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 mr1353 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 5.35E-07 5.35E-07
vg0431411704 sf0431226602 4 31411704 6.00E-07 6.00E-07
vg1104971625 sf1104967436 11 4971625 1.02E-06 1.02E-06
vg1107375253 sf1107370998 11 7375253 1.79E-06 1.79E-06
vg0130689494 sf0130688450 1 30689494 2.29E-06 2.29E-06
vg0207854825 sf0207854824 2 7854825 3.68E-06 3.68E-06