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 mr1933 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
vg0331273085 sf0331265970 3 31273085 2.92E-21 1.61E-08
vg0124114468 sf0124113424 1 24114468 3.22E-19 NA
vg0724592432 sf0724591438 7 24592432 8.89E-18 1.46E-08
vg0319913239 sf0319911750 3 19913239 1.18E-17 NA
vg0234765423 sf0234759554 2 34765423 2.05E-17 NA
vg1002842933 sf1002841910 10 2842933 4.57E-16 2.27E-06
vg0503396062 sf0503396039 5 3396062 NA 1.55E-06
vg0725235447 sf0725234453 7 25235447 NA 3.07E-06
vg0404416226 sf0404411830 4 4416226 NA 3.84E-06
vg0331256576 sf0331249461 3 31256576 NA 4.54E-06