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 mr1197 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
vg0619153685 sf0619152688 6 19153685 1.32E-07 1.32E-07
vg0819431872 sf0819429159 8 19431872 4.80E-07 4.80E-07
vg1120556042 sf1120089968 11 20556042 6.43E-07 6.43E-07
vg0705453437 sf0705452438 7 5453437 1.72E-06 1.72E-06
vg0421387991 sf0421216044 4 21387991 3.01E-06 3.01E-06
vg0619131736 sf0619130739 6 19131736 4.42E-06 4.42E-06
vg0618200340 sf0618199343 6 18200340 4.68E-06 4.68E-06