Data

Alignments

1214 fragments from the Nordborg lab 2010 project, April 2006 freeze

250k pilot data

Preliminary 250k SNP data for 93 out of the 96 accessions used by Nordborg et al (PLoS Biology, 2005). Error estimates are provided.

250k imputed SNP data

Imputed 250k SNP data for the 96 accessions used by Nordborg et al (2005), i.e., no missing data

250K imputed SNPs 051808 dump

Improved genotype calls for 250K SNPs, now for 262 samples.

Imputed 250k data (as of June 17 2008)

240,813 SNPs in 262 accessions with missing data imputed

250k data for 363 accessions

The latest imputed dataset, now with accession ids.

250K_version_3.01_file

 

250K (version 3.02)

call method 43 in db. 931 unique accessions, 21609 SNPs. Same criteria as before. Blh-1, Uod-2 and Santa Clara were removed under suspicion of contaminants.

149SNP data after filtering

Some suspicious Ecotypes and SNPs were removed. The tarball includes three files. Two are the coma-delimited genotype files with the same data in different file formats (either Strain X SNP or SNP X Strain). The columns are self-explanatory. The 3rd file is tab-delimited information related to all the ecotypes.

call-method-49.tar.gz (250k dataset 3.03)

call method 49 in db. Two Files in this tarball. One is the genotype matrix. First two columns denote the chromosome, position of all SNPs. The first row is array id (pointing to the actual affymetrix array stored in db) for each ecotype/column. The 2nd row is ecotype id (internal identifier for arabidopsis ecotypes). In total, 1018 unique accessions, 213637 SNPs. The 2nd file is a tab-delimited file containing the meta information for all ecotypes included. Uod-2 and Santa Clara were removed under suspicion of contaminants.

250k data (version 3.03)