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 mr1198 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
vg1002090827 sf1002089804 10 2090827 9.01E-13 2.41E-06
vg0817258360 sf0817255646 8 17258360 4.49E-12 NA
vg0208735762 sf0208735761 2 8735762 6.06E-12 NA
vg1217551232 sf1217545187 12 17551232 1.19E-11 NA
vg0317844794 sf0317843576 3 17844794 1.33E-11 NA
vg0216666081 sf0216660211 2 16666081 4.17E-11 6.75E-08
vg0106182650 sf0106181650 1 6182650 1.94E-10 NA
vg1215172366 sf1215169702 12 15172366 4.59E-10 4.62E-06
vg1215175187 sf1215172523 12 15175187 4.88E-10 4.60E-06
vg0314967098 sf0314965745 3 14967098 NA 5.80E-07
vg0314888685 sf0314887332 3 14888685 NA 9.78E-07
vg0808829838 sf0808828842 8 8829838 NA 3.10E-06