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 mr1971 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
vg0123720143 sf0123719099 1 23720143 2.25E-11 NA
vg0306339520 sf0306338520 3 6339520 5.49E-11 NA
vg0603088308 sf0603087309 6 3088308 5.95E-11 NA
vg0600457865 sf0600456866 6 457865 7.73E-11 NA
vg0300233526 sf0300232526 3 233526 3.51E-10 NA
vg1001249422 sf1001248399 10 1249422 1.15E-09 9.79E-07
vg0602860835 sf0602859836 6 2860835 1.74E-08 NA
vg0824030291 sf0824027577 8 24030291 3.39E-08 NA
vg0921023184 sf0921022703 9 21023184 9.63E-07 NA
vg0715150413 sf0715149420 7 15150413 3.77E-06 6.52E-06