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 mr1514 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
vg0716989182 sf0716988189 7 16989182 6.27E-07 6.27E-07
vg0717031754 sf0717030761 7 17031754 6.31E-07 6.31E-07
vg0334764145 sf0334757015 3 34764145 8.73E-07 8.73E-07
vg0506870350 sf0506870292 5 6870350 9.31E-07 9.31E-07
vg0906966618 sf0906965618 9 6966618 3.80E-06 3.80E-06
vg0802472650 sf0802471653 8 2472650 4.80E-06 4.80E-06