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 mr1864 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
vg0419235485 sf0419063523 4 19235485 1.47E-19 8.75E-12
vg0804997889 sf0804996892 8 4997889 4.62E-14 1.17E-06
vg0810884968 sf0810883973 8 10884968 9.50E-13 NA
vg0403256148 sf0403251751 4 3256148 1.73E-12 NA
vg0815520189 sf0815517475 8 15520189 5.65E-12 NA
vg0811475238 sf0811474243 8 11475238 5.37E-10 3.57E-06
vg0804864872 sf0804863875 8 4864872 1.01E-07 1.01E-06