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
vg0610813941 sf0610812942 6 10813941 9.74E-21 4.38E-18
vg0614795778 sf0614794779 6 14795778 1.44E-15 8.35E-13
vg0620057031 sf0620056034 6 20057031 9.03E-11 5.98E-09
vg0617352597 sf0617351600 6 17352597 2.29E-10 7.86E-08
vg0620153786 sf0620152789 6 20153786 5.26E-10 9.00E-09
vg0610896564 sf0610895565 6 10896564 7.46E-10 5.01E-10
vg0620501165 sf0620500168 6 20501165 1.73E-09 3.36E-09
vg0611846756 sf0611845757 6 11846756 8.06E-09 9.63E-07
vg0610649532 sf0610648533 6 10649532 NA 4.89E-07
vg0610133020 sf0610132021 6 10133020 NA 5.13E-07
vg0610694708 sf0610693709 6 10694708 NA 2.48E-06
vg0610878201 sf0610877202 6 10878201 NA 2.93E-06
vg0619834582 sf0619833585 6 19834582 NA 3.47E-06
vg0610271576 sf0610270577 6 10271576 NA 4.03E-06
vg1009886973 sf1009815794 10 9886973 NA 4.20E-06