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 mr1147 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
vg0805900956 sf0805899959 8 5900956 7.49E-08 7.49E-08
vg1214703763 sf1214701104 12 14703763 3.38E-07 3.39E-07
vg0324965295 sf0324963375 3 24965295 4.85E-07 4.85E-07
vg0414249163 sf0414239876 4 14249163 5.09E-07 5.09E-07
vg0207676313 sf0207676313 2 7676313 8.05E-07 8.05E-07
vg0130987914 sf0130986870 1 30987914 9.46E-07 9.46E-07
vg0918774898 sf0918773898 9 18774898 1.03E-06 1.03E-06
vg0722226606 sf0722225613 7 22226606 1.10E-06 1.10E-06
vg0805068073 sf0805067076 8 5068073 1.89E-06 1.89E-06
vg0223074046 sf0223068177 2 23074046 2.44E-06 2.44E-06
vg0102110388 sf0102109388 1 2110388 3.31E-06 3.31E-06
vg0335708031 sf0335700900 3 35708031 3.71E-06 3.71E-06
vg0428761895 sf0428576746 4 28761895 3.74E-06 3.74E-06
vg0905076333 sf0905075333 9 5076333 3.80E-06 3.80E-06
vg1200440277 sf1200439277 12 440277 4.24E-06 4.24E-06
vg0402378307 sf0402373902 4 2378307 4.97E-06 4.97E-06