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 mr1166 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
vg0205856474 sf0205856474 2 5856474 1.57E-13 NA
vg0232965343 sf0232959474 2 32965343 2.20E-13 NA
vg0129933023 sf0129931978 1 29933023 3.73E-13 NA
vg0335000939 sf0334993809 3 35000939 4.51E-13 3.34E-07
vg1217179765 sf1217173720 12 17179765 6.02E-13 NA
vg0400388457 sf0400387455 4 388457 1.81E-12 3.74E-06
vg1219591736 sf1219563206 12 19591736 2.86E-10 NA
vg0628049712 sf0628048714 6 28049712 NA 4.69E-07
vg0432523372 sf0432338264 4 32523372 NA 5.13E-07
vg0202722002 sf0202722000 2 2722002 NA 2.33E-06
vg0820374974 sf0820372261 8 20374974 NA 4.83E-06