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 mr1982 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
vg0208149227 sf0208149226 2 8149227 1.64E-08 NA
vg0914657992 sf0914656991 9 14657992 1.75E-08 NA
vg0120188568 sf0120187523 1 20188568 2.60E-08 7.07E-06
vg0232065371 sf0232059502 2 32065371 5.15E-08 NA
vg0819358516 sf0819355803 8 19358516 7.23E-08 NA
vg1016131635 sf1016060407 10 16131635 7.99E-08 3.59E-06
vg0908536377 sf0908535376 9 8536377 1.44E-06 3.73E-06
vg1118314742 sf1117848600 11 18314742 6.46E-06 NA