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 mr1839 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
vg0205284721 sf0205284719 2 5284721 1.21E-37 2.92E-11
vg0129863523 sf0129862478 1 29863523 1.60E-30 NA
vg0132947824 sf0132946780 1 32947824 5.01E-30 NA
vg1113344086 sf1112880407 11 13344086 9.69E-30 NA
vg0138520632 sf0138519589 1 38520632 1.63E-29 NA
vg0922486625 sf0922486144 9 22486625 6.43E-23 NA
vg0126195723 sf0126194679 1 26195723 NA 2.92E-06
vg0400488174 sf0400487172 4 488174 NA 4.63E-06
vg1014249003 sf1014177769 10 14249003 NA 4.85E-06
vg1117584893 sf1117118750 11 17584893 NA 4.96E-06