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 mr1888 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
vg0406592366 sf0406587810 4 6592366 3.38E-28 NA
vg0715323407 sf0715322414 7 15323407 5.20E-28 NA
vg0406265477 sf0406260917 4 6265477 3.38E-27 3.21E-06
vg0712400828 sf0712399835 7 12400828 1.23E-26 NA
vg0207138387 sf0207138387 2 7138387 2.18E-26 NA
vg0612831564 sf0612830565 6 12831564 2.68E-26 NA
vg0612969759 sf0612968760 6 12969759 9.72E-25 8.26E-07
vg0909042994 sf0909041993 9 9042994 3.92E-24 NA
vg0421072935 sf0420900990 4 21072935 NA 2.29E-06
vg1209997382 sf1209994793 12 9997382 NA 2.95E-06
vg1123638852 sf1123172722 11 23638852 NA 4.11E-06