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 mr1442 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
vg0231289965 sf0231284096 2 31289965 1.29E-07 1.16E-06
vg1128025024 sf1127553410 11 28025024 3.89E-07 1.83E-06
vg0232755756 sf0232749887 2 32755756 NA 3.49E-08
vg1108255008 sf1108249618 11 8255008 NA 3.09E-06
vg0401358404 sf0401353954 4 1358404 NA 3.80E-06