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 mr1985 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
vg0819444873 sf0819442160 8 19444873 2.72E-07 2.71E-07
vg0805992743 sf0805991746 8 5992743 7.99E-07 7.98E-07
vg0805321266 sf0805320269 8 5321266 3.29E-06 3.28E-06
vg0826648729 sf0826646015 8 26648729 3.45E-06 3.44E-06
vg0105758841 sf0105757841 1 5758841 3.58E-06 3.57E-06
vg0207704844 sf0207704843 2 7704844 3.64E-06 3.64E-06
vg0142909114 sf0142908070 1 42909114 4.00E-06 4.00E-06
vg0719338226 sf0719337233 7 19338226 4.34E-06 4.34E-06
vg0141821909 sf0141820866 1 41821909 4.35E-06 4.35E-06