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 mr1643 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
vg0709984451 sf0709983457 7 9984451 3.58E-07 3.58E-07
vg1210189485 sf1210186896 12 10189485 3.76E-07 3.76E-07
vg0710393331 sf0710392337 7 10393331 1.63E-06 1.63E-06
vg0712646803 sf0712645810 7 12646803 2.51E-06 2.51E-06
vg0711201796 sf0711200802 7 11201796 3.92E-06 3.92E-06
vg0712354470 sf0712353477 7 12354470 4.70E-06 4.70E-06