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 mr1303 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
vg0130773255 sf0130772211 1 30773255 7.30E-07 7.31E-07
vg1104978992 sf1104974803 11 4978992 1.61E-06 1.61E-06
vg0718838390 sf0718837397 7 18838390 2.72E-06 2.72E-06
vg0327968455 sf0327961509 3 27968455 4.45E-06 4.45E-06
vg0207854825 sf0207854824 2 7854825 4.68E-06 4.68E-06
vg0820974361 sf0820971648 8 20974361 9.80E-06 9.80E-06