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 mr1959 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
vg1000475572 sf1000474548 10 475572 2.09E-12 5.15E-10
vg1125038879 sf1124572719 11 25038879 3.90E-10 3.01E-09
vg0528146502 sf0528083857 5 28146502 9.00E-10 4.77E-08
vg1125127481 sf1124661321 11 25127481 1.03E-08 3.35E-07
vg0700359527 sf0700358527 7 359527 2.18E-08 1.55E-06
vg1124221076 sf1123754946 11 24221076 4.66E-08 5.73E-06
vg1128816376 sf1128293155 11 28816376 6.52E-08 3.16E-06
vg1119999188 sf1119533111 11 19999188 3.38E-07 2.51E-06
vg0706566801 sf0706565806 7 6566801 2.25E-06 4.85E-06
vg1125082418 sf1124616258 11 25082418 4.20E-06 1.52E-09