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 mr1827 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
vg0132541810 sf0132540766 1 32541810 1.97E-18 6.12E-07
vg0132547843 sf0132546799 1 32547843 3.38E-18 2.15E-07
vg0520363826 sf0520301299 5 20363826 1.61E-17 NA
vg0528310757 sf0528248112 5 28310757 2.94E-17 NA
vg0319456132 sf0319454643 3 19456132 1.32E-16 NA
vg0102754939 sf0102753939 1 2754939 2.73E-16 NA
vg0608532315 sf0608531316 6 8532315 1.98E-13 NA
vg0904007553 sf0904006553 9 4007553 NA 5.54E-07
vg0721954637 sf0721953644 7 21954637 NA 9.02E-07
vg0620424954 sf0620423957 6 20424954 NA 1.22E-06
vg0620747197 sf0620746200 6 20747197 NA 1.38E-06
vg0906472621 sf0906471621 9 6472621 NA 2.26E-06
vg0111955442 sf0111954416 1 11955442 NA 4.77E-06
vg0519747759 sf0519685243 5 19747759 NA 6.12E-06
vg0316269128 sf0316267775 3 16269128 NA 7.02E-06