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 mr1045 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
vg0428761895 sf0428576746 4 28761895 2.08E-10 NA
vg0130372159 sf0130371115 1 30372159 2.91E-10 NA
vg0423636908 sf0423451765 4 23636908 3.50E-10 NA
vg0125460828 sf0125459784 1 25460828 4.43E-10 NA
vg0402400401 sf0402395996 4 2400401 6.03E-10 NA
vg0420302986 sf0420131031 4 20302986 2.08E-08 NA
vg0232755756 sf0232749887 2 32755756 1.44E-07 6.84E-08
vg0812016473 sf0812015478 8 12016473 1.26E-06 NA
vg1219590404 sf1219561874 12 19590404 NA 9.13E-07