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 mr1149 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
vg0222718166 sf0222712297 2 22718166 1.04E-46 2.33E-23
vg0800545388 sf0800544388 8 545388 9.16E-18 NA
vg0908964730 sf0908963729 9 8964730 1.06E-17 NA
vg1223575079 sf1223541539 12 23575079 4.89E-17 NA
vg1203725293 sf1203724292 12 3725293 8.09E-17 NA
vg0123349791 sf0123348747 1 23349791 1.84E-14 2.10E-06
vg0311698039 sf0311696757 3 11698039 1.39E-13 3.39E-06
vg1209367960 sf1209365369 12 9367960 1.69E-13 NA
vg0222725003 sf0222719134 2 22725003 NA 5.11E-10
vg0223736992 sf0223731123 2 23736992 NA 4.57E-08
vg0224275719 sf0224269850 2 24275719 NA 6.75E-07
vg1206630456 sf1206629346 12 6630456 NA 1.13E-06
vg0800589141 sf0800588141 8 589141 NA 1.20E-06
vg1217237364 sf1217231319 12 17237364 NA 3.12E-06
vg0224242852 sf0224236983 2 24242852 NA 4.18E-06