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 mr1324 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
vg0521798367 sf0521735809 5 21798367 5.01E-19 NA
vg0411353830 sf0411344533 4 11353830 1.92E-18 NA
vg0226148109 sf0226142240 2 26148109 3.22E-18 NA
vg0721760138 sf0721759145 7 21760138 3.77E-18 NA
vg0725280982 sf0725279988 7 25280982 5.14E-18 NA
vg1215563643 sf1215560940 12 15563643 NA 1.48E-06
vg0331822672 sf0331815549 3 31822672 NA 1.70E-06
vg0224817297 sf0224811428 2 24817297 NA 2.41E-06
vg0107647091 sf0107646091 1 7647091 NA 3.51E-06
vg0308243052 sf0308241990 3 8243052 NA 4.72E-06