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 mr1679 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
vg0724506397 sf0724505403 7 24506397 1.04E-11 3.98E-09
vg0724515882 sf0724514888 7 24515882 4.54E-11 3.00E-09
vg0822936315 sf0822933602 8 22936315 2.13E-10 NA
vg1222490179 sf1222456618 12 22490179 5.38E-10 7.66E-06
vg0519857510 sf0519794986 5 19857510 8.86E-10 NA
vg1002738229 sf1002737206 10 2738229 9.32E-10 NA
vg1204616996 sf1204615984 12 4616996 1.45E-08 1.23E-07
vg0729072157 sf0729071165 7 29072157 3.80E-08 2.66E-06
vg0720805926 sf0720804933 7 20805926 8.02E-08 1.48E-08
vg0403769688 sf0403765294 4 3769688 1.12E-07 1.72E-06
vg1203995948 sf1203994936 12 3995948 5.15E-07 5.80E-06
vg0709261513 sf0709260519 7 9261513 5.83E-07 NA
vg0724340832 sf0724339838 7 24340832 NA 3.87E-08
vg0729066345 sf0729065353 7 29066345 NA 1.99E-06
vg0729234628 sf0729233636 7 29234628 NA 3.90E-06
vg0720575452 sf0720574459 7 20575452 NA 3.95E-06