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 mr1286 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
vg0315356877 sf0315355524 3 15356877 5.72E-10 NA
vg0312560454 sf0312559172 3 12560454 7.13E-10 NA
vg0819868830 sf0819866117 8 19868830 9.29E-10 NA
vg0828207340 sf0828204626 8 28207340 1.82E-09 NA
vg1106628056 sf1106623809 11 6628056 2.19E-09 NA
vg0131859112 sf0131858068 1 31859112 3.40E-08 NA
vg0323778716 sf0323776890 3 23778716 2.45E-06 2.00E-06
vg0406854976 sf0406850421 4 6854976 NA 2.88E-06
vg0406835777 sf0406831222 4 6835777 NA 3.18E-06
vg0715817404 sf0715816411 7 15817404 NA 8.08E-06