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 mr1433 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
vg1117625330 sf1117159186 11 17625330 1.17E-07 NA
vg0712648528 sf0712647535 7 12648528 5.02E-07 1.06E-06
vg0406869281 sf0406864726 4 6869281 5.92E-07 1.71E-06
vg0826160395 sf0826157681 8 26160395 6.58E-07 3.99E-06
vg0212359529 sf0212359525 2 12359529 1.35E-06 1.56E-06
vg0620348476 sf0620347479 6 20348476 1.72E-06 3.33E-06
vg0132161653 sf0132160609 1 32161653 NA 3.93E-06
vg0202138338 sf0202138338 2 2138338 NA 7.20E-06