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 mr1488 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
vg0302287012 sf0302286008 3 2287012 1.10E-11 3.80E-06
vg0330107231 sf0330100270 3 30107231 1.59E-11 NA
vg1218054771 sf1218026207 12 18054771 2.35E-11 5.35E-06
vg0623156256 sf0623155259 6 23156256 2.63E-11 NA
vg0208987778 sf0208987776 2 8987778 4.46E-11 NA
vg1105849420 sf1105845172 11 5849420 6.37E-10 NA
vg1009009289 sf1008938150 10 9009289 NA 1.29E-06