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 mr1318 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
vg1224515996 sf1224482450 12 24515996 2.29E-08 5.53E-08
vg0431872453 sf0431687347 4 31872453 4.72E-08 2.13E-06
vg1123155726 sf1122689597 11 23155726 5.31E-08 NA
vg0431889500 sf0431704395 4 31889500 2.58E-07 8.11E-08
vg0316985667 sf0316984541 3 16985667 1.69E-06 5.56E-07
vg0431240137 sf0431055027 4 31240137 3.12E-06 NA
vg0134417281 sf0134416238 1 34417281 NA 3.80E-06
vg0117060548 sf0117059502 1 17060548 NA 4.96E-06