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 mr1941 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
vg0327981236 sf0327974290 3 27981236 2.66E-07 2.66E-07
vg1215130974 sf1215128310 12 15130974 1.17E-06 1.17E-06
vg0328002759 sf0327995813 3 28002759 1.54E-06 1.54E-06
vg0700065801 sf0700064801 7 65801 1.57E-06 1.57E-06
vg0515035963 sf0514978505 5 15035963 1.81E-06 1.81E-06
vg1122446629 sf1121980500 11 22446629 1.81E-06 1.81E-06
vg0604842468 sf0604841469 6 4842468 2.98E-06 2.98E-06
vg0700107314 sf0700106314 7 107314 7.80E-06 7.80E-06