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 mr1800 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
vg0432461038 sf0432275930 4 32461038 2.47E-16 2.08E-14
vg0432446487 sf0432261379 4 32446487 4.82E-16 8.73E-15
vg0221342297 sf0221336429 2 21342297 1.70E-09 4.37E-06
vg1210236191 sf1210233603 12 10236191 1.77E-08 NA
vg0103381628 sf0103380628 1 3381628 1.86E-08 2.18E-07
vg0142030766 sf0142029723 1 42030766 3.15E-08 NA
vg0703264096 sf0703263097 7 3264096 4.52E-08 2.69E-06
vg0820892173 sf0820889460 8 20892173 5.24E-08 2.77E-06
vg0820890632 sf0820887919 8 20890632 9.13E-08 4.97E-06
vg1105377831 sf1105373582 11 5377831 4.13E-07 1.54E-06
vg1117243555 sf1116777407 11 17243555 8.83E-07 5.17E-06
vg1104889555 sf1104885366 11 4889555 9.69E-07 NA
vg0432640353 sf0432455242 4 32640353 NA 1.72E-06
vg0313045453 sf0313044171 3 13045453 NA 4.08E-06