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 mr1576 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
vg0630306971 sf0630305973 6 30306971 3.22E-11 8.07E-08
vg0420503850 sf0420331894 4 20503850 3.19E-09 2.93E-06
vg0709128655 sf0709127661 7 9128655 6.72E-09 2.02E-06
vg1207399200 sf1207396607 12 7399200 3.17E-08 3.86E-06
vg1208067607 sf1208065013 12 8067607 5.87E-08 NA
vg0417375976 sf0417204019 4 17375976 6.99E-08 4.55E-06
vg0316604658 sf0316603303 3 16604658 4.46E-07 1.91E-06
vg0115380845 sf0115379819 1 15380845 6.91E-06 3.38E-06