Difference between revisions of "Soybean"
From Applied Bioinformatics Group
(Created page with "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...") |
(→Soybean genomics) |
||
| (17 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
| − | + | == Soybean genomics == | |
| + | |||
| + | |||
| + | |||
| + | === Soybean cqProt003 supplementary data === | ||
| + | |||
| + | |||
| + | This is the supplementary data for Marsh et al. | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/cqProt-003_Supplementary_Tables.xlsx Supplementary Tables] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/cqProt-003_Supplementary_Figures.docx Supplementary Figures] | ||
| + | |||
| + | Files contain Gm20 with Wm82.a1.v4 reference | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/Gm20.INDELs.vcf.gz Raw Indels] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/Gm20.SNPs.vcf.gz Raw SNPs] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/filtered_biallelic_Gm20.INs.vcf.gz Filtered Insertions reformatted to biallelic] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/filtered_biallelic_Gm20.DELs.vcf.gz Filtered Deletions reformatted to biallelic] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/HM_input.tar.gz HaplotypeMiner input] | ||
| + | |||
| + | [https://appliedbioinformatics.com.au/download/protein_Gm20.SNPs.id.biallic_maf_0.01_geno_0.1.vcf.gz Filtered SNPs] | ||
| + | |||
| + | === Soybean pangenome === | ||
| + | |||
| + | 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. | ||
| + | |||
| + | [https://www.appliedbioinformatics.com.au/soybean JBrowse genome viewer] | ||
| + | |||
| + | 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]. | ||
| + | |||
| + | ===Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean=== | ||
| + | |||
| + | [ Supplementary tables] | ||
Latest revision as of 06:58, 18 June 2024
Contents
Soybean genomics
Soybean cqProt003 supplementary data
This is the supplementary data for Marsh et al.
Files contain Gm20 with Wm82.a1.v4 reference
Filtered Insertions reformatted to biallelic
Filtered Deletions reformatted to biallelic
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.
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]
