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 mr1978 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
vg0323845230 sf0323843404 3 23845230 2.53E-07 2.53E-07
vg0918948219 sf0918947219 9 18948219 2.56E-07 2.56E-07
vg0414114398 sf0414105113 4 14114398 1.30E-06 1.30E-06
vg0618296547 sf0618295550 6 18296547 3.78E-06 3.78E-06
vg0119705377 sf0119704332 1 19705377 3.81E-06 3.81E-06
vg1127763517 sf1127291903 11 27763517 3.82E-06 3.82E-06