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 mr1879 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
vg1217053914 sf1217047868 12 17053914 8.85E-13 2.39E-07
vg0728494505 sf0728493513 7 28494505 3.96E-11 NA
vg0310903678 sf0310902396 3 10903678 1.01E-10 NA
vg0528063279 sf0528000634 5 28063279 1.25E-10 NA
vg0805074667 sf0805073670 8 5074667 2.58E-10 NA
vg0223561654 sf0223555785 2 23561654 3.58E-10 4.68E-06
vg0107647091 sf0107646091 1 7647091 NA 2.11E-07