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 mr1728 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
vg0808728664 sf0808727668 8 8728664 1.89E-07 1.89E-07
vg0803686550 sf0803685553 8 3686550 7.32E-07 7.32E-07
vg0823006156 sf0823003443 8 23006156 1.36E-06 1.36E-06
vg0823689104 sf0823686390 8 23689104 1.53E-06 1.53E-06
vg1103859312 sf1103855214 11 3859312 1.73E-06 1.73E-06
vg1124320519 sf1123854389 11 24320519 4.44E-06 4.44E-06