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 mr1146 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
vg1002771289 sf1002770266 10 2771289 7.18E-07 7.19E-07
vg0909928084 sf0909927083 9 9928084 1.04E-06 1.04E-06
vg0808122797 sf0808121801 8 8122797 1.34E-06 1.34E-06
vg1002367995 sf1002366972 10 2367995 2.77E-06 2.77E-06
vg0224565864 sf0224559995 2 24565864 3.49E-06 3.49E-06
vg0220985543 sf0220979675 2 20985543 3.54E-06 3.54E-06
vg0807994964 sf0807993968 8 7994964 4.63E-06 4.63E-06