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 mr1824 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
vg0819603039 sf0819600326 8 19603039 7.04E-09 1.69E-07
vg1104978992 sf1104974803 11 4978992 1.23E-08 6.19E-06
vg0726964336 sf0726963342 7 26964336 1.35E-08 NA
vg0123693261 sf0123692217 1 23693261 2.37E-08 NA
vg1215165691 sf1215163027 12 15165691 3.46E-08 NA
vg0223955910 sf0223950041 2 23955910 8.89E-08 7.17E-07
vg0224007952 sf0224002083 2 24007952 5.92E-07 2.16E-06
vg0820873126 sf0820870413 8 20873126 1.07E-06 2.36E-06
vg1107370068 sf1107365813 11 7370068 1.65E-06 NA
vg1115030431 sf1114566745 11 15030431 1.83E-06 2.32E-06
vg1016429449 sf1016358223 10 16429449 2.25E-06 2.88E-07
vg1227173062 sf1227139462 12 27173062 3.98E-06 NA
vg0622384184 sf0622383187 6 22384184 9.87E-06 NA