B73 v5 VCF builder and viewer

Create a VCF file based on a given region of the B73 genome and a subset of the diverse maize accessions.

Select genomic interval

To retrieve the SNPs and INDELS within a genomic interval, select a chromosome, then enter the genome start and stop positions of your interval.

Chromosome:
Genome Start Position (bp):
Genome End Position (bp):
Loci per page:

Optional: Enter a gene model and press the "Load coordinates" button and the gene model coordinates will be auto-populated above.

Gene Model ID:

(+/- bp) (See Example)

Choose a dataset

Use the "Select" column to choose a dataset. Once you've made your selection, a list of available accessions will appear in the "Select the accessions to include" section.

Dataset	Reference Genome	Accessions	Variant Sites	Key Filters	Heterozygous Sites	INDELS	Imputation	Paper	Notes
MaizeGDB 2024 (High Quality)	B73 v5	1,498	75 million	Mapping quality (≥ 30), Genotypic coverage (≥ 50%), LD (max R² > 0.5)	✔	✔	✘	Andorf et al. 2024	See the Help and Download tabs for more information about the dataset.
MaizeGDB 2024 (High Coverage)	B73 v5	1,498	228 million	Mapping quality (≥ 30), Genotypic coverage (≥ 50%)	✔	✔	✘	Andorf et al. 2024	See the Help and Download tabs for more information about the dataset.
MaizeGDB 2024 (High Quality) + NAM	B73 v5	1,525	23 million	Mapping quality (≥ 30), Genotypic coverage (≥ 50%), LD (max R² > 0.5)	✔	✘	✘	Andorf et al. 2024 Hufford et al. 2021	This dataset represents the intersection of the MaizeGDB 2024 dataset and the variant sites identified in the NAM 2021 project. Note: The two datasets were generated using different variant calling methods.
MaizeGDB 2024 (High Coverage) + NAM	B73 v5	1,525	36 million	Mapping quality (≥ 30), Genotypic coverage (≥ 50%)	✔	✘	✘	Andorf et al. 2024 Hufford et al. 2021	This dataset represents the intersection of the MaizeGDB 2024 dataset and the variant sites identified in the NAM 2021 project. Note: The two datasets were generated using different variant calling methods.
Schnable 2023 (Imputation)	B73 v5	1,515	46 million	QualByDepth (≥ 2.0), FisherStrand (≤ 60.0), RMSMappingQuality (≥ 40.0)	✔	✔	✔	Grzybowski et al. 2023	See the paper for the full description of the methods used to generate the data.

Select the accessions to include

Upload a file of maize accessions:

The accession should listed in a single-column seperated by a tab or newline. Use the "SNPversity ID" from these lists of all maize accessions: XLSX.

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Phylogenetic tree view powered by VCF2PopTree

Construct Tree	UPGMA tree Neighbour-Joining tree (Unrooted)
Drawing options	Rectangular tree Radial tree
Output format	Newick tree Pair-wise diversity (MEGA) PHYLIP

No VCF file loaded. Use the 'Select options' tab to query the WGS database.

SNPversity 2.0 Data Downloads

Release 2.0.80 (20 September 2024)

Overview

Below you will find detailed information about the datasets available for download, along with guidelines and best practices. For more information on how the datasets were generated see the 'Help' section.

How to Download

Filtered datasets (Direct download): For the filtered datasets, click the link to the Federal Box account and identify the files to download. Check the boxes next to the files and click the download icon near the top of the page. Alternatively, click on the filename listed in one of the tables below, which is linked to the Box download page for that file.
Unfiltered datasets (Request Access): Send an email to John Portwood with the subject "WGS file access request". Once your request is received, you will receive a link and temporary password via email. This link will be active for 48 hours.