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 mr1320 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
vg0406849851 sf0406845296 4 6849851 1.24E-07 9.65E-08
vg0402234072 sf0402229667 4 2234072 1.40E-07 2.75E-07
vg0406861913 sf0406857358 4 6861913 3.84E-07 7.43E-07
vg0212825334 sf0212825330 2 12825334 8.36E-07 3.35E-06
vg1218108461 sf1218079897 12 18108461 NA 7.96E-06