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 mr1189 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
vg0413262397 sf0413253107 4 13262397 1.34E-08 1.34E-08
vg0413260469 sf0413251179 4 13260469 2.77E-08 2.77E-08
vg1006757388 sf1006773011 10 6757388 3.32E-07 3.32E-07
vg0910031361 sf0910030360 9 10031361 9.13E-07 9.13E-07
vg0203033050 sf0203033048 2 3033050 4.28E-06 4.28E-06
vg0610066552 sf0610065553 6 10066552 4.40E-06 4.40E-06