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 mr1219 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
vg0228470723 sf0228464854 2 28470723 3.96E-08 1.40E-06
vg0809657696 sf0809656700 8 9657696 5.88E-08 8.01E-07
vg0207313113 sf0207313113 2 7313113 6.64E-08 4.96E-06
vg0228442970 sf0228437101 2 28442970 6.78E-08 8.00E-07
vg1222664248 sf1222630687 12 22664248 1.27E-07 1.62E-06
vg0803345287 sf0803344290 8 3345287 1.35E-07 5.55E-06
vg0125460260 sf0125459216 1 25460260 1.36E-07 2.07E-06
vg1216455900 sf1216453193 12 16455900 1.84E-07 1.66E-07
vg0125479255 sf0125478211 1 25479255 1.86E-07 2.43E-06
vg1201180694 sf1201179694 12 1180694 2.92E-07 1.34E-06
vg0808245241 sf0808244245 8 8245241 2.08E-06 3.90E-06
vg0101093889 sf0101092889 1 1093889 3.56E-06 3.33E-06