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 mr1994 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
vg0123793333 sf0123792289 1 23793333 3.37E-08 3.37E-08
vg1117484421 sf1117018276 11 17484421 1.05E-06 1.05E-06
vg0517733960 sf0517673601 5 17733960 1.20E-06 1.20E-06
vg0706284147 sf0706283150 7 6284147 1.65E-06 1.65E-06
vg0420279302 sf0420107347 4 20279302 1.70E-06 1.70E-06
vg0909417437 sf0909416436 9 9417437 2.30E-06 2.29E-06
vg0910606255 sf0910605254 9 10606255 2.72E-06 2.72E-06
vg0225037217 sf0225031348 2 25037217 3.47E-06 3.46E-06
vg0219500936 sf0219495068 2 19500936 4.13E-06 4.13E-06
vg0910734141 sf0910733140 9 10734141 4.38E-06 4.39E-06
vg1009290760 sf1009219581 10 9290760 4.91E-06 4.90E-06
vg0208337162 sf0208337161 2 8337162 8.82E-06 8.80E-06