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 mr1125 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
vg0622528904 sf0622527907 6 22528904 4.52E-74 7.49E-06
vg0521716669 sf0521654111 5 21716669 9.85E-74 NA
vg0204272301 sf0204272298 2 4272301 1.66E-71 NA
vg0305316509 sf0305315509 3 5316509 5.14E-70 NA
vg0434433851 sf0434248745 4 34433851 7.57E-70 NA
vg0622695985 sf0622694988 6 22695985 8.17E-70 1.88E-07
vg0235268833 sf0235262964 2 35268833 1.59E-65 1.77E-07
vg0523880474 sf0523817895 5 23880474 NA 5.85E-08
vg0602769653 sf0602768654 6 2769653 NA 3.76E-07
vg0115616063 sf0115615037 1 15616063 NA 1.27E-06
vg0622173451 sf0622172454 6 22173451 NA 1.29E-06
vg0313204857 sf0313203575 3 13204857 NA 1.42E-06
vg0122953968 sf0122952924 1 22953968 NA 1.97E-06
vg0505446561 sf0505446539 5 5446561 NA 2.13E-06
vg0306636968 sf0306635968 3 6636968 NA 2.31E-06
vg0304248883 sf0304247885 3 4248883 NA 2.64E-06
vg0313235859 sf0313234577 3 13235859 NA 2.66E-06
vg1202743490 sf1202742492 12 2743490 NA 3.02E-06
vg0602813024 sf0602812025 6 2813024 NA 3.21E-06
vg1114018010 sf1113554331 11 14018010 NA 3.43E-06
vg0142981001 sf0142979957 1 42981001 NA 3.75E-06