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 mr1828 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
vg1128368057 sf1127844836 11 28368057 6.02E-08 6.02E-08
vg0421395712 sf0421223765 4 21395712 1.06E-06 1.06E-06
vg0209100423 sf0209100421 2 9100423 1.58E-06 1.58E-06
vg0709480436 sf0709479442 7 9480436 3.37E-06 3.37E-06
vg0519396234 sf0519333718 5 19396234 4.79E-06 4.79E-06