Mt4.0-based Downloads

Detailed description of the data files is available from the readme file (updated 22 April 2014). All files listed below are based on Mt4.0v1 reference genome and Mt4.0v1 annotation. Both are available from JCVI's Medicago truncatula download page. A comparison of a small region was also performed and is also available for download. Please contact us if you would like to obtain M. truncatula hapmap data that is not listed below.

SNPs: By Chromosome
SNPs for the GWAS accessions (262) by chromosome.
 
chr1-filtered-set-2014Apr15.bcf 5 GB 2014-04-15
chr1-filtered-set-2014Apr15.bcf.csi 38 KB 2014-04-15
chr2-filtered-set-2014Apr15.bcf 4 GB 2014-04-15
chr2-filtered-set-2014Apr15.bcf.csi 33 KB 2014-04-15
chr3-filtered-set-2014Apr15.bcf 5 GB 2014-04-15
chr3-filtered-set-2014Apr15.bcf.csi 40 KB 2014-04-15
chr4-filtered-set-2014Apr15.bcf 6 GB 2014-04-15
chr4-filtered-set-2014Apr15.bcf.csi 41 KB 2014-04-15
chr5-filtered-set-2014Apr15.bcf 5 GB 2014-04-15
chr5-filtered-set-2014Apr15.bcf.csi 32 KB 2014-04-15
chr6-filtered-set-2014Apr15.bcf 4 GB 2014-04-15
chr6-filtered-set-2014Apr15.bcf.csi 25 KB 2014-04-15
chr7-filtered-set-2014Apr15.bcf 5 GB 2014-04-15
chr7-filtered-set-2014Apr15.bcf.csi 35 KB 2014-04-15
chr8-filtered-set-2014Apr15.bcf 4 GB 2014-04-15
chr8-filtered-set-2014Apr15.bcf.csi 32 KB 2014-04-15
chru-filtered-set-2014Apr15.bcf 3 GB 2014-04-15
chru-filtered-set-2014Apr15.bcf.csi 40 KB 2014-04-15
SNPs: Combined
The filtered dataset represents the highest confidence SNP calls for all lines used in association studies. The complete-set files includes all calls that were filtered out, including Non-SNPs, for lines used in association studies. The everything file contains all SNP calls, including those that did not pass filters, and also contains all calls for the Sister Taxa and deeply derived lines not included in the other files.
 
complete-set-2014Apr15.bcf 55 GB 2014-04-15
complete-set-2014Apr15.bcf.csi 348 KB 2014-04-15
everything-2014Apr20.bcf 63 GB 2014-04-19
everything-2014Apr20.bcf.csi 349 KB 2014-04-21
filtered-set-2014Apr12.bcf 40 GB 2014-04-12
filtered-set-2014Apr12.bcf.csi 324 KB 2014-04-13
Gene Context
Please see README file for more information
 
Mt4_chr1_context.tsv.gz 67 MB 2014-06-24
Mt4_chr2_context.tsv.gz 59 MB 2014-06-24
Mt4_chr3_context.tsv.gz 74 MB 2014-06-24
Mt4_chr4_context.tsv.gz 74 MB 2014-06-24
Mt4_chr5_context.tsv.gz 62 MB 2014-06-24
Mt4_chr6_context.tsv.gz 47 MB 2014-06-24
Mt4_chr7_context.tsv.gz 65 MB 2014-06-24
Mt4_chr8_context.tsv.gz 60 MB 2014-06-24
Mt4_hapmap_context_files.tgz 542 MB 2014-06-25
Mt4_hapmap_context_singlefile.tsv.gz 542 MB 2014-06-25
Mt4_scaffolds_context.tsv.gz 33 MB 2014-06-24
output.vcf.gz 31 GB 2014-06-25
TASSEL Formatted Files
hapmap.tgz 2 GB 2014-06-09
Sister Taxa to M. truncatula: By Chromosome
Also includes deeply derived M. truncatula lines.
 
chr1-filtered-set-2014Apr15.bcf 955 MB 2014-04-15
chr1-filtered-set-2014Apr15.bcf.csi 38 KB 2014-04-15
chr2-filtered-set-2014Apr15.bcf 817 MB 2014-04-15
chr2-filtered-set-2014Apr15.bcf.csi 32 KB 2014-04-15
chr3-filtered-set-2014Apr15.bcf 1 GB 2014-04-15
chr3-filtered-set-2014Apr15.bcf.csi 39 KB 2014-04-15
chr4-filtered-set-2014Apr15.bcf 1 GB 2014-04-15
chr4-filtered-set-2014Apr15.bcf.csi 40 KB 2014-04-15
chr5-filtered-set-2014Apr15.bcf 835 MB 2014-04-15
chr5-filtered-set-2014Apr15.bcf.csi 31 KB 2014-04-15
chr6-filtered-set-2014Apr15.bcf 651 MB 2014-04-15
chr6-filtered-set-2014Apr15.bcf.csi 25 KB 2014-04-15
chr7-filtered-set-2014Apr15.bcf 887 MB 2014-04-15
chr7-filtered-set-2014Apr15.bcf.csi 35 KB 2014-04-15
chr8-filtered-set-2014Apr15.bcf 825 MB 2014-04-15
chr8-filtered-set-2014Apr15.bcf.csi 32 KB 2014-04-15
chru-filtered-set-2014Apr15.bcf 453 MB 2014-04-15
chru-filtered-set-2014Apr15.bcf.csi 38 KB 2014-04-15
Sister Taxa to M. truncatula: Combined
Also includes deeply diverged M. truncatula lines.
 
sister-taxa-complete-set-2014Apr15.bcf 10 GB 2014-04-15
sister-taxa-complete-set-2014Apr15.bcf.csi 337 KB 2014-04-15
sister-taxa-filtered-set-2014Apr15.bcf 7 GB 2014-04-15
sister-taxa-filtered-set-2014Apr15.bcf.csi 314 KB 2014-04-15

Site hosted by: Nevin Young's Lab at University of Minnesota. Managed By: Joseph Guhlin

Primary Collaborators: INRA - Montpellier | ENSAT - Toulouse | Noble Foundation

Co-Principal Investigators: University of Minnesota N. Young, P. Tiffin, M. Sadowsky, B. Stupar, K. Silverstein | NCGR J. Mudge, A. Farmer

Boyce Thompson Institute M. Harrison | Hamline University B. Martinez-Vaz