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 mr1154 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
vg0130670983 sf0130669939 1 30670983 2.77E-13 1.18E-09
vg1203606223 sf1203605222 12 3606223 5.52E-09 NA
vg0103512299 sf0103511299 1 3512299 6.68E-09 NA
vg0135794714 sf0135793671 1 35794714 3.33E-08 NA
vg0304269557 sf0304268559 3 4269557 7.47E-08 NA
vg0139966045 sf0139965002 1 39966045 1.03E-07 9.22E-07
vg0131232372 sf0131231328 1 31232372 NA 1.41E-06