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 mr1662 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
vg1125421780 sf1124955619 11 25421780 1.33E-09 2.85E-07
vg1127383403 sf1126911790 11 27383403 2.89E-09 2.19E-07
vg1217759068 sf1217730502 12 17759068 6.94E-08 8.30E-06
vg1125230308 sf1124764148 11 25230308 1.72E-07 6.95E-08
vg0600949542 sf0600948543 6 949542 5.89E-07 4.03E-06
vg0211188937 sf0211188934 2 11188937 6.35E-07 2.55E-06
vg1124272163 sf1123806033 11 24272163 7.12E-07 4.07E-06