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 mr1836 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
vg0317962584 sf0317961366 3 17962584 4.98E-10 1.37E-07
vg0317956486 sf0317955268 3 17956486 7.08E-10 1.40E-07
vg0321150603 sf0321149113 3 21150603 1.21E-08 5.23E-06
vg0817600286 sf0817597573 8 17600286 1.81E-08 5.28E-08
vg0818033565 sf0818030852 8 18033565 3.00E-08 3.69E-06
vg0817690102 sf0817687389 8 17690102 8.95E-08 8.34E-08
vg0320823032 sf0320821542 3 20823032 2.71E-07 3.76E-06
vg0515257828 sf0515200370 5 15257828 2.11E-06 2.05E-06
vg0401321153 sf0401316703 4 1321153 NA 4.14E-07
vg0408074000 sf0408069274 4 8074000 NA 1.51E-06