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 mr1420 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
vg1218087170 sf1218058606 12 18087170 1.70E-11 4.44E-07
vg0623156256 sf0623155259 6 23156256 2.53E-10 4.32E-06
vg0323854038 sf0323852212 3 23854038 5.58E-10 NA
vg0208849037 sf0208849035 2 8849037 1.77E-09 NA
vg0618125425 sf0618124428 6 18125425 2.42E-09 NA
vg0819094093 sf0819091380 8 19094093 3.84E-08 NA
vg1128910848 sf1128387627 11 28910848 9.87E-08 NA
vg1009009289 sf1008938150 10 9009289 NA 4.00E-06
vg0125127326 sf0125126282 1 25127326 NA 4.92E-06