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 mr1866 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
vg1215634916 sf1215632213 12 15634916 4.06E-08 NA
vg0108674689 sf0108673689 1 8674689 4.58E-08 NA
vg0413862399 sf0413853117 4 13862399 5.10E-08 7.27E-09
vg0820513390 sf0820510677 8 20513390 2.98E-07 NA
vg1004369207 sf1004385745 10 4369207 1.06E-06 NA
vg1110446917 sf1110441462 11 10446917 1.72E-06 4.70E-06
vg0317321849 sf0317320659 3 17321849 7.82E-06 NA
vg1109865325 sf1109859902 11 9865325 NA 4.72E-06