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 mr1304 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
vg0318925726 sf0318924486 3 18925726 1.54E-08 NA
vg0139790985 sf0139789942 1 39790985 3.69E-08 NA
vg0726456322 sf0726455328 7 26456322 6.50E-08 1.31E-06
vg1216084510 sf1216081806 12 16084510 7.93E-08 NA
vg0614713753 sf0614712754 6 14713753 3.18E-07 NA
vg0318752572 sf0318751332 3 18752572 6.33E-07 NA
vg1001395986 sf1001394963 10 1395986 7.19E-07 3.66E-06
vg1002823088 sf1002822065 10 2823088 NA 1.58E-06
vg0323987975 sf0323986149 3 23987975 NA 1.63E-06
vg1001183960 sf1001182937 10 1183960 NA 7.36E-06