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 mr1769 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
vg0106691981 sf0106690981 1 6691981 5.28E-42 9.25E-22
vg0106669265 sf0106668265 1 6669265 9.64E-42 5.23E-22
vg0427189711 sf0427004581 4 27189711 1.78E-21 NA
vg0102388565 sf0102387565 1 2388565 1.49E-19 1.72E-06
vg0215720831 sf0215714961 2 15720831 2.05E-19 NA
vg0801405460 sf0801404462 8 1405460 2.18E-19 NA
vg0824350881 sf0824348167 8 24350881 3.80E-18 1.58E-06
vg0102410486 sf0102409486 1 2410486 9.82E-18 1.82E-07
vg0617411606 sf0617410609 6 17411606 3.58E-17 2.11E-06
vg1125249514 sf1124783354 11 25249514 1.96E-14 4.89E-06
vg0106725146 sf0106724146 1 6725146 NA 2.87E-08
vg0408104657 sf0408099931 4 8104657 NA 2.23E-06