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 mr1599 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
vg0216851993 sf0216846123 2 16851993 6.78E-13 2.55E-06
vg0216791491 sf0216785621 2 16791491 1.44E-12 1.99E-06
vg1018443385 sf1018371942 10 18443385 2.11E-12 3.31E-06
vg0815685490 sf0815682776 8 15685490 1.01E-09 NA
vg1221060594 sf1221027144 12 21060594 1.11E-09 NA
vg1108725515 sf1108720125 11 8725515 1.13E-09 NA