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 mr1890 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
vg0215252496 sf0215246626 2 15252496 2.26E-08 2.26E-08
vg0327997014 sf0327990068 3 27997014 9.36E-07 9.36E-07
vg0314683577 sf0314682264 3 14683577 1.48E-06 1.48E-06
vg0206906369 sf0206906369 2 6906369 2.01E-06 2.01E-06
vg0402100710 sf0402096304 4 2100710 2.36E-06 2.36E-06