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 mr1054 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
vg0433017442 sf0432832328 4 33017442 1.38E-06 1.38E-06
vg1212214384 sf1212211722 12 12214384 3.03E-06 3.03E-06
vg1125009665 sf1124543505 11 25009665 3.80E-06 3.80E-06
vg0103243222 sf0103242222 1 3243222 3.86E-06 3.86E-06
vg0501601241 sf0501601225 5 1601241 4.18E-06 4.18E-06