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 mr1433 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
vg1215178307 sf1215175643 12 15178307 1.52E-07 1.52E-07
vg0138783200 sf0138782157 1 38783200 1.03E-06 1.03E-06
vg1004555361 sf1004571899 10 4555361 1.18E-06 1.18E-06
vg1104978881 sf1104974692 11 4978881 1.65E-06 1.65E-06
vg0121871143 sf0121870098 1 21871143 2.22E-06 2.22E-06
vg0825972153 sf0825969439 8 25972153 3.69E-06 3.69E-06
vg0431472905 sf0431287803 4 31472905 3.96E-06 3.96E-06
vg0300249514 sf0300248514 3 249514 5.82E-06 5.82E-06