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 mr1896 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
vg0723265983 sf0723264990 7 23265983 1.05E-08 9.76E-06
vg0805068073 sf0805067076 8 5068073 2.14E-08 NA
vg0324965295 sf0324963375 3 24965295 4.53E-08 NA
vg0130670983 sf0130669939 1 30670983 4.97E-08 NA
vg1123452646 sf1122986516 11 23452646 4.98E-08 NA
vg0228498409 sf0228492540 2 28498409 6.09E-08 NA
vg1213717956 sf1213715294 12 13717956 NA 3.35E-06