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 mr1129 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
vg1018561974 sf1018490531 10 18561974 2.47E-11 4.49E-06
vg0216744755 sf0216738885 2 16744755 1.67E-10 NA
vg0905825342 sf0905824342 9 5825342 7.46E-10 NA
vg0519497368 sf0519434852 5 19497368 9.20E-10 NA
vg0720231838 sf0720230845 7 20231838 1.29E-08 NA
vg0811476581 sf0811475586 8 11476581 1.71E-08 NA
vg1218136630 sf1218108066 12 18136630 2.66E-07 6.82E-06