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 mr1818 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
vg0217093071 sf0217087201 2 17093071 1.70E-20 1.11E-14
vg1220336354 sf1220307796 12 20336354 7.74E-10 2.59E-06
vg0211612218 sf0211612214 2 11612218 2.81E-09 1.38E-08
vg0300545002 sf0300544000 3 545002 2.94E-09 NA
vg1108225523 sf1108220133 11 8225523 7.32E-09 NA
vg1010544331 sf1010473152 10 10544331 3.96E-08 1.89E-06
vg0216601743 sf0216595873 2 16601743 4.11E-07 1.14E-06
vg0120798282 sf0120797237 1 20798282 8.29E-07 7.25E-07
vg0502367280 sf0502367255 5 2367280 2.76E-06 NA
vg0217411971 sf0217406101 2 17411971 2.82E-06 1.96E-06