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 mr1548 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
vg0615023142 sf0615022143 6 15023142 1.38E-10 7.77E-07
vg0614992514 sf0614991515 6 14992514 1.38E-10 5.72E-07
vg1124581657 sf1124115497 11 24581657 1.62E-09 2.89E-06
vg0619489522 sf0619488525 6 19489522 3.77E-09 NA
vg1203673794 sf1203672793 12 3673794 5.31E-09 NA
vg0624849062 sf0624848065 6 24849062 7.42E-09 NA
vg1011380327 sf1011309146 10 11380327 1.68E-08 1.20E-06
vg0521338672 sf0521276113 5 21338672 NA 1.32E-06
vg0122800847 sf0122799803 1 22800847 NA 2.80E-06