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 mr1604 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
vg0823144488 sf0823141775 8 23144488 2.10E-11 NA
vg1104987798 sf1104983609 11 4987798 3.18E-11 NA
vg1227173062 sf1227139462 12 27173062 4.13E-11 NA
vg0235046801 sf0235040932 2 35046801 1.10E-10 NA
vg0130364087 sf0130363043 1 30364087 1.64E-10 NA
vg0207690117 sf0207690117 2 7690117 3.26E-08 5.50E-06
vg0906603966 sf0906602966 9 6603966 1.26E-07 NA
vg0434768134 sf0434583025 4 34768134 NA 2.39E-07
vg1125669886 sf1125203725 11 25669886 NA 2.73E-06
vg0105696451 sf0105695451 1 5696451 NA 4.18E-06