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 mr1531 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
vg0507148940 sf0507148882 5 7148940 4.88E-15 1.47E-10
vg0230392490 sf0230386621 2 30392490 1.03E-11 NA
vg0229400708 sf0229394839 2 29400708 1.23E-11 NA
vg0500304693 sf0500304693 5 304693 8.72E-11 NA
vg0905251599 sf0905250599 9 5251599 1.77E-10 NA
vg0500246375 sf0500246375 5 246375 7.30E-10 2.79E-06
vg0223736839 sf0223730970 2 23736839 1.88E-07 3.57E-06
vg0232031755 sf0232025886 2 32031755 NA 3.58E-06