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 mr1228 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
vg1215106857 sf1215104194 12 15106857 1.18E-08 8.07E-07
vg0418086846 sf0417914887 4 18086846 5.43E-08 1.73E-06
vg0228612357 sf0228606488 2 28612357 6.77E-08 1.60E-06
vg0418095232 sf0417923273 4 18095232 7.60E-08 1.65E-06
vg0403315819 sf0403311422 4 3315819 7.73E-08 9.81E-07
vg0222329370 sf0222323501 2 22329370 1.35E-07 4.65E-06
vg0902893640 sf0902892640 9 2893640 3.76E-07 9.02E-07
vg0819942032 sf0819939319 8 19942032 6.60E-07 NA
vg0418087588 sf0417915629 4 18087588 1.06E-06 4.47E-06