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 mr1764 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
vg0504650681 sf0504650658 5 4650681 6.93E-08 6.93E-08
vg0221993684 sf0221987815 2 21993684 3.27E-07 3.27E-07
vg0327981236 sf0327974290 3 27981236 3.43E-06 3.43E-06
vg0714405504 sf0714404511 7 14405504 6.82E-06 6.82E-06
vg0627106014 sf0627105017 6 27106014 8.55E-06 8.55E-06