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 mr1955 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
vg0314971782 sf0314970429 3 14971782 9.25E-08 9.25E-08
vg0505448611 sf0505448589 5 5448611 1.49E-07 1.49E-07
vg1122857696 sf1122391567 11 22857696 3.06E-07 3.06E-07
vg0713864611 sf0713863618 7 13864611 3.15E-07 3.15E-07
vg1010166027 sf1010094848 10 10166027 5.11E-07 5.11E-07
vg0516598900 sf0516541382 5 16598900 6.10E-07 6.10E-07
vg0325133506 sf0325131587 3 25133506 9.55E-07 9.55E-07
vg0520392181 sf0520329653 5 20392181 1.05E-06 1.05E-06
vg0702102052 sf0702101053 7 2102052 1.20E-06 1.20E-06
vg0505172195 sf0505172173 5 5172195 1.36E-06 1.36E-06
vg0710157771 sf0710156777 7 10157771 1.62E-06 1.62E-06
vg0703377031 sf0703376032 7 3377031 2.07E-06 2.07E-06
vg1002920760 sf1002919737 10 2920760 2.66E-06 2.66E-06
vg0108679290 sf0108678290 1 8679290 3.33E-06 3.33E-06
vg1108587345 sf1108581955 11 8587345 3.34E-06 3.34E-06
vg1115168100 sf1114704414 11 15168100 3.97E-06 3.97E-06
vg0823871834 sf0823869120 8 23871834 4.61E-06 4.61E-06