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 mr1131 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
vg0719208431 sf0719207438 7 19208431 6.53E-27 2.04E-09
vg0707583684 sf0707582689 7 7583684 1.02E-22 NA
vg0304920678 sf0304919680 3 4920678 2.88E-22 NA
vg0205797280 sf0205797280 2 5797280 1.44E-21 NA
vg1201451787 sf1201450787 12 1451787 1.73E-21 NA
vg0304997671 sf0304996673 3 4997671 4.36E-20 4.07E-06
vg0719057980 sf0719056987 7 19057980 NA 1.51E-06