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 mr1683 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
vg0205285714 sf0205285712 2 5285714 4.11E-13 5.13E-06
vg0205285978 sf0205285976 2 5285978 6.37E-13 4.52E-06
vg0801628860 sf0801627862 8 1628860 1.48E-12 9.48E-07
vg1101641234 sf1101640235 11 1641234 7.54E-12 6.03E-06
vg0805992743 sf0805991746 8 5992743 1.51E-11 2.85E-07
vg0335297514 sf0335290383 3 35297514 2.41E-11 1.36E-06
vg0232480149 sf0232474280 2 32480149 4.15E-11 2.75E-06
vg1020531763 sf1020460242 10 20531763 4.65E-11 1.02E-06
vg0109580082 sf0109579058 1 9580082 1.02E-09 NA
vg0202989689 sf0202989687 2 2989689 2.25E-07 3.65E-06