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 mr1269 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
vg1105907265 sf1105903017 11 5907265 1.55E-08 1.75E-06
vg0431443433 sf0431258331 4 31443433 2.95E-08 6.76E-06
vg0506747780 sf0506747722 5 6747780 1.08E-06 2.58E-06
vg1226522030 sf1226488425 12 26522030 2.75E-06 NA
vg1204346951 sf1204345939 12 4346951 4.29E-06 1.22E-06