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 mr1273 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
vg1122571312 sf1122105183 11 22571312 3.91E-07 3.91E-07
vg0528849908 sf0528787263 5 28849908 2.59E-06 2.59E-06
vg1122689875 sf1122223746 11 22689875 2.85E-06 2.85E-06
vg0516647020 sf0516586662 5 16647020 4.35E-06 4.35E-06
vg0300255134 sf0300254134 3 255134 4.57E-06 4.55E-06
vg0527263305 sf0527200661 5 27263305 4.72E-06 4.73E-06
vg1118190858 sf1117724716 11 18190858 6.46E-06 6.44E-06