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 mr1652 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
vg0329834062 sf0329827101 3 29834062 1.05E-10 NA
vg0922565216 sf0922564735 9 22565216 1.52E-10 NA
vg0332498725 sf0332491598 3 32498725 1.71E-10 NA
vg0517802938 sf0517742424 5 17802938 2.43E-10 NA
vg0827873144 sf0827870430 8 27873144 5.24E-10 NA
vg0517819523 sf0517759009 5 17819523 1.01E-09 NA
vg0709538360 sf0709537366 7 9538360 5.24E-07 NA
vg0906168357 sf0906167357 9 6168357 1.51E-06 NA
vg0801474449 sf0801473451 8 1474449 NA 2.43E-06
vg0505677328 sf0505677266 5 5677328 NA 3.58E-06
vg0709446609 sf0709445615 7 9446609 NA 4.36E-06