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 mr1952 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
vg1208054495 sf1208051901 12 8054495 1.22E-06 1.22E-06
vg0517993776 sf0517933262 5 17993776 2.88E-06 2.88E-06
vg0627787332 sf0627786334 6 27787332 3.82E-06 3.82E-06
vg0101055689 sf0101054689 1 1055689 4.28E-06 4.28E-06
vg0722236136 sf0722235143 7 22236136 4.53E-06 4.53E-06
vg1128946610 sf1128423389 11 28946610 4.80E-06 4.81E-06