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 mr1805 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
vg0128271291 sf0128270247 1 28271291 2.26E-51 NA
vg1210385800 sf1210383213 12 10385800 1.00E-49 NA
vg0128212865 sf0128211821 1 28212865 4.37E-49 NA
vg0601388912 sf0601387913 6 1388912 2.37E-47 NA
vg0420602297 sf0420430341 4 20602297 4.56E-46 NA
vg1216986107 sf1216980061 12 16986107 5.83E-46 NA
vg0720329831 sf0720328838 7 20329831 9.77E-43 NA
vg0431162265 sf0430977156 4 31162265 NA 2.82E-08
vg0431157774 sf0430972665 4 31157774 NA 7.33E-07
vg1124648589 sf1124182429 11 24648589 NA 1.82E-06
vg0431151736 sf0430966627 4 31151736 NA 4.79E-06
vg1222217188 sf1222183735 12 22217188 NA 5.32E-06