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 mr1363 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
vg0122879183 sf0122878139 1 22879183 4.86E-08 1.11E-06
vg1212739494 sf1212736833 12 12739494 2.12E-07 3.36E-06
vg1208174078 sf1208171484 12 8174078 1.89E-06 6.12E-07
vg0142638064 sf0142637020 1 42638064 2.13E-06 5.38E-06
vg1208630420 sf1208627827 12 8630420 3.39E-06 1.18E-06
vg1104315941 sf1104311843 11 4315941 6.43E-06 4.82E-06
vg0208268939 sf0208268938 2 8268939 NA 7.40E-07