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 mr1032 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
vg0614945451 sf0614944452 6 14945451 6.93E-11 6.93E-11
vg0608909772 sf0608908773 6 8909772 1.28E-09 1.28E-09
vg0610774978 sf0610773979 6 10774978 3.47E-09 3.47E-09
vg0611846746 sf0611845747 6 11846746 3.00E-08 3.00E-08
vg0621021467 sf0621020470 6 21021467 2.43E-07 2.43E-07