Difference between revisions of "Soybean"

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(Soybean genomics)
 
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We have been working to develop and analyse a large collection of soybean germplasm. A manuscript has been submitted and supplementary information relating to this manuscript is available below.
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== Soybean genomics  ==
  
Supplementary Tables: [http://www.appliedbioinformatics.com.au/download/Soybean_pangenome_Supp_Tables.xlsx Download here]
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=== Soybean cqProt003 supplementary data ===
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This is the supplementary data for Marsh et al.   
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[https://appliedbioinformatics.com.au/download/cqProt-003_Supplementary_Tables.xlsx Supplementary Tables]
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[https://appliedbioinformatics.com.au/download/cqProt-003_Supplementary_Figures.docx Supplementary Figures]
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Files contain Gm20 with Wm82.a1.v4 reference
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[https://appliedbioinformatics.com.au/download/Gm20.INDELs.vcf.gz Raw Indels]
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[https://appliedbioinformatics.com.au/download/Gm20.SNPs.vcf.gz Raw SNPs]
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[https://appliedbioinformatics.com.au/download/filtered_biallelic_Gm20.INs.vcf.gz Filtered Insertions reformatted to biallelic]
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[https://appliedbioinformatics.com.au/download/filtered_biallelic_Gm20.DELs.vcf.gz Filtered Deletions reformatted to biallelic]
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[https://appliedbioinformatics.com.au/download/HM_input.tar.gz HaplotypeMiner input]
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[https://appliedbioinformatics.com.au/download/protein_Gm20.SNPs.id.biallic_maf_0.01_geno_0.1.vcf.gz Filtered SNPs]
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=== Soybean pangenome ===
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Supplementary information relating to Bayer et al. 2021, [https://acsess.onlinelibrary.wiley.com/doi/10.1002/tpg2.20109 Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding], is available below.
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[https://www.appliedbioinformatics.com.au/soybean JBrowse genome viewer]
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Supplementary Tables: [https://www.appliedbioinformatics.com.au/download/Soybean_pangenome_Supp_Tables.xlsx Download here]
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The data can also be viewed on [https://soybase.org/projects/SoyBase.C2020.02.php soybase] and [https://research-repository.uwa.edu.au/en/datasets/soybean-pangenome-snps-assembly-annotation-pav UWA Research Repository].
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===Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean===
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[ Supplementary tables]

Latest revision as of 06:58, 18 June 2024

Soybean genomics

Soybean cqProt003 supplementary data

This is the supplementary data for Marsh et al.

Supplementary Tables

Supplementary Figures

Files contain Gm20 with Wm82.a1.v4 reference

Raw Indels

Raw SNPs

Filtered Insertions reformatted to biallelic

Filtered Deletions reformatted to biallelic

HaplotypeMiner input

Filtered SNPs

Soybean pangenome

Supplementary information relating to Bayer et al. 2021, Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding, is available below.

JBrowse genome viewer

Supplementary Tables: Download here

The data can also be viewed on soybase and UWA Research Repository.

Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean

[ Supplementary tables]