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 mr1811 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
vg0222002131 sf0221996262 2 22002131 7.95E-08 7.96E-08
vg0805900956 sf0805899959 8 5900956 9.99E-08 9.99E-08
vg1001247868 sf1001246845 10 1247868 4.46E-07 4.46E-07
vg0335297514 sf0335290383 3 35297514 5.29E-07 5.29E-07
vg0606307455 sf0606306456 6 6307455 8.37E-07 8.37E-07
vg0124420479 sf0124419435 1 24420479 1.37E-06 1.37E-06
vg0801698743 sf0801697746 8 1698743 1.46E-06 1.46E-06
vg0324965295 sf0324963375 3 24965295 1.86E-06 1.86E-06
vg0509233251 sf0509233180 5 9233251 2.01E-06 2.01E-06
vg0112179197 sf0112178171 1 12179197 2.26E-06 2.26E-06
vg0207698155 sf0207698154 2 7698155 3.30E-06 3.30E-06
vg0131361719 sf0131360675 1 31361719 4.72E-06 4.72E-06