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 mr1308 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
vg1019998215 sf1019926714 10 19998215 5.33E-12 3.69E-07
vg1217257158 sf1217251113 12 17257158 1.85E-10 NA
vg0815981055 sf0815978341 8 15981055 2.33E-09 NA
vg0724098043 sf0724097049 7 24098043 4.96E-09 NA
vg0506364463 sf0506364402 5 6364463 5.09E-09 NA