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 mr1776 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
vg0916428508 sf0916427507 9 16428508 9.37E-12 NA
vg1002049704 sf1002048681 10 2049704 9.72E-12 NA
vg0623156256 sf0623155259 6 23156256 1.72E-11 NA
vg0327698923 sf0327691976 3 27698923 1.84E-11 NA
vg0500284719 sf0500284719 5 284719 1.88E-11 NA
vg1120838492 sf1120372395 11 20838492 3.41E-11 3.90E-06
vg0316990859 sf0316989733 3 16990859 7.33E-11 3.30E-06
vg0919712999 sf0919712589 9 19712999 5.11E-09 NA
vg0503050458 sf0503050434 5 3050458 2.71E-08 1.56E-06