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 mr1833 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
vg0711831639 sf0711830645 7 11831639 7.51E-08 7.51E-08
vg0223380868 sf0223270029 2 23380868 4.67E-07 4.68E-07
vg0919632209 sf0919631799 9 19632209 5.62E-07 5.62E-07
vg1022578618 sf1022507092 10 22578618 1.55E-06 1.55E-06
vg0118124341 sf0118123295 1 18124341 2.73E-06 2.73E-06
vg0728386858 sf0728385866 7 28386858 3.00E-06 3.00E-06
vg0920652722 sf0920652241 9 20652722 4.03E-06 4.04E-06
vg0728245843 sf0728244851 7 28245843 4.19E-06 4.19E-06