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 mr1300 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
vg0601001133 sf0601000134 6 1001133 6.96E-08 6.96E-08
vg0714095299 sf0714094306 7 14095299 7.43E-08 7.43E-08
vg0406334961 sf0406330401 4 6334961 1.24E-07 1.24E-07
vg0708022997 sf0708022002 7 8022997 2.08E-07 2.08E-07
vg1222445637 sf1222412076 12 22445637 2.35E-07 2.35E-07
vg1209709241 sf1209706650 12 9709241 2.87E-07 2.87E-07
vg0706932173 sf0706931178 7 6932173 3.20E-07 3.20E-07
vg0519671296 sf0519608780 5 19671296 6.40E-07 6.40E-07
vg0413034382 sf0413025092 4 13034382 9.60E-07 9.60E-07
vg1211445891 sf1211443227 12 11445891 1.18E-06 1.18E-06
vg0901431167 sf0901430167 9 1431167 1.62E-06 1.62E-06
vg0430365122 sf0430179999 4 30365122 2.03E-06 2.03E-06
vg0137704063 sf0137703020 1 37704063 2.48E-06 2.47E-06
vg0225795212 sf0225789343 2 25795212 3.36E-06 3.36E-06
vg0614462370 sf0614461371 6 14462370 3.69E-06 3.69E-06
vg0121204502 sf0121203457 1 21204502 3.74E-06 3.74E-06
vg1209659109 sf1209656518 12 9659109 4.38E-06 4.38E-06
vg1118086655 sf1117620513 11 18086655 4.66E-06 4.66E-06