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 mr1538 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
vg0137838253 sf0137837210 1 37838253 1.34E-22 3.05E-16
vg1003424037 sf1003423014 10 3424037 2.30E-22 1.15E-15
vg1003068805 sf1003067782 10 3068805 3.74E-22 1.49E-16
vg0137798144 sf0137797101 1 37798144 5.37E-22 2.16E-15
vg0137834118 sf0137833075 1 37834118 4.50E-18 9.89E-13
vg0717727644 sf0717726651 7 17727644 1.72E-10 1.47E-06
vg1003718301 sf1003717278 10 3718301 3.59E-10 6.55E-06
vg1003059277 sf1003058254 10 3059277 5.31E-10 1.53E-06
vg0717726887 sf0717725894 7 17726887 7.22E-10 1.56E-07
vg1003717312 sf1003716289 10 3717312 1.56E-09 2.28E-06
vg0712651082 sf0712650089 7 12651082 3.35E-08 4.17E-06
vg1104938434 sf1104934245 11 4938434 2.61E-07 NA
vg0136593923 sf0136592880 1 36593923 2.87E-07 3.85E-06
vg0137414650 sf0137413607 1 37414650 5.66E-06 1.54E-06