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 mr1172 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
vg0909014180 sf0909013179 9 9014180 4.70E-14 NA
vg0920273401 sf0920272920 9 20273401 4.90E-14 NA
vg0104304529 sf0104303529 1 4304529 2.01E-13 NA
vg0626132398 sf0626131401 6 26132398 4.11E-13 NA
vg1115418543 sf1114954855 11 15418543 5.08E-13 NA
vg0922565216 sf0922564735 9 22565216 NA 8.86E-06