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 mr1479 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
vg0224249043 sf0224243174 2 24249043 1.19E-08 4.51E-06
vg0224797537 sf0224791668 2 24797537 1.29E-08 1.09E-06
vg0916441676 sf0916440675 9 16441676 2.10E-08 NA
vg0404315243 sf0404310849 4 4315243 2.11E-06 6.50E-06
vg1121697590 sf1121231467 11 21697590 2.55E-06 NA
vg0415621401 sf0415612088 4 15621401 4.00E-06 4.79E-06