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 mr1582 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
vg0100431870 sf0100430870 1 431870 5.95E-11 9.63E-06
vg0624609971 sf0624608974 6 24609971 6.19E-10 NA
vg1209056273 sf1209053682 12 9056273 1.57E-09 NA
vg0619806827 sf0619805830 6 19806827 3.07E-09 NA
vg0314128708 sf0314127397 3 14128708 7.55E-09 NA
vg1109920086 sf1109914663 11 9920086 2.95E-07 3.83E-07
vg0600800692 sf0600799693 6 800692 4.42E-07 NA
vg0516076751 sf0516019235 5 16076751 7.40E-06 NA