Genomic variation for 104 rice elite cultivars, landraces and wild relatives

Genomic variation obtained from analysis of high throughput sequencing (HTS) illumina data for 94 varieties of Oryza sativa and 10 wild relatives from O. rufipogon and O. nivara. The 94 O. sativa varieties include 21 latin american elite cultivars from the CIAT rice breeding program, 33 north american elite cultivars from USDA, as well as 40 landraces and 10 wild relatives sequenced and previously analyzed (doi: 10.1038/nbt.2050). Raw sequencing data was analyzed using the NGSEP pipeline (http://sourceforge.net/projects/ngsep/). Details of the analysis and the main research outcomes obtained from these data can be found here (doi: 10.1371/journal.pone.0124617). SNPs and small indels for the 104 varieties are provided as a single VCF file, whereas predictions of copy number variation (CNVs), large indels and inversions are provided as one file per sample in GFF format.