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 mr1847 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
vg0716322335 sf0716321342 7 16322335 1.92E-08 NA
vg0607988535 sf0607987536 6 7988535 1.28E-07 4.23E-06
vg0323164411 sf0323162899 3 23164411 3.22E-06 1.94E-06
vg0222807259 sf0222801390 2 22807259 4.63E-06 2.57E-06
vg0102009968 sf0102008968 1 2009968 NA 2.80E-06
vg1220409333 sf1220380775 12 20409333 NA 3.90E-06