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 mr1382 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
vg0521601877 sf0521539318 5 21601877 1.17E-06 7.21E-07
vg0312535741 sf0312534459 3 12535741 1.91E-06 1.99E-06
vg1117431373 sf1116965228 11 17431373 4.15E-06 4.37E-06
vg1216729892 sf1216723846 12 16729892 7.42E-06 1.25E-06
vg0407630134 sf0407625401 4 7630134 NA 2.83E-06
vg0419331192 sf0419159230 4 19331192 NA 7.71E-06