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 mr1686 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
vg0914770963 sf0914769962 9 14770963 9.22E-32 NA
vg0917625534 sf0917624533 9 17625534 2.77E-31 NA
vg0702153429 sf0702152430 7 2153429 4.12E-31 NA
vg0504748577 sf0504748554 5 4748577 6.90E-31 NA
vg1014032601 sf1013961367 10 14032601 2.84E-30 NA
vg1202398699 sf1202397700 12 2398699 1.63E-27 NA
vg0500706163 sf0500706163 5 706163 5.38E-27 NA
vg0225036220 sf0225030351 2 25036220 NA 2.13E-07
vg0708904930 sf0708903936 7 8904930 NA 2.71E-06
vg1220070336 sf1220041778 12 20070336 NA 3.23E-06
vg0716748284 sf0716747291 7 16748284 NA 3.98E-06
vg1216914223 sf1216908177 12 16914223 NA 5.11E-06