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 mr1432 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
vg1215829261 sf1215826558 12 15829261 1.62E-06 1.62E-06
vg0810647541 sf0810646545 8 10647541 2.78E-06 2.78E-06
vg0316514218 sf0316512863 3 16514218 3.21E-06 3.21E-06
vg0714594330 sf0714593337 7 14594330 4.17E-06 4.17E-06
vg0223170170 sf0223164301 2 23170170 4.39E-06 4.39E-06
vg0316516127 sf0316514772 3 16516127 6.16E-06 6.16E-06
vg0710286016 sf0710285022 7 10286016 8.60E-06 8.60E-06