DNA composition dynamics across genomes of diverse taxonomy is a major sub- ject of genome analyses. DNA composition changes are characteristics of both replication and repair machineries. We investigated 3,611,007 single nucleotide polymorphisms (SNPs) generated by comparing two sequenced rice genomes from distant inbred lines (subspecies), including those from 242,811 introns and 45,462 protein-coding sequences (CDSs). Neighboring-nucleotide e?ects (NNEs) of these SNPs are diverse, depending on structural content-based classifications (genome- wide, intronic, and CDS) and sequence context-based categories (A/C, A/G, A/T, C/G, C/T, and G/T substitutions) of the analyzed SNPs. Strong and evident NNEs and nucleotide proportion biases surrounding the analyzed SNPs were ob- served in 1–3 bp sequences on both sides of an SNP. Strong biases were observed around neighboring nucleotides of protein-coding SNPs, which exhibit a periodicity of three in nucleotide content, constrained by a combined e?ect of codon-related rules and DNA repair mechanisms. Unlike a previous finding in the human genome, we found negative correlation between GC contents of chromosomes and the mag- nitude of corresponding bias of nucleotide C at ?1 site and G at +1 site. These results will further our understanding of the mutation mechanism in rice as well as its evolutionary implications. DNA composition dynamics are genomes of diverse taxonomy is a major sub- ject of genome analyzes. DNA composition changes are characteristics of both replication and repair machineries. We investigated 3,611,007 single nucleotide polymorphisms (SNPs) generated by comparing two sequenced rice genomes from distant inbred lines (subspecies), including those from 242,811 introns and 45,462 protein-coding sequences (CDSs). Neighboring-nucleotide ects (NNEs) of these SNPs are diverse, depending on structural content-based classifications (genome- wide, intronic, and CDS ) and sequence context-based categories (A / C, A / G, A / T, C / G, C / T, and G / T substitutions) of the analyzed SNPs. Strong and evident NNEs and nucleotide proportion biases surrounding analyzed SNPs were ob- served in 1-3 bp sequences on both sides of an SNP. Strong biases were observed around nearby nucleotides of protein-coding SNPs, which exhibit a periodicity of three in nucleotide content, constrained by a comb ined e? ect of codon-related rules and DNA repair mechanisms. Unlike a previous finding in the human genome, we found negative correlation between GC contents of chromosomes and the mag- nitude of corresponding bias of nucleotide C at? 1 site and G at +1 site. These results will further our understanding of the mutation mechanism in rice as well as its evolutionary implications.