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 mr1914 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
vg0217124073 sf0217118203 2 17124073 2.00E-29 3.87E-15
vg0217102196 sf0217096326 2 17102196 1.76E-22 5.39E-18
vg0217108891 sf0217103021 2 17108891 2.08E-22 3.31E-18
vg0217124463 sf0217118593 2 17124463 4.05E-21 4.01E-18
vg0808046261 sf0808045265 8 8046261 3.92E-16 NA
vg1205555293 sf1205554279 12 5555293 1.33E-15 NA
vg0205331757 sf0205331756 2 5331757 4.13E-15 NA
vg0216573861 sf0216567991 2 16573861 NA 2.98E-06
vg0217615900 sf0217610030 2 17615900 NA 5.95E-06