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 mr1369 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
vg0329834062 sf0329827101 3 29834062 1.34E-11 NA
vg0922565216 sf0922564735 9 22565216 4.40E-11 NA
vg0332523541 sf0332516414 3 32523541 5.50E-11 NA
vg0126542310 sf0126541266 1 26542310 1.32E-10 NA
vg0315489079 sf0315487726 3 15489079 2.91E-10 NA
vg0103416626 sf0103415626 1 3416626 3.40E-08 NA
vg0625073430 sf0625072433 6 25073430 1.72E-07 2.43E-06