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 mr1315 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
vg0623833223 sf0623832226 6 23833223 3.32E-08 3.32E-08
vg0140479964 sf0140478921 1 40479964 1.43E-07 1.44E-07
vg1117584893 sf1117118750 11 17584893 2.81E-07 2.81E-07
vg0705087118 sf0705086119 7 5087118 2.89E-06 2.89E-06
vg1127125428 sf1126653815 11 27125428 3.27E-06 3.27E-06