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 mr1027 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
vg1007550477 sf1007566089 10 7550477 2.41E-07 2.41E-07
vg0824309188 sf0824306474 8 24309188 3.74E-07 3.74E-07
vg1011363524 sf1011292343 10 11363524 1.18E-06 1.18E-06
vg1003093171 sf1003092148 10 3093171 1.21E-06 1.21E-06
vg1207669371 sf1207666775 12 7669371 1.80E-06 1.80E-06
vg0904707656 sf0904706656 9 4707656 1.97E-06 1.98E-06
vg0802736687 sf0802735690 8 2736687 2.48E-06 2.48E-06
vg0803043978 sf0803042981 8 3043978 3.14E-06 3.14E-06
vg0110928636 sf0110927612 1 10928636 3.37E-06 3.37E-06
vg0623505200 sf0623504203 6 23505200 3.75E-06 3.75E-06
vg1006579796 sf1006595419 10 6579796 4.12E-06 4.12E-06
vg1205975370 sf1205974351 12 5975370 4.37E-06 4.37E-06