collections are gzipped JSON Lines (one document per line) except the SNP catalog, which is gzipped BSON (mongodump) and is restored with mongorestore. See the README and METADATA documents for details.

Climate-factor GWAS (study)

Ferrero-Serrano Á, Assmann SM (2019). Nat. Ecol. Evol. 3, 274-285. doi:10.1038/s41559-018-0754-5

AraGWAS Catalog (study)

Togninalli M et al. (2018). Nucleic Acids Res. 46(D1), D1150-D1156. doi:10.1093/nar/gkx954

SNP, haplotype, proteotype & structure assays

Derived from the 1001 Genomes panel — 1001 Genomes Consortium (2016). Cell 166, 481-491. doi:10.1016/j.cell.2016.05.063

Cross-assay lookup tables

Accession metadata derived from the 1001 Genomes panel (Cell 2016, 166, 481-491).

Programmatic data access (API)

The full Arabidopsis thaliana / 1001 Genomes GWAS dataset can be accessed programmatically through the public AraGWAS REST API: https://aragwas.1001genomes.org/api/.

If you use this resource, please cite snpStar. The Collaborative Research Centre CRC 1664 is funded by Deutsche Forschungsgemeinschaft (DFG).

Credits

• Pseudogenomes (download FASTA files from the 1001 Genomes Data Center) were generated by Alexander Platzer.
• GWAS analysis was performed by Francesco Pezzini with the software GEMMA . Every climate factor was used as a phenotype and for every climate factor, one analysis run was carried out. In a data preprocessing step ecotypes related to missing values were filtered out from the phenotype vector. Minor allele frequency (MAF) and linkage disequilibrium (LD) thresholds in GEMMA were set to 1% and 0.8 respectively. This means only SNPs with a MAF of 1% or high were analysed. The obtained P-values were corrected for multiple comparisons using the Benjamini-Yekutieli method. The climate factor data was taken from the paper by Ferrero-Serrano and Assmann.
• The de-novo GWAS are computed with TASSEL 5.0 (https://tassel.bitbucket.io/).
• The analysis of the SNP data was performed by Lasse Feldhahn .
• This tool was built on the basis of the 1001 Genomes Tool Pseudogenomes ( Github page) developed by Joffrey Fitz.
• The additional web app and database development was done by Benjamin Schmidt. The webapp uses bootstrap, selectize, jquery, popper the calipho-sib feature-viewer and sequence-viewer and the webix datatable .

References

• 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana 1001 Genomes Consortium Cell (2016), 166(2) 481-91.
• Angel Ferrero-Serrano, Sarah Mary Assmann: Phenotypic and genome-wide association with the local environment of Arabidopsis: Source of the climate factors used for the gwas analysis.