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 mr1654 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
vg0113517997 sf0113516971 1 13517997 4.11E-11 NA
vg0908709564 sf0908708563 9 8709564 8.01E-10 NA
vg0305147989 sf0305146991 3 5147989 1.27E-09 2.00E-06
vg1118243944 sf1117777803 11 18243944 2.74E-09 NA
vg0523764434 sf0523701855 5 23764434 1.15E-08 NA
vg0114538326 sf0114537300 1 14538326 1.08E-06 3.57E-06
vg0119954347 sf0119953302 1 19954347 5.36E-06 NA