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 mr1243 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
vg0216772798 sf0216766928 2 16772798 6.82E-15 3.36E-13
vg0216721532 sf0216715662 2 16721532 4.04E-10 1.01E-08
vg0220342684 sf0220336816 2 20342684 5.16E-09 2.28E-07
vg0804975535 sf0804974538 8 4975535 4.47E-08 2.57E-06
vg1112935039 sf1112471360 11 12935039 7.91E-08 2.04E-06
vg0218518468 sf0218512599 2 18518468 8.83E-08 1.87E-06
vg1114473442 sf1114009759 11 14473442 1.62E-07 2.52E-06
vg1005364262 sf1005380799 10 5364262 1.31E-06 3.82E-06
vg0107383822 sf0107382822 1 7383822 NA 4.25E-06