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 mr1514 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
vg0506869876 sf0506869818 5 6869876 5.85E-11 1.73E-10
vg0203405625 sf0203405623 2 3405625 9.70E-10 2.65E-09
vg1009362935 sf1009291756 10 9362935 1.18E-09 7.74E-09
vg0506943710 sf0506943652 5 6943710 1.98E-09 1.01E-08
vg0510421589 sf0510421518 5 10421589 1.08E-08 1.34E-08
vg1001247140 sf1001246117 10 1247140 2.79E-08 3.75E-07
vg0514519530 sf0514462073 5 14519530 3.68E-08 1.49E-08
vg1213203956 sf1213201294 12 13203956 1.15E-07 3.58E-07
vg1003777399 sf1003776375 10 3777399 3.62E-07 1.31E-06
vg0500863102 sf0500863084 5 863102 9.74E-07 3.06E-06
vg1109539652 sf1109534229 11 9539652 1.35E-06 2.62E-06
vg0519252225 sf0519189709 5 19252225 2.80E-06 4.54E-06
vg0917229617 sf0917228616 9 17229617 NA 3.76E-06