Raw Genotypes:

chr01  chr02  chr03  chr04  chr05  chr06  chr07  chr08  chr09  chr10  chr11  chr12 

Imputed Genotypes:

Tab-separated genotype files

chr01  chr02  chr03  chr04  chr05  chr06  chr07  chr08  chr09  chr10  chr11  chr12 

VCF format

Note: For variants that showed up as missing genotypes in a large number of high-coverage sequenced varieties (depth > 12×), we assigned the corresponding genotypes in these varieties as “DEL” for the situation indicates that these varieties probably have large deletions at these positions compared with the reference genome, which are difficult to identify using GATK. You can choose to download files with or without "DEL" depending on your needs.

With 'DEL':

rice4k_geno_add_del.vcf.gz

Without 'DEL':

rice4k_geno_no_del.vcf.gz

Plink format

With 'DEL':

rice4k_geno_add_del.bed  rice4k_geno_add_del.bim  rice4k_geno_add_del.fam 

Without 'DEL':

rice4k_geno_no_del.bed  rice4k_geno_no_del.bim  rice4k_geno_no_del.fam 

Phenotypes:

Phenotype data

Raw sequence data:

The raw sequence data can be downloaded from the NCBI or EBI European Nucleotide Archive under accession numbers PRJNA171289, ERP000106, ERP000729 and PRJEB6180.