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 mr1037 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
vg0402389835 sf0402385430 4 2389835 1.29E-17 1.57E-10
vg0921456103 sf0921455622 9 21456103 2.37E-12 9.57E-09
vg0402237717 sf0402233312 4 2237717 4.97E-11 5.97E-06
vg0404388307 sf0404383911 4 4388307 9.17E-11 NA
vg0622359913 sf0622358916 6 22359913 4.01E-10 NA
vg0910063949 sf0910062948 9 10063949 2.22E-06 4.81E-06
vg0205700559 sf0205700559 2 5700559 2.88E-06 6.95E-07
vg0614703627 sf0614702628 6 14703627 NA 2.45E-06