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 mr1477 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
vg0137605963 sf0137604920 1 37605963 2.49E-10 NA
vg0138093125 sf0138092082 1 38093125 1.50E-09 4.33E-06
vg1222399385 sf1222365824 12 22399385 9.28E-09 NA
vg1217341446 sf1217335401 12 17341446 2.22E-08 NA
vg0526986295 sf0526923651 5 26986295 5.07E-08 NA
vg0518363321 sf0518302807 5 18363321 8.49E-06 1.81E-06
vg0502125341 sf0502125315 5 2125341 NA 6.85E-06