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 mr1885 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
vg0820968372 sf0820965659 8 20968372 1.47E-11 NA
vg0128529554 sf0128528509 1 28529554 3.13E-11 NA
vg0616757478 sf0616756480 6 16757478 3.38E-11 7.42E-06
vg1218957771 sf1218929206 12 18957771 1.60E-10 NA
vg0914990285 sf0914989284 9 14990285 3.59E-10 NA
vg1115066964 sf1114603278 11 15066964 2.99E-09 7.55E-06
vg1219556254 sf1219527724 12 19556254 2.23E-08 NA
vg0605513869 sf0605512870 6 5513869 NA 2.06E-06