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 mr1685 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
vg1003779182 sf1003778158 10 3779182 1.64E-06 3.73E-06
vg0209233917 sf0209233915 2 9233917 3.28E-06 2.08E-06
vg1218127805 sf1218099241 12 18127805 4.68E-06 3.20E-06
vg1018711746 sf1018640303 10 18711746 5.42E-06 NA
vg1106569715 sf1106565468 11 6569715 7.65E-06 2.01E-06