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 mr1475 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
vg1214822308 sf1214819649 12 14822308 2.19E-07 2.19E-07
vg0431655631 sf0431470524 4 31655631 4.04E-07 4.04E-07
vg0431472905 sf0431287803 4 31472905 4.13E-07 4.13E-07
vg1107375253 sf1107370998 11 7375253 1.13E-06 1.13E-06
vg0820974361 sf0820971648 8 20974361 1.43E-06 1.43E-06
vg1214600105 sf1214597445 12 14600105 1.59E-06 1.59E-06
vg0709984451 sf0709983457 7 9984451 1.66E-06 1.67E-06
vg0431411704 sf0431226602 4 31411704 2.06E-06 2.06E-06
vg1104978992 sf1104974803 11 4978992 2.08E-06 2.08E-06
vg1210390475 sf1210387888 12 10390475 2.76E-06 2.76E-06