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 mr1606 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
vg1215546652 sf1215543949 12 15546652 2.40E-08 NA
vg1212988162 sf1212985501 12 12988162 3.53E-08 NA
vg0228217298 sf0228211429 2 28217298 7.88E-08 NA
vg0603938117 sf0603937118 6 3938117 9.15E-08 9.84E-06
vg1002308179 sf1002307156 10 2308179 1.68E-07 NA
vg1214331785 sf1214329125 12 14331785 2.50E-07 NA