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 mr1004 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
vg0921524668 sf0921524187 9 21524668 2.84E-13 1.87E-10
vg0726031887 sf0726030893 7 26031887 3.12E-08 4.17E-06
vg1003150061 sf1003149038 10 3150061 4.25E-08 7.90E-08
vg0206307094 sf0206307094 2 6307094 5.12E-08 NA
vg1217386148 sf1217380103 12 17386148 1.47E-07 1.06E-06
vg0724979429 sf0724978435 7 24979429 2.63E-07 7.46E-07
vg1108677068 sf1108671678 11 8677068 3.76E-06 1.79E-06
vg0827379782 sf0827377068 8 27379782 7.67E-06 NA
vg1215306171 sf1215303469 12 15306171 NA 2.06E-06