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 mr1696 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
vg0910719144 sf0910718143 9 10719144 3.85E-07 4.34E-06
vg0312535741 sf0312534459 3 12535741 1.64E-06 3.90E-06
vg0521601877 sf0521539318 5 21601877 8.43E-06 1.90E-06
vg0105231400 sf0105230400 1 5231400 8.92E-06 NA
vg1022634833 sf1022563307 10 22634833 9.02E-06 NA