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 mr1532 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
vg0709128655 sf0709127661 7 9128655 5.55E-09 2.81E-06
vg0306909345 sf0306908343 3 6909345 1.70E-08 NA
vg0207019221 sf0207019221 2 7019221 8.19E-08 1.22E-06
vg1023134936 sf1023063408 10 23134936 3.09E-07 1.10E-06
vg0417136797 sf0416964838 4 17136797 NA 3.06E-06
vg1000984389 sf1000983365 10 984389 NA 3.73E-06
vg1017226656 sf1017155429 10 17226656 NA 3.90E-06