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 mr1027 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
vg0521003207 sf0520940648 5 21003207 2.41E-76 NA
vg0206010341 sf0206010341 2 6010341 2.31E-75 NA
vg0208996721 sf0208996719 2 8996721 1.76E-74 NA
vg0133616436 sf0133615392 1 33616436 2.18E-74 3.97E-07
vg0133476794 sf0133475750 1 33476794 4.22E-74 1.78E-07
vg0215052036 sf0215046166 2 15052036 7.51E-74 NA
vg1008681328 sf1008610190 10 8681328 NA 3.08E-07
vg1006430096 sf1006445719 10 6430096 NA 7.78E-07
vg0124426824 sf0124425780 1 24426824 NA 3.67E-06
vg1007792154 sf1007807764 10 7792154 NA 4.22E-06
vg0207187961 sf0207187961 2 7187961 NA 6.27E-06
vg0610636473 sf0610635474 6 10636473 NA 6.75E-06