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 mr1035 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
vg0427385115 sf0427199979 4 27385115 9.59E-08 9.60E-08
vg0404351840 sf0404347444 4 4351840 3.27E-07 3.27E-07
vg0405488386 sf0405483827 4 5488386 9.98E-07 9.98E-07
vg0628751779 sf0628750781 6 28751779 1.48E-06 1.48E-06
vg0231593943 sf0231588074 2 31593943 1.86E-06 1.86E-06
vg0524512577 sf0524449998 5 24512577 2.17E-06 2.17E-06
vg0404350615 sf0404346219 4 4350615 3.21E-06 3.21E-06
vg0404351848 sf0404347452 4 4351848 3.85E-06 3.85E-06
vg0404256297 sf0404251903 4 4256297 4.24E-06 4.24E-06