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 mr1444 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
vg0315312443 sf0315311090 3 15312443 3.81E-09 NA
vg0312522964 sf0312521682 3 12522964 5.25E-09 NA
vg0820434015 sf0820431302 8 20434015 4.00E-08 NA
vg1117514629 sf1117048484 11 17514629 4.18E-08 7.33E-06
vg0507694055 sf0507693996 5 7694055 5.93E-08 NA
vg0141047242 sf0141046199 1 41047242 5.67E-06 NA
vg0320463339 sf0320461850 3 20463339 9.54E-06 1.69E-06
vg0104000380 sf0103999380 1 4000380 NA 4.87E-06