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 mr1114 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
vg0222673217 sf0222667348 2 22673217 1.59E-46 7.73E-22
vg0222675535 sf0222669666 2 22675535 1.40E-44 6.34E-22
vg1110425815 sf1110420360 11 10425815 2.31E-30 7.87E-11
vg0505887711 sf0505887649 5 5887711 1.15E-25 2.38E-06
vg0526731344 sf0526668702 5 26731344 4.19E-25 1.03E-06
vg0500483303 sf0500483303 5 483303 6.05E-25 4.86E-06
vg1117963441 sf1117497299 11 17963441 1.34E-24 7.65E-09
vg0528277698 sf0528215053 5 28277698 3.66E-24 1.03E-07
vg0624499979 sf0624498982 6 24499979 9.00E-24 4.35E-08
vg0818212763 sf0818210050 8 18212763 9.38E-24 4.98E-08
vg1108600295 sf1108594905 11 8600295 1.40E-21 2.24E-07
vg0501379198 sf0501379182 5 1379198 2.46E-21 1.06E-07
vg0222988287 sf0222982418 2 22988287 1.04E-20 2.99E-08
vg0434773299 sf0434588190 4 34773299 1.35E-18 1.06E-07
vg0305905054 sf0305904054 3 5905054 1.25E-17 2.78E-08
vg0222722554 sf0222716685 2 22722554 NA 1.85E-14
vg0222952563 sf0222946694 2 22952563 NA 2.44E-13
vg0222926098 sf0222920229 2 22926098 NA 1.40E-09
vg0141556686 sf0141555643 1 41556686 NA 4.21E-09
vg0403136311 sf0403131914 4 3136311 NA 1.10E-08
vg0129623631 sf0129622586 1 29623631 NA 1.43E-08
vg1005950387 sf1005966925 10 5950387 NA 1.99E-08
vg0626215270 sf0626214273 6 26215270 NA 3.08E-08
vg1009512226 sf1009441047 10 9512226 NA 4.09E-08
vg0506230550 sf0506230489 5 6230550 NA 9.97E-08
vg0434765214 sf0434580105 4 34765214 NA 1.19E-07
vg0419662846 sf0419490881 4 19662846 NA 1.63E-07
vg1204507349 sf1204506337 12 4507349 NA 1.98E-07
vg0232925929 sf0232920060 2 32925929 NA 2.50E-07
vg0709501453 sf0709500459 7 9501453 NA 1.22E-06