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 mr1452 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
vg0114197089 sf0114196063 1 14197089 8.57E-07 8.57E-07
vg1207119817 sf1207118707 12 7119817 1.31E-06 1.31E-06
vg0309690725 sf0309689661 3 9690725 1.62E-06 1.62E-06
vg0107647091 sf0107646091 1 7647091 2.65E-06 2.65E-06
vg0403579142 sf0403574744 4 3579142 2.97E-06 2.97E-06
vg0512292895 sf0512292825 5 12292895 3.97E-06 3.97E-06
vg0430941234 sf0430756114 4 30941234 3.97E-06 3.97E-06
vg0316453911 sf0316452556 3 16453911 4.47E-06 4.47E-06