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 mr1813 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
vg1104978992 sf1104974803 11 4978992 3.13E-08 5.84E-06
vg0123692227 sf0123691183 1 23692227 9.91E-08 NA
vg0820888052 sf0820885339 8 20888052 3.88E-07 3.03E-06
vg0205080708 sf0205080705 2 5080708 7.36E-07 3.89E-06
vg1204560575 sf1204559563 12 4560575 2.12E-06 1.97E-06
vg1106375766 sf1106371518 11 6375766 3.11E-06 3.08E-06
vg1016429449 sf1016358223 10 16429449 5.99E-06 1.79E-06
vg1214822308 sf1214819649 12 14822308 9.51E-06 NA