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 mr1207 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
vg0106103383 sf0106102383 1 6103383 4.58E-12 7.71E-07
vg0106854990 sf0106853990 1 6854990 1.28E-10 1.28E-07
vg0606713553 sf0606712554 6 6713553 2.06E-10 NA
vg1215352870 sf1215350168 12 15352870 3.81E-10 2.70E-06
vg0205107721 sf0205107718 2 5107721 2.58E-09 NA
vg0316759586 sf0316758232 3 16759586 3.50E-09 NA
vg0808039960 sf0808038964 8 8039960 2.12E-08 NA
vg0727868341 sf0727867348 7 27868341 3.30E-08 3.42E-06
vg0106494338 sf0106493338 1 6494338 NA 9.69E-10