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 mr1836 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
vg0817816804 sf0817814091 8 17816804 3.81E-08 3.81E-08
vg0318816925 sf0318815685 3 18816925 9.55E-07 9.56E-07
vg0816073881 sf0816071167 8 16073881 1.60E-06 1.60E-06
vg0408046336 sf0408041608 4 8046336 2.16E-06 2.16E-06
vg0818395231 sf0818392518 8 18395231 2.50E-06 2.50E-06
vg0908706109 sf0908705108 9 8706109 2.90E-06 2.90E-06
vg0431086715 sf0430901604 4 31086715 4.05E-06 4.05E-06
vg0320620607 sf0320619117 3 20620607 4.70E-06 4.70E-06
vg1017015504 sf1016944276 10 17015504 4.81E-06 4.81E-06