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 mr1125 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
vg0602898411 sf0602897412 6 2898411 2.08E-09 NA
vg0235782900 sf0235777031 2 35782900 2.11E-09 NA
vg0808423022 sf0808422026 8 8423022 4.65E-09 NA
vg0602901938 sf0602900939 6 2901938 5.27E-09 2.96E-06
vg0123888552 sf0123887508 1 23888552 6.84E-09 NA
vg0428346851 sf0428161709 4 28346851 1.03E-08 NA
vg0224385795 sf0224379926 2 24385795 6.60E-07 NA
vg1126520444 sf1126048859 11 26520444 7.42E-07 NA
vg0219643578 sf0219637710 2 19643578 9.21E-07 NA
vg0906841924 sf0906840924 9 6841924 NA 3.99E-06