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 mr1846 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
vg0407382502 sf0407377771 4 7382502 6.64E-19 4.81E-11
vg0411115062 sf0411105763 4 11115062 1.05E-18 5.76E-11
vg0411410586 sf0411401287 4 11410586 1.67E-18 3.14E-11
vg1115982424 sf1115517296 11 15982424 4.82E-13 3.69E-08
vg0406325095 sf0406320535 4 6325095 5.00E-12 4.79E-06
vg0402381225 sf0402376820 4 2381225 7.45E-12 NA
vg0211848242 sf0211848238 2 11848242 3.98E-11 3.35E-06
vg0406877690 sf0406873135 4 6877690 8.64E-11 1.56E-06