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 mr1862 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
vg1019004923 sf1018933480 10 19004923 2.39E-15 2.77E-07
vg1219345800 sf1219317270 12 19345800 1.02E-13 NA
vg1004756810 sf1004773347 10 4756810 1.06E-11 NA
vg0139831768 sf0139830725 1 39831768 1.50E-11 NA
vg0506270948 sf0506270887 5 6270948 3.63E-11 NA