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 mr1436 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
vg0719041786 sf0719040793 7 19041786 2.17E-11 2.17E-11
vg0719065500 sf0719064507 7 19065500 1.63E-09 1.63E-09
vg1213429246 sf1213426584 12 13429246 1.85E-07 1.85E-07
vg1216198926 sf1216196222 12 16198926 1.91E-07 1.91E-07
vg0406192421 sf0406187861 4 6192421 2.12E-07 2.12E-07
vg0107198487 sf0107197487 1 7198487 3.42E-07 3.42E-07
vg0517737761 sf0517677402 5 17737761 4.47E-07 4.47E-07
vg1020494793 sf1020423272 10 20494793 1.99E-06 1.99E-06
vg0124666730 sf0124665686 1 24666730 2.71E-06 2.71E-06
vg0408294186 sf0408289460 4 8294186 2.72E-06 2.72E-06
vg0228933475 sf0228927606 2 28933475 2.77E-06 2.77E-06
vg0602255305 sf0602254306 6 2255305 3.51E-06 3.51E-06
vg0726455031 sf0726454037 7 26455031 4.09E-06 4.09E-06