Difference between revisions of "Soybean"

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(Soybean genomics)
 
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This is the supplementary data for Marsh et al.   
  
1. Raw InDels
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[https://appliedbioinformatics.com.au/download/cqProt-003_Supplementary_Tables.xlsx Supplementary Tables]
2. Raw SNPs
 
3. Filtered Insertions reformatted to biallelic
 
4. Filtered Deletions reformatted to biallelic
 
5. HaplotypeMiner inputs
 
6. Filtered SNPs
 
  
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[https://appliedbioinformatics.com.au/download/cqProt-003_Supplementary_Figures.docx Supplementary Figures]
  
This is the supplementary data for Marsh et al.   
 
 
Files contain Gm20 with Wm82.a1.v4 reference
 
Files contain Gm20 with Wm82.a1.v4 reference
  
[http://appliedbioinformatics.com.au/download/Gm20.INDELs.vcf.gz Raw Indels]
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[https://appliedbioinformatics.com.au/download/Gm20.INDELs.vcf.gz Raw Indels]
  
[http://appliedbioinformatics.com.au/download/Gm20.SNPs.vcf.gz Raw SNPs]
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[https://appliedbioinformatics.com.au/download/Gm20.SNPs.vcf.gz Raw SNPs]
  
[http://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.INs.vcf.gz Filtered Insertions reformatted to biallelic]
  
[http://appliedbioinformatics.com.au/download/filtered_biallelic_Gm20.DELs.vcf.gz Filtered Deletions reformatted to biallelic]
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[https://appliedbioinformatics.com.au/download/filtered_biallelic_Gm20.DELs.vcf.gz Filtered Deletions reformatted to biallelic]
  
[http://appliedbioinformatics.com.au/download/HM_input.tar.gz HaplotypeMiner input]
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[https://appliedbioinformatics.com.au/download/HM_input.tar.gz HaplotypeMiner input]
  
[http://appliedbioinformatics.com.au/download/protein_Gm20.SNPs.id.biallic_maf_0.01_geno_0.1.vcf.gz Filtered SNPs]
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[https://appliedbioinformatics.com.au/download/protein_Gm20.SNPs.id.biallic_maf_0.01_geno_0.1.vcf.gz Filtered SNPs]
  
 
=== Soybean pangenome ===
 
=== 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.
 
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.
  
[http://www.appliedbioinformatics.com.au/soybean JBrowse genome viewer]
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[https://www.appliedbioinformatics.com.au/soybean JBrowse genome viewer]
  
Supplementary Tables: [http://www.appliedbioinformatics.com.au/download/Soybean_pangenome_Supp_Tables.xlsx Download here]
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Supplementary Tables: [https://www.appliedbioinformatics.com.au/download/Soybean_pangenome_Supp_Tables.xlsx Download here]
  
 
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].
 
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]