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 mr1964 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
vg0418242514 sf0418070560 4 18242514 2.61E-08 3.35E-06
vg0902272767 sf0902271767 9 2272767 1.39E-06 NA
vg0220199951 sf0220194083 2 20199951 1.76E-06 4.41E-06
vg0407784068 sf0407779336 4 7784068 4.60E-06 NA
vg0434013322 sf0433828213 4 34013322 NA 4.62E-06