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 mr1462 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
vg1122531667 sf1122065538 11 22531667 2.40E-09 2.31E-06
vg0107647091 sf0107646091 1 7647091 2.41E-08 4.82E-08
vg0916032111 sf0916031110 9 16032111 2.56E-08 NA
vg0627981060 sf0627980062 6 27981060 5.59E-08 NA
vg1122976068 sf1122509939 11 22976068 6.54E-08 NA
vg1122886718 sf1122420589 11 22886718 2.68E-06 4.89E-06
vg1002941120 sf1002940097 10 2941120 NA 4.69E-06
vg0214178528 sf0214172658 2 14178528 NA 5.52E-06