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 mr1274 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
vg0313808304 sf0313807021 3 13808304 2.45E-09 4.93E-07
vg0406561685 sf0406557128 4 6561685 6.90E-09 1.01E-06
vg0140818805 sf0140817762 1 40818805 1.75E-08 3.25E-07
vg0707304077 sf0707303082 7 7304077 2.46E-08 9.37E-07
vg0401488518 sf0401484068 4 1488518 2.78E-08 1.33E-06
vg0207313113 sf0207313113 2 7313113 4.19E-08 8.11E-07
vg0808245241 sf0808244245 8 8245241 7.16E-08 6.65E-07
vg1104497863 sf1104493765 11 4497863 7.79E-08 1.15E-06
vg0122322284 sf0122321239 1 22322284 1.39E-07 3.54E-07
vg0900355549 sf0900354549 9 355549 2.35E-07 2.27E-06
vg0405035806 sf0405031245 4 5035806 1.89E-06 NA