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 mr1971 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
vg0615169965 sf0615168966 6 15169965 2.19E-12 1.07E-09
vg0610774978 sf0610773979 6 10774978 1.78E-10 2.09E-07
vg0611519166 sf0611518167 6 11519166 3.15E-10 5.65E-09
vg0608909772 sf0608908773 6 8909772 3.01E-09 3.27E-07
vg0611846746 sf0611845747 6 11846746 3.90E-09 1.04E-07
vg0608926537 sf0608925538 6 8926537 1.35E-08 2.84E-07
vg0611482314 sf0611481315 6 11482314 6.04E-08 1.91E-07
vg0728961881 sf0728960889 7 28961881 NA 8.36E-09
vg0118403800 sf0118402754 1 18403800 NA 2.03E-07
vg0620701377 sf0620700380 6 20701377 NA 3.52E-06
vg0322429158 sf0322427647 3 22429158 NA 4.37E-06
vg0618089803 sf0618088806 6 18089803 NA 4.55E-06