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 mr1612 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
vg0811149556 sf0811148561 8 11149556 4.65E-08 4.65E-08
vg0525142231 sf0525079652 5 25142231 7.58E-08 7.58E-08
vg0224923406 sf0224917537 2 24923406 2.37E-06 2.37E-06
vg0406837723 sf0406833168 4 6837723 2.54E-06 2.54E-06
vg0913973334 sf0913972333 9 13973334 2.68E-06 2.68E-06
vg0503604454 sf0503604431 5 3604454 3.44E-06 3.44E-06