Genome wide variations of rice detected by PED

Next generation sequence data of 'World Rice Core Collection' and 'Rice Core Collection of Japanese Landraces' distributing NARO genebank have been analyzed by the software 'Polymorphic Edge Detection'. This data is an additional supplementary data of the PED paper.

Polymorphisms between Japonica rice Nipponbare (wrc01) and other cultivars were detected by the PED software. More than 2 million polymorphic loci were detected. 

Lists are separated by 12 rice chromosomes.

Column order is chromosome number, position, cultivar name, ref, alt, genotype, allele frequency, number of reads, mutation type, gene name, RAP ID, position of nucleotide sequence of gene, position of amino acid sequence of gene, left primer, right primer, amplified size.

Accession Numbers of NGS data are listed in Japanese page 'World Rice Core Collection' and in NCBI SRA page 'Rice Core Collection of Japanese Landraces'.

The PED software is available at: https://github.com/akiomiyao/ped

Miyao, A., Kiyomiya, J.S., Iida, K. et al. Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data. BMC Bioinformatics 20, 362 (2019). https://doi.org/10.1186/s12859-019-2955-6