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 mr1823 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
vg0918774898 sf0918773898 9 18774898 2.10E-07 2.10E-07
vg0324965295 sf0324963375 3 24965295 2.11E-06 2.11E-06
vg0805900956 sf0805899959 8 5900956 3.84E-06 3.84E-06
vg0207698155 sf0207698154 2 7698155 3.86E-06 3.86E-06
vg0314986971 sf0314985618 3 14986971 4.76E-06 4.76E-06