Fig. 3

Rice Population Reference Panel (RPRP) [15] pan-genome variant analysis. a Circos plot depicts the distribution of genomic attributes along the IRGSP RefSeq (window size = 500 Kb). b Comparison of genomic attributes, i.e., genes, SNPs, Pi, and Theta on chromosome 9 across the 16 RPRP pan-genome data sets (window size = 10 Kb). c Rice Gene Index (RGI) comparison of the Sub loci across the 16 RPRP pan-genome data set. d Phylogenetic analysis of Sub1A, Sub1B, and Sub1C across the 16 RPRP pan-genome data set. e Amino acid alignment of the Sub1A gene across the RPRP. f Survey of SNPs within the Sub1A gene across the 3 K-RGP resequencing data set. This analysis revealed the genomic status of the Sub1A gene (presence/absence; submergence tolerance/intolerance) across the 3 K-RGP data set