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 mr1851 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
vg0419232798 sf0419060836 4 19232798 2.12E-21 4.00E-19
vg0334059893 sf0334052763 3 34059893 2.12E-08 1.57E-06
vg0419282874 sf0419110912 4 19282874 4.72E-08 1.18E-06
vg1209048534 sf1209045943 12 9048534 1.80E-07 4.48E-06
vg0620348476 sf0620347479 6 20348476 8.70E-06 1.42E-07