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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

From: The 3,000 rice genomes project

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
  1. 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.
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