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 mr1287 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
vg1117484883 sf1117018738 11 17484883 1.67E-08 8.15E-06
vg1001363211 sf1001362188 10 1363211 1.86E-08 NA
vg0315350100 sf0315348747 3 15350100 4.26E-08 NA
vg0414197719 sf0414188435 4 14197719 4.44E-08 NA
vg1117574960 sf1117108817 11 17574960 4.50E-08 NA
vg0700312059 sf0700311059 7 312059 6.12E-08 NA
vg0909402515 sf0909401514 9 9402515 1.11E-06 NA
vg0103143509 sf0103142509 1 3143509 NA 3.58E-07
vg1002941120 sf1002940097 10 2941120 NA 7.65E-07
vg0715817404 sf0715816411 7 15817404 NA 4.69E-06