Data from: Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection

Duitama J, Silva A, Sanabria Y, Cruz DF, Quintero C, Ballen C, Lorieux M, Scheffler B, Farmer A, Torres E, Oard J, Tohme J

Date Published: May 13, 2015

DOI: http://dx.doi.org/10.5061/dryad.8hg32

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Structural variants WGSOryza_CIAT_LSU_USDA_NCGR
Downloaded 38 times
Description Structural variation identified for the 104 varieties analyzed in this study in GFF format (one file per sample). Genomic coordinates are relative to IRGSP1.0.
Download WGSOryza_CIAT_LSU_USDA_NCGR_SV.tar.gz (44.27 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr1_0.vcf
Downloaded 19 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 1 from basepairs 1 to 15000000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (723.6 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr2_0.vcf
Downloaded 11 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 2 from basepairs 1 to 15000000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (789.2 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr3_0.vcf
Downloaded 12 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 3 from basepairs 1 to 15000000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (568.7 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr1_1.vcf
Downloaded 7 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 1 from basepairs 15,000,000 to 30,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (889.7 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr1_2.vcf
Downloaded 6 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 1 from basepairs 30,000,000 to 43,270,923
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (503.3 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr2_1.vcf
Downloaded 6 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 2 from basepairs 15,000,000 to 30,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (725.5 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr2_2.vcf
Downloaded 5 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 2 from basepairs 30,000,000 to 35,937,250
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (209.5 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr3_1.vcf
Downloaded 5 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 3 from basepairs 15,000,000 to 30,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (847.2 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr3_2.vcf
Downloaded 6 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 3 from basepairs 30,000,000 to 36,413,819
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (233.1 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr5_0.vcf
Downloaded 4 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 5 from basepairs 1 to 15,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (977.0 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr5_1.vcf
Downloaded 4 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 5 from basepairs 15,000,000 to 29,958,434
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (719.2 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr6_0.vcf
Downloaded 4 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 6 from basepairs 1 to 16,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (954.0 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr6_1.vcf
Downloaded 4 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 6 from basepairs 16,000,000 to 31,248,787
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (840.2 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr7_0.vcf
Downloaded 4 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 7 from basepairs 1 to 15,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (955.1 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr7_1.vcf
Downloaded 5 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 7 from basepairs 15,000,000 to 29,697,621
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (736.8 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr8_0.vcf
Downloaded 3 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 8 from basepairs 1 to 12,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (782.5 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr8_1.vcf
Downloaded 3 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 8 from basepairs 12,000,000 to 24,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (811.6 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr8_2.vcf
Downloaded 3 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 8 from basepairs 24,000,000 to 28,443,022
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (177.0 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr4_0.vcf
Downloaded 2 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 4 from basepairs 1 to 10,000,000.
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (846.5 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr4_1.vcf
Downloaded 4 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 4 from basepairs 10,000,000 to 20,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (645.4 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr4_2.vcf
Downloaded 3 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 4 from basepairs 20,000,000 to 30,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (389.7 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr4_3.vcf
Downloaded 3 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 4 from basepairs 30,000,000 to 35,502,694
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (211.3 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr9_0.vcf
Downloaded 4 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 9 from basepairs 1 to 12,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (852.7 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr9_1.vcf
Downloaded 3 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 9 from basepairs 12,000,000 to 23,012,720
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (478.7 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr10_0.vcf
Downloaded 2 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 10 from basepairs 1 to 12,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (960.1 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr10_1.vcf
Downloaded 3 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 10 from basepairs 12,000,000 to 23,207,287
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (505.8 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr11_0.vcf
Downloaded 2 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 11 from basepairs 1 to 15,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (952.2 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr11_1.vcf
Downloaded 3 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 11 from basepairs 15,000,000 to 29,021,106
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (908.7 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr12_0.vcf
Downloaded 4 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 12 from basepairs 1 to 12,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (758.7 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr12_1.vcf
Downloaded 3 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 12 from basepairs 12,000,000 to 24,000,000
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (812.2 Mb)
Details View File Details
Title WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_Chr12_2.vcf
Downloaded 3 times
Description SNPs and small indels identified for the 104 varieties analyzed in this study. All genotypes have an NGSEP genotyping quality score larger or equal than 40. Genomic coordinates are relative to IRGSP1.0. This file contains chromosome 12 from basepairs 24,000,000 to 27,531,856
Download WGSOryza_CIAT_LSU_USDA_NCGR_Q40_annotated_...cf.gz (150.8 Mb)
Details View File Details

When using this data, please cite the original publication:

Duitama J, Silva A, Sanabria Y, Cruz DF, Quintero C, Ballen C, Lorieux M, Scheffler B, Farmer A, Torres E, Oard J, Tohme J (2015) Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. PLOS ONE 10(4): e0124617. http://dx.doi.org/10.1371/journal.pone.0124617

Additionally, please cite the Dryad data package:

Duitama J, Silva A, Sanabria Y, Cruz DF, Quintero C, Ballen C, Lorieux M, Scheffler B, Farmer A, Torres E, Oard J, Tohme J (2015) Data from: Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8hg32
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: