Variants from "The role of deleterious substitutions in crop genomes"
2016-07-26
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Title
Variants from "The role of deleterious substitutions in crop genomes"
Published Date
2016-07-26
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Kono, Thomas J Y
konox006@umn.edu
konox006@umn.edu
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Genomics Data
Genomics Data
Abstract
SNP calls in protein coding regions were obtained from 15 barley and 8 soybean lines. Non synonymous SNPs were predicted to be deleterious or not using three approaches.
Description
There are two gzipped VCF (variant call format) files with variant calls for barley and soybean. A total of 652,797 SNPs were identified in the barley lines, which consisted of 13 cultivars and 2 wild accessions. For soybean, 7 cultivars and 1 wild accession were used, and 586,102 SNPs were called. Whether a variant is deleterious or not was determined using SIFT (http://sift.jcvi.org/), PolyPhen2 (http://genetics.bwh.harvard.edu/pph2/), and a likelihood ratio test of sequence conservation. Raw reads are available through the SRA accession numbers in Table S1 of Kono et al. 2016. The code used for this research, BAD_Mutations, is open source and freely available at https://github.com/MorrellLAB/BAD_Mutations.
Referenced by
The method used to extract the genetic material from the plant samples is described in: Mascher M, Richmond TA, Gerhardt DJ, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D'Ascenzo M, Akhunov ED, Hedley PE, Gonzales AM, Morrell PL, Kilian B, Blattner FR, Scholz U, Mayer KF, Flavell AJ, Muehlbauer GJ, Waugh R, Jeddeloh JA, Stein N. (2013). Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. The Plant Journal, 2013, Vol.76(3), pp.494-505 doi: 10.1111/tpj.12294.
http://dx.doi.org/10.1111/tpj.12294
Published article: Thomas J. Y. Kono, Fengli Fu1, Mohsen Mohammadi, Paul J. Hoffman, Chaochih Liu, Robert M. Stupar, Kevin P. Smith, Peter Tiffin, Justin C. Fay and Peter L. Morrell. (2016). The Role of Deleterious Substitutions in Crop Genomes. Mol Biol Evol. doi: 10.1093/molbev/msw102
http://dx.doi.org/10.1093/molbev/msw102
Original preprint can be found in BioRxiv:
http://dx.doi.org/10.1101/033175
http://dx.doi.org/10.1111/tpj.12294
Published article: Thomas J. Y. Kono, Fengli Fu1, Mohsen Mohammadi, Paul J. Hoffman, Chaochih Liu, Robert M. Stupar, Kevin P. Smith, Peter Tiffin, Justin C. Fay and Peter L. Morrell. (2016). The Role of Deleterious Substitutions in Crop Genomes. Mol Biol Evol. doi: 10.1093/molbev/msw102
http://dx.doi.org/10.1093/molbev/msw102
Original preprint can be found in BioRxiv:
http://dx.doi.org/10.1101/033175
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Funding information
USDA NIFA National Needs Fellowship (Appropriation No. 5430-21000-006-00D)
MnDrive 2014 Food Security Fellowship
Minnesota Agricultural Experiment Station Variety Development fund
United Soybean Board
U.S. NSF Plant Genome Program (BDI-1339393)
MnDrive 2014 Food Security Fellowship
Minnesota Agricultural Experiment Station Variety Development fund
United Soybean Board
U.S. NSF Plant Genome Program (BDI-1339393)
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Suggested citation
Kono, Thomas J Y; Fu, Fengli; Mohammadi, Mohsen; Hoffman, Paul J; Liu, Chaochih; Stupar, Robert M; Smith, Kevin P; Tiffin, Peter; Fay, Justin C; Morrell, Peter L. (2016). Variants from "The role of deleterious substitutions in crop genomes". Retrieved from the Data Repository for the University of Minnesota (DRUM), http://doi.org/10.13020/D65C7D.
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Description
Size
BadMutationsI_SNP_Calls_Barley.vcf.gz
Gzipped variant calling of barley SNPs
(121.53 MB)
BadMutationsI_SNP_Calls_Soy.vcf.gz
Gzipped variant calling of soybean SNPs
(48.41 MB)
Header_SNP_Calls_Barley.txt
Format and Info lines from header of Barley variant calls file
(139 B)
Header_SNP_Calls_Soy.txt
Format and Info lines from header of Soybean variant calls file
(3.29 KB)
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