Legacy SNPs

Legacy SNPs designed from Sanger sequencing data (context sequences provided); Genotyping results from traditional SNP assays such as the Illumina Golden Gate SNP assay or the Sequenom single-base extension assay.

[Citation] http://www.panzea.org

File NameDescriptionRef.ChrFormatRelease DateSize
panzea_SNPs_20160417.zipThese are legacy SNPs from the previous version panzea web site. There are 4 files in this directory:
SNPpos_agpv2.bed: SNP positions in B73 agpv2 coordinates.
SNPpos_agpv3.bed: SNP positions in B73 agpv3 coordinates.
context_full.fasta: Context sequence of the SNPs. One sequence for each SNP.
context_left_right.fasta: Context sequence of the SNPs. Two flanking sequences for each SNP. Both sequences are in the same orientation as the sequences in the file context_full.fasta.
The BED file format is as described in https://genome.ucsc.edu/FAQ/FAQformat.html#format1 . You can open this file in Excel. The columns are:
1) chromosome name;
2) start position (0-based, the first nucleotide of the chromsome is position 0);
3) end position (1-based, the first nucleotide of the chromsome is position 1);
4) SNP name;
5) score. This value is the percentage of identical nucleotides in the alignment between context and reference times 1000 ;
6) strand. The relative strand of the context vs the reference genome

Some of SNPs with context sequences, but not in the bed files. This is because we cannot identify a postion based on the alignment between context sequence and the reference genome.
agpv2 and agpv3 bed and fasta4/17/20161.15mb
NAM_map_and_genos-120731.zipGenotypes and genetic map for the 1144 SNPs consituting the maize NAM map in McMullen et al. 2009. Genetic properties of the maize Nested Association Mapping population. Science 325:737AGPv1 & v2 zip20090807 

[CyVerse Data Store file path*]: /iplant/home/shared/panzea/genotypes/SNPs/
* Linux users can use iCommands to download the data files.  Click this link for instructions of using iCommands.
* Windows and Mac users can use Cyberduck to download the data files. Here is the instruction for Cyberduck.