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 mr1039 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
vg1204697263 sf1204696251 12 4697263 2.21E-10 NA
vg0211188937 sf0211188934 2 11188937 3.12E-10 3.80E-06
vg0805970880 sf0805969883 8 5970880 4.14E-10 1.21E-06
vg0216929890 sf0216924020 2 16929890 4.17E-10 6.29E-06
vg0142134296 sf0142133253 1 42134296 1.53E-09 NA
vg0806225198 sf0806224203 8 6225198 7.97E-09 1.29E-06
vg0506870350 sf0506870292 5 6870350 1.77E-07 1.61E-08
vg0207729665 sf0207729664 2 7729665 1.87E-07 NA
vg0817018173 sf0817015459 8 17018173 NA 8.81E-07