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 mr1149 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
vg0222718166 sf0222712297 2 22718166 5.77E-31 8.69E-20
vg0223769163 sf0223763294 2 23769163 1.26E-12 1.09E-07
vg0224293556 sf0224287687 2 24293556 6.64E-10 1.58E-06
vg0224832365 sf0224826496 2 24832365 8.80E-10 6.45E-06
vg1112606104 sf1112142307 11 12606104 8.40E-09 NA
vg0222673059 sf0222667190 2 22673059 3.23E-07 1.16E-07
vg1217237364 sf1217231319 12 17237364 1.54E-06 2.62E-06
vg0711574504 sf0711573510 7 11574504 6.97E-06 3.04E-06