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 mr1830 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
vg0805959456 sf0805958459 8 5959456 5.46E-10 1.38E-07
vg1215060377 sf1215057719 12 15060377 7.14E-09 NA
vg0805934301 sf0805933304 8 5934301 1.15E-08 1.42E-07
vg0726517533 sf0726516539 7 26517533 4.08E-08 8.67E-06
vg1005864251 sf1005880789 10 5864251 4.86E-08 NA
vg1204133974 sf1204132962 12 4133974 6.03E-08 NA
vg0726533898 sf0726532904 7 26533898 7.08E-08 4.83E-06
vg0824561001 sf0824558287 8 24561001 1.41E-07 1.48E-06