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 mr1126 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
vg0816195208 sf0816192494 8 16195208 3.92E-07 4.35E-06
vg0212169170 sf0212169166 2 12169170 1.64E-06 NA
vg1220063865 sf1220035307 12 20063865 2.16E-06 NA
vg1128469268 sf1127946047 11 28469268 2.24E-06 3.77E-06
vg1127976659 sf1127505045 11 27976659 NA 2.42E-06