The 3,000 rice genomes project

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Table 1 Characteristics of the single nucleotide polymorphisms (SNPs) identified in the 3,000 rice genomes when aligned to the reference japonica Nipponbare genome IRGSP-1.0

Chrom.	Gene	mRNA	5’-UTR	CDS	Intron	3’-UTR	Intergenic	Total	Syn	Non-syn	Total	Non-syn/Syn
Chr1	634,912	630,396	25,880	291,817	286,601	26,098	1,252,989	1,887,901	118,095	173,722	291,817	1.471
Chr2	528,417	524,172	20,087	243,967	238,738	21,380	1,013,475	1,541,892	97,306	146,661	243,967	1.507
Chr3	490,402	487,611	19,899	223,196	224,129	20,387	962,304	1,452,706	88,477	134,719	223,196	1.523
Chr4	730,310	727,473	19,018	388,220	301,071	19,164	1,176,274	1,906,584	160,101	228,115	388,220	1.425
Chr5	489,370	485,848	13,623	257,327	200,307	14,591	867,799	1,357,169	103,723	153,604	257,327	1.481
Chr6	560,506	557,361	16,943	280,933	242,635	16,850	1,023,473	1,583,979	114,625	166,308	280,933	1.451
Chr7	548,266	546,569	16,210	280,994	231,797	17,568	973,670	1,521,936	115,332	165,662	280,994	1.436
Chr8	582,068	580,181	16,396	302,785	244,991	16,009	998,651	1,580,719	124,025	178,759	302,785	1.441
Chr9	436,037	434,440	10,692	222,916	190,025	10,807	763,771	1,199,808	90,299	132,617	222,916	1.469
Chr10	476,710	473,603	11,735	258,013	192,214	11,641	806,940	1,283,650	109,451	148,561	258,013	1.357
Chr11	684,803	681,891	16,642	354,874	291,049	19,326	1,148,735	1,833,538	140,772	214,101	354,874	1.521
Chr12	607,336	603,783	16,549	319,401	251,103	16,730	1,055,044	1,662,380	129,296	190,105	319,401	1.470
ChrUn	19,706	19,706	0	12,615	7,091	0	26,669	46,375	5,819	6,796	12,615	1.168
ChrSy	11,463	11,463	0	7,913	3,550	0	15,043	26,506	3,846	4,067	7,913	1.057
Total	6,800,306	6,764,497	203,674	3,444,971	2,905,301	210,551	12,084,837	18,885,143	1,401,167	2,043,797	3,444,971	1.459

The MSU V7.0 rice gene annotation for 55,986 genes and 66,338 mRNA [13] as a raw gff3 file type was downloaded from the Rice Genome Project Annotation ftp site [19]. Prior to categorization of SNP types, the raw gff3 file was processed 1) to remove all but the primary mRNA transcript and 2) to select the gene models with the highest support in cases where there are overlapping gene models. Hence, SNP characteristics are reported here for 55,107 of the 55,986 gene models. Characteristics of SNPs in pseudogenes or where the reference base is N (unknown or missing) are not reported. Syn = synonymous; Non-syn = non-synonymous.