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 mr1146 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
vg0222746050 sf0222740181 2 22746050 2.00E-41 3.33E-23
vg0602873086 sf0602872087 6 2873086 3.67E-19 NA
vg0327464410 sf0327457463 3 27464410 6.98E-19 NA
vg0626585095 sf0626584098 6 26585095 2.73E-18 NA
vg0525138543 sf0525075964 5 25138543 3.45E-18 NA
vg0315944031 sf0315942678 3 15944031 1.55E-16 NA
vg0222725003 sf0222719134 2 22725003 NA 4.53E-13
vg0222634177 sf0222628308 2 22634177 NA 6.86E-08
vg0224876386 sf0224870517 2 24876386 NA 6.06E-07
vg0224640486 sf0224634617 2 24640486 NA 1.57E-06
vg0223506504 sf0223500635 2 23506504 NA 2.13E-06
vg0224830269 sf0224824400 2 24830269 NA 2.86E-06