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 mr1333 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
vg0519079761 sf0519017245 5 19079761 4.42E-09 NA
vg0619807095 sf0619806098 6 19807095 1.53E-06 NA
vg0721760138 sf0721759145 7 21760138 5.29E-06 NA
vg1122688601 sf1122222472 11 22688601 7.79E-06 NA
vg0221470237 sf0221464368 2 21470237 NA 3.69E-06