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 mr1549 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
vg1104609253 sf1104605155 11 4609253 4.77E-08 4.30E-06
vg1214799098 sf1214796439 12 14799098 8.02E-07 2.95E-06
vg1104204113 sf1104200015 11 4204113 1.22E-06 1.03E-06
vg0119732348 sf0119731303 1 19732348 3.88E-06 3.31E-06
vg1205728884 sf1205727866 12 5728884 6.83E-06 NA
vg1104596397 sf1104592299 11 4596397 NA 3.78E-06