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 mr1534 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
vg0430538314 sf0430353189 4 30538314 5.76E-13 1.82E-08
vg0916498845 sf0916497844 9 16498845 1.95E-09 1.80E-06
vg0114807948 sf0114806922 1 14807948 2.65E-09 NA
vg0225162124 sf0225156255 2 25162124 1.29E-08 NA
vg0434888110 sf0434703002 4 34888110 2.42E-08 NA