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 mr1181 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
vg0715665085 sf0715664092 7 15665085 1.87E-32 NA
vg0620988799 sf0620987802 6 20988799 3.48E-31 NA
vg0718993703 sf0718992710 7 18993703 4.91E-31 NA
vg0612896542 sf0612895543 6 12896542 2.67E-30 NA
vg0428607142 sf0428421993 4 28607142 3.76E-30 NA
vg0719317459 sf0719316466 7 19317459 8.69E-28 NA
vg0724558639 sf0724557645 7 24558639 2.00E-26 2.21E-07
vg0804382774 sf0804381777 8 4382774 2.82E-26 2.60E-06