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 mr1326 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
vg0519281720 sf0519219204 5 19281720 1.90E-09 NA
vg0315486151 sf0315484798 3 15486151 1.27E-08 1.62E-06
vg0300375981 sf0300374979 3 375981 3.27E-08 NA
vg0415328744 sf0415319460 4 15328744 4.55E-08 NA
vg1122770823 sf1122304694 11 22770823 8.25E-08 NA
vg0519159149 sf0519096633 5 19159149 1.47E-07 3.08E-06
vg0706513088 sf0706512093 7 6513088 7.89E-07 2.10E-06
vg1000404968 sf1000403968 10 404968 8.52E-06 NA
vg0816417852 sf0816415138 8 16417852 9.64E-06 NA
vg0328066679 sf0328059733 3 28066679 NA 4.22E-06