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 mr1891 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
vg0710985476 sf0710984482 7 10985476 5.86E-09 5.86E-09
vg0907175535 sf0907174535 9 7175535 1.21E-07 1.21E-07
vg0130689494 sf0130688450 1 30689494 8.05E-07 8.05E-07
vg0229752031 sf0229746162 2 29752031 1.48E-06 1.48E-06
vg0130836121 sf0130835077 1 30836121 1.71E-06 1.71E-06
vg0501827640 sf0501827623 5 1827640 2.00E-06 2.00E-06
vg0501785216 sf0501785199 5 1785216 2.06E-06 2.06E-06
vg0215735517 sf0215729647 2 15735517 2.75E-06 2.75E-06
vg0404029438 sf0404025045 4 4029438 3.27E-06 3.27E-06
vg1121614615 sf1121148492 11 21614615 3.72E-06 3.72E-06