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 mr1364 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
vg0720317869 sf0720316876 7 20317869 1.51E-15 7.58E-06
vg0132166543 sf0132165499 1 32166543 4.93E-15 NA
vg0720047684 sf0720046691 7 20047684 3.79E-14 2.08E-06
vg0129594569 sf0129593524 1 29594569 1.99E-13 NA
vg0721444659 sf0721443666 7 21444659 3.38E-13 NA
vg0628021635 sf0628020637 6 28021635 4.06E-13 NA
vg0720034658 sf0720033665 7 20034658 4.35E-10 3.33E-06
vg1217465756 sf1217459711 12 17465756 5.92E-10 2.81E-06
vg0720103928 sf0720102935 7 20103928 3.10E-09 4.79E-06
vg0404474445 sf0404470049 4 4474445 5.68E-09 2.91E-06
vg0223811221 sf0223805352 2 23811221 NA 1.56E-06
vg0111292103 sf0111291079 1 11292103 NA 2.40E-06