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 mr1156 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
vg1000453123 sf1000452099 10 453123 7.22E-22 3.65E-06
vg1000651713 sf1000650689 10 651713 3.29E-20 3.93E-07
vg1210414239 sf1210411652 12 10414239 5.70E-20 8.22E-06
vg1210520286 sf1210517699 12 10520286 1.31E-19 1.07E-06
vg0406944785 sf0406940053 4 6944785 2.91E-19 NA
vg0314904428 sf0314903075 3 14904428 7.15E-19 NA
vg1016877035 sf1016805807 10 16877035 1.09E-18 NA
vg0305373006 sf0305372006 3 5373006 4.34E-16 NA
vg0322154741 sf0322153248 3 22154741 7.36E-16 NA
vg1212386844 sf1212384183 12 12386844 NA 4.19E-07
vg0526725308 sf0526662666 5 26725308 NA 3.77E-06
vg0500172077 sf0500172077 5 172077 NA 6.47E-06