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 mr1460 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
vg1105811378 sf1105807130 11 5811378 7.23E-07 7.23E-07
vg1105852239 sf1105847991 11 5852239 1.90E-06 1.90E-06
vg0607344108 sf0607343109 6 7344108 1.92E-06 1.92E-06
vg0105478106 sf0105477106 1 5478106 2.61E-06 2.61E-06
vg0203293759 sf0203293757 2 3293759 3.50E-06 3.50E-06
vg0505812393 sf0505812331 5 5812393 4.46E-06 4.46E-06