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 mr1691 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
vg1204844332 sf1204843317 12 4844332 1.34E-11 9.02E-08
vg0720805926 sf0720804933 7 20805926 2.10E-11 1.31E-08
vg0700863821 sf0700862821 7 863821 2.54E-11 9.34E-07
vg1204816499 sf1204815484 12 4816499 4.09E-11 5.89E-08
vg0700862842 sf0700861842 7 862842 1.18E-10 6.15E-07
vg1223869700 sf1223836153 12 23869700 2.21E-10 3.35E-06
vg0106100583 sf0106099583 1 6100583 1.59E-09 9.19E-06
vg0105995926 sf0105994926 1 5995926 1.90E-09 1.96E-06
vg1203346568 sf1203345571 12 3346568 5.98E-08 NA