Barley Genotyping SNPs Annotated using SNPMeta

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Collection period

2013
2013

Date completed

2013

Date updated

Time period coverage

Geographic coverage

Source information

Probe contextual sequences were obtained from Tables S6-10 from Close et al. 2009

Journal Title

Journal ISSN

Volume Title

Title

Barley Genotyping SNPs Annotated using SNPMeta

Published Date

2016-07-18

Group

Author Contact

Kono, Thomas J Y
konox006@umn.edu

Type

Dataset
Genomics Data

Abstract

SNPs annotations were derived from publicly available DNA sequences in GenBank using BLAST. Gene name, functional impact, and other information are returned using the program SNPMeta available for download at https://github.com/MorrellLAB/SNPMeta.

Description

These are SNPs on two Illumina GoldenGate genotyping arrays and one 9k iSelect genotyping array. The ascertainment scheme for the SNPs is available in Close, Timothy J., et al. "Development and implementation of high-throughput SNP genotyping in barley." BMC genomics 10.1 (2009): 1.

Referenced by

Kono, T. J. Y., Seth, K., Poland, J. A. and Morrell, P. L. (2014), SNPMeta: SNP annotation and SNP metadata collection without a reference genome. Molecular Ecology Resources, 14: 419–425. doi: 10.1111/1755-0998.12183
http://dx.doi.org/10.1111/1755-0998.12183

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Publisher

Funding information

US National Institute for Food and Agriculture (NIFA) (2011-68002-30029)
USDA National Needs Fellowship (USDA NIFA 2011-38420-20068)
USDA - Agricultural Research Service (Appropriation No. 5430-21000-006-00D)
Kansas State University

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Previously Published Citation

Suggested citation

Kono, Thomas J Y; Kiran, Seth; Poland, Jesse A; Morrell, Peter L. (2016). Barley Genotyping SNPs Annotated using SNPMeta. Retrieved from the Data Repository for the University of Minnesota (DRUM), http://doi.org/10.13020/D63K53.
View/Download file
File View/OpenDescriptionSize
Barley_SNP_Annotations.txtBarley SNP Annotations1.33 MB
Readme_BarleySNPAnnotations.txtDescription of the Annotation Column Fields and Notes4.23 KB

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