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 mr1020 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
vg0614107939 sf0614106940 6 14107939 8.23E-11 1.53E-08
vg0610762995 sf0610761996 6 10762995 2.43E-10 9.65E-08
vg0610778838 sf0610777839 6 10778838 3.02E-10 4.89E-08
vg0616691629 sf0616690631 6 16691629 4.27E-10 1.36E-07
vg0611482704 sf0611481705 6 11482704 NA 7.27E-07
vg0322427276 sf0322425765 3 22427276 NA 4.44E-06