Detailed knowledge of the genetic variations in diverse crop populations forms the basis for genetic crop improvement and gene functional studies. In the present study, we analyzed a super-large-scale rice population (10,548 samples) to construct a rice super-population variation map (RSPVM). This map consisted of 54,378,986 single nucleotide polymorphisms (SNPs) and 11,119,947 insertion/deletion mutations (InDels) derived from 10,548 cultivated and wild accessions of rice. 356 Asian cultivated rice long sequencing reads data were collected and structural variants were identified. And based on this, a graph pangenome was constructed, and then 184,736 presence/absence variations (PAVs) were identified in 10,548 accessions.
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