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 mr1165 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
vg0611588754 sf0611587755 6 11588754 5.49E-09 5.49E-09
vg0615169965 sf0615168966 6 15169965 1.32E-08 1.32E-08
vg0608909772 sf0608908773 6 8909772 2.00E-08 2.00E-08
vg0611311887 sf0611310888 6 11311887 7.56E-08 7.56E-08
vg0620548889 sf0620547892 6 20548889 4.02E-07 4.02E-07
vg0617344026 sf0617343029 6 17344026 9.80E-07 9.80E-07
vg0619937082 sf0619936085 6 19937082 3.11E-06 3.11E-06
vg0611357651 sf0611356652 6 11357651 3.88E-06 3.88E-06