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 mr1888 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
vg0203000556 sf0203000554 2 3000556 4.54E-08 7.42E-06
vg0406465683 sf0406461126 4 6465683 2.99E-07 2.31E-08
vg1204382187 sf1204381175 12 4382187 1.97E-06 NA
vg0810864582 sf0810863587 8 10864582 4.39E-06 4.22E-06
vg0714249759 sf0714248766 7 14249759 5.33E-06 4.37E-06
vg0406056794 sf0406052233 4 6056794 NA 1.13E-06