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 mr1535 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
vg0405710877 sf0405706316 4 5710877 1.03E-14 NA
vg0100779931 sf0100778931 1 779931 3.58E-14 NA
vg0919812604 sf0919812123 9 19812604 5.82E-14 NA
vg0139829401 sf0139828358 1 39829401 1.28E-13 NA
vg0133158489 sf0133157445 1 33158489 3.14E-13 NA
vg0604924928 sf0604923929 6 4924928 3.45E-11 NA
vg0715862869 sf0715861876 7 15862869 3.23E-10 1.47E-06
vg0919872267 sf0919871786 9 19872267 1.26E-08 NA
vg0520358656 sf0520296129 5 20358656 NA 4.27E-07
vg1209154479 sf1209151888 12 9154479 NA 2.64E-06