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 mr1908 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
vg0122441794 sf0122440749 1 22441794 1.29E-08 2.80E-07
vg0122407241 sf0122406196 1 22407241 4.61E-08 1.08E-06
vg0122403766 sf0122402721 1 22403766 7.29E-08 2.27E-06
vg1126538466 sf1126066881 11 26538466 2.28E-07 1.94E-06
vg1126327328 sf1125855741 11 26327328 3.81E-07 3.94E-06
vg0221218849 sf0221212981 2 21218849 1.94E-06 8.81E-06
vg0114463521 sf0114462495 1 14463521 6.45E-06 1.33E-06