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 mr1804 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
vg0211092649 sf0211092646 2 11092649 1.75E-09 1.75E-09
vg1115212225 sf1114748539 11 15212225 4.20E-07 4.20E-07
vg1121950694 sf1121484565 11 21950694 2.49E-06 2.49E-06
vg1117899452 sf1117433310 11 17899452 4.31E-06 4.31E-06
vg1108623696 sf1108618306 11 8623696 4.38E-06 4.38E-06