Supplemental links of
”Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms”
Toshio Yamamoto, Hideki Nagasaki, Jun-ichi Yonemaru, Kaworu Ebana, Maiko Nakajima, Taeko Shibaya, Masahiro Yano
BMC Genomics. 2010 Apr 27;11(1):267. doi:10.1186/1471-2164-11-267. PMID:20423466.

All the detailed information of the 67051 SNPs detected between the two Japanese japonica cultivars, Koshihikari and Nipponbare, are stored as styles of both gbrowse and Microsoft ExcelTM.

To find a specific SNP(s) by chromosomal position,
  1. go directly to gbrowse site and enter appropriate information.
  2. go distribution map of the SNPs and click the position.

To get a list of SNP(s) by gene functional category, select any of the files below. Detailed explanation of each file is described on README.
  1. SupTable_SNP_nonSynonymous.xls (889 kb)
  2. SupTable_SNP_Synonymous.xls (764 kb)
  3. SupTable_SNP_intron.xls (2.3 Mb)
  4. SupTable_SNP_UTRs.xls (1.3 kb)
  5. SupTable_SNP_intergenic.xls (19.3 Mb)
Total number of all the SNPs is over 67051. Because some of the SNPs belong to more than one category.

To find detail of the 1917 SNP(s) for genotyping and result of genotyping on the 151 varieties , select following files.
  1. SupTable_SNP_ForTyping.xls (726 kb)
  2. JSNP151x1917.xls (18.2 Mb)

Pseudomolecules and contigs by whole genome shotgun sequencing method of the Koshihikari genome are available from search site of DDBJ under accession nos. DG000025 to DG000036 and BABO01000001 to BABO01654543, respectivery.
Short reads of Koshihikari are also avairable from DDBJ Read Archive website under accession nos. DRA000010.

Copyright © National Institute of Agrobiological Sciences. 2009 All rights reserved.