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 mr1894 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
vg1117584893 sf1117118750 11 17584893 1.74E-07 1.74E-07
vg0507616861 sf0507616802 5 7616861 7.09E-07 7.09E-07
vg0140613900 sf0140612857 1 40613900 1.07E-06 1.07E-06
vg0507626279 sf0507626220 5 7626279 1.35E-06 1.35E-06
vg0808451668 sf0808450672 8 8451668 1.42E-06 1.42E-06
vg0507614897 sf0507614838 5 7614897 3.72E-06 3.72E-06
vg0210259508 sf0210259506 2 10259508 3.99E-06 3.99E-06
vg0808817077 sf0808816081 8 8817077 4.60E-06 4.60E-06