Download SoySNP50K haplotypes for a subset of the cultivars

Paste a list of cultivar names, one per line, into the box below or use the Browse button to navigate to a plain text file on your computer that contains a list of cultivar names. Note that the tool is designed to download less than 1000 cultivars at a time. If you attempt to download more than that you will recieve a error message. To download greater than 1000 cultivars as a single request, get the VCF file and extract your list of cultivars using BCFtools.

The submit button will initiate a download to your computer of the SoySNP50K haplotypes for the cultivars you provide.

Load Examples

Select Assembly Version Wm82.a2 (Current Assembly)
Wm82.a1

Or use our shopping cart tool to select cultivars of interest from the complete list of cultivars haplotyped by Song et al.

Readme Text:
(Included in download)

Including this READ ME there are three files returned for a cultivar-haplotype search. 
All data are in plain text files with tab delimiters between columns.

1. This READ ME file

2. submitted_list_report_Williams_82.aX_XXXXXXXXXX.txt

This file contains a summary of the requested SoySNP50K haplotype data in SoyBase. Although in previous data releases 
some cultivars were named using nonstandard variants, only the official GRIN names are used in this release of the 
SoySNP50K data. Specifically, leading zero padding and incorrect underscores (eg. PI012345 -> PI12345, FC01234 -> FC1234, 
and PI123456_1 -> PI123456-1) have been corrected.

Column 1 shows the names that will be used in the haplotype file.
Column 2 indicates whether a SoySNP50K haplotype is available for that cultivar.
  Found - Haplotype data was found using the submitted cultivar name. The haplotype data 
               are included in the snp50k allele report.
  Not found - This cultivar is not in the SoySNP50K haplotype data set. This could indicate that 
                    the cultivar has not yet been genotyped with the SoySNP50K chip or there was an 
                    error in the cultivar name submitted. Please contact the SoyBase Curator if help 
                    with cultivar names is needed.

Cultivar Name			Search Result
PI518671			Found
Hutton				Found
FC30282				Found
PI56742-1			Found
PI987431			Not Found

3. snp50k_allele_report_Williams_82.aX_XXXXXXXXXX.txt

This file contains the SoySNP50K haplotypes. Heterozygous loci are indicated with an H. Missing data are reported as U.

chromosome		position	SNP name		PI518671		PI548557		PI548506	...
Gm01			24939		ss715578788		A			H			A		...
Gm01			25990		ss715578818		C			C			C		...
Gm01			29658		ss715578923		A			A			U		...
...
...

Funded by the USDA-ARS. Developed by the USDA-ARS SoyBase and Legume Clade Database group at the Iowa State University, Ames, IA

U.S. Public Domain