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 mr1622 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
vg1007139747 sf1007155370 10 7139747 3.50E-10 NA
vg1007055373 sf1007070996 10 7055373 5.22E-10 3.65E-06
vg0619902184 sf0619901187 6 19902184 1.37E-09 NA
vg1117580481 sf1117114338 11 17580481 1.66E-09 NA
vg0629645562 sf0629644564 6 29645562 1.90E-09 7.68E-06
vg0819202971 sf0819200258 8 19202971 2.56E-09 NA
vg0819131129 sf0819128416 8 19131129 8.74E-09 1.91E-06
vg0407000775 sf0406996046 4 7000775 1.11E-08 NA
vg1200185437 sf1200184437 12 185437 2.82E-08 NA
vg0405034359 sf0405029798 4 5034359 1.46E-07 NA
vg1006899494 sf1006915117 10 6899494 2.89E-07 3.42E-07
vg0218156828 sf0218150959 2 18156828 1.33E-06 NA
vg0112338981 sf0112337955 1 12338981 1.55E-06 NA
vg1213936119 sf1213933457 12 13936119 1.93E-06 1.77E-06
vg1020949886 sf1020878365 10 20949886 2.82E-06 NA
vg1013275525 sf1013204295 10 13275525 NA 5.92E-07
vg0222645252 sf0222639383 2 22645252 NA 1.66E-06