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 mr1045 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
vg0130736687 sf0130735643 1 30736687 4.39E-11 9.75E-07
vg0726962702 sf0726961708 7 26962702 1.08E-09 NA
vg1104978992 sf1104974803 11 4978992 1.13E-08 NA
vg0125460621 sf0125459577 1 25460621 1.54E-08 NA
vg0111722806 sf0111721780 1 11722806 2.56E-08 NA
vg0820974361 sf0820971648 8 20974361 5.47E-07 2.94E-06
vg0802040250 sf0802039253 8 2040250 6.37E-06 NA
vg0914525816 sf0914524815 9 14525816 6.98E-06 NA
vg0714836122 sf0714835129 7 14836122 8.43E-06 NA
vg1219556254 sf1219527724 12 19556254 9.17E-06 NA