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 mr1456 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
vg1210023832 sf1210021243 12 10023832 2.57E-10 2.57E-10
vg1215994922 sf1215992218 12 15994922 7.70E-09 7.70E-09
vg0528279181 sf0528216536 5 28279181 1.54E-07 1.54E-07
vg1218209454 sf1218180890 12 18209454 3.15E-07 3.15E-07
vg0805616881 sf0805615884 8 5616881 3.56E-07 3.56E-07
vg0315572376 sf0315571023 3 15572376 7.43E-07 7.43E-07
vg1210574208 sf1210571621 12 10574208 9.88E-07 9.88E-07
vg0216525301 sf0216519431 2 16525301 1.73E-06 1.73E-06
vg1210415899 sf1210413312 12 10415899 1.87E-06 1.87E-06
vg1106186411 sf1106182163 11 6186411 2.77E-06 2.77E-06
vg1116820455 sf1116355333 11 16820455 3.10E-06 3.10E-06
vg0705190029 sf0705189030 7 5190029 3.84E-06 3.84E-06
vg1215609346 sf1215606643 12 15609346 4.32E-06 4.32E-06
vg1215609371 sf1215606668 12 15609371 6.70E-06 6.70E-06