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 mr1276 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
vg0412166795 sf0412157506 4 12166795 3.30E-20 7.47E-07
vg0725044153 sf0725043159 7 25044153 5.95E-18 NA
vg0820742977 sf0820740264 8 20742977 7.98E-18 NA
vg1013305458 sf1013234227 10 13305458 1.18E-17 NA
vg0613133735 sf0613132736 6 13133735 1.53E-17 NA
vg0625011849 sf0625010852 6 25011849 1.69E-17 2.45E-06
vg0916243027 sf0916242026 9 16243027 NA 8.88E-07
vg1126973835 sf1126502222 11 26973835 NA 9.45E-07
vg0819107411 sf0819104698 8 19107411 NA 1.02E-06