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 mr1015 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
vg0133595333 sf0133594289 1 33595333 1.90E-124 5.37E-27
vg0130086873 sf0130085828 1 30086873 9.62E-93 NA
vg0221063004 sf0221057136 2 21063004 1.11E-90 NA
vg0137837960 sf0137836917 1 37837960 1.83E-90 NA
vg0212494179 sf0212494175 2 12494179 8.25E-89 NA
vg0133497043 sf0133495999 1 33497043 NA 1.30E-08
vg0210314544 sf0210314542 2 10314544 NA 6.61E-08
vg1208143024 sf1208140430 12 8143024 NA 1.36E-06
vg0627634217 sf0627633219 6 27634217 NA 2.31E-06
vg0608384983 sf0608383984 6 8384983 NA 3.48E-06
vg0718004907 sf0718003914 7 18004907 NA 4.01E-06