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 mr1064 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
vg0430612192 sf0430427067 4 30612192 2.06E-14 1.48E-09
vg0916498845 sf0916497844 9 16498845 3.52E-09 1.54E-06
vg0115022018 sf0115020992 1 15022018 6.74E-09 4.21E-06
vg0426938787 sf0426753659 4 26938787 9.36E-09 6.46E-06
vg0114940313 sf0114939287 1 14940313 1.20E-08 2.08E-06
vg0707514298 sf0707513303 7 7514298 1.47E-08 NA
vg0430528176 sf0430343051 4 30528176 1.98E-06 1.10E-06