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 mr1804 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
vg0702575620 sf0702574621 7 2575620 1.31E-10 3.68E-06
vg1207192862 sf1207190252 12 7192862 1.49E-10 NA
vg0321124152 sf0321122662 3 21124152 1.76E-10 NA
vg0312535741 sf0312534459 3 12535741 4.68E-10 NA
vg0405066237 sf0405061676 4 5066237 6.78E-10 NA
vg0520272415 sf0520209888 5 20272415 1.12E-09 NA
vg0702447742 sf0702446743 7 2447742 1.62E-09 1.21E-06
vg1115212225 sf1114748539 11 15212225 4.03E-09 9.96E-06
vg0328324322 sf0328317376 3 28324322 4.97E-09 1.15E-06
vg0322105332 sf0322103839 3 22105332 NA 3.81E-07
vg0410956225 sf0410946926 4 10956225 NA 1.51E-06