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 mr1727 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
vg1214649624 sf1214646964 12 14649624 1.64E-08 8.25E-07
vg0316048632 sf0316047279 3 16048632 1.72E-08 NA
vg0134544774 sf0134543731 1 34544774 1.80E-08 NA
vg0316733441 sf0316732087 3 16733441 1.90E-08 NA
vg0316454459 sf0316453104 3 16454459 2.68E-08 NA
vg1214632415 sf1214629755 12 14632415 3.33E-08 5.76E-07
vg0702613671 sf0702612672 7 2613671 3.25E-07 NA
vg1017103250 sf1017032022 10 17103250 6.70E-06 1.31E-06
vg1017179262 sf1017108035 10 17179262 NA 7.20E-06