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 mr1403 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
vg0432598231 sf0432413122 4 32598231 1.04E-09 3.30E-07
vg0409069254 sf0409064529 4 9069254 1.05E-09 NA
vg0432446683 sf0432261575 4 32446683 1.86E-09 2.45E-07
vg0411837967 sf0411828678 4 11837967 2.14E-09 NA
vg0402380608 sf0402376203 4 2380608 5.53E-09 NA
vg1002814950 sf1002813927 10 2814950 7.55E-09 NA
vg0414370101 sf0414360814 4 14370101 1.27E-06 NA
vg1218431169 sf1218402605 12 18431169 1.42E-06 NA