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 mr1653 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
vg0424114621 sf0423929482 4 24114621 3.66E-07 8.03E-06
vg0323869447 sf0323867621 3 23869447 1.00E-06 NA
vg1009677908 sf1009606729 10 9677908 1.59E-06 6.30E-06
vg1006468934 sf1006484557 10 6468934 4.25E-06 9.70E-06
vg1125889993 sf1125423912 11 25889993 5.82E-06 NA