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 mr1781 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
vg1219761706 sf1219733176 12 19761706 5.11E-15 NA
vg0904366177 sf0904365177 9 4366177 2.90E-14 NA
vg0616045271 sf0616044273 6 16045271 3.83E-14 6.87E-06
vg0820982018 sf0820979305 8 20982018 3.92E-14 3.55E-06
vg0232206014 sf0232200145 2 32206014 5.65E-14 NA
vg0821013869 sf0821011156 8 21013869 1.18E-13 1.72E-06
vg1107364083 sf1107359828 11 7364083 3.22E-13 1.28E-06
vg1227405673 sf1227372073 12 27405673 1.19E-11 NA
vg0615248067 sf0615247068 6 15248067 1.19E-11 NA
vg1117363278 sf1116897130 11 17363278 NA 9.92E-07
vg0720751948 sf0720750955 7 20751948 NA 2.59E-06
vg0909181183 sf0909180182 9 9181183 NA 2.69E-06