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 mr1205 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
vg0140499546 sf0140498503 1 40499546 1.28E-07 1.28E-07
vg0140571065 sf0140570022 1 40571065 1.43E-07 1.43E-07
vg0500663880 sf0500663880 5 663880 9.68E-07 9.68E-07
vg1213198324 sf1213195662 12 13198324 1.64E-06 1.64E-06
vg0905688587 sf0905687587 9 5688587 1.66E-06 1.66E-06
vg1005148582 sf1005165119 10 5148582 2.59E-06 2.59E-06
vg0501173671 sf0501173655 5 1173671 2.96E-06 2.97E-06
vg0407630134 sf0407625401 4 7630134 3.49E-06 3.50E-06
vg1118328578 sf1117862436 11 18328578 4.01E-06 4.01E-06