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 mr1982 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
vg0420711795 sf0420539838 4 20711795 2.66E-08 2.66E-08
vg0623981969 sf0623980972 6 23981969 1.81E-07 1.81E-07
vg0907175535 sf0907174535 9 7175535 3.07E-07 3.07E-07
vg0403140954 sf0403136557 4 3140954 6.07E-07 6.07E-07
vg0421031231 sf0420859284 4 21031231 6.43E-07 6.43E-07
vg0421384856 sf0421212909 4 21384856 2.15E-06 2.15E-06
vg0516381476 sf0516323958 5 16381476 4.11E-06 4.11E-06
vg1013490779 sf1013419549 10 13490779 4.40E-06 4.40E-06