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 mr1591 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
vg0328874978 sf0328868031 3 28874978 1.37E-07 1.37E-07
vg0402100710 sf0402096304 4 2100710 6.16E-07 6.16E-07
vg0222021204 sf0222015335 2 22021204 1.95E-06 1.95E-06
vg0215252496 sf0215246626 2 15252496 2.91E-06 2.91E-06
vg0502159367 sf0502159342 5 2159367 3.23E-06 3.24E-06
vg1104228568 sf1104224470 11 4228568 4.52E-06 4.52E-06