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 mr1856 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
vg0522014819 sf0521952261 5 22014819 1.26E-07 4.91E-06
vg1214616089 sf1214613429 12 14616089 2.96E-07 3.01E-06
vg0131774075 sf0131773031 1 31774075 3.32E-07 4.95E-06
vg0125127326 sf0125126282 1 25127326 7.53E-07 5.28E-06
vg0800190791 sf0800189791 8 190791 1.33E-06 4.83E-06
vg0618433395 sf0618432398 6 18433395 1.39E-06 1.73E-06
vg0620354393 sf0620353396 6 20354393 1.60E-06 3.74E-06
vg0914211024 sf0914210023 9 14211024 2.15E-06 2.32E-06
vg0806619995 sf0806619000 8 6619995 2.63E-06 2.76E-06
vg0623833223 sf0623832226 6 23833223 4.13E-06 1.55E-06
vg0910108488 sf0910107487 9 10108488 4.38E-06 3.10E-06