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 mr1478 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
vg0610849825 sf0610848826 6 10849825 3.46E-07 3.46E-07
vg0620630387 sf0620629390 6 20630387 7.18E-07 7.18E-07
vg0725097326 sf0725096332 7 25097326 2.10E-06 2.10E-06
vg0504828513 sf0504828490 5 4828513 2.58E-06 2.58E-06
vg0401505122 sf0401500672 4 1505122 4.08E-06 4.08E-06