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 mr1513 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
vg0729692653 sf0729691661 7 29692653 5.36E-07 5.36E-07
vg0407000775 sf0406996046 4 7000775 5.72E-07 5.72E-07
vg1218074554 sf1218045990 12 18074554 7.13E-07 7.13E-07
vg1122446629 sf1121980500 11 22446629 1.61E-06 1.61E-06
vg1107376701 sf1107372446 11 7376701 2.00E-06 2.01E-06
vg1117569414 sf1117103271 11 17569414 3.56E-06 3.56E-06
vg1104315941 sf1104311843 11 4315941 3.78E-06 3.78E-06
vg0913973334 sf0913972333 9 13973334 3.88E-06 3.88E-06
vg0312535741 sf0312534459 3 12535741 4.21E-06 4.21E-06