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 mr1724 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
vg0406869281 sf0406864726 4 6869281 5.21E-08 5.21E-08
vg1117178010 sf1116711862 11 17178010 9.59E-07 9.59E-07
vg0601214799 sf0601213800 6 1214799 1.10E-06 1.10E-06
vg0724951834 sf0724950840 7 24951834 3.39E-06 3.40E-06
vg1002941120 sf1002940097 10 2941120 3.88E-06 3.88E-06
vg0212359529 sf0212359525 2 12359529 3.92E-06 3.92E-06
vg1117625330 sf1117159186 11 17625330 4.14E-06 4.15E-06
vg0620348476 sf0620347479 6 20348476 4.64E-06 4.64E-06
vg0501390670 sf0501390654 5 1390670 4.79E-06 4.79E-06
vg0202138338 sf0202138338 2 2138338 9.06E-06 9.05E-06