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 mr1381 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
vg0616757478 sf0616756480 6 16757478 NA 1.05E-06
vg0807410855 sf0807409860 8 7410855 NA 2.80E-06
vg1219590404 sf1219561874 12 19590404 NA 2.81E-06
vg0528175919 sf0528113274 5 28175919 NA 3.10E-06
vg1219850678 sf1219822148 12 19850678 NA 3.82E-06