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 mr1046 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
vg0431515534 sf0431330433 4 31515534 2.83E-06 2.84E-06
vg0815304114 sf0815301400 8 15304114 3.58E-06 3.59E-06
vg0115899007 sf0115897981 1 15899007 4.21E-06 4.22E-06
vg0719511488 sf0719510495 7 19511488 4.82E-06 4.83E-06
vg0608111689 sf0608110690 6 8111689 4.92E-06 4.92E-06