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 mr1347 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
vg0303941671 sf0303940667 3 3941671 3.82E-11 NA
vg0310800399 sf0310799117 3 10800399 1.26E-10 NA
vg1215699227 sf1215696524 12 15699227 1.31E-10 NA
vg0728979771 sf0728978779 7 28979771 1.70E-10 NA
vg0332021398 sf0332014275 3 32021398 3.19E-10 NA
vg0804419898 sf0804418901 8 4419898 2.25E-08 2.29E-08
vg0919319021 sf0919318611 9 19319021 1.74E-07 NA
vg0804308209 sf0804307212 8 4308209 NA 8.37E-08