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 mr1036 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
vg0223174676 sf0223168807 2 23174676 1.08E-07 1.08E-07
vg0221882859 sf0221876990 2 21882859 1.88E-07 1.88E-07
vg0625671188 sf0625670191 6 25671188 7.69E-07 7.69E-07
vg1124874746 sf1124408586 11 24874746 8.68E-07 8.69E-07
vg0714889859 sf0714888866 7 14889859 1.45E-06 1.45E-06
vg0225258958 sf0225253089 2 25258958 1.45E-06 1.45E-06
vg0722526631 sf0722525638 7 22526631 1.93E-06 1.93E-06
vg0620542201 sf0620541204 6 20542201 2.70E-06 2.70E-06
vg0715642858 sf0715641865 7 15642858 3.34E-06 3.35E-06
vg0111239136 sf0111238112 1 11239136 3.96E-06 3.96E-06
vg0105021483 sf0105020483 1 5021483 4.22E-06 4.22E-06
vg0706707109 sf0706706114 7 6707109 4.66E-06 4.66E-06
vg0916496482 sf0916495481 9 16496482 4.70E-06 4.70E-06
vg0305150792 sf0305149794 3 5150792 4.82E-06 4.82E-06