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 mr1954 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
vg0202781823 sf0202781821 2 2781823 2.97E-06 2.97E-06
vg0915815902 sf0915814901 9 15815902 3.32E-06 3.32E-06
vg1206974574 sf1206973464 12 6974574 3.79E-06 3.79E-06
vg0314910245 sf0314908892 3 14910245 4.62E-06 4.62E-06
vg1214799094 sf1214796435 12 14799094 4.87E-06 4.87E-06
vg0218747822 sf0218741953 2 18747822 6.86E-06 6.86E-06
vg1104596397 sf1104592299 11 4596397 8.33E-06 8.33E-06