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 mr1034 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
vg0130113615 sf0130112570 1 30113615 1.84E-09 NA
vg0217651623 sf0217645753 2 17651623 2.89E-09 NA
vg1101359273 sf1101358274 11 1359273 1.81E-08 5.24E-06
vg0110154128 sf0110153104 1 10154128 8.53E-08 NA
vg1220078311 sf1220049753 12 20078311 2.06E-07 NA
vg0820586619 sf0820583906 8 20586619 1.48E-06 1.26E-06
vg0808705088 sf0808704092 8 8705088 6.77E-06 NA