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 mr1021 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
vg1222403923 sf1222370362 12 22403923 8.46E-09 9.21E-06
vg0137605963 sf0137604920 1 37605963 1.23E-08 NA
vg1217341446 sf1217335401 12 17341446 2.25E-08 NA
vg1222579005 sf1222545444 12 22579005 1.72E-07 1.09E-06
vg0515943111 sf0515885618 5 15943111 8.47E-07 NA
vg0518363321 sf0518302807 5 18363321 5.39E-06 8.75E-07
vg0225887862 sf0225881993 2 25887862 5.63E-06 NA
vg0915432595 sf0915431594 9 15432595 NA 1.62E-06