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 mr1860 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
vg0404394964 sf0404390568 4 4394964 9.83E-11 1.60E-06
vg0518324346 sf0518263832 5 18324346 3.90E-10 2.03E-06
vg0919394402 sf0919393992 9 19394402 1.10E-09 NA
vg0225981053 sf0225975184 2 25981053 1.88E-09 NA
vg1212822297 sf1212819636 12 12822297 1.97E-09 NA
vg1005050526 sf1005067063 10 5050526 1.56E-08 3.02E-06
vg0402217448 sf0402213043 4 2217448 NA 2.23E-06
vg1119840928 sf1119363397 11 19840928 NA 3.70E-06