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 mr1358 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
vg0306341565 sf0306340565 3 6341565 8.62E-12 NA
vg1210818720 sf1210816086 12 10818720 1.44E-10 NA
vg0132025675 sf0132024631 1 32025675 4.01E-10 NA
vg0526399169 sf0526336532 5 26399169 5.08E-10 NA
vg0125510468 sf0125509424 1 25510468 5.74E-10 NA
vg1214408077 sf1214405418 12 14408077 9.59E-09 7.23E-07
vg1214600105 sf1214597445 12 14600105 3.57E-08 2.11E-07
vg0525794122 sf0525731543 5 25794122 6.23E-08 4.51E-06
vg0206101296 sf0206101296 2 6101296 4.52E-07 NA
vg0528175919 sf0528113274 5 28175919 1.09E-06 NA
vg0630306971 sf0630305973 6 30306971 2.22E-06 4.12E-06