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 mr1634 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
vg0205851172 sf0205851172 2 5851172 4.50E-08 4.50E-08
vg0112384462 sf0112383436 1 12384462 1.41E-06 1.41E-06
vg0124420479 sf0124419435 1 24420479 1.68E-06 1.68E-06
vg0808428148 sf0808427152 8 8428148 2.68E-06 2.68E-06
vg0228320179 sf0228314310 2 28320179 3.66E-06 3.66E-06
vg1120839610 sf1120373513 11 20839610 3.99E-06 3.99E-06
vg0610852582 sf0610851583 6 10852582 4.58E-06 4.58E-06
vg1117799956 sf1117333812 11 17799956 4.76E-06 4.76E-06