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 mr1208 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
vg0403546886 sf0403542490 4 3546886 3.97E-09 1.44E-06
vg0611960936 sf0611959937 6 11960936 4.38E-09 9.31E-07
vg0904473538 sf0904472538 9 4473538 7.00E-08 NA
vg0901841716 sf0901840716 9 1841716 2.11E-07 NA
vg0300249514 sf0300248514 3 249514 1.65E-06 7.62E-06
vg1124078519 sf1123612389 11 24078519 NA 2.77E-06