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 mr1977 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
vg0301124195 sf0301123193 3 1124195 9.86E-07 2.03E-06
vg1217706014 sf1217699969 12 17706014 2.81E-06 NA
vg0601745967 sf0601744968 6 1745967 3.10E-06 NA
vg0434406763 sf0434221657 4 34406763 8.68E-06 NA
vg0526341867 sf0526279230 5 26341867 NA 2.02E-06
vg0611545338 sf0611544339 6 11545338 NA 3.15E-06
vg0140618489 sf0140617446 1 40618489 NA 6.40E-06