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 mr1440 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
vg0528836237 sf0528773592 5 28836237 1.35E-07 1.37E-06
vg0220342715 sf0220336847 2 20342715 1.65E-07 3.65E-06
vg0805322127 sf0805321130 8 5322127 2.31E-07 2.25E-06
vg0112179197 sf0112178171 1 12179197 4.15E-07 1.01E-06
vg0325806113 sf0325804131 3 25806113 7.78E-07 1.55E-06
vg0102110388 sf0102109388 1 2110388 1.57E-06 1.92E-06
vg0126250228 sf0126249184 1 26250228 7.10E-06 3.65E-06
vg0816229266 sf0816226552 8 16229266 8.88E-06 2.51E-06
vg0223425489 sf0223419620 2 23425489 NA 6.88E-07
vg0916030541 sf0916029540 9 16030541 NA 2.04E-06
vg1210723067 sf1210720480 12 10723067 NA 3.54E-06