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 mr1474 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
vg0300330721 sf0300329719 3 330721 9.91E-10 NA
vg0306341565 sf0306340565 3 6341565 1.81E-08 NA
vg1207382181 sf1207379588 12 7382181 2.47E-08 NA
vg0125967068 sf0125966024 1 25967068 6.08E-08 NA
vg0210693850 sf0210693848 2 10693850 6.35E-08 NA
vg0401249611 sf0401245161 4 1249611 1.11E-06 NA
vg0306142106 sf0306141106 3 6142106 1.28E-06 2.90E-06
vg0137230062 sf0137229019 1 37230062 NA 1.16E-06
vg0820796944 sf0820794231 8 20796944 NA 2.85E-06