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 mr1597 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
vg0317009509 sf0317008383 3 17009509 1.21E-07 1.21E-07
vg0317009541 sf0317008415 3 17009541 1.21E-07 1.21E-07
vg0613793879 sf0613792880 6 13793879 1.70E-06 1.70E-06
vg0810860589 sf0810859594 8 10860589 2.67E-06 2.67E-06
vg0323847195 sf0323845369 3 23847195 2.87E-06 2.87E-06
vg0325617211 sf0325615229 3 25617211 3.16E-06 3.16E-06
vg0824883472 sf0824880758 8 24883472 4.31E-06 4.31E-06
vg1125736814 sf1125270653 11 25736814 4.45E-06 4.45E-06
vg0330585710 sf0330578599 3 30585710 4.56E-06 4.56E-06