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 mr1179 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
vg0500170952 sf0500170952 5 170952 8.05E-11 4.26E-07
vg0502159367 sf0502159342 5 2159367 1.36E-10 3.01E-07
vg0524666547 sf0524603967 5 24666547 6.38E-07 8.55E-07
vg1119904700 sf1119438623 11 19904700 7.28E-07 7.14E-06
vg1117539909 sf1117073764 11 17539909 5.76E-06 NA