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 mr1233 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
vg0719300893 sf0719299900 7 19300893 4.68E-19 1.56E-14
vg0719208938 sf0719207945 7 19208938 1.42E-17 8.85E-15
vg0228211032 sf0228205163 2 28211032 6.24E-10 3.79E-06
vg0719140447 sf0719139454 7 19140447 6.59E-10 1.46E-07
vg0719465974 sf0719464981 7 19465974 1.02E-08 1.40E-07
vg0336364525 sf0336357395 3 36364525 2.60E-08 1.30E-06
vg0228210940 sf0228205071 2 28210940 3.30E-08 2.50E-06
vg0715949888 sf0715948895 7 15949888 3.48E-08 1.28E-06
vg0336362940 sf0336355810 3 36362940 5.76E-08 9.21E-07
vg1207833484 sf1207830890 12 7833484 8.59E-08 2.96E-06
vg0718994741 sf0718993748 7 18994741 2.64E-07 1.34E-06
vg0610442617 sf0610441618 6 10442617 3.07E-07 4.52E-06
vg1216729892 sf1216723846 12 16729892 3.32E-07 2.21E-07
vg0718984214 sf0718983221 7 18984214 4.00E-07 2.28E-08
vg1106800673 sf1106796426 11 6800673 5.07E-07 7.12E-07
vg0118543379 sf0118542333 1 18543379 8.46E-07 NA
vg0719453364 sf0719452371 7 19453364 2.74E-06 1.60E-06
vg0808431667 sf0808430671 8 8431667 NA 1.90E-06
vg0808426459 sf0808425463 8 8426459 NA 2.07E-06
vg1121543479 sf1121077356 11 21543479 NA 3.97E-06
vg1214384242 sf1214381583 12 14384242 NA 4.90E-06
vg0525497182 sf0525434603 5 25497182 NA 8.39E-06