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 mr1485 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
vg0805900956 sf0805899959 8 5900956 1.39E-08 1.39E-08
vg0317372993 sf0317371803 3 17372993 8.10E-07 8.10E-07
vg0804905723 sf0804904726 8 4905723 1.61E-06 1.61E-06
vg0138706549 sf0138705506 1 38706549 2.41E-06 2.41E-06
vg0810822568 sf0810821573 8 10822568 4.36E-06 4.36E-06