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 mr1729 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
vg0414235746 sf0414226459 4 14235746 3.04E-14 3.87E-08
vg0414211322 sf0414202035 4 14211322 3.84E-12 1.55E-08
vg0314622348 sf0314621035 3 14622348 5.89E-12 NA
vg0315006527 sf0315005174 3 15006527 2.06E-11 1.74E-06
vg0414207978 sf0414198694 4 14207978 2.70E-11 1.91E-06
vg0315008841 sf0315007488 3 15008841 3.08E-11 4.80E-06
vg1100779104 sf1100778105 11 779104 6.81E-11 NA
vg0728386754 sf0728385762 7 28386754 7.22E-11 NA
vg1000080430 sf1000079430 10 80430 4.39E-10 NA