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 mr1084 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
vg1214822308 sf1214819649 12 14822308 4.43E-08 1.00E-06
vg1104978992 sf1104974803 11 4978992 4.77E-08 NA
vg0130290451 sf0130289406 1 30290451 9.24E-08 7.02E-06
vg0726847020 sf0726846026 7 26847020 1.30E-07 6.81E-06
vg0431655631 sf0431470524 4 31655631 1.88E-07 1.42E-06
vg0906503065 sf0906502065 9 6503065 6.78E-07 2.45E-06
vg1106375766 sf1106371518 11 6375766 9.15E-06 5.34E-06