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 mr1591 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
vg1104978992 sf1104974803 11 4978992 3.20E-09 3.20E-09
vg0820865298 sf0820862585 8 20865298 1.29E-07 1.29E-07
vg0130689494 sf0130688450 1 30689494 2.37E-07 2.37E-07
vg1105750981 sf1105746733 11 5750981 2.53E-06 2.53E-06
vg0511023890 sf0511023819 5 11023890 2.56E-06 2.56E-06
vg0228600547 sf0228594678 2 28600547 3.75E-06 3.75E-06
vg0514184495 sf0514127039 5 14184495 4.69E-06 4.69E-06