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 mr1097 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
vg0130670983 sf0130669939 1 30670983 2.08E-20 2.64E-15
vg0519983192 sf0519920668 5 19983192 9.35E-11 NA
vg0433013078 sf0432827964 4 33013078 9.50E-11 9.00E-07
vg0122013723 sf0122012678 1 22013723 1.71E-10 NA
vg1200417909 sf1200416909 12 417909 1.88E-10 NA
vg0432678602 sf0432493491 4 32678602 6.31E-09 6.98E-06
vg0432725120 sf0432540006 4 32725120 1.04E-08 8.91E-07
vg0507517974 sf0507517916 5 7517974 2.09E-06 NA
vg0130861999 sf0130860955 1 30861999 NA 2.07E-07