Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1940 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0121172559 sf0121171514 1 21172559 1.90E-09 1.90E-09
vg0434580936 sf0434395828 4 34580936 6.53E-09 6.53E-09
vg0401779398 sf0401774994 4 1779398 9.87E-09 9.87E-09
vg0912801939 sf0912800938 9 12801939 5.11E-08 5.11E-08
vg0200274146 sf0200274146 2 274146 1.10E-07 1.10E-07
vg0507480268 sf0507480210 5 7480268 1.83E-07 1.83E-07
vg0107554036 sf0107553036 1 7554036 1.88E-07 1.88E-07
vg0919039056 sf0919038056 9 19039056 2.11E-07 2.11E-07
vg1207772422 sf1207769828 12 7772422 2.26E-07 2.25E-07
vg0139109454 sf0139108411 1 39109454 7.02E-07 7.02E-07
vg0335027666 sf0335020536 3 35027666 7.63E-07 7.63E-07
vg0722719316 sf0722718323 7 22719316 8.34E-07 8.34E-07
vg0124523825 sf0124522781 1 24523825 1.54E-06 1.54E-06
vg1215125172 sf1215122508 12 15125172 2.02E-06 2.02E-06
vg0902893640 sf0902892640 9 2893640 3.28E-06 3.28E-06
vg0308773264 sf0308772202 3 8773264 4.93E-06 4.93E-06