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 mr1651 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
vg0424008068 sf0423822926 4 24008068 3.99E-07 3.99E-07
vg0402982636 sf0402978242 4 2982636 8.87E-07 8.87E-07
vg0105363238 sf0105362238 1 5363238 1.65E-06 1.65E-06
vg0105366812 sf0105365812 1 5366812 2.14E-06 2.14E-06
vg0510928675 sf0510928604 5 10928675 2.39E-06 2.39E-06
vg1214852727 sf1214850068 12 14852727 2.91E-06 2.91E-06
vg0916034764 sf0916033763 9 16034764 4.03E-06 4.03E-06
vg0406789502 sf0406784947 4 6789502 4.13E-06 4.13E-06