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 mr1302 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
vg1117584893 sf1117118750 11 17584893 2.62E-07 2.62E-07
vg0313073263 sf0313071981 3 13073263 4.42E-07 4.42E-07
vg0504650681 sf0504650658 5 4650681 4.60E-07 4.60E-07
vg0623833223 sf0623832226 6 23833223 7.67E-07 7.67E-07
vg0626047468 sf0626046471 6 26047468 5.60E-06 5.60E-06