This database is constructed using the genome sequences of Nipponbare, a cultivar of japonica, and 93-11, a cultivar of indica. It contains 1,703,176 single nucleotide polymorphisms (SNPs) and 479,406 Insertion/Deletions (InDels), approximately one SNP every 268 bp and one InDel every 953 bp in rice genome. It can be downloaded and distributed without any limitations.

Column Headings:
1. Chromosome: 1 thru 12
2. BAC_Accession: GenBank/EMBL/DDBJ accession, ordered by position in chromosome
3. BAC_Name: P for RGP PAC Clone; B for RGP BAC Clone; OSJNB for CUGI BAC Clone; OJ for              Monsanto BAC Clone.
4. BAC_Length: in bp
5. LeftCoor: The coordinate of the base to the left of the polymorphic location. See below.
6. RightCoor: The coordinate of the base to the left of the polymorphic location. See below.
7. Direction: Plus (two strands of Nipponbare and 93-11 with same direction) or Minus               (two strands of Nipponbare and 93-11 with different direction)
8. ContigName: strandard BGI contig name http://btn.genomics.org.cn/rice/
9. ContigLength: in bp
10. Identity: overall sequence similarity between contigs of 93-11 and BAC clones.
11. PLM_Type: SNP, Single Nucleotide Polymorphism; IND, Insertion/Deletion ; #”, large               chunks of rearranged, inverted or inserted sequence; “No extension” , regions               of no similarity while their flanking sequences are quite similar.
12. SNP_Base: changed nucleotide. Nipponbare/93-11 e.g. A/T means A in Nipponbare and T in               93-11.
13. IND_Size: size of insertion or deletion in Nipponbare. e.g. -4 means a 4bp deletion in               Nipponbare and 4 means a 4bp insertion in Nipponbare.
14. Left_Flank: 20 bp directly to the left of the polymorphic location
15. Right_Flank: 20bp directly to the right of the polymorphic location.
16. Restriction_sites (N): restriction sites in Nipponbar from the SNP
17. Restriction_sites (9): restriction sites in 93-11 from the SNP

Note:

Please note that the genome sequence of Nipponbare released on Sep 9, 2003 was used to construct the rice DNA polymorphism database. From then on, some of BAC sequences were further annotated and new version was released. The “LeftCoor” and “RightCoor” might be not accurate for some of new released clones. In these cases, flanking sequences (Left_Flank and Right_Flank) could be used to blast rice genome sequence database and the locations of polymorphisms in the new clones could be identified.

Rice DNA polymorphism database

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If you have any questions ,please Contact us. mailto:joradmwc2003.wang@vip.sina.com