The first maize PHG database is composed of haplotypes derived from the assemblies of the NAM founders. For broader compatibility with existing genotyping platforms and data, we chose B73 as the base reference. The B73 v5 genic regions define the reference ranges implemented for the identification of haplotype start and end coordinates. The current version of the database allows for the exporting of imputed haplotypes and SNPs.
MUMMER4 was used to generate pairwise alignments of equivalent chromosomes from each NAM founder against B73. The alignments were then filtered and processed, with the valid ones used to define the haplotypes on each taxon for each B73 reference range. For taxa with a reference range that did not include a valid alignment, the processing designated the haplotype as missing.
Due to the size of the maize PHG file, it is made available through the CyVerse Data Store. Please use iCommands (Linux) or Cyberduck (Windows and Mac) software to download the file rather than downloading through the CyVerse/iPlant web page.
You will need to login as a CyVerse (iPlant) user in order to see the data file. Anonymous data access is not allowed. If you do not have an account, you can register at CyVerse (iPlant). When using the software for downloading, you will need the CyVerse data store file path (see below) to locate the maize PHG file. The instruction links for iCommand and Cyberduck are provided below as well.
[CyVerse Data Store file path*]:/iplant/home/shared/panzea/panGenome/PHG_db_maize
* Linux users can use iCommands to download the data files. Here are the instructions for iCommands.
* Windows and Mac users can use Cyberduck to download the data files. Here are the instructions for Cyberduck.