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 mr1111 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
vg0610588684 sf0610587685 6 10588684 2.02E-12 1.57E-09
vg0610737979 sf0610736980 6 10737979 1.10E-11 4.09E-12
vg0610118958 sf0610117959 6 10118958 3.27E-10 6.11E-08
vg0610756191 sf0610755192 6 10756191 1.27E-09 2.56E-09
vg1214763416 sf1214760757 12 14763416 1.20E-08 7.53E-06
vg0616129303 sf0616128305 6 16129303 9.79E-07 3.39E-06