Table 2. Classified SNPs in exon regions.

Region	Effects on translation	Genes in category I–IVa	All protein-coding genesb
5′UTR		23454 [3.3×10−3/site]c	51881
ORF	Total	85233 [2.7×10−3/site]	96164
	Synonymous	37484 [4.1×10−3 /site]	40484
	Nonsynonymous	46261 [2.1×10−3 /site]	53754
	AA↔Terd	938	1258
	Unclassifiede	398	421
Stop codon	Total	152	247
	Synonymous	63	88
	Ter↔AAd	89	159
3′UTR		69691 [3.3×10−3/site]	104510
Total		178378	252555

^aRepresentative transcripts in 23,717 genes whose function were defined or suggested (similarity category I–III) and genes annotated as conserved hypothetical proteins (similarity category IV).

^bRepresentative transcripts in all protein-coding genes (36,712) including genes in similarity category I–IV plus similarity category V–VII (hypothetical protein, hypothetical short protein, and pseudogene candidate, respectively).

^cDensities of polymorphisms are shown in brackets as average number of polymorphisms per site. The average lengths of the 5′UTR, ORF and 3′UTR regions in 23717 genes were 303.9 bp, 1343.5 bp, and 877.6 bp, respectively. The densities of SNPs for synonymous, nonsynonymous and nonsense SNPs in ORFs were calculated based on the numbers of potential nucleotide sites for synonymous, nonsynonymous and nonsense mutations in coding regions. The density of nonsense SNPs is shown in Table 3.

^dSNPs causing changes between amino acids and stop codons.