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
vg0314683577 sf0314682264 3 14683577 3.50E-07 3.50E-07
vg1012153349 sf1012082164 10 12153349 4.46E-07 4.46E-07
vg0329708419 sf0329701459 3 29708419 2.42E-06 2.42E-06
vg0402100710 sf0402096304 4 2100710 2.69E-06 2.69E-06
vg0215252496 sf0215246626 2 15252496 4.36E-06 4.36E-06
vg0314862466 sf0314861113 3 14862466 4.72E-06 4.72E-06
vg1216136207 sf1216133503 12 16136207 6.05E-06 6.05E-06