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 mr1834 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
vg0912998506 sf0912997505 9 12998506 1.29E-09 1.33E-07
vg1019855843 sf1019784343 10 19855843 6.24E-09 7.66E-07
vg0333662864 sf0333655734 3 33662864 2.14E-08 3.17E-07
vg0911021962 sf0911020961 9 11021962 9.17E-08 4.78E-06
vg1119850034 sf1119354291 11 19850034 4.39E-07 4.95E-06
vg0508125097 sf0508125037 5 8125097 1.99E-06 7.22E-07
vg0817979262 sf0817976549 8 17979262 2.16E-06 1.41E-06
vg0525960946 sf0525898367 5 25960946 2.49E-06 4.86E-07
vg0620734924 sf0620733927 6 20734924 8.76E-06 2.18E-06
vg0917926619 sf0917925618 9 17926619 NA 2.24E-06
vg1014078448 sf1014007214 10 14078448 NA 4.97E-06