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 mr1711 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
vg0607961607 sf0607960608 6 7961607 2.29E-06 2.30E-06
vg0805959456 sf0805958459 8 5959456 2.84E-06 2.84E-06
vg1211852525 sf1211849861 12 11852525 3.01E-06 3.01E-06
vg0608026705 sf0608025706 6 8026705 3.19E-06 3.19E-06
vg0509300373 sf0509300302 5 9300373 4.15E-06 4.15E-06
vg0805067670 sf0805066673 8 5067670 4.40E-06 4.39E-06