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 mr1823 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
vg0819603039 sf0819600326 8 19603039 2.25E-12 4.95E-10
vg0726964336 sf0726963342 7 26964336 1.11E-08 NA
vg0123708079 sf0123707035 1 23708079 2.11E-08 NA
vg0217846554 sf0217840685 2 17846554 5.76E-08 NA
vg0819985140 sf0819982427 8 19985140 9.39E-08 7.69E-06
vg0820873126 sf0820870413 8 20873126 2.69E-07 4.44E-07
vg0127428591 sf0127427547 1 27428591 2.95E-06 1.61E-06
vg0113652030 sf0113651004 1 13652030 5.51E-06 2.11E-06
vg0807847137 sf0807846141 8 7847137 NA 8.38E-06