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 mr1558 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
vg1020402835 sf1020331315 10 20402835 7.34E-66 3.71E-10
vg1020720683 sf1020649162 10 20720683 8.83E-63 2.16E-08
vg1020563532 sf1020492011 10 20563532 1.07E-60 5.70E-12
vg0132925911 sf0132924867 1 32925911 1.87E-55 NA
vg0332643360 sf0332636231 3 32643360 4.56E-55 NA
vg0211098718 sf0211098715 2 11098718 9.82E-54 NA
vg0233373837 sf0233367968 2 33373837 2.10E-53 NA
vg1209700334 sf1209697743 12 9700334 NA 1.90E-06
vg0715057249 sf0715056256 7 15057249 NA 5.82E-06
vg1209592277 sf1209589686 12 9592277 NA 6.37E-06
vg0702609879 sf0702608880 7 2609879 NA 7.49E-06