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 mr1166 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
vg0910776286 sf0910775285 9 10776286 3.45E-22 3.69E-06
vg0606987803 sf0606986804 6 6987803 9.96E-19 NA
vg0336362784 sf0336355654 3 36362784 1.23E-18 NA
vg0107395608 sf0107394608 1 7395608 2.10E-18 NA
vg0420417885 sf0420245929 4 20417885 3.56E-18 NA
vg1003146570 sf1003145547 10 3146570 5.95E-14 4.37E-08
vg0907792919 sf0907791919 9 7792919 NA 4.98E-09
vg0327425445 sf0327418498 3 27425445 NA 1.76E-08
vg0327424324 sf0327417377 3 27424324 NA 4.15E-08
vg1005967804 sf1005984342 10 5967804 NA 2.39E-07
vg1127981469 sf1127509855 11 27981469 NA 3.41E-07
vg0222961957 sf0222956088 2 22961957 NA 4.50E-07
vg0620348476 sf0620347479 6 20348476 NA 1.67E-06
vg0400362758 sf0400361756 4 362758 NA 2.33E-06
vg0400995844 sf0400991396 4 995844 NA 2.47E-06
vg0325688031 sf0325686049 3 25688031 NA 2.55E-06
vg0525540452 sf0525477873 5 25540452 NA 3.61E-06
vg0202735231 sf0202735229 2 2735231 NA 4.24E-06
vg1119463807 sf1118997495 11 19463807 NA 5.94E-06