Maize Data

Exploring NGS data of zea mays

zmAGP Reference Genome

zmWGS

zmHapMap

Current Version downloaded on 8/22/2016 using iget.

Maize HapMapV3.2.1 genotypes (without imputation), for more information refer to panzea.

icd /iplant/home/shared/panzea/hapmap3/hmp321/unimputed/

Basic statistics

1. WGS data from 1,210 maize lines.
2. 83 million SNPs (30 million SNPs marked with LLD are high confidence markers)

ZeaGBS

The current version is ZeaGBSv2.7. I get the data via the following path on CyVerse (iPlant):

icd /iplant/home/shared/panzea/genotypes/GBS/v27/
iget AllZeaGBSv2.7_publicSamples_imputedV3b_agpv3_sorted.vcf.gz

1. It contains genotypes for 955,690 SNPs at more than 60K taxa (samples), 17,280 of which are public.
2. AGPv3 coordinates in hapmap and VCF formats.

zmTx Transcriptome

zmMe Methylome

License

This repo is open source, licensed under GPLv3. But most of the data were collected from various online resources generated by different groups. Please refer data usage policies to the original providers.