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 mr1915 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
vg0525628187 sf0525565608 5 25628187 8.03E-10 3.91E-07
vg0525627816 sf0525565237 5 25627816 1.39E-09 3.98E-07
vg0623056011 sf0623055014 6 23056011 3.11E-09 NA
vg0824221287 sf0824218573 8 24221287 1.77E-08 NA
vg0221741384 sf0221735515 2 21741384 1.78E-08 NA
vg1118091992 sf1117625850 11 18091992 1.95E-08 NA
vg0828022960 sf0828020246 8 28022960 6.42E-08 NA
vg0308948024 sf0308946962 3 8948024 3.10E-07 NA
vg0817698022 sf0817695309 8 17698022 5.93E-07 2.82E-06
vg0132460481 sf0132459437 1 32460481 2.92E-06 NA
vg1219645684 sf1219617154 12 19645684 NA 3.25E-07
vg0518984986 sf0518922470 5 18984986 NA 6.99E-07
vg0820974361 sf0820971648 8 20974361 NA 9.62E-07
vg1227356558 sf1227322958 12 27356558 NA 1.04E-06
vg0523035315 sf0522972756 5 23035315 NA 4.16E-06