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 mr1845 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
vg0309414251 sf0309413187 3 9414251 3.54E-07 3.54E-07
vg0600058626 sf0600057626 6 58626 6.03E-07 6.04E-07
vg0320912059 sf0320910569 3 20912059 7.33E-07 7.34E-07
vg0229180325 sf0229174456 2 29180325 1.02E-06 1.02E-06
vg0423536187 sf0423351044 4 23536187 1.45E-06 1.45E-06
vg0403406131 sf0403401734 4 3406131 1.85E-06 1.85E-06
vg1118012029 sf1117545887 11 18012029 3.92E-06 3.92E-06
vg0421232041 sf0421060093 4 21232041 3.99E-06 3.99E-06
vg1104173599 sf1104169501 11 4173599 3.99E-06 3.99E-06
vg0204366436 sf0204366433 2 4366436 6.26E-06 6.26E-06