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 mr1403 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
vg0414207803 sf0414198519 4 14207803 5.87E-11 NA
vg0408052694 sf0408047966 4 8052694 1.02E-10 NA
vg1220040338 sf1220011780 12 20040338 1.71E-09 NA
vg0408089486 sf0408084760 4 8089486 1.05E-08 NA
vg0410703197 sf0410693899 4 10703197 1.45E-08 NA
vg0126378704 sf0126377660 1 26378704 1.67E-08 NA
vg0225362516 sf0225356647 2 25362516 8.86E-08 NA
vg1009642237 sf1009571058 10 9642237 NA 5.29E-06
vg0103148298 sf0103147298 1 3148298 NA 5.61E-06