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 mr1219 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
vg0707304077 sf0707303082 7 7304077 4.01E-10 1.44E-08
vg0916716723 sf0916715722 9 16716723 6.32E-09 1.39E-06
vg1201180694 sf1201179694 12 1180694 9.19E-09 8.90E-08
vg0228470723 sf0228464854 2 28470723 5.32E-08 6.89E-07
vg0809657696 sf0809656700 8 9657696 6.30E-08 2.49E-07
vg0228442970 sf0228437101 2 28442970 9.51E-08 4.84E-07
vg0623254583 sf0623253586 6 23254583 2.68E-07 7.76E-07
vg1104497863 sf1104493765 11 4497863 5.08E-07 4.42E-06
vg0808245241 sf0808244245 8 8245241 6.89E-07 2.87E-06
vg1010065690 sf1009994511 10 10065690 9.63E-07 9.68E-07
vg0106723726 sf0106722726 1 6723726 2.85E-06 2.29E-06