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 mr1346 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
vg0500881578 sf0500881560 5 881578 2.34E-07 4.06E-06
vg0825288365 sf0825285651 8 25288365 9.50E-07 2.66E-06
vg0407728955 sf0407724222 4 7728955 1.30E-06 1.19E-06
vg1205810555 sf1205809537 12 5810555 4.71E-06 3.55E-06
vg0122738881 sf0122737837 1 22738881 5.14E-06 NA