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 mr1554 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
vg0420626329 sf0420454372 4 20626329 3.96E-12 1.67E-06
vg0335647105 sf0335639974 3 35647105 4.31E-12 NA
vg0420625673 sf0420453716 4 20625673 4.94E-12 1.13E-06
vg0728887297 sf0728886305 7 28887297 7.76E-12 NA
vg0526373535 sf0526310898 5 26373535 4.57E-11 NA
vg0323555815 sf0323553989 3 23555815 5.25E-11 NA
vg0815304114 sf0815301400 8 15304114 1.15E-06 6.09E-06
vg1214365279 sf1214362619 12 14365279 NA 1.09E-07
vg0307901966 sf0307900904 3 7901966 NA 2.73E-07
vg0420626346 sf0420454389 4 20626346 NA 4.22E-07
vg0420626339 sf0420454382 4 20626339 NA 1.35E-06
vg0335560373 sf0335553242 3 35560373 NA 1.79E-06