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 mr1033 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
vg0613474765 sf0613473766 6 13474765 3.44E-133 5.28E-31
vg0613465733 sf0613464734 6 13465733 1.06E-131 2.69E-36
vg0617844295 sf0617843298 6 17844295 1.01E-125 4.84E-25
vg0617831675 sf0617830678 6 17831675 7.35E-124 4.33E-27
vg0620693330 sf0620692333 6 20693330 9.51E-107 NA
vg0621021040 sf0621020043 6 21021040 1.49E-97 4.73E-11
vg0613452716 sf0613451717 6 13452716 NA 1.75E-18
vg0613478814 sf0613477815 6 13478814 NA 4.15E-13
vg0618987742 sf0618986745 6 18987742 NA 1.08E-09
vg0617852766 sf0617851769 6 17852766 NA 2.64E-09
vg0506428153 sf0506428093 5 6428153 NA 1.14E-08