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 mr1249 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
vg0334118102 sf0334110972 3 34118102 8.60E-12 4.81E-07
vg0103417456 sf0103416456 1 3417456 2.04E-11 NA
vg0724953161 sf0724952167 7 24953161 2.30E-11 NA
vg0818017838 sf0818015125 8 18017838 5.67E-11 NA
vg0920575377 sf0920574896 9 20575377 7.81E-11 NA
vg0132744722 sf0132743678 1 32744722 3.01E-10 1.96E-06
vg0135794714 sf0135793671 1 35794714 8.04E-10 NA
vg0142100552 sf0142099509 1 42100552 4.37E-08 3.97E-07
vg0431700870 sf0431515763 4 31700870 1.35E-07 NA
vg0334389176 sf0334382046 3 34389176 NA 1.66E-09
vg0335759426 sf0335752295 3 35759426 NA 2.47E-08
vg0334985144 sf0334978014 3 34985144 NA 3.17E-08
vg0334584462 sf0334577332 3 34584462 NA 1.16E-07
vg0826635155 sf0826632441 8 26635155 NA 6.11E-07
vg0335111562 sf0335104432 3 35111562 NA 1.07E-06
vg0142910448 sf0142909404 1 42910448 NA 1.22E-06