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 mr1898 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
vg1214948506 sf1214945848 12 14948506 2.72E-09 9.80E-08
vg0922186933 sf0922186452 9 22186933 2.43E-08 1.27E-06
vg0700711476 sf0700710476 7 711476 3.27E-08 2.72E-06
vg0922187496 sf0922187015 9 22187496 6.91E-08 3.65E-06
vg1215172477 sf1215169813 12 15172477 1.29E-07 4.98E-06
vg1013325243 sf1013254012 10 13325243 1.99E-07 2.88E-06
vg1214950798 sf1214948140 12 14950798 3.35E-07 8.49E-08
vg1214985021 sf1214982363 12 14985021 5.13E-07 1.47E-07
vg1214620614 sf1214617954 12 14620614 6.24E-06 3.42E-06
vg0403668748 sf0403664354 4 3668748 NA 2.23E-06